Merge branch 'main' of github.com:PhasicFlow/phasicFlow

.gitignore

@@ -37,11 +37,15 @@
 *.out
 *.app
 
-# directories
+# Exclude specific directories wherever they appear
 build/**
 include/**
 bin/**
 lib/**
+**/build/
+**/include/
+**/bin/
+**/lib/
 test*/**
 **/**notnow
 doc/code-documentation/
@@ -61,3 +65,5 @@ doc/DTAGS
 **/[0-9]*.[0-9][0-9][0-9][0-9][0-9][0-9][0-9]
 **/[0-9]*.[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]
 **/VTK
+
+

DEMSystems/DEMSystem/DEMSystem.hpp

@@ -96,7 +96,7 @@ public:
 		return Control_();
 	}
 
-	auto inline constexpr usingDoulle()const
+	auto inline constexpr usingDouble()const
 	{
 		return pFlow::usingDouble__;
 	}

src/Interaction/sphereInteraction/sphereInteraction/sphereInteraction.cpp

@@ -359,7 +359,7 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::hearChanges
 	if(msg.equivalentTo(message::ITEMS_REARRANGE))
 	{
 		notImplementedFunction;
-		return false;
+		return true;
 	}
 	
 	fatalErrorInFunction<<"Event "<< msg.eventNames()<<

src/PostprocessData/fieldsDataBase/fieldsDataBase.cpp

@@ -467,7 +467,7 @@ pFlow::postprocessData::fieldsDataBase::fieldsDataBase
     systemControl& control,
     const dictionary& postDict,
     bool inSimulation,
-    timeValue startTime
+    TimeValueType startTime
 )
 :
     time_(control.time()),
@@ -492,7 +492,7 @@ pFlow::postprocessData::fieldsDataBase::fieldsDataBase
     }
 }
 
-pFlow::timeValue pFlow::postprocessData::fieldsDataBase::currentTime() const
+pFlow::TimeValueType pFlow::postprocessData::fieldsDataBase::currentTime() const
 {
     return time_.currentTime();
 }
@@ -914,7 +914,7 @@ pFlow::uniquePtr<pFlow::postprocessData::fieldsDataBase>
     systemControl& control, 
     const dictionary& postDict, 
     bool inSimulation,
-    timeValue startTime
+    TimeValueType startTime
 )
 {
     word dbType;

src/PostprocessData/fieldsDataBase/fieldsDataBase.hpp

@@ -78,7 +78,7 @@ private:
         anyList             allFields_;
 
         /// Map to store the last capture time of each field
-        wordMap<timeValue>  captureTime_;
+        wordMap<TimeValueType>  captureTime_;
 
         /// Reference to the Time object
         Time&               time_; 
@@ -178,7 +178,7 @@ public:
             systemControl& control, 
             const dictionary& postDict,
             bool inSimulation,
-            timeValue startTime);
+            TimeValueType startTime);
 
         /// no copy constructor
         fieldsDataBase(const fieldsDataBase&) = delete;
@@ -203,7 +203,7 @@ public:
                 systemControl& control, 
                 const dictionary& postDict, 
                 bool inSimulation,
-                timeValue startTime
+                TimeValueType startTime
             ),
             (control, postDict, inSimulation, startTime)
         );
@@ -211,7 +211,7 @@ public:
     
     // - Public Access Functions
         /// returns the current time
-        timeValue currentTime()const;
+        TimeValueType currentTime()const;
 
         /// const ref to object Time 
         const Time& time()const 
@@ -282,7 +282,7 @@ public:
         /// Get the next avaiable time folder after the current time folder 
         /// This is only used for post-simulation processing 
         virtual
-        timeValue getNextTimeFolder()const
+        TimeValueType getNextTimeFolder()const
         {
             return -1.0;
         }
@@ -291,7 +291,7 @@ public:
         /// This is used only for post-simulation processing
         /// @returns the time value of the next folder.
         virtual 
-        timeValue setToNextTimeFolder()
+        TimeValueType setToNextTimeFolder()
         {
             return -1.0;
         }
@@ -300,7 +300,7 @@ public:
         /// This is used only for post-simulation processing 
         /// @returns the time value of the skipped folder 
         virtual 
-        timeValue skipNextTimeFolder()
+        TimeValueType skipNextTimeFolder()
         {
             return -1.0;
         }
@@ -316,7 +316,7 @@ public:
         systemControl& control, 
         const dictionary& postDict, 
         bool inSimulation,
-        timeValue startTime);
+        TimeValueType startTime);
 };
 
 } // namespace pFlow::postprocessData

src/PostprocessData/fieldsDataBase/simulationFieldsDataBase.cpp

@@ -49,7 +49,7 @@ pFlow::postprocessData::simulationFieldsDataBase::simulationFieldsDataBase
     systemControl &control,
     const dictionary& postDict, 
     bool inSimulation,
-    timeValue startTime
+    TimeValueType startTime
 )
 :
     fieldsDataBase(control, postDict, inSimulation, startTime),

src/PostprocessData/fieldsDataBase/simulationFieldsDataBase.hpp

@@ -60,7 +60,7 @@ public:
         systemControl& control, 
         const dictionary& postDict,
         bool inSimulation,
-        timeValue startTime);
+        TimeValueType startTime);
 
     ~simulationFieldsDataBase() override = default;
 

src/PostprocessData/operation/includeMask/IncludeMask.hpp

@@ -86,12 +86,12 @@ private:
     word                    fieldName_;
     
     /// Timestamp when mask was last updated (-1 indicates never updated)
-    timeValue               lastUpdated_ = -1;
+    TimeValueType               lastUpdated_ = -1;
 
     /// Updates the mask based on current field values if needed, returns true if successful
     bool updateMask()
     {
-        timeValue t = database().currentTime();
+        TimeValueType t = database().currentTime();
         
         if( equal( t, lastUpdated_)) return true;
         
@@ -206,11 +206,11 @@ private:
 	
     std::vector<bool>       mask_;
 
-    timeValue               lastUpdated_ = -1;
+    TimeValueType               lastUpdated_ = -1;
 
     bool updateMask()
     {
-        timeValue t = database().currentTime();
+        TimeValueType t = database().currentTime();
         
         if( equal( t, lastUpdated_)) return true;
         

src/PostprocessData/operation/postprocessOperation/postprocessOperationFunctions.hpp

@@ -46,7 +46,7 @@ inline
 bool writeField
 (
     iOstream&             os,
-    timeValue             t,
+    TimeValueType             t,
     const regionField<T>  field,
     uint32                threshold,
     const T&              defValue=T{}    

src/PostprocessData/postprocessComponent/particleProbePostprocessComponent/particleProbePostprocessComponent.cpp

@@ -52,7 +52,7 @@ template<typename T>
 inline bool writeField
 (
     iOstream&             os,
-    timeValue             t,
+    TimeValueType             t,
     const regionField<T>& field,
     const regionPoints&   regPoints,
     const T&              invalidVal = T{}

src/PostprocessData/postprocessData/postprocessData.cpp

@@ -27,7 +27,7 @@ Licence:
 pFlow::postprocessData::postprocessData::postprocessData
 (
     const systemControl &control,
-    timeValue startTime
+    TimeValueType startTime
 )
 :
     auxFunctions(control),
@@ -50,7 +50,7 @@ pFlow::postprocessData::postprocessData::postprocessData
     if( !dict_.fileExist() || !dict_.headerOk() )
     {
         WARNING<<"You requested postprocessData function while,"
-            <<" the dictionary system/postprocessDataDict does not exist."
+            <<" the dictionary settings/postprocessDataDict does not exist."
             <<" This feature is disabled in the current run."<<END_WARNING;
         return;
     }

src/PostprocessData/postprocessData/postprocessData.hpp

@@ -85,7 +85,7 @@ public:
     ///  this constructor is used when postprocesing is active
     ///  during simulation.
     /// @param control const reference to systemControl 
-    postprocessData(const systemControl& control, timeValue startTime = -1.0);
+    postprocessData(const systemControl& control, TimeValueType startTime = -1.0);
 
     ~postprocessData()override = default;
 

src/phasicFlow/containers/span/span.hpp

@@ -55,7 +55,7 @@ private:
 
     mutable T*     data_ = nullptr;
  
-    index          size_ = 0;
+    IndexType      size_ = 0;
 
 public:
     
@@ -104,7 +104,7 @@ public:
 
     /// Returns the number of elements in the span
     INLINE_FUNCTION_HD
-    index size() const
+    IndexType size() const
     {
         return size_;
     }
@@ -139,14 +139,14 @@ public:
 
     /// Returns a reference to the element at the specified index
     INLINE_FUNCTION_HD
-    T& operator[](index i)
+    T& operator[](IndexType i)
     {
         return data_[i];
     }
 
     /// Returns a const reference to the element at the specified index
     INLINE_FUNCTION_HD
-    T& operator[](index i)const
+    T& operator[](IndexType i)const
     {
         return data_[i];
     }

src/phasicFlow/repository/Time/baseTimeControl.cpp

@@ -23,21 +23,21 @@ Licence:
 
 void pFlow::baseTimeControl::setTimeControl
 (
-	timeValue startTime, 
-	timeValue endTime, 
-	timeValue interval, 
+	TimeValueType startTime, 
+	TimeValueType endTime, 
+	TimeValueType interval, 
 	const word &intervalPrefix
 )
 {
 	isTimeStep_ = false;
 	intervalPrefix_ = intervalPrefix;
-	rRange_ = stridedRange<timeValue>(startTime, endTime, interval);
+	rRange_ = stridedRange<TimeValueType>(startTime, endTime, interval);
 }
 
 pFlow::baseTimeControl::baseTimeControl(
     const dictionary &dict,
     const word &intervalPrefix,
-    timeValue defStartTime)
+    TimeValueType defStartTime)
     : intervalPrefix_(intervalPrefix)
 {
 	auto tControl = dict.getVal<word>("timeControl");
@@ -59,10 +59,10 @@ pFlow::baseTimeControl::baseTimeControl(
 
 	if(!isTimeStep_)
 	{
-		auto startTime = (dict.getValOrSet<timeValue>("startTime", defStartTime));
-    	auto endTime = (dict.getValOrSet<timeValue>("endTime", largeValue));
-		auto interval = dict.getVal<timeValue>(intervalWord);
-		rRange_ = stridedRange<timeValue>(startTime, endTime, interval);
+		auto startTime = (dict.getValOrSet<TimeValueType>("startTime", defStartTime));
+    	auto endTime = (dict.getValOrSet<TimeValueType>("endTime", largeValue));
+		auto interval = dict.getVal<TimeValueType>(intervalWord);
+		rRange_ = stridedRange<TimeValueType>(startTime, endTime, interval);
 
 	}
 	else
@@ -78,9 +78,9 @@ pFlow::baseTimeControl::baseTimeControl(
 pFlow::baseTimeControl::baseTimeControl
 (
 	const dictionary& dict,
-	const timeValue   defInterval,
+	const TimeValueType   defInterval,
 	const word&       intervalPrefix,
-	const timeValue   defStartTime
+	const TimeValueType   defStartTime
 )
 :
 	intervalPrefix_(intervalPrefix)
@@ -104,10 +104,10 @@ pFlow::baseTimeControl::baseTimeControl
 
 	if(!isTimeStep_)
 	{
-		auto startTime = (dict.getValOrSet<timeValue>("startTime", defStartTime));
-    	auto endTime = (dict.getValOrSet<timeValue>("endTime", largeValue));
-		auto interval = dict.getValOrSet<timeValue>(intervalWord, defInterval);
-		rRange_ = stridedRange<timeValue>(startTime, endTime, interval);
+		auto startTime = (dict.getValOrSet<TimeValueType>("startTime", defStartTime));
+    	auto endTime = (dict.getValOrSet<TimeValueType>("endTime", largeValue));
+		auto interval = dict.getValOrSet<TimeValueType>(intervalWord, defInterval);
+		rRange_ = stridedRange<TimeValueType>(startTime, endTime, interval);
 
 	}
 	else
@@ -131,9 +131,9 @@ pFlow::baseTimeControl::baseTimeControl(int32 start, int32 end, int32 stride, co
 
 pFlow::baseTimeControl::baseTimeControl
 (
-	timeValue start, 
-	timeValue end, 
-	timeValue stride, 
+	TimeValueType start, 
+	TimeValueType end, 
+	TimeValueType stride, 
 	const word &intervalPrefix
 )
 :
@@ -147,7 +147,7 @@ pFlow::baseTimeControl::baseTimeControl
 { 
 }
 
-bool pFlow::baseTimeControl::eventTime(uint32 iter, timeValue t, timeValue dt) const
+bool pFlow::baseTimeControl::eventTime(uint32 iter, TimeValueType t, TimeValueType dt) const
 {
 	if(isTimeStep_)
 	{	
@@ -166,7 +166,7 @@ bool pFlow::baseTimeControl::eventTime(const timeInfo &ti) const
 }
 
 bool
-pFlow::baseTimeControl::isInRange(uint32 iter, timeValue t, timeValue dt) const
+pFlow::baseTimeControl::isInRange(uint32 iter, TimeValueType t, TimeValueType dt) const
 {
 	if(isTimeStep_)
 	{
@@ -178,7 +178,7 @@ pFlow::baseTimeControl::isInRange(uint32 iter, timeValue t, timeValue dt) const
 	}
 }
 
-pFlow::timeValue
+pFlow::TimeValueType
 pFlow::baseTimeControl::startTime() const
 {
 	if(!isTimeStep_)
@@ -191,7 +191,7 @@ pFlow::baseTimeControl::startTime() const
 	return 0;
 }
 
-pFlow::timeValue
+pFlow::TimeValueType
 pFlow::baseTimeControl::endTime() const
 {
 	if(!isTimeStep_)
@@ -204,7 +204,7 @@ pFlow::baseTimeControl::endTime() const
 	return 0;
 }
 
-pFlow::timeValue
+pFlow::TimeValueType
 pFlow::baseTimeControl::rInterval() const
 {
 	if(!isTimeStep_)

src/phasicFlow/repository/Time/baseTimeControl.hpp

@@ -36,16 +36,16 @@ private:
 
     int32StridedRagne        iRange_;
 
-    stridedRange<timeValue>  rRange_;
+    stridedRange<TimeValueType>  rRange_;
 
     word                      intervalPrefix_;
 
 protected:
 
 	void setTimeControl(
-		timeValue startTime, 
-		timeValue endTime, 
-		timeValue interval, 
+		TimeValueType startTime, 
+		TimeValueType endTime, 
+		TimeValueType interval, 
 		const word& intervalPrefix);
 
 public:
@@ -53,14 +53,14 @@ public:
 	baseTimeControl(
 	  const dictionary& dict,
 	  const word&       intervalPrefix = "",
-	  timeValue         defStartTime   = 0.0
+	  TimeValueType         defStartTime   = 0.0
 	);
 
 	baseTimeControl(
 		const dictionary&  dict,
-		const timeValue	   defInterval,
+		const TimeValueType	   defInterval,
 		const word&        intervalPrefix="",
-		const timeValue    defStartTime=0.0);
+		const TimeValueType    defStartTime=0.0);
 
 	baseTimeControl(
 		int32 start,
@@ -70,9 +70,9 @@ public:
 	); 
 
 	baseTimeControl(
-		timeValue start,
-		timeValue end,
-		timeValue stride,
+		TimeValueType start,
+		TimeValueType end,
+		TimeValueType stride,
 		const word& intervalPrefix = ""
 	);
 
@@ -99,17 +99,17 @@ public:
 		return isTimeStep_;
 	}
 
-	bool eventTime(uint32 iter, timeValue t, timeValue dt) const;
+	bool eventTime(uint32 iter, TimeValueType t, TimeValueType dt) const;
 
 	bool eventTime(const timeInfo& ti)const;
 
-	bool  isInRange(uint32 iter, timeValue t, timeValue dt) const;
+	bool  isInRange(uint32 iter, TimeValueType t, TimeValueType dt) const;
 
-	timeValue  startTime() const;
+	TimeValueType  startTime() const;
 
-	timeValue  endTime() const;
+	TimeValueType  endTime() const;
 
-	timeValue  rInterval() const;
+	TimeValueType  rInterval() const;
 
 	int32 startIter() const;
 

src/phasicFlow/repository/Time/timeControl.cpp

@@ -36,16 +36,16 @@ pFlow::timeControl::timeControl
 	ti_(dict),
 	startTime_
 	(
-		dict.getVal<timeValue>("startTime")
+		dict.getVal<TimeValueType>("startTime")
 	),
 	endTime_
 	(
-		dict.getVal<timeValue>("endTime")
+		dict.getVal<TimeValueType>("endTime")
 	),
 	stopAt_(endTime_),
 	saveInterval_
 	(
-		dict.getVal<timeValue>("saveInterval")
+		dict.getVal<TimeValueType>("saveInterval")
 	),
 	lastSaved_(startTime_),
 	performSorting_
@@ -65,9 +65,9 @@ pFlow::timeControl::timeControl
 
 pFlow::timeControl::timeControl(
 		dictionary& dict,
-		timeValue startTime,
-		timeValue endTime,
-		timeValue saveInterval,
+		TimeValueType startTime,
+		TimeValueType endTime,
+		TimeValueType saveInterval,
 		word startTimeName)
 :
 	ti_(startTime, dict),
@@ -95,9 +95,9 @@ pFlow::timeControl::timeControl(
 	checkForOutputToFile();
 }
 
-pFlow::timeValue pFlow::timeControl::setTime(timeValue t)
+pFlow::TimeValueType pFlow::timeControl::setTime(TimeValueType t)
 {
-	timeValue tmp = ti_.currentTime();
+	TimeValueType tmp = ti_.currentTime();
 	ti_.currentTime_ = t;
 	lastSaved_ = t;
 	checkForOutputToFile();

src/phasicFlow/repository/Time/timeControl.hpp

@@ -37,7 +37,7 @@ class dictionary;
 class timeControl
 {
 public:
-	using timeStridedRange = stridedRange<timeValue>;
+	using timeStridedRange = stridedRange<TimeValueType>;
 private:
 
 
@@ -47,19 +47,19 @@ private:
 		timeInfo 		ti_;
 		
 		// - start time of simulation
-		timeValue startTime_;
+		TimeValueType startTime_;
 
 		// - end time of simulation 
-		timeValue endTime_;
+		TimeValueType endTime_;
 
 		// - stopAt
-		timeValue stopAt_;	
+		TimeValueType stopAt_;	
 
 		// - time interval for time folder output 
-		timeValue saveInterval_;
+		TimeValueType saveInterval_;
 
 		// - the last time folder that was saved
-		timeValue lastSaved_;
+		TimeValueType lastSaved_;
 
 		bool  managedExternaly_ = false;
 
@@ -80,7 +80,7 @@ private:
 		inline word  timeName_ = "wrongSettings"; // for managedExternamly
 
 		static
-		inline timeValue 	writeTime_ = 0; // for managedExternamly
+		inline TimeValueType 	writeTime_ = 0; // for managedExternamly
 
 		void checkForOutputToFile();
 		
@@ -92,22 +92,22 @@ public:
 
 	timeControl(
 		dictionary& dict,
-		timeValue startTime,
-		timeValue endTime,
-		timeValue saveInterval,
+		TimeValueType startTime,
+		TimeValueType endTime,
+		TimeValueType saveInterval,
 		word startTimeName);
 	
 	virtual ~timeControl() = default;
 	
-	timeValue dt()const
+	TimeValueType dt()const
 	{
 		return ti_.dt();
 	}
 
-	timeValue setTime(timeValue t);
+	TimeValueType setTime(TimeValueType t);
 	
 
-	void setStopAt(timeValue sT)
+	void setStopAt(TimeValueType sT)
 	{
 		if(managedExternaly_)
 		{
@@ -115,24 +115,24 @@ public:
 		}
 	}
 
-	timeValue startTime()const
+	TimeValueType startTime()const
 	{
 		return startTime_;
 	}
 
-	timeValue endTime()const
+	TimeValueType endTime()const
 	{
 		return endTime_;
 	}
 
-	timeValue saveInterval()const
+	TimeValueType saveInterval()const
 	{
 		return saveInterval_;
 	}
 
 	word timeName()const;	
 
-	timeValue currentTime() const 
+	TimeValueType currentTime() const 
 	{
 		return ti_.currentTime();
 	}

src/phasicFlow/repository/Time/timeInfo.hpp

@@ -36,16 +36,16 @@ private:
 	uint32 		currentIter_;
 
 	// - current time of simulation
-	timeValue   currentTime_;
+	TimeValueType   currentTime_;
 
 	// - integration time step
-	timeValue   dt_;
+	TimeValueType   dt_;
 
 	inline static uint32 presicion_ = 5;
 
 public:
 
-	timeInfo(uint32 cIter, timeValue cTime, timeValue dt)
+	timeInfo(uint32 cIter, TimeValueType cTime, TimeValueType dt)
 	  : currentIter_(cIter),
 	    currentTime_(cTime),
 	    dt_(dt)
@@ -55,31 +55,31 @@ public:
 	timeInfo(const dictionary& dict)
 	:
 		currentIter_(0),
-		currentTime_(dict.getVal<timeValue>("startTime")),
-		dt_( dict.getVal<timeValue>("dt"))
+		currentTime_(dict.getVal<TimeValueType>("startTime")),
+		dt_( dict.getVal<TimeValueType>("dt"))
 	{
 		presicion_ = dict.getValOrSet<uint32>("timePrecision",5);
 	}
 
-	timeInfo(timeValue currentTime, const dictionary& dict)
+	timeInfo(TimeValueType currentTime, const dictionary& dict)
 	:
 		currentIter_(0),
 		currentTime_(currentTime),
-		dt_( dict.getVal<timeValue>("dt"))
+		dt_( dict.getVal<TimeValueType>("dt"))
 	{
 		presicion_ = dict.getValOrSet<int32>("timePrecision",5);
 	}
 
-	inline const timeValue& currentTime()const
+	inline const TimeValueType& currentTime()const
 	{
 		return currentTime_;
 	}
 
-	inline const timeValue& t() const
+	inline const TimeValueType& t() const
 	{
 		return currentTime_;
 	}
-	inline const timeValue& dt() const
+	inline const TimeValueType& dt() const
 	{
 		return dt_;
 	}
@@ -109,7 +109,7 @@ public:
 	inline 
 	word prevTimeName()const
 	{
-		return real2FixedStripZeros( max(currentTime_-dt_, timeValue(0)), presicion_);
+		return real2FixedStripZeros( max(currentTime_-dt_, TimeValueType(0)), presicion_);
 	}
 
 	static

src/phasicFlow/repository/systemControl/sampleDictionary/settingsDict

@@ -0,0 +1,55 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	settingsDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// list of libraries that should be loaded during runtime;
+// for example, "libPostprocessData.so" (optional)
+libs  ();       
+
+// Auxiliary function to be run during simulation (optional) 
+auxFunctions    postprocessData;
+
+// time step for integration in seconds, (mandatory) 
+dt 				  0.00001; 	                     
+
+// start time for simulation, can be any valid value. Simulation starts from 
+// time folder with the same name 
+startTime 		  0; 
+
+// end time for simulation (mandatory)
+endTime 		  10;
+
+// time interval between each data save on disk, (mandatory)
+saveInterval 	  0.01; 
+
+// maximum number of digits for time folder, (opetional, default is 5)
+timePrecision     5; 
+
+// gravitational acceleration vector (m/s2), (mandatory)
+g 			      (0 -9.8 0);                         // gravity vector (m/s2) 
+
+// include a list of objects that are not normally in the save list on disk, (optional) 
+includeObjects (diameter);                       
+
+// exculde a list of objects from saving on the disk, (optional)
+excludeObjects (); 
+
+// integration method for position and velocity, (mandatory)
+integrationMethod 		AdamsBashforth2; 
+
+// if keep the integeration history under timeFolder/integeration or not, (optional, default is no)
+integrationHistory              Yes;
+
+// data writting format (ascii or binary), (mandatory)
+writeFormat				          ascii;         
+
+// report timers (Yes or No)?, (optional, default is Yes)
+timersReport 			            Yes;  	     
+
+// time interval between each timer report, (optional, default is 0.04)
+timersReportInterval   	           0.01;	     // time interval for reporting timers

src/phasicFlow/repository/systemControl/timeFolder.hpp

@@ -27,11 +27,11 @@ Licence:
 namespace pFlow
 {
 
-Map<timeValue, fileSystem> getTimeFolders(const fileSystem& path);
+Map<TimeValueType, fileSystem> getTimeFolders(const fileSystem& path);
 
 class timeFolder
 {
-	using timeList = Map<timeValue, fileSystem>;
+	using timeList = Map<TimeValueType, fileSystem>;
 
 protected:
 	
@@ -61,14 +61,14 @@ public:
 	}
 
 	inline
-	timeValue currentTime()const
+	TimeValueType currentTime()const
 	{
 		if(folders_.empty()) return -1;
 		return currentFolder_->first;
 	}
 
 	inline
-	timeValue nextTime()const
+	TimeValueType nextTime()const
 	{
 		auto next = currentFolder_;
 		next++;
@@ -98,7 +98,7 @@ public:
 		return !finished();
 	}
 
-	bool setTime(timeValue upto)
+	bool setTime(TimeValueType upto)
 	{
 		timeList::iterator orgFolder = currentFolder_;
 		
@@ -140,14 +140,14 @@ public:
 		return false;
 	}
 
-	timeValue startTime()const
+	TimeValueType startTime()const
 	{
 		if(folders_.empty()) return -1;
 		auto [t,f] = *folders_.begin();
 		return t;
 	}
 
-	timeValue endTime()const
+	TimeValueType endTime()const
 	{
 		if(folders_.empty()) return -1;
 		auto [t,f] = *(--folders_.end());
@@ -162,16 +162,16 @@ public:
 };
 
 inline
-Map<timeValue, fileSystem> getTimeFolders(const fileSystem& path)
+Map<TimeValueType, fileSystem> getTimeFolders(const fileSystem& path)
 {
-	Map<timeValue, fileSystem> tFolders;
+	Map<TimeValueType, fileSystem> tFolders;
 
 	auto subDirs = subDirectories(path);
 
 	for(auto& subD: subDirs)
 	{
 		auto timeName = tailName(subD.wordPath(), '/');
-		timeValue TIME;
+		TimeValueType TIME;
 		if( auto success = readReal(timeName, TIME); success)
 		{
 			if(!tFolders.insertIf(TIME, subD))

src/phasicFlow/structuredData/domain/sampleDictionary/domainDict

@@ -0,0 +1,64 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	domainDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        
+{
+	min (-0.12 -0.12 0.00);
+	max (0.12   0.12 0.11); 
+}
+
+
+pointSorting
+{
+	active 			Yes; // optional (default: No)
+
+	dx 				0.01; // optional (default: 0.01)	
+
+	timeControl 	simulationTime; // runTime, or timeStep
+	
+	startTime 		0.0; 
+	
+	endTime 		100; // optional (default: very large number)
+
+	sortingInterval 0.1; // in seconds 
+}
+
+boundaries
+{
+	left
+	{
+		type     exit;	                  // other options: periodict, reflective 
+	}
+
+	right
+	{
+		type     exit;                    // other options: periodict, reflective 
+	}
+
+	bottom
+	{
+		type     exit;                    // other options: periodict, reflective 
+	}
+
+	top
+	{
+		type     exit;                    // other options: periodict, reflective 
+	}
+
+	rear
+	{
+		type     exit;                    // other options: periodict, reflective 
+	}
+
+	front
+	{
+		type     exit;                    // other options: periodict, reflective 
+	}
+}

src/phasicFlow/structuredData/pointStructure/pointStructure/pointSorting/pointSorting.cpp

@@ -32,15 +32,23 @@ pFlow::pointSorting::pointSorting(const dictionary & dict)
     dx_(
         performSorting_()?
             dict.getVal<real>("dx"):
-            1.0
+            0.01
     )
 {
     if( performSorting_() )
-        REPORT(2)<<"Point sorting is "<<Yellow_Text("active")<<" in simulation"<<END_REPORT;
-    else
-       REPORT(2)<<"Point sorting is "<<Yellow_Text("inactive")<<" in simulation"<<END_REPORT;
+    {
+        REPORT(2)<<"Point sorting is "<<Yellow_Text("active")<<" in the simulation"<<END_REPORT;
+        dictionary dict2("pointSorting");
+        dict2.add("avtive", performSorting_);
+        dict2.add("dx", dx_);
+        timeControl_.write(dict2);
+        output.incrIndent();
+            output<<dict2<<endl;
+        output.decrIndent();
+    }
         
 }
+
 pFlow::uint32IndexContainer 
 pFlow::pointSorting::getSortedIndices(
     const box& boundingBox, 

src/phasicFlow/structuredData/pointStructure/pointStructure/pointSorting/pointSorting.hpp

@@ -50,9 +50,9 @@ public:
 		return performSorting_();
 	}
 
-	bool sortTime(uint32 iter, real t, real dt)const
+	bool sortTime(const timeInfo& ti)const
 	{
-		return performSorting_() && timeControl_.eventTime(iter, t, dt);
+		return performSorting_() && timeControl_.eventTime(ti);
 	}
 
 	uint32IndexContainer getSortedIndices(

src/phasicFlow/structuredData/pointStructure/pointStructure/pointStructure.cpp

@@ -178,7 +178,7 @@ bool pFlow::pointStructure::beforeIteration()
 {
     const timeInfo ti = TimeInfo();
 
-    if(pointSorting_().sortTime(ti.iter(), ti.t(), ti.dt()))
+    if(pointSorting_().sortTime(ti))
     {
         auto sortedIndices = pointSorting_().getSortedIndices(
             simulationDomain_().globalBox(),

src/phasicFlow/types/basicTypes/Logical.cpp

@@ -25,11 +25,14 @@ Licence:
 
 pFlow::Logical::Logical(const word& l)
 {
-	if (!evaluteWord(l, s_, yesNoSet_))
+	bool s;
+	int yesNoSet;
+	if (!evaluteWord(l, s, yesNoSet))
 	{
 		fatalErrorInFunction << "  invalid input for Logical: " << l << endl;
 		fatalExit;
 	}
+	*this = Logical(s, yesNoSet);
 }
 
 pFlow::Logical::Logical(const char* ch)
@@ -42,7 +45,7 @@ pFlow::Logical::evaluteWord(const word& l, bool& b, int& yesNoSet)
 {
 	auto Ul = toUpper(l);
 
-	for (int i = 0; i < 4; ++i)
+	for (int i = 1; i < 5; ++i)
 	{
 		if (toUpper(YesNo__[i][0]) == Ul)
 		{
@@ -89,20 +92,26 @@ pFlow::Logical::read(iIstream& is)
 		is.setBad();
 		return false;
 	}
-
-	return evaluteWord(w, s_, yesNoSet_);
+	bool s;
+	int yesNoSet;
+	if( evaluteWord(w, s, yesNoSet) )
+	{
+		*this = Logical(s, yesNoSet);
+		return true;
+	}
+	return false;
 }
 
 bool
 pFlow::Logical::write(iOstream& os) const
 {
-	if (s_)
+	if (s_ > 0)
 	{
-		os << YesNo__[yesNoSet_][0];
+		os << YesNo__[s_][0];
 	}
 	else
 	{
-		os << YesNo__[yesNoSet_][1];
+		os << YesNo__[-s_][1];
 	}
 	return os.check(FUNCTION_NAME);
 }

src/phasicFlow/types/basicTypes/Logical.hpp

@@ -41,24 +41,30 @@ class Logical
 private:
 
 	/// bool value
-	bool                     s_ = false;
+	/// negative value means false 
+	/// positive value means true
+	/// 0 means not set, but still valid as true
+	int8_t                     s_ = -1;
 
-	/// Set numbe of of Yes or No
-	int                      yesNoSet_ = 0;
 	
 	/// Set of Yes or Nos
-	inline static const word YesNo__[4][2] = { { "Yes", "No" },
+	inline static const word YesNo__[5][2] = { { "Y", "Y" },
+											   { "Yes", "No" },
 		                                       { "on", "off" },
 		                                       { "true", "false" },
 		                                       { "Ok", "No" } };
 
 	/// Construct from bool and set number
-	inline explicit Logical(bool s, int yns)
-	  : s_(s),
-	    yesNoSet_(yns)
+	inline Logical(bool s, int yns)
 	{
+		yns = std::max(1, std::min(4, yns));
+		s_ = s ? static_cast<int8_t>(yns) : static_cast<int8_t>(-yns);
 	}
 
+	inline explicit Logical(int8_t s)
+	{
+		s_ = s;
+	}
 public:
 
 	/// Type info
@@ -79,7 +85,8 @@ public:
 
 	/// Construct from bool
 	inline explicit Logical(bool s)
-	  : s_(s)
+	: 
+		Logical(s, 1)
 	{
 	}
 
@@ -104,8 +111,7 @@ public:
 	/// Assignment with bool
 	inline Logical& operator=(const bool& b)
 	{
-		s_        = b;
-		yesNoSet_ = 0;
+		*this = Logical(b);
 		return *this;
 	}
 
@@ -114,19 +120,19 @@ public:
 	/// () operator, return bool value
 	inline bool operator()() const
 	{
-		return s_;
+		return s_ > 0;
 	}
 
 	/// Return bool value
 	inline explicit operator bool() const
 	{
-		return s_;
+		return s_ > 0;
 	}
 
 	/// Not operator
 	inline Logical operator!() const
 	{
-		return Logical(!s_, yesNoSet_);
+		return  Logical(static_cast<int8_t>(-s_));
 	}
 
 	//// IO operations

src/phasicFlow/types/basicTypes/bTypesFunctions.hpp

@@ -21,7 +21,6 @@ Licence:
 
     \brief Helper functions for built-in types.
  */
-
 #ifndef __bTypesFunctions_hpp__
 #define __bTypesFunctions_hpp__
 

src/phasicFlow/types/basicTypes/builtinTypes.hpp

@@ -61,19 +61,20 @@ using uint64 = unsigned long long int;
 
 using word = std::string;
 
-using timeValue = double;
+/// type for time values
+using TimeValueType = double;
 
+/// type for indexing arrays and vectors 
 #ifdef pFlow_Build_Index64
 	#define Index64 1
-	using index = std::size_t;
+	using IndexType = std::size_t;
 	inline const char* IndexType__ = "std::size_t";
 #else
 	#define Index64 0
-	using index = uint32;
+	using IndexType = uint32;
 	inline const char* IndexType__ = "uint32";
 #endif
 
-
 inline word
 floatingPointDescription()
 {

thirdParty/README.md

@@ -0,0 +1,11 @@
+# Third-party packages used in PhasicFlow
+
+This folder contains the third-party packages that are used by PhasicFlow. Since the source code is under the main directory of the project, they are downloaded with the source code. But this does not mean that these packages are maintained by PhasicFlow or they are a part of the project.
+
+## [Zoltan](./Zoltan/)
+This package is used for space-decomposition and load balancing for MPI execution of the code. 
+
+## Thrust
+This package is a parallel library developed by NVIDIA. It is built for either CUDA or OpenMP depending of the type of build.  
+
+

thirdParty/Zoltan/CMakeLists.txt

@@ -0,0 +1,133 @@
+
+
+#
+# A) Define the package
+#
+
+TRIBITS_PACKAGE(Zoltan)
+
+#
+# B) Set up package-specific options
+#
+
+TRIBITS_ADD_OPTION_AND_DEFINE( ${PACKAGE_NAME}_ENABLE_UINT_IDS
+  UNSIGNED_INT_GLOBAL_IDS
+  "typedef unsigned int ZOLTAN_ID_TYPE"
+  OFF )
+
+TRIBITS_ADD_OPTION_AND_DEFINE( ${PACKAGE_NAME}_ENABLE_ULONG_IDS
+  UNSIGNED_LONG_GLOBAL_IDS
+  "typedef unsigned long ZOLTAN_ID_TYPE"
+  OFF )
+
+TRIBITS_ADD_OPTION_AND_DEFINE( ${PACKAGE_NAME}_ENABLE_ULLONG_IDS
+  UNSIGNED_LONG_LONG_GLOBAL_IDS
+  "typedef unsigned long long ZOLTAN_ID_TYPE"
+  OFF )
+
+TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_HUND
+  HAVE_ZOLTAN_HUND
+  "Enable support for HUND in ${PACKAGE_NAME}."
+  OFF )
+
+TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_KNUTH_HASH
+  HAVE_ZOLTAN_KNUTH_HASH
+  "Enable support for Knuth's hash function in ${PACKAGE_NAME}."
+  OFF )
+
+TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_F90INTERFACE
+  BUILD_ZOLTAN_F90_INTERFACE
+  "Enable build of F90 interface to ${PACKAGE_NAME}."
+  OFF )
+
+TRIBITS_ADD_OPTION_AND_DEFINE(${PACKAGE_NAME}_ENABLE_PURIFY
+  HAVE_PURIFY
+  "Enable work-arounds to purify bugs."
+  OFF )
+
+OPTION(${PACKAGE_NAME}_ENABLE_CPPDRIVER
+  "Enable C++ driver for ${PACKAGE_NAME}."
+  ${${PROJECT_NAME}_ENABLE_CXX} )
+
+IF (${PROJECT_NAME}_ENABLE_CXX) 
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK")
+ENDIF()
+
+IF(${PROJECT_NAME}_ENABLE_Fortran AND BUILD_ZOLTAN_F90_INTERFACE)
+
+  # Special Fortran compiler-specific flags
+  IF (${CMAKE_Fortran_COMPILER_ID} MATCHES "PGI")
+    SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DPGI")
+    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DPGI")
+  ENDIF()
+
+  IF (${CMAKE_Fortran_COMPILER_ID} MATCHES "LAHEY")
+    SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DFUJITSU")
+    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DFUJITSU")
+  ENDIF()
+
+  SET(ZOLTAN_BUILD_ZFDRIVE YES)
+ENDIF()
+
+#
+# C) Add the libraries, tests, and examples
+#
+
+IF (NOT TPL_ENABLE_MPI)
+  ADD_SUBDIRECTORY(siMPI)
+  SET(ZOLTAN_BUILD_ZFDRIVE NO)
+ENDIF()
+
+ADD_SUBDIRECTORY(src)
+
+TRIBITS_ADD_TEST_DIRECTORIES(src/driver)
+
+IF(ZOLTAN_BUILD_ZFDRIVE)
+  # CMAKE version > 2.6.4 is needed; earlier versions use C++ compiler to link
+  # fdriver, while fdriver needs F90.
+  TRIBITS_ADD_TEST_DIRECTORIES(src/fdriver)
+ENDIF()
+
+TRIBITS_ADD_TEST_DIRECTORIES(test)
+
+TRIBITS_ADD_EXAMPLE_DIRECTORIES(example)
+
+TRIBITS_EXCLUDE_FILES(
+  test/ch_brack2_3
+  test/ch_bug
+  test/ch_degenerate
+  test/ch_degenerateAA
+  test/ch_drake
+  test/ch_grid20x19
+  test/ch_hammond
+  test/ch_hammond2
+  test/ch_hughes
+  test/ch_nograph
+  test/ch_onedbug
+  test/ch_random
+  test/ch_serial
+  test/ch_slac
+  test/hg_cage10
+  test/hg_diag500_4
+  test/hg_ewgt
+  test/hg_felix
+  test/hg_ibm03
+  test/hg_ml27
+  test/hg_nograph
+  test/hg_vwgt
+  test/nem_ti_20k
+  test/nem_ti_4k
+  test/misc_siefert
+  test/th
+  test/bin
+  doc/Zoltan_html/tu_html
+  src/ZoltanComponent
+  src/driver_old
+  src/fdriver_old
+  )
+
+#
+# D) Do standard postprocessing
+#
+
+TRIBITS_PACKAGE_POSTPROCESS()

thirdParty/Zoltan/COPYRIGHT_AND_LICENSE

@@ -0,0 +1,45 @@
+/* 
+ * @HEADER
+ *
+ * ***********************************************************************
+ *
+ *  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+ *                  Copyright 2012 Sandia Corporation
+ *
+ * Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+ * the U.S. Government retains certain rights in this software.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ *
+ * 3. Neither the name of the Corporation nor the names of the
+ * contributors may be used to endorse or promote products derived from
+ * this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * Questions? Contact Karen Devine	kddevin@sandia.gov
+ *                    Erik Boman	egboman@sandia.gov
+ *
+ * ***********************************************************************
+ *
+ * @HEADER
+ */

thirdParty/Zoltan/Disclaimer

@@ -0,0 +1,17 @@
+
+Zoltan Library for Parallel Applications
+
+Neither Sandia, the government, the DOE, nor any of their employees, makes
+any warranty, express or implied, or assumes any legal liability or
+responsibility for the accuracy, completeness, or usefulness of any
+information, apparatus, product, or process disclosed, or represents that
+its use would not infringe privately owned rights. This information is made
+available on an "AS-IS" basis.
+ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+EXCLUDED HEREUNDER.
+Neither Sandia nor the Government, nor their agents, officers and employees
+shall be liable for any loss, damage (including, incidental, consequential
+and special), injury or other casualty of whatsoever kind, or by whomsoever
+caused, to the person or property of anyone arising out of or resulting from
+this information, or the accuracy and validity of this information. 

thirdParty/Zoltan/Known_Problems

@@ -0,0 +1,251 @@
+Problems existing in Zoltan.
+This file was last updated on $Date$
+
+-------------------------------------------------------------------------------
+ERROR CONDITIONS IN ZOLTAN
+When a processor returns from Zoltan to the application due to an error
+condition, other processors do not necessarily return the same condition.
+In fact, other processors may not know that the processor has quit Zoltan,
+and may hang in a communication (waiting for a message that is not sent 
+due to the error condition).  The parallel error-handling capabilities of
+Zoltan will be improved in future releases.
+-------------------------------------------------------------------------------
+RCB/RIB ON ASCI RED
+On ASCI Red, the number of context IDs (e.g., MPI Communicators) is limited
+to 8192.  The environment variable MPI_REUSE_CONTEXT_IDS must be set to 
+reuse the IDs; setting this variable, however, slows performance.
+An alternative is to set Zoltan_Parameter TFLOPS_SPECIAL to "1".  With 
+TFLOPS_SPECIAL set, communicators in RCB/RIB are not split and, thus, the
+application is less likely to run out of context IDs.  However, ASCI Red
+also has a bug that is exposed by TFLOPS_SPECIAL; when messages that use
+MPI_Send/MPI_Recv within RCB/RIB exceed the MPI_SHORT_MSG_SIZE, MPI_Recv 
+hangs.  We do not expect these conditions to exist on future platforms and,
+indeed, plan to make TFLOPS_SPECIAL obsolete in future versions of Zoltan
+rather than re-work it with MPI_Irecv.  -- KDD 10/5/2004
+-------------------------------------------------------------------------------
+ERROR CONDITIONS IN OCTREE, PARMETIS AND JOSTLE
+On failure, OCTREE, ParMETIS and Jostle methods abort rather than return 
+error codes.  
+-------------------------------------------------------------------------------
+ZOLTAN_INITIALIZE BUT NO ZOLTAN_FINALIZE
+If Zoltan_Initialize calls MPI_Init, then MPI_Finalize
+will never be called because there is no Zoltan_Finalize routine.
+If the application uses MPI and calls MPI_Init and MPI_Finalize,
+then there is no problem.
+-------------------------------------------------------------------------------
+HETEROGENEOUS ENVIRONMENTS
+Some parts of Zoltan currently assume that basic data types like 
+integers and real numbers (floats) have identical representation
+on all processors. This may not be true in a heterogeneous
+environment. Specifically, the unstructured (irregular) communication
+library is unsafe in a heterogeneous environment. This problem
+will be corrected in a future release of Zoltan for heterogeneous
+systems.
+-------------------------------------------------------------------------------
+F90 ISSUES
+Pacific Sierra Research (PSR) Vastf90 is not currently supported due to bugs 
+in the compiler with no known workarounds. It is not known when or if this 
+compiler will be supported. 
+
+N.A.Software FortranPlus is not currently supported due to problems with the 
+query functions. We anticipate that this problem can be overcome, and support 
+will be added soon. 
+-------------------------------------------------------------------------------
+PROBLEMS EXISTING IN PARMETIS 
+(Reported to the ParMETIS development team at the University of Minnesota,
+ metis@cs.umn.edu)
+
+Name: Free-memory write in PartGeomKway
+Version: ParMETIS 3.1.1
+Symptom: Free-memory write reported by Purify and Valgrind for graphs with
+         no edges.
+Description:
+  For input graphs with no (or, perhaps, few) edges, Purify and Valgrind
+  report writes to already freed memory as shown below.
+FMW: Free memory write:
+  * This is occurring while in thread 22199:
+        SetUp(void)    [setup.c:80]
+        PartitionSmallGraph(void) [weird.c:39]
+        ParMETIS_V3_PartGeomKway [gkmetis.c:214]
+        Zoltan_ParMetis [parmetis_interface.c:280]
+        Zoltan_LB      [lb_balance.c:384]
+        Zoltan_LB_Partition [lb_balance.c:91]
+        run_zoltan     [dr_loadbal.c:581]
+        main           [dr_main.c:386]
+        __libc_start_main [libc.so.6]
+        _start         [crt1.o]
+  * Writing 4 bytes to 0xfcd298 in the heap.
+  * Address 0xfcd298 is at the beginning of a freed block of 4 bytes.
+  * This block was allocated from thread -1781075296:
+        malloc         [rtlib.o]
+        GKmalloc(void) [util.c:151]
+        idxmalloc(void) [util.c:100]
+        AllocateWSpace [memory.c:28]
+        ParMETIS_V3_PartGeomKway [gkmetis.c:123]
+        Zoltan_ParMetis [parmetis_interface.c:280]
+        Zoltan_LB      [lb_balance.c:384]
+        Zoltan_LB_Partition [lb_balance.c:91]
+        run_zoltan     [dr_loadbal.c:581]
+        main           [dr_main.c:386]
+        __libc_start_main [libc.so.6]
+        _start         [crt1.o]
+  * There have been 10 frees since this block was freed from thread 22199:
+        GKfree(void)   [util.c:168]
+        Mc_MoveGraph(void) [move.c:92]
+        ParMETIS_V3_PartGeomKway [gkmetis.c:149]
+        Zoltan_ParMetis [parmetis_interface.c:280]
+        Zoltan_LB      [lb_balance.c:384]
+        Zoltan_LB_Partition [lb_balance.c:91]
+        run_zoltan     [dr_loadbal.c:581]
+        main           [dr_main.c:386]
+        __libc_start_main [libc.so.6]
+        _start         [crt1.o]
+Reported: Reported 8/31/09 http://glaros.dtc.umn.edu/flyspray/task/50
+Status:   Reported 8/31/09
+
+Name: PartGeom limitation
+Version: ParMETIS 3.0, 3.1
+Symptom: inaccurate number of partitions when # partitions != # processors
+Description:
+  ParMETIS method PartGeom produces decompositions with #-processor 
+  partitions only.  Zoltan parameters NUM_GLOBAL_PARTITIONS and 
+  NUM_LOCAL_PARTITIONS will be ignored.
+Reported: Not yet reported.  
+Status: Not yet reported.
+
+Name: vsize array freed in ParMetis 
+Version: ParMETIS 3.0 and 3.1
+Symptom: seg. fault, core dump at runtime
+Description:
+  When calling ParMETIS_V3_AdaptiveRepart with the vsize parameter,
+  ParMetis will try to free the vsize array even if it was
+  allocated in Zoltan. Zoltan will then try to free vsize again
+  later, resulting in a fatal error. As a temporary fix,
+  Zoltan will never call ParMetis with the vsize parameter. 
+Reported: 11/25/2003.
+Status: Acknowledged by George Karypis.
+
+Name: ParMETIS_V3_AdaptiveRepart and ParMETIS_V3_PartKWay crash 
+      for zero-sized partitions.
+Version: ParMETIS 3.1
+Symptom: run-time error "killed by signal 8" on DEC.  FPE, divide-by-zero.
+Description:
+  Metis divides by partition size; thus, zero-sized partitions
+  cause a floating-point exception. 
+Reported: 9/9/2003.
+Status: ?
+
+Name: ParMETIS_V3_AdaptiveRepart dies for zero-sized partitions.
+Version: ParMETIS 3.0
+Symptom: run-time error "killed by signal 8" on DEC.  FPE, divide-by-zero.
+Description:
+   ParMETIS_V3_AdaptiveRepart divides by partition size; thus, zero-sized 
+   partitions cause a floating-point exception.  This problem is exhibited in 
+   adaptive-partlocal3 tests.  The tests actually run on Sun and Linux machines 
+   (which don't seem to care about the divide-by-zero), but cause an FPE 
+   signal on DEC (Compaq) machines.
+Reported: 1/23/2003.
+Status: Fixed in ParMetis 3.1, but new problem appeared (see above).
+
+Name: ParMETIS_V3_AdaptiveRepart crashes when no edges.
+Version: ParMETIS 3.0
+Symptom: Floating point exception, divide-by-zero.
+Description:
+   Divide-by-zero in ParMETISLib/adrivers.c, function Adaptive_Partition, 
+   line 40.
+Reported: 1/23/2003.
+Status: Fixed in ParMetis 3.1.
+
+Name: Uninitialized memory read in akwayfm.c.
+Version: ParMETIS 3.0
+Symptom: UMR warning.
+Description:
+   UMR in ParMETISLib/akwayfm.c, function Moc_KWayAdaptiveRefine, near line 520.
+Reported: 1/23/2003.
+Status: Fixed in ParMetis 3.1.
+
+Name: Memory leak in wave.c
+Version: ParMETIS 3.0
+Symptom: Some memory not freed.
+Description:
+   Memory leak in ParMETISLib/wave.c, function WavefrontDiffusion;
+   memory for the following variables is not always freed:
+   solution, perm, workspace, cand
+   We believe the early return near line 111 causes the problem.
+Reported: 1/23/2003.
+Status: Fixed in ParMetis 3.1.
+
+Name: tpwgts ignored for small graphs.
+Version: ParMETIS 3.0
+Symptom: incorrect output (partitioning)
+Description:
+   When using ParMETIS_V3_PartKway to partition into partitions
+   of unequal sizes, the input array tpwgts is ignored and
+   uniform-sized partitions are computed. This bug shows up when
+   (a) the number of vertices is < 10000 and (b) only one weight
+   per vertex is given (ncon=1).
+Reported: Reported to George Karypis and metis@cs.umn.edu on 2002/10/30.
+Status: Fixed in ParMetis 3.1.
+
+
+Name: AdaptiveRepart crashes on partless test.
+Version: ParMETIS 3.0
+Symptom: run-time segmentation violation. 
+Description:
+   ParMETIS_V3_AdaptiveRepart crashes with a SIGSEGV if
+   the input array _part_ contains any value greater then
+   the desired number of partitions, nparts. This shows up
+   in Zoltan's "partless" test cases. 
+Reported: Reported to George Karypis and metis@cs.umn.edu on 2002/12/02.
+Status: Fixed in ParMetis 3.1.
+
+
+Name: load imbalance tolerance
+Version: ParMETIS 2.0
+Symptom: missing feature
+Description:
+   The load imbalance parameter UNBALANCE_FRACTION can
+   only be set at compile-time. With Zoltan it is
+   necessary to be able to set this parameter at run-time.
+Reported: Reported to metis@cs.umn.edu on 19 Aug 1999.
+Status: Fixed in version 3.0.
+
+
+Name: no edges
+Version: ParMETIS 2.0
+Symptom: segmentation fault at run time
+Description:
+   ParMETIS crashes if the input graph has no edges and
+   ParMETIS_PartKway is called. We suspect all the graph based
+   methods crash. From the documentation it is unclear if
+   a NULL pointer is a valid input for the adjncy array.
+   Apparently, the bug occurs both with NULL as input or
+   a valid pointer to an array.
+Reported: Reported to metis@cs.umn.edu on 5 Oct 1999.
+Status: Fixed in version 3.0.
+
+
+Name: no vertices
+Version: ParMETIS 2.0, 3.0, 3.1
+Symptom: segmentation fault at run time
+Description:
+   ParMETIS may crash if a processor owns no vertices.
+   The extent of this bug is not known (which methods are affected).
+   Again, it is unclear if NULL pointers are valid input.
+Reported: Reported to metis@cs.umn.edu on 6 Oct 1999.
+Status: Fixed in 3.0 and 3.1 for the graph methods, but not the geometric methods.
+        New bug report sent on 2003/08/20.
+
+
+Name: partgeom bug
+Version: ParMETIS 2.0
+Symptom: floating point exception
+Description:
+   For domains where the global delta_x, delta_y, or delta_z (in 3D)
+   is zero (e.g., all nodes lie along the y-axis), a floating point
+   exception can occur when the partgeom algorithm is used.
+Reported: kirk@cs.umn.edu in Jan 2001.
+Status: Fixed in version 3.0.
+
+-------------------------------------------------------------------------------
+

thirdParty/Zoltan/Makefile.am

@@ -0,0 +1,370 @@
+# @HEADER
+#
+########################################################################
+#
+#  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+#                  Copyright 2012 Sandia Corporation
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Questions? Contact Karen Devine	kddevin@sandia.gov
+#                    Erik Boman	        egboman@sandia.gov
+#
+########################################################################
+#
+# @HEADER
+
+
+## #######################################################################
+## Options to automake (rarely used - don't worry about it)
+## #######################################################################
+AUTOMAKE_OPTIONS = foreign
+
+## #######################################################################
+## Aclocal command (rarely used - don't worry about it)
+## #######################################################################
+ACLOCAL_AMFLAGS = -I config
+
+## #######################################################################
+## Additional files to be included in distribution for 'make dist'
+## #######################################################################
+ZOLTAN_TESTS = \
+    test/test_zoltan \
+    test/runtests \
+    test/ctest_zoltan.pl \
+    test/ch_simple \
+    test/hg_simple 
+
+ZOLTAN_DOCS = \
+    doc/Zoltan_html/Zoltan.html \
+    doc/Zoltan_html/Zoltan_FAQ.html \
+    doc/Zoltan_html/Zoltan_bugreport.html \
+    doc/Zoltan_html/Zoltan_cite.html \
+    doc/Zoltan_html/Zoltan_construction.html \
+    doc/Zoltan_html/Zoltan_phil.html \
+    doc/Zoltan_html/Zoltan_pubs.html \
+    doc/Zoltan_html/dev_html/brack3d.png \
+    doc/Zoltan_html/dev_html/dev.html \
+    doc/Zoltan_html/dev_html/dev_add.html \
+    doc/Zoltan_html/dev_html/dev_add_interface.html \
+    doc/Zoltan_html/dev_html/dev_add_lb.html \
+    doc/Zoltan_html/dev_html/dev_add_memory.html \
+    doc/Zoltan_html/dev_html/dev_add_params.html \
+    doc/Zoltan_html/dev_html/dev_add_remap.html \
+    doc/Zoltan_html/dev_html/dev_add_struct.html \
+    doc/Zoltan_html/dev_html/dev_cpp.html \
+    doc/Zoltan_html/dev_html/dev_degenerate.html \
+    doc/Zoltan_html/dev_html/dev_dist.html \
+    doc/Zoltan_html/dev_html/dev_dist_compile.html \
+    doc/Zoltan_html/dev_html/dev_dist_cvs.html \
+    doc/Zoltan_html/dev_html/dev_dist_dir.html \
+    doc/Zoltan_html/dev_html/dev_driver.html \
+    doc/Zoltan_html/dev_html/dev_fortran.html \
+    doc/Zoltan_html/dev_html/dev_hier.html \
+    doc/Zoltan_html/dev_html/dev_hsfc.html \
+    doc/Zoltan_html/dev_html/dev_intro.html \
+    doc/Zoltan_html/dev_html/dev_intro_coding.html \
+    doc/Zoltan_html/dev_html/dev_intro_philosophy.html \
+    doc/Zoltan_html/dev_html/dev_intro_sqe.html \
+    doc/Zoltan_html/dev_html/dev_lb.html \
+    doc/Zoltan_html/dev_html/dev_lb_interface.html \
+    doc/Zoltan_html/dev_html/dev_lb_structs.html \
+    doc/Zoltan_html/dev_html/dev_lb_types.html \
+    doc/Zoltan_html/dev_html/dev_mig.html \
+    doc/Zoltan_html/dev_html/dev_parmetis.html \
+    doc/Zoltan_html/dev_html/dev_phg.html \
+    doc/Zoltan_html/dev_html/dev_rcb.html \
+    doc/Zoltan_html/dev_html/dev_refs.html \
+    doc/Zoltan_html/dev_html/dev_reftree.html \
+    doc/Zoltan_html/dev_html/dev_rib.html \
+    doc/Zoltan_html/dev_html/dev_services.html \
+    doc/Zoltan_html/dev_html/dev_services_debug.html \
+    doc/Zoltan_html/dev_html/dev_services_hash.html \
+    doc/Zoltan_html/dev_html/dev_services_objlist.html \
+    doc/Zoltan_html/dev_html/dev_services_parallel.html \
+    doc/Zoltan_html/dev_html/dev_services_params.html \
+    doc/Zoltan_html/dev_html/dev_services_time.html \
+    doc/Zoltan_html/dev_html/dev_services_zoltantimer.html \
+    doc/Zoltan_html/dev_html/dev_test_script.html \
+    doc/Zoltan_html/dev_html/dev_view.html \
+    doc/Zoltan_html/dev_html/film2d.png \
+    doc/Zoltan_html/dev_html/hammondMesh.png \
+    doc/Zoltan_html/dev_html/hammondPoints.png \
+    doc/Zoltan_html/dev_html/zdrive.inp \
+    doc/Zoltan_html/ug_html/figures/arrow.gif \
+    doc/Zoltan_html/ug_html/figures/HGFigure.gif \
+    doc/Zoltan_html/ug_html/figures/hierexample.fig \
+    doc/Zoltan_html/ug_html/figures/hierexample.gif \
+    doc/Zoltan_html/ug_html/figures/Z.gif \
+    doc/Zoltan_html/ug_html/ug.html \
+    doc/Zoltan_html/ug_html/ug_alg.html \
+    doc/Zoltan_html/ug_html/ug_alg_block.html \
+    doc/Zoltan_html/ug_html/ug_alg_geom.html \
+    doc/Zoltan_html/ug_html/ug_alg_graph.html \
+    doc/Zoltan_html/ug_html/ug_alg_hier.html \
+    doc/Zoltan_html/ug_html/ug_alg_hsfc.html \
+    doc/Zoltan_html/ug_html/ug_alg_hypergraph.html \
+    doc/Zoltan_html/ug_html/ug_alg_jostle.html \
+    doc/Zoltan_html/ug_html/ug_alg_oct.html \
+    doc/Zoltan_html/ug_html/ug_alg_parkway.html \
+    doc/Zoltan_html/ug_html/ug_alg_parmetis.html \
+    doc/Zoltan_html/ug_html/ug_alg_patoh.html \
+    doc/Zoltan_html/ug_html/ug_alg_phg.html \
+    doc/Zoltan_html/ug_html/ug_alg_ptscotch.html \
+    doc/Zoltan_html/ug_html/ug_alg_random.html \
+    doc/Zoltan_html/ug_html/ug_alg_rcb.html \
+    doc/Zoltan_html/ug_html/ug_alg_reftree.html \
+    doc/Zoltan_html/ug_html/ug_alg_rib.html \
+    doc/Zoltan_html/ug_html/ug_alg_simple.html \
+    doc/Zoltan_html/ug_html/ug_backward.html \
+    doc/Zoltan_html/ug_html/ug_color.html \
+    doc/Zoltan_html/ug_html/ug_color_parallel.html \
+    doc/Zoltan_html/ug_html/ug_cpp.html \
+    doc/Zoltan_html/ug_html/ug_examples.html \
+    doc/Zoltan_html/ug_html/ug_examples_init.html \
+    doc/Zoltan_html/ug_html/ug_examples_lb.html \
+    doc/Zoltan_html/ug_html/ug_examples_mig.html \
+    doc/Zoltan_html/ug_html/ug_examples_query.html \
+    doc/Zoltan_html/ug_html/ug_fortran.html \
+    doc/Zoltan_html/ug_html/ug_graph_vs_hg.html \
+    doc/Zoltan_html/ug_html/ug_index.html \
+    doc/Zoltan_html/ug_html/ug_interface.html \
+    doc/Zoltan_html/ug_html/ug_interface_augment.html \
+    doc/Zoltan_html/ug_html/ug_interface_color.html \
+    doc/Zoltan_html/ug_html/ug_interface_init.html \
+    doc/Zoltan_html/ug_html/ug_interface_lb.html \
+    doc/Zoltan_html/ug_html/ug_interface_mig.html \
+    doc/Zoltan_html/ug_html/ug_interface_order.html \
+    doc/Zoltan_html/ug_html/ug_intro.html \
+    doc/Zoltan_html/ug_html/ug_order.html \
+    doc/Zoltan_html/ug_html/ug_order_parmetis.html \
+    doc/Zoltan_html/ug_html/ug_order_ptscotch.html \
+    doc/Zoltan_html/ug_html/ug_param.html \
+    doc/Zoltan_html/ug_html/ug_query.html \
+    doc/Zoltan_html/ug_html/ug_query_lb.html \
+    doc/Zoltan_html/ug_html/ug_query_mig.html \
+    doc/Zoltan_html/ug_html/ug_refs.html \
+    doc/Zoltan_html/ug_html/ug_release.html \
+    doc/Zoltan_html/ug_html/ug_usage.html \
+    doc/Zoltan_html/ug_html/ug_util.html \
+    doc/Zoltan_html/ug_html/ug_util_comm.html \
+    doc/Zoltan_html/ug_html/ug_util_dd.html \
+    doc/Zoltan_html/ug_html/ug_util_mem.html 
+
+ZOLTAN_SAMPLE = \
+       SampleConfigurationScripts/mac_osX_no_fortran \
+       SampleConfigurationScripts/linux_with_purify_zoltan_only \
+       SampleConfigurationScripts/mac_osX_zoltan_only \
+       SampleConfigurationScripts/linux_zoltan_only \
+       SampleConfigurationScripts/linux_trilinos_runtests        \
+       SampleConfigurationScripts/linux_zoltan_dist  \
+       SampleConfigurationScripts/mac_osX_zoltan_dist
+
+
+ZOLTAN_CMAKE = \
+       CMakeLists.txt \
+       src/CMakeLists.txt \
+       src/driver/CMakeLists.txt \
+       src/fdriver/CMakeLists.txt \
+       test/CMakeLists.txt \
+       test/ch_simple/CMakeLists.txt \
+       test/hg_simple/CMakeLists.txt \
+       cmake/Dependencies.cmake  \
+       cmake/Zoltan_config.h.in
+
+EXTRA_DIST = config/generate-makeoptions.pl \
+       README.html README.txt \
+       config/strip_dup_incl_paths.pl config/strip_dup_libs.pl \
+       config/replace-install-prefix.pl config/string-replace.pl \
+       config/token-replace.pl \
+       Disclaimer GNU_Lesser_GPL.txt Known_Problems VERSION \
+       $(ZOLTAN_DOCS) $(ZOLTAN_SAMPLE) $(ZOLTAN_TESTS)
+
+
+## #######################################################################
+## Tools in the auxillary directory 
+## #######################################################################
+AUX_DIST = config/install-sh config/missing config/mkinstalldirs 
+
+## #######################################################################
+## Files to be deleted by 'make maintainer-clean'
+## #######################################################################
+MAINTAINERCLEANFILES = Makefile.in aclocal.m4 autom4te.cache/* \
+	configure config.status config.log \
+	src/common/config-h.in src/common/stamp-h.in \
+	$(AUX_DIST) 
+
+#The following line helps the test harness recover from build errors.
+
+all-local:
+	@echo ""
+	@echo "Trilinos package zoltan built successfully."
+	@echo ""
+
+## #######################################################################
+## Subdirectories to be make'd recursively
+## #######################################################################
+
+#We now build tests and examples through separate make targets, rather than
+#during "make".  We still need to conditionally include the test and example
+#in SUBDIRS, even though BUILD_TESTS and BUILD_EXAMPLES will never be
+#defined, so that the tests and examples are included in the distribution
+#tarball.
+
+#Add this later
+if SUB_TEST
+TEST_SUBDIR=
+endif
+
+if SUB_EXAMPLE
+EXAMPLE_SUBDIR=example
+endif
+
+if BUILD_TESTS
+tests: examples
+	@echo ""
+	@echo "Now building zoltan tests."
+	@echo ""
+	@echo "Zoltan tests use drivers and input files; no compilation necessary."
+	@echo ""
+	@echo "Finished building zoltan tests."
+	@echo ""
+else
+tests:
+	@echo "zoltan tests were disabled at configure time"
+endif
+
+if BUILD_EXAMPLES
+examples:
+	@echo ""
+	@echo "Now building zoltan examples."
+	@echo ""
+	cd $(top_builddir)/example && $(MAKE)
+	@echo ""
+	@echo "Finished building zoltan examples."
+	@echo ""
+
+install-examples:
+	cd $(top_builddir)/example && $(MAKE) install
+else
+examples:
+	@echo "zoltan examples were disabled at configure time"
+
+install-examples:
+	@echo "zoltan examples were disabled at configure time"
+endif
+
+clean-tests:
+	cd $(top_builddir)/test && $(MAKE) clean
+
+clean-examples:
+	cd $(top_builddir)/example && $(MAKE) clean
+
+everything:
+	$(MAKE) && $(MAKE) examples && $(MAKE) tests
+
+clean-everything:
+	$(MAKE) clean-examples && $(MAKE) clean-tests && $(MAKE) clean
+
+install-everything:
+	$(MAKE) install && $(MAKE) install-examples
+
+if HAVE_MPI
+SIMPI_SUBDIR=
+else
+SIMPI_SUBDIR=siMPI
+endif
+
+SUBDIRS = $(SIMPI_SUBDIR) src $(EXAMPLE_SUBDIR) $(TEST_SUBDIR) 
+
+## #######################################################################
+## The below targets allow you to use the new
+## testharness to run the test suite as make targets
+## #######################################################################
+
+TRILINOS_HOME_DIR=@abs_top_srcdir@/../..
+TRILINOS_BUILD_DIR=@abs_top_builddir@/../..
+TRILINOS_MPI_MAX_PROC=4
+TRILINOS_TEST_CATEGORY=INSTALL
+
+runtests-serial :
+	$(PERL_EXE) $(TRILINOS_HOME_DIR)/commonTools/test/utilities/runtests \
+  --trilinos-dir=$(TRILINOS_HOME_DIR) \
+  --comm=serial \
+  --build-dir=$(TRILINOS_BUILD_DIR) \
+  --category=$(TRILINOS_TEST_CATEGORY) \
+  --output-dir=@abs_top_builddir@/test/runtests-results \
+  --verbosity=1 \
+  --packages=zoltan
+
+runtests-mpi :
+	$(PERL_EXE) $(TRILINOS_HOME_DIR)/commonTools/test/utilities/runtests \
+  --trilinos-dir=$(TRILINOS_HOME_DIR) \
+  --comm=mpi \
+  --mpi-go=$(TRILINOS_MPI_GO) \
+  --build-dir=$(TRILINOS_BUILD_DIR) \
+  --max-proc=$(TRILINOS_MPI_MAX_PROC) \
+  --category=$(TRILINOS_TEST_CATEGORY) \
+  --output-dir=@abs_top_builddir@/test/runtests-results \
+  --verbosity=1 \
+  --packages=zoltan
+
+## #######################################################################
+## Export makefile stuff
+## #######################################################################
+
+if USING_EXPORT_MAKEFILES
+
+install-exec-hook:	
+	mkdir -p $(DESTDIR)$(includedir)
+	cp $(top_builddir)/Makefile.export.zoltan $(DESTDIR)$(includedir)/.
+	$(PERL_EXE) $(top_srcdir)/config/replace-install-prefix.pl \
+		--exec-prefix=$(exec_prefix) \
+		--my-export-makefile=Makefile.export.zoltan \
+		--my-abs-top-srcdir=@abs_top_srcdir@ \
+		--my-abs-incl-dirs=@abs_top_builddir@/src:@abs_top_srcdir@/src \
+		--my-abs-lib-dirs=@abs_top_builddir@/src
+	$(PERL_EXE) $(top_srcdir)/config/generate-makeoptions.pl $(top_builddir)/src/Makefile ZOLTAN > $(DESTDIR)$(includedir)/Makefile.export.zoltan.macros
+
+uninstall-hook:
+	rm -f $(includedir)/Makefile.export.zoltan
+	rm -f $(includedir)/Makefile.export.zoltan.macros
+
+else 
+
+install-exec-hook:
+
+uninstall-hook:
+
+endif
+
+## #######################################################################
+

thirdParty/Zoltan/Makefile.export.zoltan.in

@@ -0,0 +1,80 @@
+@HAVE_MPI_FALSE@SIMPI_INCDIR = -I@abs_top_srcdir@/siMPI/pyMPI/siMPI
+@HAVE_MPI_FALSE@SIMPI_LIBS = -L@abs_top_builddir@/siMPI/pyMPI/siMPI -lsimpi
+
+ZOLTAN_INCLUDES = -I@abs_top_builddir@/src/include -I@abs_top_srcdir@/src/include $(SIMPI_INCDIR)
+
+#@BUILD_FORTRAN90DRIVER_TRUE@ZFORLIBS = @FCLIBS@
+@USE_FORTRAN_TRUE@ZFLIBS = @FLIBS@
+#The following line can be edited in the case that -lm is not available
+@USE_FORTRAN_FALSE@ZFLIBS = -lm
+#@BUILD_FORTRAN90DRIVER_FALSE@ZFORLIBS = $(ZFLIBS)
+ZFORLIBS = $(ZFLIBS)
+
+ZOLTAN_LIBS = @LDFLAGS@ -L@abs_top_builddir@/src -lzoltan @LIBS@ $(ZFORLIBS) $(SIMPI_LIBS) 
+
+ZOLTAN_LIBRARY_INCLUDES = -I@abs_top_builddir@/src/include -I@abs_top_srcdir@/src/include -I@abs_top_srcdir@/src/all -I@abs_top_srcdir@/src/coloring -I@abs_top_srcdir@/src/ha -I@abs_top_srcdir@/src/hier -I@abs_top_srcdir@/src/hsfc -I@abs_top_srcdir@/src/lb -I@abs_top_srcdir@/src/oct -I@abs_top_srcdir@/src/order -I@abs_top_srcdir@/src/par -I@abs_top_srcdir@/src/params -I@abs_top_srcdir@/src/tpls -I@abs_top_srcdir@/src/ccolamd -I@abs_top_srcdir@/src/phg -I@abs_top_srcdir@/src/rcb -I@abs_top_srcdir@/src/reftree -I@abs_top_srcdir@/src/timer -I@abs_top_srcdir@/src/Utilities/Communication -I@abs_top_srcdir@/src/Utilities/Timer -I@abs_top_srcdir@/src/Utilities/DDirectory -I@abs_top_srcdir@/src/Utilities/Memory -I@abs_top_srcdir@/src/Utilities/shared -I@abs_top_srcdir@/src/zz -I@abs_top_srcdir@/src/graph -I@abs_top_srcdir@/src/matrix -I@abs_top_srcdir@/src/simple $(SIMPI_INCDIR)
+
+ZOLTAN_DEPS = @abs_top_builddir@/src/libzoltan.a
+
+############################################################################
+#
+# Export MPI settings
+#
+############################################################################
+
+# MPI libraries
+ZOLTAN_MPI_LIBS = @MPI_LIBS@
+
+# MPI include path
+ZOLTAN_MPI_INC = @MPI_INC@
+
+# Path to MPI libraries
+ZOLTAN_MPI_LIBDIR = @MPI_LIBDIR@
+
+# Path to MPI root
+ZOLTAN_MPI_DIR = @MPI_DIR@
+
+############################################################################
+#
+# Export Fortran libraries
+#
+############################################################################
+
+# Fortran & standard math libs
+#ZOLTAN_FCLIBS = @FCLIBS@
+ZOLTAN_FLIBS = $(ZFLIBS)
+
+# Extra libraries
+ZOLTAN_EXTRA_LIBS = @LIBS@
+
+############################################################################
+#
+# Export compiler settings
+#
+############################################################################
+
+# Extra definitions
+ZOLTAN_DEFS = @DEFS@
+
+# Fortran compilation flags
+@BUILD_FORTRAN90DRIVER_TRUE@ZOLTAN_FCFLAGS = @FCFLAGS@
+@USE_FORTRAN_TRUE@ZOLTAN_FFLAGS = @FFLAGS@
+ 
+# C compilation flags
+ZOLTAN_CFLAGS = @CFLAGS@
+
+# C++ compilation flags
+ZOLTAN_CXXFLAGS = @CXXFLAGS@
+
+# linker flags
+ZOLTAN_LDFLAGS = @LDFLAGS@
+
+
+############################################################################
+#
+# Export the ranlib and archiver to be used
+#
+############################################################################
+
+ZOLTAN_RANLIB = @RANLIB@
+

thirdParty/Zoltan/README

@@ -0,0 +1,94 @@
+# @HEADER
+#
+########################################################################
+#
+#  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+#                  Copyright 2012 Sandia Corporation
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Questions? Contact Karen Devine	kddevin@sandia.gov
+#                    Erik Boman	        egboman@sandia.gov
+#
+########################################################################
+#
+# @HEADER
+@HEADER
+
+**********************************************************************
+
+ Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+                 Copyright 2012 Sandia Corporation
+
+Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+the U.S. Government retains certain rights in this software.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the Corporation nor the names of the
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Questions? Contact Karen Devine	kddevin@sandia.gov
+                   Erik Boman	egboman@sandia.gov
+
+@HEADER
+
+##############################################################################
+
+INSTALLATION
+------------
+Instructions for building and installing Zoltan using CMAKE or Autotools
+are at the following web site:
+
+ http://www.cs.sandia.gov/zoltan/ug_html/ug_usage.html
+

thirdParty/Zoltan/README.developer

@@ -0,0 +1,166 @@
+# @HEADER
+#
+########################################################################
+#
+#  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+#                  Copyright 2012 Sandia Corporation
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Questions? Contact Karen Devine	kddevin@sandia.gov
+#                    Erik Boman	        egboman@sandia.gov
+#
+########################################################################
+#
+# @HEADER
+lriesen@sandia.gov
+November 29, 2010
+
+Notes on typedefs that were just introduced in order to support 64-bit global counts and IDs:
+
+ZOLTAN_ID_TYPE:
+==============
+
+A ZOLTAN_ID_TYPE is still the type that we use for global IDs passed in by the user.  However now the ZOLTAN_ID_TYPE can be set at configuration time.  It can be unsigned int, unsigned long, or unsigned long long.  The default is unsigned int.
+
+In CMake you can choose: 
+
+-D Zoltan_ENABLE_UINT_IDS:Bool=ON
+-D Zoltan_ENABLE_ULONG_IDS:Bool=ON
+-D Zoltan_ENABLE_ULLONG_IDS:Bool=ON
+
+Using autoconf it's:
+
+--with-id-type=uint
+--with-id-type=ulong
+--with-id-type=ullong
+
+To print a ZOLTAN_ID_TYPE use ZOLTAN_ID_SPEC:
+
+printf("GID: " ZOLTAN_ID_SPEC ", LID %d\n", my_gid, my_lid);
+
+To send a ZOLTAN_ID_TYPE in an MPI message, use ZOLTAN_ID_MPI_TYPE:
+
+MPI_Bcast(&gid, 1, ZOLTAN_ID_MPI_TYPE, 0, MPI_COMM_WORLD);
+
+To silence compiler warnings, you can properly specify a constant of type ZOLTAN_ID_TYPE using ZOLTAN_ID_CONSTANT:
+
+a = ZOLTAN_ID_CONSTANT(99)
+
+ZOLTAN_GNO_TYPE:
+===============
+ZOLTAN_GNO_TYPE is a new typedef which Zoltan uses for global counts and for internal global IDs regardless of the definition of ZOLTAN_ID_TYPE.  It is defined to be ssize_t, so it is signed and it will be 64 bits on a 64-bit architecture and 32 bits on a 32-bit architecture.  
+
+The MPI_Datatype for ZOLTAN_GNO_TYPE is returned by Zoltan_mpi_gno_type().
+
+Any time that Zoltan creates a new problem from the application supplied problem it uses ZOLTAN_GNO_TYPE for the object IDs.
+
+indextype and weighttype:
+========================
+
+At compile time, the Zoltan library defines indextype and weighttype to coincide with the third party graph libraries, if any, that it has been configured to work with.  
+
+The "indextype" will be the data type used by the third party library (TPL) for global IDs.
+
+The "weighttype" will be the data type used by the TPL for weights.
+
+Based on configure-time parameters, Zoltan will recognize and correcty set types for Metis, ParMetis, 32- or 64-bit Scotch or 32- or 64-bit PTScotch.
+
+As a developer, it is important to know where the boundary is in the code for the use of Zoltan's types (ZOLTAN_ID_TYPE, ZOLTAN_GNO_TYPE, float) versus the types used by the TPL (indextype, weighttype).  A simplified explanation is that indextype and weighttype are only used in source code that is in the "tpls" directory.
+
+More specifically, it goes like this:
+
+1. Zoltan calls the application query functions to obtain the graph using Zoltan's data types for IDs and weights.
+
+2. Zoltan builds graph and matrix structures in Zoltan_ZG_Build using Zoltan's data types.  (I suspect the "ZG" stands for "Zoltan Graph").
+
+3. The graph is exported to the TPL data structures in Zoltan_ZG_Export.  This is the point where arrays are converted if necessary to the data types used by the third party libraries.  The C-structures with names like ZOLTAN_Third_* and others found in tpls/third_library.h use the indextype and weighttype data types.
+
+4. Of course the TPL is called with indextype and weighttype objects.
+
+5. Zoltan_Postprocess_Graph is called on the TPL structures and writes the ZOLTAN_Output_Part structure which uses Zoltan's data types.
+
+6. Zoltan_Third_Export_User uses the ZOLTAN_Output_Part structure to write the part assignments to the structures returned to the user.
+
+To print a indextype or weighttype use TPL_IDX_SPEC or TPL_WGT_SPEC respectively.
+
+If the TPL weight type is a floating point type, then TPL_FLOAT_WEIGHT will be defined.
+
+If the TPL weight type is an integral type, then TPL_INTEGRAL_WEIGHT will be defined.
+
+Other useful TPL configuration macro definitions can be found in tpls/third_library_const.h.
+
+Zoltan can be configured to use both Scotch and ParMetis as long as the 32-bit version of Scotch is used.
+
+Assumptions:
+===========
+
+sizeof(ZOLTAN_GNO_TYPE) >= sizeof(ZOLTAN_ID_TYPE)
+sizeof(ZOLTAN_ID_TYPE) >= sizeof(int)
+
+Some changes to support 64-bit IDs:
+==================================
+
+Zoltan_Map_Create() used to assume it was handling keys that were multiples of ZOLTAN_ID_TYPEs.  Now you supply the number of bytes in the key, not the number of ZOLTAN_ID_TYPEs.
+
+Because testing of this branch involves running large memory problems, I added the function Zoltan_write_linux_meminfo() which will write out the contents of /proc/meminfo on a Linux machine.  The new function Zoltan_Memory_Get_Debug() returns the debug level set in mem.c by Zoltan_Memory_Debug().  zdrive has a new input option
+
+  zoltan memory debug level = n
+
+which will set the debug level.  Then after partitioning, zdrive checks the debug level and if there was an error and it is running on a linux machine it will dump out /proc/meminfo.
+
+I modified the configure script to define HOST_LINUX on a linux machine.
+
+I wrote three tests in tests/Large_Data that test PHG, RCB and RIB with arbitrarily large numbers of objects.  They have signal handlers that call Zoltan_write_linux_meminfo() on a Linux machine.  One test can be configured to use 64-bit IDs when it has less than 2*10^9 IDs.
+
+Limitations:
+===========
+The reftree and oct methods have not been converted to support 64-bit global IDs and global numbers.
+
+INTERESTING CHART:
+=================
+
+32 and 64 bit data models (ILP - integer/long/pointer):
+
+type            LP32    ILP32   ILP64   LLP64   LP64
+
+char            8       8       8       8       8
+short           16      16      16      16      16
+_int32                          32
+int             16      32      64      32      32
+long            32      32      64      32      64
+long long                               64
+pointer         32      32      64      64      64
+
+ILP32 is most widely used.
+LP64 is most widely used.
+
+LLP64 is ILP32 with new 64 bit int added to it - used for Win64.

thirdParty/Zoltan/README.md

@@ -0,0 +1,38 @@
+# Zoltan
+Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit -- Distribution site
+
+The most up-to-date version of Zoltan is in the Trilinos framework at https://github.com/trilinos/Trilinos.  
+
+This site provides stand-alone releases of Zoltan, separate from Trilinos:  https://github.com/sandialabs/Zoltan/releases.  Stand-alone releases of Zoltan may lag the Trilinos repo code. 
+
+You can download individual releases of Zoltan from this site, or clone the Trilinos repository 
+https://github.com/trilinos/Trilinos to get the most up-to-date version of Zoltan.  Individual releases are tarballs that can be unzipped and built with autotools/make.  
+
+Trilinos clones include Zoltan in directory Trilinos/packages/zoltan.  In this directory, you can 
+build Zoltan separately from Trilinos using autotools/make.  Or in the Trilinos repository, 
+you can build Zoltan using Trilinos' cmake system.
+
+The main Zoltan page is https://sandialabs.github.io/Zoltan/
+
+See https://sandialabs.github.io/Zoltan/ug_html/ug_usage.html
+for details on building Zoltan.
+
+Release history:  https://sandialabs.github.io/Zoltan/ug_html/ug_release.html
+* Version 3.90 (4/08/21; as in Trilinos v13; d328e0e2a8a5c48a4e01d6541cd8c0eb7f364823)
+* Version 3.83 (1/28/16; as in Trilinos v12.6; aaf328db7e43001ee2d3148f72f12147e51c3293)
+* Version 3.82 (5/1/15; as in Trilinos v12)
+* Version 3.81 (11/06/14; as in Trilinos v11.12.2)
+* Version 3.8 (10/28/13; as in Trilinos v10.11)
+* Version 3.6 (11/2/11; as in Trilinos v10.8)
+* Version 3.501 (5/12/11; as in Trilinos v10.6 with additions) 
+* Version 3.3 (7/31/10; as in Trilinos v10.4)
+* Version 3.2 (10/5/09)
+* Version 3.1 (9/30/08)
+* Version 3.0 (5/30/07)
+* Version 2.1 (10/05/06)
+* Version 2.0 (7/17/06)
+* Version 1.5 (5/29/03)
+* Version 1.4 (6/18/02)
+* Version 1.3 (3/27/02) -- the Original
+
+Questions?  Email zoltan-dev@software.sandia.gov

thirdParty/Zoltan/ReleaseNotes.txt

@@ -0,0 +1,60 @@
+Zoltan release notes for Trilinos v12.8
+
+Improved robustness of RCB partitioner for problems where many objects have
+weight = 0 (e.g., PIC codes).  Convergence is faster and the stopping 
+criteria are more robust.
+
+Fixed bug that occurred when RETURN_LIST=PARTS and (Num_GID > 1 or Num_LID > 1);
+GIDs and LIDs are now copied correctly into return lists.
+
+Fixed a bug related to struct padding in the siMPI serial MPI interface.
+
+-----------------------
+
+Zoltan release notes for Trilinos v12.6
+
+Minor code cleanup and bug fixes.
+
+New Zoltan_Get_Fn interface returning pointers to callback functions.
+See zoltan/src/include/zoltan.h for details.
+
+Closest stand-alone Zoltan release is v3.83.  
+http://www.cs.sandia.gov/Zoltan
+
+-----------------------
+
+Zoltan release notes for Trilinos v11.8
+
+Revised Scotch TPL specification in Trilinos' CMake environment to link
+with all libraries needed by Scotch v6.
+
+Fixed bug in interface to ParMETIS v4 when multiple vertex weights are used.
+Fixed bug in interface to Scotch when some processor has no vertices.
+
+-----------------------
+
+Zoltan release notes for Trilinos v11.
+
+Highlights are listed below; for more details, see 
+Trilinos/packages/zoltan/doc/Zoltan_html/ug_html/ug_release.html .
+
+-  Zoltan is now released under Trilinos' BSD license.
+
+-  The following Zoltan features are no longer supported in Trilinos v11:
+   +  Zoltan v1 interface (as described in Zoltan include file lbi_const.h)
+   +  Partitioning method OCTPART: use partitioning method HSFC instead.
+
+
+-  Hierarchical partitioning received several performance, interface and 
+   testing improvements.  An easier-to-use interface has been 
+   added using simple parameters (HIER_ASSIST, PLATFORM_NAME, TOPOLOGY)
+   instead of callback functions; the callback function interface is still
+   supported. 
+
+-  Memory usage in Zoltan Distributed Data Directories is improved, leading to
+   faster execution times for data directories and hierarchical partitioning.
+
+-  Compilation with gcc 4.7 is now supported.
+
+-  Zoltan supports PT-Scotch v5.1.12 and ParMETIS v4, as well as some older
+   versions of these TPLs. 

thirdParty/Zoltan/SampleCmakeScripts/linux_zoltan_gid_64_only

@@ -0,0 +1,31 @@
+#!/bin/csh
+# Sample script for building using CMAKE on linux workstation octopi.
+# 64-bit, Zoltan only.
+
+# Clean up the mess from previous configurations.
+/bin/rm -r cmake* CMake* CPack* CTest* Dart* Trilinos* Testing packages Makefile OUT* 
+
+cmake \
+-D CMAKE_INSTALL_PREFIX:FILEPATH="/home/lriesen/projects/Trilinos/build" \
+-D TPL_ENABLE_MPI:BOOL=ON \
+-D CMAKE_C_FLAGS:STRING="-m64 -g -DZOLTAN_ID_TYPE_LONG -std=c99" \
+-D CMAKE_CXX_FLAGS:STRING="-m64 -g" \
+-D CMAKE_Fortran_FLAGS:STRING="-m64 -g" \
+-D CMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+-D MPIEXEC_MAX_NUMPROCS:STRING=11 \
+-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
+-D Trilinos_ENABLE_EXAMPLES:BOOL=ON \
+-D Trilinos_VERBOSE_CONFIGURE:BOOL=ON \
+-D Trilinos_ENABLE_Zoltan:BOOL=ON \
+-D Zoltan_ENABLE_EXAMPLES:BOOL=ON \
+-D Zoltan_ENABLE_TESTS:BOOL=ON \
+-D Zoltan_ENABLE_ParMETIS:BOOL=ON \
+-D ParMETIS_INCLUDE_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/all/src/ParMETIS3_1" \
+-D ParMETIS_LIBRARY_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/lib/openmpi/ParMETIS3_1" \
+-D Zoltan_ENABLE_Scotch:BOOL=OFF \
+-D Zoltan_ENABLE_PaToH:BOOL=OFF \
+.. |& tee OUTPUT.CMAKE
+
+make |& tee OUTPUT.MAKE
+make install |& tee OUTPUT.INSTALL
+

thirdParty/Zoltan/SampleCmakeScripts/linux_zoltan_only

@@ -0,0 +1,36 @@
+#!/bin/csh
+# Sample script for building using CMAKE on linux workstation octopi.
+# 64-bit, Zoltan only.
+# Run in Trilinos/Obj_cmake.
+
+# Clean up the mess from previous configurations.
+/bin/rm -r cmake* CMake* CPack* CTest* Dart* Trilinos* Testing packages Makefile
+
+cmake \
+-D CMAKE_INSTALL_PREFIX:FILEPATH="/Net/local/homes/kddevin/code/trilinos/Obj_cmake" \
+-D TPL_ENABLE_MPI:BOOL=ON \
+-D CMAKE_C_FLAGS:STRING="-m64 -g" \
+-D CMAKE_CXX_FLAGS:STRING="-m64 -g" \
+-D CMAKE_Fortran_FLAGS:STRING="-m64 -g" \
+-D CMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+-D MPI_EXEC_MAX_NUMPROCS:STRING=11 \
+-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
+-D Trilinos_ENABLE_EXAMPLES:BOOL=ON \
+-D Trilinos_VERBOSE_CONFIGURE:BOOL=ON \
+-D Trilinos_ENABLE_Zoltan:BOOL=ON \
+-D Zoltan_ENABLE_EXAMPLES:BOOL=ON \
+-D Zoltan_ENABLE_TESTS:BOOL=ON \
+-D Zoltan_ENABLE_ParMETIS:BOOL=ON \
+-D ParMETIS_INCLUDE_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/all/src/ParMETIS3_1" \
+-D ParMETIS_LIBRARY_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/lib/openmpi/ParMETIS3_1" \
+-D Zoltan_ENABLE_Scotch:BOOL=ON \
+-D Scotch_INCLUDE_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/all/src/Scotch5" \
+-D Scotch_LIBRARY_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/lib/openmpi/Scotch5" \
+-D Zoltan_ENABLE_PaToH:BOOL=ON \
+-D PaToH_LIBRARY_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/lib" \
+-D PaToH_INCLUDE_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/PaToH" \
+.. |& tee OUTPUT.CMAKE
+
+make |& tee OUTPUT.MAKE
+make install |& tee OUTPUT.INSTALL
+

thirdParty/Zoltan/SampleCmakeScripts/linux_zoltan_only_purify

@@ -0,0 +1,42 @@
+#!/bin/csh
+# Sample script for building using CMAKE, LAM, and purify on octopi.
+# 64-bit, Zoltan only.
+# Run in Trilinos/Obj_pure.
+
+# Clean up the mess from previous configurations.
+/bin/rm -r cmake* CMake* CPack* CTest* Dart* Trilinos* Testing packages Makefile OUTPUT* include lib install*
+set MPICCEXTRACOMP="`/opt/lam714-gcc346-pure/bin/mpicc --showme:compile`"
+set MPICXXEXTRACOMP="`/opt/lam714-gcc346-pure/bin/mpiCC --showme:compile`"
+set MPIEXTRALINK="`/opt/lam714-gcc346-pure/bin/mpiCC --showme:link`"
+set PURIFY="/usr/local/rational/releases/PurifyPlus.7.0/i386_linux2/bin/purify"
+set GCC="/usr/bin/gcc346"
+set GCXX="/usr/bin/g++346"
+
+/home/kddevin/cmake/bin/cmake \
+-D CMAKE_INSTALL_PREFIX:FILEPATH="/Net/local/homes/kddevin/code/Trilinos/Obj_pure" \
+-D TPL_ENABLE_MPI:BOOL=ON \
+-D MPI_USE_COMPILER_WRAPPERS:BOOL=OFF \
+-D MPI_BIN_DIR:STRING="/opt/lam714-gcc346-pure/bin" \
+-D CMAKE_C_COMPILER:STRING="$PURIFY" \
+-D CMAKE_C_FLAGS:STRING="-best-effort -follow-child-processes=yes -cache-dir=/tmp/purify -chain-length=20 $GCC -m64 -g $MPICCEXTRACOMP" \
+-D CMAKE_CXX_COMPILER:STRING="$PURIFY" \
+-D CMAKE_CXX_FLAGS:STRING="-best-effort -follow-child-processes=yes -cache-dir=/tmp/purify -chain-length=20 $GCXX -m64 -g $MPICXXEXTRACOMP" \
+-D Trilinos_EXTRA_LINK_FLAGS:STRING="$MPIEXTRALINK" \
+-D CMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+-D MPI_EXEC_MAX_NUMPROCS:STRING=11 \
+-D Trilinos_ENABLE_Fortran:BOOL=OFF \
+-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
+-D Trilinos_ENABLE_EXAMPLES:BOOL=ON \
+-D Trilinos_VERBOSE_CONFIGURE:BOOL=ON \
+-D Trilinos_ENABLE_Zoltan:BOOL=ON \
+-D Zoltan_ENABLE_EXAMPLES:BOOL=OFF \
+-D Zoltan_ENABLE_TESTS:BOOL=ON \
+-D Zoltan_ENABLE_ParMETIS:BOOL=ON \
+-D ParMETIS_LIBRARY_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/lib/lam/ParMETIS3" \
+-D ParMETIS_INCLUDE_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/all/src/ParMETIS3" \
+-D Zoltan_ENABLE_Scotch:BOOL=ON \
+-D Scotch_LIBRARY_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/linux64/lib/lam/Scotch5" \
+-D Scotch_INCLUDE_DIRS:FILEPATH="/Net/local/proj/zoltan/arch/all/src/Scotch5" \
+.. |& tee OUTPUT.CMAKE
+
+make |& tee OUTPUT.MAKE

thirdParty/Zoltan/SampleCmakeScripts/linux_zoltan_only_serial

@@ -0,0 +1,29 @@
+#!/bin/csh
+# Sample script for building in serial mode using CMAKE on linux machine godel.
+# 64-bit, Zoltan only.
+# Run in Trilinos/Obj_cmake.
+
+# Clean up the mess from previous configurations.
+/bin/rm -r cmake* CMake* CPack* CTest* Dart* Trilinos* Testing packages Makefile
+
+cmake \
+-D CMAKE_INSTALL_PREFIX:FILEPATH="/home/kddevin/code/Trilinos/Obj_cmake_serial" \
+-D TPL_ENABLE_MPI:BOOL=OFF \
+-D CMAKE_C_FLAGS:STRING="-m64 -g" \
+-D CMAKE_CXX_FLAGS:STRING="-m64 -g" \
+-D CMAKE_Fortran_FLAGS:STRING="-m64 -g" \
+-D CMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
+-D Trilinos_ENABLE_EXAMPLES:BOOL=ON \
+-D Trilinos_VERBOSE_CONFIGURE:BOOL=ON \
+-D Trilinos_ENABLE_Zoltan:BOOL=ON \
+-D Trilinos_EXTRA_LINK_FLAGS:STRING="-lsimpi" \
+-D Zoltan_ENABLE_EXAMPLES:BOOL=ON \
+-D Zoltan_ENABLE_TESTS:BOOL=ON \
+-D Zoltan_ENABLE_ParMETIS:BOOL=ON \
+-D ParMETIS_INCLUDE_DIRS:FILEPATH="/home/kddevin/code/ParMETIS3_1_siMPI" \
+-D ParMETIS_LIBRARY_DIRS:FILEPATH="/home/kddevin/code/ParMETIS3_1_siMPI" \
+.. |& tee OUTPUT.CMAKE
+
+make |& tee OUTPUT.MAKE
+make install |& tee OUTPUT.INSTALL

thirdParty/Zoltan/SampleCmakeScripts/mac_osX_zoltan_only

@@ -0,0 +1,57 @@
+#!
+# Sample script for building using CMAKE on Karen's Mac OS X system.
+# 64-bit, Zoltan only.
+# TPLs = ParMETIS, Scotch and PaToH.
+# Run in Trilinos/Obj_cmake.
+
+# Clean up the mess from previous configurations.
+/bin/rm -r cmake* CMake* CPack* CTest* Dart* Trilinos* Testing packages Makefile
+
+setenv F77 /Users/kddevin/code/lib-m64/lam-7.1.4/bin/mpif77
+
+cmake \
+-D CMAKE_INSTALL_PREFIX:FILEPATH="/Users/kddevin/code/trilinos/Obj_cmake" \
+-D TPL_ENABLE_MPI:BOOL=ON \
+-D CMAKE_C_FLAGS:STRING="-m64 -g" \
+-D CMAKE_CXX_FLAGS:STRING="-m64 -g" \
+-D CMAKE_Fortran_FLAGS:STRING="-m64 -g" \
+-D CMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+-D MPI_EXEC_MAX_NUMPROCS:STRING=11 \
+-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
+-D Trilinos_ENABLE_EXAMPLES:BOOL=ON \
+-D Trilinos_VERBOSE_CONFIGURE:BOOL=ON \
+-D Trilinos_ENABLE_Zoltan:BOOL=ON \
+-D Trilinos_EXTRA_LINK_FLAGS:STRING="-framework vecLib" \
+-D Zoltan_ENABLE_EXAMPLES:BOOL=ON \
+-D Zoltan_ENABLE_TESTS:BOOL=ON \
+-D Zoltan_ENABLE_ParMETIS:BOOL=ON \
+-D ParMETIS_INCLUDE_DIRS:FILEPATH="/Users/kddevin/code/lib-m64/ParMETIS3_1" \
+-D ParMETIS_LIBRARY_DIRS:FILEPATH="/Users/kddevin/code/lib-m64/ParMETIS3_1" \
+-D Zoltan_ENABLE_Scotch:BOOL=ON \
+-D Scotch_INCLUDE_DIRS:FILEPATH="/Users/kddevin/code/lib-m64/scotch_5.1/include" \
+-D Scotch_LIBRARY_DIRS:FILEPATH="/Users/kddevin/code/lib-m64/scotch_5.1/lib" \
+-D Zoltan_ENABLE_PaToH:BOOL=ON \
+-D PaToH_INCLUDE_DIRS:FILEPATH="/Users/kddevin/code/lib-m64/PaToH/dist" \
+-D PaToH_LIBRARY_DIRS:FILEPATH="/Users/kddevin/code/lib-m64/PaToH/dist" \
+.. |& tee OUTPUT.CMAKE
+
+make |& tee OUTPUT.MAKE
+make install |& tee OUTPUT.INSTALL
+
+#Other useful flags.
+#-D Trilinos_ENABLE_Epetra:BOOL=ON \
+#-D Trilinos_ENABLE_Tpetra:BOOL=ON \
+#-D Trilinos_ENABLE_Isorropia:BOOL=ON \
+#-D Trilinos_ENABLE_EpetraExt:BOOL=ON \
+#-D Trilinos_ENABLE_Fortran:BOOL=OFF \
+#-D MPI_EXTRA_LIBRARY:FILEPATH="" \
+#-D CMAKE_CXX_COMPILER:FILEPATH="mpic++" \
+#-D CMAKE_C_COMPILER:FILEPATH="mpicc" \
+
+# NOTE:  I hacked my version of CMAKE, as it had errors trying to find
+# install_name_tool.  I changed the following file to check for 
+# CMAKE_INSTALL_NAME_TOOL before running FIND_PROGRAM to find it.
+# I don't know why it had problems only with install_name_tool, as the
+# linker, ranlib, etc., were found with no difficulty.
+# /Applications/CMake\ 2.6-2.app/Contents/share/cmake-2.6/Modules/CMakeFindBinUtils.cmake
+

thirdParty/Zoltan/SampleConfigurationScripts/linux_trilinos_runtests

@@ -0,0 +1,5 @@
+#!/bin/tcsh
+which lamboot
+lamboot
+make runtests-mpi TRILINOS_MPI_GO="'mpirun -np '"
+

thirdParty/Zoltan/SampleConfigurationScripts/linux_with_purify_zoltan_only

@@ -0,0 +1,34 @@
+# Script for building Zoltan with purify on linux workstation octopi 
+# with openmpi.
+# This is a 64-bit installation.
+
+/bin/rm -r Makefile Makefile.export.zoltan OUTPUT.C OUTPUT.I OUTPUT.M config.cache config.log config.status* example/ include/ lib/ siMPI/ src/
+
+set path=(/usr/local/bin $path)
+setenv PURE_CC "purify -best-effort -follow-child-processes=yes -cache-dir=/tmp/purify -chain-length=20"
+setenv CC  "$PURE_CC gcc34  -Wall -Werror-implicit-function-declaration"
+setenv CXX "$PURE_CC g++34  -Wall -Werror-implicit-function-declaration"
+setenv CFLAGS "-m64 -g"
+setenv CXXFLAGS "-m64 -g"
+setenv CPPFLAGS "-m64 -g"
+setenv FCFLAGS "-m64 -g"
+setenv MPIINC `mpicc --showme:compile`
+setenv MPILIB `mpicc --showme:link`
+
+../configure -C \
+  --prefix=/Net/local/homes/kddevin/code/zoltan_v3.2/Obj_pure \
+  --enable-mpi  \
+  --with-mpi-compilers=no \
+  --disable-fortran \
+  --with-gnumake \
+  --disable-zoltan-cppdriver \
+  --with-libs="$MPILIB" \
+  --with-incdirs="$MPIINC" \
+   |& tee OUTPUT.C
+make everything |& tee OUTPUT.M
+make install |& tee OUTPUT.I
+
+#  --with-parmetis \
+#  --with-parmetis-incdir="/Net/local/proj/zoltan/arch/all/src/ParMETIS3" \
+#  --with-parmetis-libdir="/Net/local/proj/zoltan/arch/linux64/lib/openmpi/ParMETIS3_1" \
+

thirdParty/Zoltan/SampleConfigurationScripts/linux_zoltan_dist

@@ -0,0 +1,15 @@
+#Script for building the Zoltan tarball on a 64-bit Linux workstation
+#with OpenMPI.
+#This script builds the Zoltan tarball from the Zoltan package directory.
+#Assuming running script from 
+#/Net/local/homes/kddevin/code/zoltan_v3.1/Obj_DIST.
+set path=(/usr/local/bin $path)
+setenv CFLAGS -m64
+setenv CXXFLAGS -m64
+setenv CPPFLAGS -m64
+setenv FCFLAGS -m64
+
+../configure -C \
+  --prefix=/Net/local/homes/kddevin/code/zoltan_v3.1/OBJ_DIST \
+  --with-gnumake |& tee OUTPUT.C
+make dist |& tee OUTPUT.D

thirdParty/Zoltan/SampleConfigurationScripts/linux_zoltan_only

@@ -0,0 +1,22 @@
+#Script for building Zoltan only on a 64-bit Linux workstation
+#with OpenMPI.
+#This script builds only Zoltan from the Zoltan package directory.
+#Assuming running script from 
+#/Net/local/homes/kddevin/code/zoltan_v3.1/Obj_linux64.
+set path=(/usr/local/bin $path)
+setenv CFLAGS -m64
+setenv CXXFLAGS -m64
+setenv CPPFLAGS -m64
+setenv FCFLAGS -m64
+
+../configure -C \
+  --prefix=/Net/local/homes/kddevin/code/zoltan_v3.1/Obj_linux64 \
+  --with-parmetis \
+  --with-parmetis-incdir="/Net/local/proj/zoltan/arch/all/src/ParMETIS3_1" \
+  --with-parmetis-libdir="/Net/local/proj/zoltan/arch/linux64/lib/openmpi/ParMETIS3_1" \
+  --with-scotch \
+  --with-scotch-incdir="/Net/local/proj/zoltan/arch/all/src/Scotch5" \
+  --with-scotch-libdir="/Net/local/proj/zoltan/arch/linux64/lib/openmpi/Scotch5" \
+  --with-gnumake |& tee OUTPUT.C
+make everything |& tee OUTPUT.M
+make install |& tee OUTPUT.I

thirdParty/Zoltan/SampleConfigurationScripts/mac_osX_no_fortran

@@ -0,0 +1,25 @@
+#Script for building Zoltan and Isorropia on a 64-bit Mac OS X
+#with LAM MPI on a machine with NO FORTRAN COMPILER.  Note the option
+#--disable-fortran.
+#This script builds only Zoltan but builds it from the top-level Trilinos
+#directory.
+#Assuming running script from /Users/kddevin/code/trilinos_v9.0/Obj_mac64.
+set path=(/Users/kddevin/code/lib-m64/lam-7.1.4/bin $path)
+setenv CC /Users/kddevin/code/lib-m64/lam-7.1.4/bin/mpicc
+setenv CXX /Users/kddevin/code/lib-m64/lam-7.1.4/bin/mpic++
+setenv FC /Users/kddevin/code/lib-m64/lam-7.1.4/bin/mpif77
+setenv CFLAGS -m64
+setenv CXXFLAGS -m64
+setenv CPPFLAGS -m64
+setenv FCFLAGS -m64
+
+../configure -C \
+  --prefix=/Users/kddevin/code/trilinos_v9.0/Obj_mac64 \
+  --with-parmetis \
+  --with-parmetis-incdir="/Users/kddevin/code/lib-m64/ParMETIS3_1" \
+  --with-parmetis-libdir="/Users/kddevin/code/lib-m64/ParMETIS3_1" \
+  --with-libs="-framework vecLib" \
+  --with-gnumake \
+  --with-cxxflags="-DLAM_BUILDING" |& tee OUTPUT.C
+make everything |& tee OUTPUT.M
+make install |& tee OUTPUT.I

thirdParty/Zoltan/SampleConfigurationScripts/mac_osX_zoltan_dist

@@ -0,0 +1,4 @@
+# Since Mac OS X is case-insensitive, autoconf produces a bad Makefile.in
+# Don't use Mac OS X until this bug is fixed.
+
+echo "Due to bug in autoconf Makefile.in, do not make dist on a case-insensitive system."

thirdParty/Zoltan/SampleConfigurationScripts/mac_osX_zoltan_only

@@ -0,0 +1,18 @@
+#Script for building Zoltan only on a 64-bit Mac OS X with LAM mpi 
+#Assuming running this script from /Users/kddevin/code/zoltan_v3.1/OBJ_MAC64.
+
+setenv CFLAGS -m64
+setenv CXXFLAGS -m64
+../configure \
+  --prefix=/Users/kddevin/code/zoltan_v3.1/OBJ_MAC64 \
+  --with-gnumake \
+  --with-parmetis \
+  --with-parmetis-incdir="/Users/kddevin/code/lib-m64/ParMETIS3_1" \
+  --with-parmetis-libdir="/Users/kddevin/code/lib-m64/ParMETIS3_1" \
+  --with-patoh \
+  --with-patoh-incdir="/Users/kddevin/code/lib-m64/PaToH/dist" \
+  --with-patoh-libdir="/Users/kddevin/code/lib-m64/PaToH/dist" \
+ |& tee OUTPUT.C
+make everything |& tee OUTPUT.M
+make install |& tee OUTPUT.I
+

thirdParty/Zoltan/VERSION

@@ -0,0 +1,2 @@
+To determine the exact version number, type
+  grep ZOLTAN_VERSION_NUMBER src/include/zoltan.h

thirdParty/Zoltan/bootstrap-local

@@ -0,0 +1,3 @@
+#! /bin/csh
+setenv AUTOHEADER 'echo SkippingAutoHeader'
+autoreconf -i -f -v

thirdParty/Zoltan/buildlib

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+rm -rf build/ include/ lib/
+mkdir build
+
+cd build
+
+../configure \
+--prefix=$HOME/PhasicFlow/phasicFlow-v-1.0/thirdParty/Zoltan/ \
+--with-gnumake \
+--with-id-type=uint
+--disable-tests
+--disable-examples
+
+make everything -j4
+make install
+
+cd ../

thirdParty/Zoltan/cmake/Dependencies.cmake

@@ -0,0 +1,8 @@
+SET(LIB_REQUIRED_DEP_PACKAGES)
+SET(LIB_OPTIONAL_DEP_PACKAGES)
+SET(TEST_REQUIRED_DEP_PACKAGES)
+SET(TEST_OPTIONAL_DEP_PACKAGES)
+SET(LIB_REQUIRED_DEP_TPLS)
+SET(LIB_OPTIONAL_DEP_TPLS MPI METIS ParMETIS PaToH Scotch Zlib CCOLAMD OVIS)
+SET(TEST_REQUIRED_DEP_TPLS)
+SET(TEST_OPTIONAL_DEP_TPLS)

thirdParty/Zoltan/cmake/Zoltan_config.h.in

@@ -0,0 +1,74 @@
+/* src/include/Zoltan_config.h.in.  Generated from configure.ac by autoheader.  */
+
+/* KDD Copied F77 macros from packages/epetra/cmake/Epetra_config.h.in. */
+/* Define to dummy `main' function (if any) required to link to the Fortran
+   libraries. */
+#cmakedefine F77_DUMMY_MAIN
+
+/* Define to a macro mangling the given C identifier (in lower and upper
+   case), which must not contain underscores, for linking with Fortran. */
+#ifndef FC_FUNC
+  #define FC_FUNC@F77_FUNC@
+#endif
+
+/* As FC_FUNC, but for C identifiers containing underscores. */
+#ifndef FC_FUNC_
+  #define FC_FUNC_@F77_FUNC_@
+#endif
+
+/* Define if F77 and FC dummy `main' functions are identical. */
+#cmakedefine FC_DUMMY_MAIN_EQ_F77
+
+/* ZOLTAN_ID_TYPE is unsigned int */
+#cmakedefine UNSIGNED_INT_GLOBAL_IDS
+
+/* ZOLTAN_ID_TYPE is unsigned long */
+#cmakedefine UNSIGNED_LONG_GLOBAL_IDS
+
+/* ZOLTAN_ID_TYPE is unsigned long long */
+#cmakedefine UNSIGNED_LONG_LONG_GLOBAL_IDS
+
+/* define if we want to use MPI */
+#cmakedefine HAVE_MPI
+
+/* Define if want to build with nemesis_exodus enabled */
+#cmakedefine HAVE_NEMESIS_EXODUS
+
+/* Define if want to build with parmetis enabled */
+#cmakedefine HAVE_METIS
+
+/* Define if want to build with parmetis enabled */
+#cmakedefine HAVE_PARMETIS
+
+/* Define if want to build with patoh enabled */
+#cmakedefine HAVE_PATOH
+
+/* Define if want to build with scotch enabled */
+#cmakedefine HAVE_SCOTCH
+
+/* Define if want to build with OVIS enabled */
+#cmakedefine HAVE_OVIS
+
+/* Define if want to build with OVIS enabled */
+#cmakedefine HAVE_PURIFY
+
+/* Define if DON'T want support for MPI TPL */
+#ifndef HAVE_MPI
+#define NO_MPI_TPL
+#endif
+
+/* Define if want to build with zlib enabled */
+#cmakedefine ZHAVE_GZIP
+
+/* Use to have only filename when debugging memory */
+#define SHORT_FILE
+
+/* HUND support */
+#cmakedefine HAVE_ZOLTAN_HUND
+
+/* Revert to Old Hash function support */
+#cmakedefine HAVE_ZOLTAN_KNUTH_HASH
+
+#ifdef HAVE_ZOLTAN_HUND
+#define CEDRIC_2D_PARTITIONS
+#endif

thirdParty/Zoltan/config/ax_f90_module_case.m4

@@ -0,0 +1,50 @@
+dnl Check case (upper or lower) of F90 module files.  
+dnl Also checks module suffix, but we return only ax_cv_f90_modulecase.
+AC_DEFUN([AX_F90_MODULE_CASE],[
+AC_CACHE_CHECK([fortran 90 module file suffix and case],
+ax_cv_f90_modulecase,
+[
+rm -f conftest*
+cat >conftest.f <<EOF
+	module conftest
+        integer n
+        parameter (n=1)
+        end module conftest
+EOF
+# SGI and absoft compilers generates module name in upper case!
+testname="conftest"
+modcase="lower"
+echo "KDDKDD CASE 1" ${FC}
+if ${FC} -c conftest.f > conftest.out 2>&1 ; then
+    FCMODSUFFIX=`ls conftest* | grep -v conftest.f | grep -v conftest.o`
+    echo "KDDKDD CASE 2" ${FCMODSUFFIX}
+    FCMODSUFFIX=`echo "${FCMODSUFFIX}" | sed -e 's/conftest\.//g'`
+    if test -z "${FCMODSUFFIX}" ; then
+	FCMODSUFFIX=`ls CONFTEST* 2>/dev/null \
+		| grep -v CONFTEST.f | grep -v CONFTEST.o`
+        FCMODSUFFIX=`echo "${FCMODSUFFIX}" | sed -e 's/CONFTEST\.//g'`
+	if test -n "${FCMODSUFFIX}" ; then
+	    testname="CONFTEST"
+	    modcase="upper"
+	fi
+    fi
+    if test -z "${FCMODSUFFIX}" ; then 
+        AC_MSG_RESULT(unknown)
+	# Use mod if we can't figure it out
+	FCMODSUFFIX="mod"   
+    else
+        AC_MSG_RESULT(${FCMODSUFFIX})
+    fi
+else
+    AC_MSG_RESULT(unknown)
+fi
+#AC_SUBST(FCMODSUFFIX)
+AC_MSG_CHECKING(for case of module names)
+if test "${modcase}" = "lower" ; then
+    AC_MSG_RESULT(lower)
+    ax_cv_f90_modulecase="lower"
+else
+    AC_MSG_RESULT(upper)
+    ax_cv_f90_modulecase="upper"
+fi
+])])

thirdParty/Zoltan/config/ax_f90_module_flag.m4

@@ -0,0 +1,67 @@
+# ===========================================================================
+#       http://www.nongnu.org/autoconf-archive/ax_f90_module_flag.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_F90_MODULE_FLAG
+#
+# DESCRIPTION
+#
+#   Find Fortran 90 modules inclusion flag. The module inclusion flag is
+#   stored in the cached variable ax_f90_modflag. An error is triggered if
+#   the flag cannot be found. Supported are the -I GNU compilers flag, the
+#   -M SUN compilers flag, and the -p Absoft Pro Fortran compiler flag.
+#
+# LICENSE
+#
+#   Copyright (c) 2009 Luc Maisonobe <luc@spaceroots.org>
+#   Copyright (c) 2009 Julian C. Cummings <cummings@cacr.caltech.edu>
+#   Copyright (c) 2009 Alexander Pletzer <pletzer@txcorp.com>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved.
+
+AC_DEFUN([AX_F90_MODULE_FLAG],[
+AC_CACHE_CHECK([fortran 90 modules inclusion flag],
+ax_cv_f90_modflag,
+[AC_LANG_PUSH(Fortran)
+i=0
+while test \( -f tmpdir_$i \) -o \( -d tmpdir_$i \) ; do
+  i=`expr $i + 1`
+done
+mkdir tmpdir_$i
+cd tmpdir_$i
+AC_COMPILE_IFELSE([
+!234567
+      module conftest_module
+      contains
+      subroutine conftest_routine
+      write(*,'(a)') 'gotcha!'
+      end subroutine conftest_routine
+      end module conftest_module
+  ],[],[])
+cd ..
+ax_cv_f90_modflag="not found"
+for ax_flag in "-I " "-M" "-p"; do
+  if test "$ax_cv_f90_modflag" = "not found" ; then
+    ax_save_FCFLAGS="$FCFLAGS"
+    FCFLAGS="$ax_save_FCFLAGS ${ax_flag}tmpdir_$i"
+    AC_COMPILE_IFELSE([
+!234567
+      program conftest_program
+      use conftest_module
+      call conftest_routine
+      end program conftest_program
+      ],[ax_cv_f90_modflag="$ax_flag"],[])
+    FCFLAGS="$ax_save_FCFLAGS"
+  fi
+done
+rm -fr tmpdir_$i
+if test "$ax_cv_f90_modflag" = "not found" ; then
+  AC_MSG_ERROR([unable to find compiler flag for modules inclusion])
+fi
+AC_LANG_POP(Fortran)
+])])
+

thirdParty/Zoltan/config/compile

@@ -0,0 +1,310 @@
+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2012-01-04.17; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2009, 2010, 2012 Free
+# Software Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+nl='
+'
+
+# We need space, tab and new line, in precisely that order.  Quoting is
+# there to prevent tools from complaining about whitespace usage.
+IFS=" ""	$nl"
+
+file_conv=
+
+# func_file_conv build_file lazy
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts. If the determined conversion
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+  file=$1
+  case $file in
+    / | /[!/]*) # absolute file, and not a UNC file
+      if test -z "$file_conv"; then
+	# lazily determine how to convert abs files
+	case `uname -s` in
+	  MINGW*)
+	    file_conv=mingw
+	    ;;
+	  CYGWIN*)
+	    file_conv=cygwin
+	    ;;
+	  *)
+	    file_conv=wine
+	    ;;
+	esac
+      fi
+      case $file_conv/,$2, in
+	*,$file_conv,*)
+	  ;;
+	mingw/*)
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+	  ;;
+	cygwin/*)
+	  file=`cygpath -m "$file" || echo "$file"`
+	  ;;
+	wine/*)
+	  file=`winepath -w "$file" || echo "$file"`
+	  ;;
+      esac
+      ;;
+  esac
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+  # Assume a capable shell
+  lib_path=
+  shared=:
+  linker_opts=
+  for arg
+  do
+    if test -n "$eat"; then
+      eat=
+    else
+      case $1 in
+	-o)
+	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
+	  eat=1
+	  case $2 in
+	    *.o | *.[oO][bB][jJ])
+	      func_file_conv "$2"
+	      set x "$@" -Fo"$file"
+	      shift
+	      ;;
+	    *)
+	      func_file_conv "$2"
+	      set x "$@" -Fe"$file"
+	      shift
+	      ;;
+	  esac
+	  ;;
+	-I*)
+	  func_file_conv "${1#-I}" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-l*)
+	  lib=${1#-l}
+	  found=no
+	  save_IFS=$IFS
+	  IFS=';'
+	  for dir in $lib_path $LIB
+	  do
+	    IFS=$save_IFS
+	    if $shared && test -f "$dir/$lib.dll.lib"; then
+	      found=yes
+	      set x "$@" "$dir/$lib.dll.lib"
+	      break
+	    fi
+	    if test -f "$dir/$lib.lib"; then
+	      found=yes
+	      set x "$@" "$dir/$lib.lib"
+	      break
+	    fi
+	  done
+	  IFS=$save_IFS
+
+	  test "$found" != yes && set x "$@" "$lib.lib"
+	  shift
+	  ;;
+	-L*)
+	  func_file_conv "${1#-L}"
+	  if test -z "$lib_path"; then
+	    lib_path=$file
+	  else
+	    lib_path="$lib_path;$file"
+	  fi
+	  linker_opts="$linker_opts -LIBPATH:$file"
+	  ;;
+	-static)
+	  shared=false
+	  ;;
+	-Wl,*)
+	  arg=${1#-Wl,}
+	  save_ifs="$IFS"; IFS=','
+	  for flag in $arg; do
+	    IFS="$save_ifs"
+	    linker_opts="$linker_opts $flag"
+	  done
+	  IFS="$save_ifs"
+	  ;;
+	-Xlinker)
+	  eat=1
+	  linker_opts="$linker_opts $2"
+	  ;;
+	-*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+	  func_file_conv "$1"
+	  set x "$@" -Tp"$file"
+	  shift
+	  ;;
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+	  func_file_conv "$1" mingw
+	  set x "$@" "$file"
+	  shift
+	  ;;
+	*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+      esac
+    fi
+    shift
+  done
+  if test -n "$linker_opts"; then
+    linker_opts="-link$linker_opts"
+  fi
+  exec "$@" $linker_opts
+  exit 1
+}
+
+eat=
+
+case $1 in
+  '')
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file 'INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+    func_cl_wrapper "$@"      # Doesn't return...
+    ;;
+esac
+
+ofile=
+cfile=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as 'compile cc -o foo foo.c'.
+	# So we strip '-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no '-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # '.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

thirdParty/Zoltan/config/depcomp

@@ -0,0 +1,688 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2011-12-04.11; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009, 2010,
+# 2011 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
+
+case $1 in
+  '')
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+  depmode     Dependency tracking mode.
+  source      Source file read by `PROGRAMS ARGS'.
+  object      Object file output by `PROGRAMS ARGS'.
+  DEPDIR      directory where to store dependencies.
+  depfile     Dependency file to output.
+  tmpdepfile  Temporary file to use when outputting dependencies.
+  libtool     Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "depcomp $scriptversion"
+    exit $?
+    ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+  echo "depcomp: Variables source, object and depmode must be set" 1>&2
+  exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+  sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags.  We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write.  Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+  # HP compiler uses -M and no extra arg.
+  gccflag=-M
+  depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+   # This is just like dashmstdout with a different argument.
+   dashmflag=-xM
+   depmode=dashmstdout
+fi
+
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+   # This is just like msvisualcpp but w/o cygpath translation.
+   # Just convert the backslash-escaped backslashes to single forward
+   # slashes to satisfy depend.m4
+   cygpath_u='sed s,\\\\,/,g'
+   depmode=msvisualcpp
+fi
+
+if test "$depmode" = msvc7msys; then
+   # This is just like msvc7 but w/o cygpath translation.
+   # Just convert the backslash-escaped backslashes to single forward
+   # slashes to satisfy depend.m4
+   cygpath_u='sed s,\\\\,/,g'
+   depmode=msvc7
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want.  Yay!  Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff.  Hmm.
+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
+## the command line argument order; so add the flags where they
+## appear in depend2.am.  Note that the slowdown incurred here
+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
+  for arg
+  do
+    case $arg in
+    -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
+    *)  set fnord "$@" "$arg" ;;
+    esac
+    shift # fnord
+    shift # $arg
+  done
+  "$@"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  mv "$tmpdepfile" "$depfile"
+  ;;
+
+gcc)
+## There are various ways to get dependency output from gcc.  Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+##   up in a subdir.  Having to rename by hand is ugly.
+##   (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+##   -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+##   than renaming).
+  if test -z "$gccflag"; then
+    gccflag=-MD,
+  fi
+  "$@" -Wp,"$gccflag$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+  sed -e 's/^[^:]*: / /' \
+      -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header).  We avoid this by adding
+## dummy dependencies for each header file.  Too bad gcc doesn't do
+## this for us directly.
+  tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'.  On the theory
+## that the space means something, we add a space to the output as
+## well.  hp depmode also adds that space, but also prefixes the VPATH
+## to the object.  Take care to not repeat it in the output.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
+      | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+hp)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
+sgi)
+  if test "$libtool" = yes; then
+    "$@" "-Wp,-MDupdate,$tmpdepfile"
+  else
+    "$@" -MDupdate "$tmpdepfile"
+  fi
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+
+  if test -f "$tmpdepfile"; then  # yes, the sourcefile depend on other files
+    echo "$object : \\" > "$depfile"
+
+    # Clip off the initial element (the dependent).  Don't try to be
+    # clever and replace this with sed code, as IRIX sed won't handle
+    # lines with more than a fixed number of characters (4096 in
+    # IRIX 6.2 sed, 8192 in IRIX 6.5).  We also remove comment lines;
+    # the IRIX cc adds comments like `#:fec' to the end of the
+    # dependency line.
+    tr ' ' '
+' < "$tmpdepfile" \
+    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+    tr '
+' ' ' >> "$depfile"
+    echo >> "$depfile"
+
+    # The second pass generates a dummy entry for each header file.
+    tr ' ' '
+' < "$tmpdepfile" \
+   | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+   >> "$depfile"
+  else
+    # The sourcefile does not contain any dependencies, so just
+    # store a dummy comment line, to avoid errors with the Makefile
+    # "include basename.Plo" scheme.
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile"
+  ;;
+
+aix)
+  # The C for AIX Compiler uses -M and outputs the dependencies
+  # in a .u file.  In older versions, this file always lives in the
+  # current directory.  Also, the AIX compiler puts `$object:' at the
+  # start of each line; $object doesn't have directory information.
+  # Version 6 uses the directory in both cases.
+  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+  test "x$dir" = "x$object" && dir=
+  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+  if test "$libtool" = yes; then
+    tmpdepfile1=$dir$base.u
+    tmpdepfile2=$base.u
+    tmpdepfile3=$dir.libs/$base.u
+    "$@" -Wc,-M
+  else
+    tmpdepfile1=$dir$base.u
+    tmpdepfile2=$dir$base.u
+    tmpdepfile3=$dir$base.u
+    "$@" -M
+  fi
+  stat=$?
+
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+    exit $stat
+  fi
+
+  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+  do
+    test -f "$tmpdepfile" && break
+  done
+  if test -f "$tmpdepfile"; then
+    # Each line is of the form `foo.o: dependent.h'.
+    # Do two passes, one to just change these to
+    # `$object: dependent.h' and one to simply `dependent.h:'.
+    sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+    # That's a tab and a space in the [].
+    sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+  else
+    # The sourcefile does not contain any dependencies, so just
+    # store a dummy comment line, to avoid errors with the Makefile
+    # "include basename.Plo" scheme.
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile"
+  ;;
+
+icc)
+  # Intel's C compiler understands `-MD -MF file'.  However on
+  #    icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+  # ICC 7.0 will fill foo.d with something like
+  #    foo.o: sub/foo.c
+  #    foo.o: sub/foo.h
+  # which is wrong.  We want:
+  #    sub/foo.o: sub/foo.c
+  #    sub/foo.o: sub/foo.h
+  #    sub/foo.c:
+  #    sub/foo.h:
+  # ICC 7.1 will output
+  #    foo.o: sub/foo.c sub/foo.h
+  # and will wrap long lines using \ :
+  #    foo.o: sub/foo.c ... \
+  #     sub/foo.h ... \
+  #     ...
+
+  "$@" -MD -MF "$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  # Each line is of the form `foo.o: dependent.h',
+  # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+  # Do two passes, one to just change these to
+  # `$object: dependent.h' and one to simply `dependent.h:'.
+  sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+  # Some versions of the HPUX 10.20 sed can't process this invocation
+  # correctly.  Breaking it into two sed invocations is a workaround.
+  sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+    sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+hp2)
+  # The "hp" stanza above does not work with aCC (C++) and HP's ia64
+  # compilers, which have integrated preprocessors.  The correct option
+  # to use with these is +Maked; it writes dependencies to a file named
+  # 'foo.d', which lands next to the object file, wherever that
+  # happens to be.
+  # Much of this is similar to the tru64 case; see comments there.
+  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+  test "x$dir" = "x$object" && dir=
+  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+  if test "$libtool" = yes; then
+    tmpdepfile1=$dir$base.d
+    tmpdepfile2=$dir.libs/$base.d
+    "$@" -Wc,+Maked
+  else
+    tmpdepfile1=$dir$base.d
+    tmpdepfile2=$dir$base.d
+    "$@" +Maked
+  fi
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+     rm -f "$tmpdepfile1" "$tmpdepfile2"
+     exit $stat
+  fi
+
+  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
+  do
+    test -f "$tmpdepfile" && break
+  done
+  if test -f "$tmpdepfile"; then
+    sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+    # Add `dependent.h:' lines.
+    sed -ne '2,${
+	       s/^ *//
+	       s/ \\*$//
+	       s/$/:/
+	       p
+	     }' "$tmpdepfile" >> "$depfile"
+  else
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile" "$tmpdepfile2"
+  ;;
+
+tru64)
+   # The Tru64 compiler uses -MD to generate dependencies as a side
+   # effect.  `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+   # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+   # dependencies in `foo.d' instead, so we check for that too.
+   # Subdirectories are respected.
+   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+   test "x$dir" = "x$object" && dir=
+   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+   if test "$libtool" = yes; then
+      # With Tru64 cc, shared objects can also be used to make a
+      # static library.  This mechanism is used in libtool 1.4 series to
+      # handle both shared and static libraries in a single compilation.
+      # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+      #
+      # With libtool 1.5 this exception was removed, and libtool now
+      # generates 2 separate objects for the 2 libraries.  These two
+      # compilations output dependencies in $dir.libs/$base.o.d and
+      # in $dir$base.o.d.  We have to check for both files, because
+      # one of the two compilations can be disabled.  We should prefer
+      # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+      # automatically cleaned when .libs/ is deleted, while ignoring
+      # the former would cause a distcleancheck panic.
+      tmpdepfile1=$dir.libs/$base.lo.d   # libtool 1.4
+      tmpdepfile2=$dir$base.o.d          # libtool 1.5
+      tmpdepfile3=$dir.libs/$base.o.d    # libtool 1.5
+      tmpdepfile4=$dir.libs/$base.d      # Compaq CCC V6.2-504
+      "$@" -Wc,-MD
+   else
+      tmpdepfile1=$dir$base.o.d
+      tmpdepfile2=$dir$base.d
+      tmpdepfile3=$dir$base.d
+      tmpdepfile4=$dir$base.d
+      "$@" -MD
+   fi
+
+   stat=$?
+   if test $stat -eq 0; then :
+   else
+      rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+      exit $stat
+   fi
+
+   for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+   do
+     test -f "$tmpdepfile" && break
+   done
+   if test -f "$tmpdepfile"; then
+      sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+      # That's a tab and a space in the [].
+      sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+   else
+      echo "#dummy" > "$depfile"
+   fi
+   rm -f "$tmpdepfile"
+   ;;
+
+msvc7)
+  if test "$libtool" = yes; then
+    showIncludes=-Wc,-showIncludes
+  else
+    showIncludes=-showIncludes
+  fi
+  "$@" $showIncludes > "$tmpdepfile"
+  stat=$?
+  grep -v '^Note: including file: ' "$tmpdepfile"
+  if test "$stat" = 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  # The first sed program below extracts the file names and escapes
+  # backslashes for cygpath.  The second sed program outputs the file
+  # name when reading, but also accumulates all include files in the
+  # hold buffer in order to output them again at the end.  This only
+  # works with sed implementations that can handle large buffers.
+  sed < "$tmpdepfile" -n '
+/^Note: including file:  *\(.*\)/ {
+  s//\1/
+  s/\\/\\\\/g
+  p
+}' | $cygpath_u | sort -u | sed -n '
+s/ /\\ /g
+s/\(.*\)/	\1 \\/p
+s/.\(.*\) \\/\1:/
+H
+$ {
+  s/.*/	/
+  G
+  p
+}' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+msvc7msys)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
+#nosideeffect)
+  # This comment above is used by automake to tell side-effect
+  # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout, regardless of -o.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test "X$1" != 'X--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
+  for arg
+  do
+    case $arg in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    *)
+      set fnord "$@" "$arg"
+      shift # fnord
+      shift # $arg
+      ;;
+    esac
+  done
+
+  test -z "$dashmflag" && dashmflag=-M
+  # Require at least two characters before searching for `:'
+  # in the target name.  This is to cope with DOS-style filenames:
+  # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+  "$@" $dashmflag |
+    sed 's:^[  ]*[^: ][^:][^:]*\:[    ]*:'"$object"'\: :' > "$tmpdepfile"
+  rm -f "$depfile"
+  cat < "$tmpdepfile" > "$depfile"
+  tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+dashXmstdout)
+  # This case only exists to satisfy depend.m4.  It is never actually
+  # run, as this mode is specially recognized in the preamble.
+  exit 1
+  ;;
+
+makedepend)
+  "$@" || exit $?
+  # Remove any Libtool call
+  if test "$libtool" = yes; then
+    while test "X$1" != 'X--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+  # X makedepend
+  shift
+  cleared=no eat=no
+  for arg
+  do
+    case $cleared in
+    no)
+      set ""; shift
+      cleared=yes ;;
+    esac
+    if test $eat = yes; then
+      eat=no
+      continue
+    fi
+    case "$arg" in
+    -D*|-I*)
+      set fnord "$@" "$arg"; shift ;;
+    # Strip any option that makedepend may not understand.  Remove
+    # the object too, otherwise makedepend will parse it as a source file.
+    -arch)
+      eat=yes ;;
+    -*|$object)
+      ;;
+    *)
+      set fnord "$@" "$arg"; shift ;;
+    esac
+  done
+  obj_suffix=`echo "$object" | sed 's/^.*\././'`
+  touch "$tmpdepfile"
+  ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+  rm -f "$depfile"
+  # makedepend may prepend the VPATH from the source file name to the object.
+  # No need to regex-escape $object, excess matching of '.' is harmless.
+  sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
+  sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile" "$tmpdepfile".bak
+  ;;
+
+cpp)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test "X$1" != 'X--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
+  for arg
+  do
+    case $arg in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    *)
+      set fnord "$@" "$arg"
+      shift # fnord
+      shift # $arg
+      ;;
+    esac
+  done
+
+  "$@" -E |
+    sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+       -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+    sed '$ s: \\$::' > "$tmpdepfile"
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  cat < "$tmpdepfile" >> "$depfile"
+  sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+msvisualcpp)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test "X$1" != 'X--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  IFS=" "
+  for arg
+  do
+    case "$arg" in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+	set fnord "$@"
+	shift
+	shift
+	;;
+    *)
+	set fnord "$@" "$arg"
+	shift
+	shift
+	;;
+    esac
+  done
+  "$@" -E 2>/dev/null |
+  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
+  echo "	" >> "$depfile"
+  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+msvcmsys)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
+none)
+  exec "$@"
+  ;;
+
+*)
+  echo "Unknown depmode $depmode" 1>&2
+  exit 1
+  ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

thirdParty/Zoltan/config/generate-makeoptions.pl

@@ -0,0 +1,88 @@
+#!/usr/bin/perl -w
+#
+# This perl script graps a bunch of make macro definitions
+# generated for Teuchos that can be used in other makefiles.
+# This is dumped to stdout and can be redirected to build
+# a makefile.
+#
+# Note, this script must be maintained to be current for
+# the Teuchos makefile.
+#
+use strict;
+
+if( !((@ARGV) && scalar(@ARGV)==2) ) {
+  die "Error, this script takes two and only two arguments (makefile_name package_name).!\n";
+}
+
+my $makefile_name = shift;
+my $package_name  = shift;
+
+#
+# List the macros you want to grep and include in the output
+#
+my @macros =
+	(
+	 "CC"
+	 ,"CXX"
+	 ,"F77"
+	 ,"FC"
+	 ,"CXXLD"
+	 ,"DEFS"
+	 ,"CPPFLAGS"
+	 ,"CFLAGS"
+	 ,"CXXFLAGS"
+	 ,"FFLAGS"
+	 ,"FCFLAGS"
+	 ,"LDFLAGS"
+	 ,"FLIBS"
+	 ,"BLAS_LIBS"
+	 ,"LAPACK_LIBS"
+	 ,"prefix"
+	 ,"AR"
+	 ,"ALTERNATE_AR"
+	 ,"libteuchos_a_AR"
+	 ,"RANLIB"
+	 );
+
+open FILE_IN, "<$makefile_name" || die "The file $makefile_name could not be opended for input\n";
+my @makefile_name_array = <FILE_IN>;
+close FILE_IN;
+
+#
+# Find the above macros and append "${package_name}_" to the beginning.
+#
+my @new_macros;
+my $add_next_line = 0;
+foreach( @makefile_name_array ) {
+	my $line = $_;
+	if($add_next_line) {
+		push @new_macros, $line;
+		if( substr($line,-1,1) eq "\\" ) {
+			$add_next_line = 1;
+		}
+		else {
+			$add_next_line = 0;
+		}
+		next;
+	}
+	#print "Line = $line";
+	foreach( @macros ) {
+		my $macro_search = "^${_} ";
+		#print "Macro search = \'$macro_search\'\n";
+		if( $line=~/$macro_search/ ) {
+			#print "Adding Macro!\n";
+      my $find_str = '\(CXX\)';
+      my $replace_str = "(${package_name}_CXX)";
+      $line=~s/$find_str/$replace_str/;
+			push @new_macros, "${package_name}_${line}";
+			if( substr($line,-2,1) eq "\\" ) {
+				$add_next_line = 1;
+			}
+			else {
+				$add_next_line = 0;
+			}
+		}
+	}
+}
+
+print join("",@new_macros);

thirdParty/Zoltan/config/install-sh

@@ -0,0 +1,527 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2011-01-19.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" ""	$nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+  doit_exec=exec
+else
+  doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+  test "$posix_glob" != "?" || {
+    if (set -f) 2>/dev/null; then
+      posix_glob=
+    else
+      posix_glob=:
+    fi
+  }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+   or: $0 [OPTION]... SRCFILES... DIRECTORY
+   or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+   or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+     --help     display this help and exit.
+     --version  display version info and exit.
+
+  -c            (ignored)
+  -C            install only if different (preserve the last data modification time)
+  -d            create directories instead of installing files.
+  -g GROUP      $chgrpprog installed files to GROUP.
+  -m MODE       $chmodprog installed files to MODE.
+  -o USER       $chownprog installed files to USER.
+  -s            $stripprog installed files.
+  -t DIRECTORY  install into DIRECTORY.
+  -T            report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+  CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+  RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+  case $1 in
+    -c) ;;
+
+    -C) copy_on_change=true;;
+
+    -d) dir_arg=true;;
+
+    -g) chgrpcmd="$chgrpprog $2"
+	shift;;
+
+    --help) echo "$usage"; exit $?;;
+
+    -m) mode=$2
+	case $mode in
+	  *' '* | *'	'* | *'
+'*	  | *'*'* | *'?'* | *'['*)
+	    echo "$0: invalid mode: $mode" >&2
+	    exit 1;;
+	esac
+	shift;;
+
+    -o) chowncmd="$chownprog $2"
+	shift;;
+
+    -s) stripcmd=$stripprog;;
+
+    -t) dst_arg=$2
+	# Protect names problematic for `test' and other utilities.
+	case $dst_arg in
+	  -* | [=\(\)!]) dst_arg=./$dst_arg;;
+	esac
+	shift;;
+
+    -T) no_target_directory=true;;
+
+    --version) echo "$0 $scriptversion"; exit $?;;
+
+    --)	shift
+	break;;
+
+    -*)	echo "$0: invalid option: $1" >&2
+	exit 1;;
+
+    *)  break;;
+  esac
+  shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+  # When -d is used, all remaining arguments are directories to create.
+  # When -t is used, the destination is already specified.
+  # Otherwise, the last argument is the destination.  Remove it from $@.
+  for arg
+  do
+    if test -n "$dst_arg"; then
+      # $@ is not empty: it contains at least $arg.
+      set fnord "$@" "$dst_arg"
+      shift # fnord
+    fi
+    shift # arg
+    dst_arg=$arg
+    # Protect names problematic for `test' and other utilities.
+    case $dst_arg in
+      -* | [=\(\)!]) dst_arg=./$dst_arg;;
+    esac
+  done
+fi
+
+if test $# -eq 0; then
+  if test -z "$dir_arg"; then
+    echo "$0: no input file specified." >&2
+    exit 1
+  fi
+  # It's OK to call `install-sh -d' without argument.
+  # This can happen when creating conditional directories.
+  exit 0
+fi
+
+if test -z "$dir_arg"; then
+  do_exit='(exit $ret); exit $ret'
+  trap "ret=129; $do_exit" 1
+  trap "ret=130; $do_exit" 2
+  trap "ret=141; $do_exit" 13
+  trap "ret=143; $do_exit" 15
+
+  # Set umask so as not to create temps with too-generous modes.
+  # However, 'strip' requires both read and write access to temps.
+  case $mode in
+    # Optimize common cases.
+    *644) cp_umask=133;;
+    *755) cp_umask=22;;
+
+    *[0-7])
+      if test -z "$stripcmd"; then
+	u_plus_rw=
+      else
+	u_plus_rw='% 200'
+      fi
+      cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+    *)
+      if test -z "$stripcmd"; then
+	u_plus_rw=
+      else
+	u_plus_rw=,u+rw
+      fi
+      cp_umask=$mode$u_plus_rw;;
+  esac
+fi
+
+for src
+do
+  # Protect names problematic for `test' and other utilities.
+  case $src in
+    -* | [=\(\)!]) src=./$src;;
+  esac
+
+  if test -n "$dir_arg"; then
+    dst=$src
+    dstdir=$dst
+    test -d "$dstdir"
+    dstdir_status=$?
+  else
+
+    # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+    # might cause directories to be created, which would be especially bad
+    # if $src (and thus $dsttmp) contains '*'.
+    if test ! -f "$src" && test ! -d "$src"; then
+      echo "$0: $src does not exist." >&2
+      exit 1
+    fi
+
+    if test -z "$dst_arg"; then
+      echo "$0: no destination specified." >&2
+      exit 1
+    fi
+    dst=$dst_arg
+
+    # If destination is a directory, append the input filename; won't work
+    # if double slashes aren't ignored.
+    if test -d "$dst"; then
+      if test -n "$no_target_directory"; then
+	echo "$0: $dst_arg: Is a directory" >&2
+	exit 1
+      fi
+      dstdir=$dst
+      dst=$dstdir/`basename "$src"`
+      dstdir_status=0
+    else
+      # Prefer dirname, but fall back on a substitute if dirname fails.
+      dstdir=`
+	(dirname "$dst") 2>/dev/null ||
+	expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	     X"$dst" : 'X\(//\)[^/]' \| \
+	     X"$dst" : 'X\(//\)$' \| \
+	     X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+	echo X"$dst" |
+	    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\/\)[^/].*/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\/\)$/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\).*/{
+		   s//\1/
+		   q
+		 }
+		 s/.*/./; q'
+      `
+
+      test -d "$dstdir"
+      dstdir_status=$?
+    fi
+  fi
+
+  obsolete_mkdir_used=false
+
+  if test $dstdir_status != 0; then
+    case $posix_mkdir in
+      '')
+	# Create intermediate dirs using mode 755 as modified by the umask.
+	# This is like FreeBSD 'install' as of 1997-10-28.
+	umask=`umask`
+	case $stripcmd.$umask in
+	  # Optimize common cases.
+	  *[2367][2367]) mkdir_umask=$umask;;
+	  .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+	  *[0-7])
+	    mkdir_umask=`expr $umask + 22 \
+	      - $umask % 100 % 40 + $umask % 20 \
+	      - $umask % 10 % 4 + $umask % 2
+	    `;;
+	  *) mkdir_umask=$umask,go-w;;
+	esac
+
+	# With -d, create the new directory with the user-specified mode.
+	# Otherwise, rely on $mkdir_umask.
+	if test -n "$dir_arg"; then
+	  mkdir_mode=-m$mode
+	else
+	  mkdir_mode=
+	fi
+
+	posix_mkdir=false
+	case $umask in
+	  *[123567][0-7][0-7])
+	    # POSIX mkdir -p sets u+wx bits regardless of umask, which
+	    # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+	    ;;
+	  *)
+	    tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+	    trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+	    if (umask $mkdir_umask &&
+		exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+	    then
+	      if test -z "$dir_arg" || {
+		   # Check for POSIX incompatibilities with -m.
+		   # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+		   # other-writeable bit of parent directory when it shouldn't.
+		   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
+		   case $ls_ld_tmpdir in
+		     d????-?r-*) different_mode=700;;
+		     d????-?--*) different_mode=755;;
+		     *) false;;
+		   esac &&
+		   $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+		     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+		     test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+		   }
+		 }
+	      then posix_mkdir=:
+	      fi
+	      rmdir "$tmpdir/d" "$tmpdir"
+	    else
+	      # Remove any dirs left behind by ancient mkdir implementations.
+	      rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+	    fi
+	    trap '' 0;;
+	esac;;
+    esac
+
+    if
+      $posix_mkdir && (
+	umask $mkdir_umask &&
+	$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+      )
+    then :
+    else
+
+      # The umask is ridiculous, or mkdir does not conform to POSIX,
+      # or it failed possibly due to a race condition.  Create the
+      # directory the slow way, step by step, checking for races as we go.
+
+      case $dstdir in
+	/*) prefix='/';;
+	[-=\(\)!]*) prefix='./';;
+	*)  prefix='';;
+      esac
+
+      eval "$initialize_posix_glob"
+
+      oIFS=$IFS
+      IFS=/
+      $posix_glob set -f
+      set fnord $dstdir
+      shift
+      $posix_glob set +f
+      IFS=$oIFS
+
+      prefixes=
+
+      for d
+      do
+	test X"$d" = X && continue
+
+	prefix=$prefix$d
+	if test -d "$prefix"; then
+	  prefixes=
+	else
+	  if $posix_mkdir; then
+	    (umask=$mkdir_umask &&
+	     $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+	    # Don't fail if two instances are running concurrently.
+	    test -d "$prefix" || exit 1
+	  else
+	    case $prefix in
+	      *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+	      *) qprefix=$prefix;;
+	    esac
+	    prefixes="$prefixes '$qprefix'"
+	  fi
+	fi
+	prefix=$prefix/
+      done
+
+      if test -n "$prefixes"; then
+	# Don't fail if two instances are running concurrently.
+	(umask $mkdir_umask &&
+	 eval "\$doit_exec \$mkdirprog $prefixes") ||
+	  test -d "$dstdir" || exit 1
+	obsolete_mkdir_used=true
+      fi
+    fi
+  fi
+
+  if test -n "$dir_arg"; then
+    { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+    { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+      test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+  else
+
+    # Make a couple of temp file names in the proper directory.
+    dsttmp=$dstdir/_inst.$$_
+    rmtmp=$dstdir/_rm.$$_
+
+    # Trap to clean up those temp files at exit.
+    trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+    # Copy the file name to the temp name.
+    (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+    # and set any options; do chmod last to preserve setuid bits.
+    #
+    # If any of these fail, we abort the whole thing.  If we want to
+    # ignore errors from any of these, just make sure not to ignore
+    # errors from the above "$doit $cpprog $src $dsttmp" command.
+    #
+    { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+    { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+    { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+    # If -C, don't bother to copy if it wouldn't change the file.
+    if $copy_on_change &&
+       old=`LC_ALL=C ls -dlL "$dst"	2>/dev/null` &&
+       new=`LC_ALL=C ls -dlL "$dsttmp"	2>/dev/null` &&
+
+       eval "$initialize_posix_glob" &&
+       $posix_glob set -f &&
+       set X $old && old=:$2:$4:$5:$6 &&
+       set X $new && new=:$2:$4:$5:$6 &&
+       $posix_glob set +f &&
+
+       test "$old" = "$new" &&
+       $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+    then
+      rm -f "$dsttmp"
+    else
+      # Rename the file to the real destination.
+      $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+      # The rename failed, perhaps because mv can't rename something else
+      # to itself, or perhaps because mv is so ancient that it does not
+      # support -f.
+      {
+	# Now remove or move aside any old file at destination location.
+	# We try this two ways since rm can't unlink itself on some
+	# systems and the destination file might be busy for other
+	# reasons.  In this case, the final cleanup might fail but the new
+	# file should still install successfully.
+	{
+	  test ! -f "$dst" ||
+	  $doit $rmcmd -f "$dst" 2>/dev/null ||
+	  { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+	    { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+	  } ||
+	  { echo "$0: cannot unlink or rename $dst" >&2
+	    (exit 1); exit 1
+	  }
+	} &&
+
+	# Now rename the file to the real destination.
+	$doit $mvcmd "$dsttmp" "$dst"
+      }
+    fi || exit 1
+
+    trap '' 0
+  fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

thirdParty/Zoltan/config/missing

@@ -0,0 +1,331 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2012-01-06.13; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+  echo 1>&2 "Try \`$0 --help' for more information"
+  exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+  configure_ac=configure.ac
+else
+  configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+  # Try to run requested program, and just exit if it succeeds.
+  run=
+  shift
+  "$@" && exit 0
+  # Exit code 63 means version mismatch.  This often happens
+  # when the user try to use an ancient version of a tool on
+  # a file that requires a minimum version.  In this case we
+  # we should proceed has if the program had been absent, or
+  # if --run hadn't been passed.
+  if test $? = 63; then
+    run=:
+    msg="probably too old"
+  fi
+  ;;
+
+  -h|--h|--he|--hel|--help)
+    echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+  -h, --help      display this help and exit
+  -v, --version   output version information and exit
+  --run           try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+  aclocal      touch file \`aclocal.m4'
+  autoconf     touch file \`configure'
+  autoheader   touch file \`config.h.in'
+  autom4te     touch the output file, or create a stub one
+  automake     touch all \`Makefile.in' files
+  bison        create \`y.tab.[ch]', if possible, from existing .[ch]
+  flex         create \`lex.yy.c', if possible, from existing .c
+  help2man     touch the output file
+  lex          create \`lex.yy.c', if possible, from existing .c
+  makeinfo     touch the output file
+  yacc         create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake@gnu.org>."
+    exit $?
+    ;;
+
+  -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+    echo "missing $scriptversion (GNU Automake)"
+    exit $?
+    ;;
+
+  -*)
+    echo 1>&2 "$0: Unknown \`$1' option"
+    echo 1>&2 "Try \`$0 --help' for more information"
+    exit 1
+    ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+  s/^gnu-//; t
+  s/^gnu//; t
+  s/^g//; t'`
+
+# Now exit if we have it, but it failed.  Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program).  This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+  lex*|yacc*)
+    # Not GNU programs, they don't have --version.
+    ;;
+
+  *)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+       # Could not run --version or --help.  This is probably someone
+       # running `$TOOL --version' or `$TOOL --help' to check whether
+       # $TOOL exists and not knowing $TOOL uses missing.
+       exit 1
+    fi
+    ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+  aclocal*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`acinclude.m4' or \`${configure_ac}'.  You might want
+         to install the \`Automake' and \`Perl' packages.  Grab them from
+         any GNU archive site."
+    touch aclocal.m4
+    ;;
+
+  autoconf*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`${configure_ac}'.  You might want to install the
+         \`Autoconf' and \`GNU m4' packages.  Grab them from any GNU
+         archive site."
+    touch configure
+    ;;
+
+  autoheader*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`acconfig.h' or \`${configure_ac}'.  You might want
+         to install the \`Autoconf' and \`GNU m4' packages.  Grab them
+         from any GNU archive site."
+    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+    test -z "$files" && files="config.h"
+    touch_files=
+    for f in $files; do
+      case $f in
+      *:*) touch_files="$touch_files "`echo "$f" |
+				       sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+      *) touch_files="$touch_files $f.in";;
+      esac
+    done
+    touch $touch_files
+    ;;
+
+  automake*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+         You might want to install the \`Automake' and \`Perl' packages.
+         Grab them from any GNU archive site."
+    find . -type f -name Makefile.am -print |
+	   sed 's/\.am$/.in/' |
+	   while read f; do touch "$f"; done
+    ;;
+
+  autom4te*)
+    echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+         You might have modified some files without having the
+         proper tools for further handling them.
+         You can get \`$1' as part of \`Autoconf' from any GNU
+         archive site."
+
+    file=`echo "$*" | sed -n "$sed_output"`
+    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+    if test -f "$file"; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo "#! /bin/sh"
+	echo "# Created by GNU Automake missing as a replacement of"
+	echo "#  $ $@"
+	echo "exit 0"
+	chmod +x $file
+	exit 1
+    fi
+    ;;
+
+  bison*|yacc*)
+    echo 1>&2 "\
+WARNING: \`$1' $msg.  You should only need it if
+         you modified a \`.y' file.  You may need the \`Bison' package
+         in order for those modifications to take effect.  You can get
+         \`Bison' from any GNU archive site."
+    rm -f y.tab.c y.tab.h
+    if test $# -ne 1; then
+        eval LASTARG=\${$#}
+	case $LASTARG in
+	*.y)
+	    SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+	    if test -f "$SRCFILE"; then
+	         cp "$SRCFILE" y.tab.c
+	    fi
+	    SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+	    if test -f "$SRCFILE"; then
+	         cp "$SRCFILE" y.tab.h
+	    fi
+	  ;;
+	esac
+    fi
+    if test ! -f y.tab.h; then
+	echo >y.tab.h
+    fi
+    if test ! -f y.tab.c; then
+	echo 'main() { return 0; }' >y.tab.c
+    fi
+    ;;
+
+  lex*|flex*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified a \`.l' file.  You may need the \`Flex' package
+         in order for those modifications to take effect.  You can get
+         \`Flex' from any GNU archive site."
+    rm -f lex.yy.c
+    if test $# -ne 1; then
+        eval LASTARG=\${$#}
+	case $LASTARG in
+	*.l)
+	    SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+	    if test -f "$SRCFILE"; then
+	         cp "$SRCFILE" lex.yy.c
+	    fi
+	  ;;
+	esac
+    fi
+    if test ! -f lex.yy.c; then
+	echo 'main() { return 0; }' >lex.yy.c
+    fi
+    ;;
+
+  help2man*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+	 you modified a dependency of a manual page.  You may need the
+	 \`Help2man' package in order for those modifications to take
+	 effect.  You can get \`Help2man' from any GNU archive site."
+
+    file=`echo "$*" | sed -n "$sed_output"`
+    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+    if test -f "$file"; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo ".ab help2man is required to generate this page"
+	exit $?
+    fi
+    ;;
+
+  makeinfo*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified a \`.texi' or \`.texinfo' file, or any other file
+         indirectly affecting the aspect of the manual.  The spurious
+         call might also be the consequence of using a buggy \`make' (AIX,
+         DU, IRIX).  You might want to install the \`Texinfo' package or
+         the \`GNU make' package.  Grab either from any GNU archive site."
+    # The file to touch is that specified with -o ...
+    file=`echo "$*" | sed -n "$sed_output"`
+    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+    if test -z "$file"; then
+      # ... or it is the one specified with @setfilename ...
+      infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+      file=`sed -n '
+	/^@setfilename/{
+	  s/.* \([^ ]*\) *$/\1/
+	  p
+	  q
+	}' $infile`
+      # ... or it is derived from the source name (dir/f.texi becomes f.info)
+      test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+    fi
+    # If the file does not exist, the user really needs makeinfo;
+    # let's fail without touching anything.
+    test -f $file || exit 1
+    touch $file
+    ;;
+
+  *)
+    echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+         You might have modified some files without having the
+         proper tools for further handling them.  Check the \`README' file,
+         it often tells you about the needed prerequisites for installing
+         this package.  You may also peek at any GNU archive site, in case
+         some other package would contain this missing \`$1' program."
+    exit 1
+    ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

thirdParty/Zoltan/config/replace-install-prefix.pl

@@ -0,0 +1,89 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+#
+# This script is called to do a set of text replacements for installing
+# a Makefile.export.package file so that external clients can use it.
+#
+# Read in commandline arguments
+#
+my $exec_prefix = "";           # [required] Abs path to base installation directory (i.e. --prefix=??? option passed to configure)
+my $my_export_makefile = "";    # [required] Name only of installed Makefile.export.package file
+my $my_top_srcdir = "";         # [required] Abs path to this package's top source directory
+my $my_incl_dirs = "";          # [required] Abs path to this package's include directories
+my $my_lib_dirs = "";           # [optional] Abs path to this package's library directories (if any exist)
+my $dep_package_builddirs = ""; # [optional] Abs paths to other directly dependent framework package build directories (if any exist)
+GetOptions(
+  "exec-prefix=s"                   => \$exec_prefix,
+  "my-export-makefile=s"            => \$my_export_makefile,
+  "my-abs-top-srcdir=s"             => \$my_top_srcdir,
+  "my-abs-incl-dirs=s"              => \$my_incl_dirs,
+  "my-abs-lib-dirs=s"               => \$my_lib_dirs,
+  "dep-package-abs-builddirs=s"     => \$dep_package_builddirs
+  );
+#
+# Validate commandline arguments
+#
+scalar(@ARGV) == 0 || die;
+$exec_prefix ne "" || die;
+$my_export_makefile ne "" || die;
+$my_top_srcdir ne "" || die;
+$my_incl_dirs ne "" || die;
+#
+# Interpret commandline arguments
+#
+$exec_prefix = remove_rel_paths($exec_prefix);
+my @my_incl_dirs = split(":",$my_incl_dirs);
+my @my_lib_dirs = split(":",$my_lib_dirs);
+my @dep_export_package_builddirs = split(":",$dep_package_builddirs);
+#
+# Do the replacements
+#
+my $my_abs_export_makefile = "${exec_prefix}/include/${my_export_makefile}";
+
+my $cmnd_base = "${my_top_srcdir}/config/token-replace.pl ";
+#
+foreach(@dep_export_package_builddirs) {
+  if($_ ne "") {
+    run_cmnd($cmnd_base . "${_} ${exec_prefix}/include ${my_abs_export_makefile} ${my_abs_export_makefile}");
+  }
+}
+#
+foreach(@my_incl_dirs) {
+  if($_ ne "") {
+    run_cmnd($cmnd_base . "-I${_} -I${exec_prefix}/include ${my_abs_export_makefile} ${my_abs_export_makefile}");
+  }
+}
+#
+foreach(@my_lib_dirs) {
+  if($_ ne "") {
+    run_cmnd($cmnd_base . "-L${_} -L${exec_prefix}/lib ${my_abs_export_makefile} ${my_abs_export_makefile}");
+  }
+}
+#
+run_cmnd($cmnd_base . "${my_top_srcdir}/config ${exec_prefix}/include ${my_abs_export_makefile} ${my_abs_export_makefile}");
+#
+# Subroutines
+#
+sub remove_rel_paths {
+	my $entry_in = shift;
+	if ($entry_in=~/-L\.\./) {
+		return $entry_in;
+	}
+	my @paths = split("/",$entry_in);
+	my @new_paths;
+	foreach( @paths ) {
+		if( !($_=~/\.\./) ) {
+			push @new_paths, $_;
+		}
+		else {
+			pop @new_paths
+		}
+	}
+	return join("/",@new_paths);
+}
+sub run_cmnd {
+  my $cmnd = shift;
+  #print "\n", $cmnd, "\n";
+  system($cmnd)==0 || die;
+}

thirdParty/Zoltan/config/string-replace.pl

@@ -0,0 +1,43 @@
+#!/usr/bin/perl -w
+#
+# This perl script replaces a string with another string.
+# Here it is allowd for file_in and file_out to be the
+# same file.
+#
+use strict;
+#
+my $g_use_msg =
+  "Use: string-replace.pl find_string replacement_string file_in file_out\n";
+if( scalar(@ARGV) < 4 ) {
+  print STDERR $g_use_msg;
+  exit(-1);
+}
+#
+my $find_string        = shift;
+my $replacement_string = shift;
+my $file_in_name       = shift;
+my $file_out_name      = shift;
+#
+#
+if($file_in_name=~/CVS/) {
+#  print "Do not replace in CVS\n";
+  exit;
+}
+#
+open FILE_IN, "<$file_in_name" || die "The file $file_in_name could not be opended for input\n";
+my @file_in_array = <FILE_IN>;
+close FILE_IN;
+#
+my @file_out_array;
+my $did_replacement = 0;
+foreach(@file_in_array) {
+  #print $_;
+  $did_replacement = 1 if $_=~s/$find_string/$replacement_string/g;
+  #print $_;
+  push @file_out_array, $_;
+}
+if($did_replacement || $file_out_name ne $file_in_name) {
+  open FILE_OUT, ">$file_out_name" || die "The file $file_out_name could not be opended for output\n";
+  print FILE_OUT @file_out_array;
+  close FILE_OUT;
+}

thirdParty/Zoltan/config/strip_dup_incl_paths.pl

@@ -0,0 +1,44 @@
+#!/usr/bin/perl -w
+# This perl script removes duplicate include paths left to the right
+use strict;
+my @all_incl_paths = @ARGV;
+my @cleaned_up_incl_paths;
+foreach( @all_incl_paths ) {
+	$_ = remove_rel_paths($_);
+	if( !($_=~/-I/) ) {
+		push @cleaned_up_incl_paths, $_;
+	}
+	elsif( !entry_exists($_,\@cleaned_up_incl_paths) ) {
+		push @cleaned_up_incl_paths, $_;
+	}
+}
+print join( " ", @cleaned_up_incl_paths );
+#
+# Subroutines
+#
+sub entry_exists {
+	my $entry = shift; # String
+	my $list  = shift; # Reference to an array
+	foreach( @$list ) {
+		if( $entry eq $_ ) { return 1; }
+	}
+	return 0;
+}
+#
+sub remove_rel_paths {
+	my $entry_in = shift;
+	if ($entry_in=~/-I\.\./) {
+		return $entry_in;
+	}
+	my @paths = split("/",$entry_in);
+	my @new_paths;
+	foreach( @paths ) {
+		if( !($_=~/\.\./) ) {
+			push @new_paths, $_;
+		}
+		else {
+			pop @new_paths
+		}
+	}
+	return join("/",@new_paths);
+}

thirdParty/Zoltan/config/strip_dup_libs.pl

@@ -0,0 +1,69 @@
+#!/usr/bin/perl -w
+# This perl script removes duplicate libraries from the right to the left and
+# removes duplicate -L library paths from the left to the right
+use strict;
+
+my @all_libs = @ARGV;
+#
+# Move from left to right and remove duplicate -l libraries
+#
+my @cleaned_up_libs_first;
+foreach( reverse @all_libs ) {
+	$_ = remove_rel_paths($_);
+	if( $_=~/-L/ ) {
+		unshift @cleaned_up_libs_first, $_;
+	}
+	else {
+		if( !entry_exists($_,\@cleaned_up_libs_first) ) {
+			unshift @cleaned_up_libs_first, $_;
+		}
+	}
+}
+
+#
+# Move from right to left and remove duplicate -L library paths
+#
+my @cleaned_up_libs;
+foreach( @cleaned_up_libs_first ) {
+	$_ = remove_rel_paths($_);
+	if( !($_=~/-L/) ) {
+		push @cleaned_up_libs, $_;
+	}
+	elsif( !entry_exists($_,\@cleaned_up_libs) ) {
+		push @cleaned_up_libs, $_;
+	}
+}
+#
+# Print the new list of libraries and paths
+#
+print join( " ", @cleaned_up_libs );
+
+#
+# Subroutines
+#
+sub entry_exists {
+	my $entry = shift; # String
+	my $list  = shift; # Reference to an array
+	foreach( @$list ) {
+		if( $entry eq $_ ) { return 1; }
+	}
+	return 0;
+}
+#
+sub remove_rel_paths {
+	my $entry_in = shift;
+	if ($entry_in=~/-L\.\./) {
+		return $entry_in;
+	}
+	my @paths = split("/",$entry_in);
+	my @new_paths;
+	foreach( @paths ) {
+		if( !($_=~/\.\./) ) {
+			push @new_paths, $_;
+		}
+		else {
+			pop @new_paths
+		}
+	}
+	return join("/",@new_paths);
+}

thirdParty/Zoltan/config/tac_arg_check_mpi.m4

@@ -0,0 +1,67 @@
+dnl @synopsis TAC_ARG_CHECK_MPI
+dnl
+dnl Check to make sure any definitions set in TAC_ARG_CONFIG_MPI
+dnl are valid, set the MPI flags.  Test MPI compile using C++ compiler.
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_CHECK_MPI],
+[
+
+if test "X${HAVE_PKG_MPI}" = "Xyes"; then
+
+  if test -n "${MPI_DIR}" && test -z "${MPI_INC}"; then
+    MPI_INC="${MPI_DIR}/include"
+  fi
+
+  if test -n "${MPI_INC}"; then
+    CPPFLAGS="${CPPFLAGS} -I${MPI_INC}"
+  fi
+
+  AC_LANG_CPLUSPLUS 
+  AC_MSG_CHECKING(for mpi.h)
+  AC_TRY_CPP([#include "mpi.h"],
+    [AC_MSG_RESULT(yes)], 
+    [
+     AC_MSG_RESULT(no)  
+     echo "-----"
+     echo "Cannot link simple MPI program."
+     echo "Try --with-mpi-compilers to specify MPI compilers."
+     echo "Or try --with-mpi-libs, --with-mpi-incdir, --with-mpi-libdir"
+     echo "to specify all the specific MPI compile options."
+     echo "-----"
+     AC_MSG_ERROR(MPI cannot link)
+    ])
+
+  if test -n "${MPI_DIR}" && test -z "${MPI_LIBDIR}"; then
+    MPI_LIBDIR="${MPI_DIR}/lib"
+  fi
+
+  if test -n "${MPI_LIBDIR}"; then
+    LDFLAGS="${LDFLAGS} -L${MPI_LIBDIR}"
+  fi
+
+  if test -z "${MPI_LIBS}" && test -n "${MPI_LIBDIR}"; then
+    MPI_LIBS="-lmpi"
+  fi
+
+  if test -n "${MPI_LIBS}"; then
+    LIBS="${MPI_LIBS} ${LIBS}"
+  fi
+
+#   AC_LANG_CPLUSPLUS 
+#   AC_MSG_CHECKING(whether MPI will link using C++ compiler)
+#   AC_TRY_LINK([#include <mpi.h>],
+#   [int c; char** v; MPI_Init(&c,&v);],
+#   [AC_MSG_RESULT(yes)], 
+#   [AC_MSG_RESULT(no)  
+#    echo "-----"
+#    echo "Cannot link simple MPI program."
+#    echo "Or try --with-mpi-libs, --with-mpi-incdir, --with-mpi-libdir"
+#    echo "to specify all the specific MPI compile options."
+#    echo "-----"
+#    AC_MSG_ERROR(MPI cannot link)]
+#   )
+
+fi
+])

thirdParty/Zoltan/config/tac_arg_config_mpi.m4

@@ -0,0 +1,232 @@
+dnl @synopsis TAC_ARG_CONFIG_MPI
+dnl
+dnl Test a variety of MPI options:
+dnl --enable-mpi       - Turns MPI compiling mode on
+dnl --with-mpi         - specify root directory of MPI
+dnl --with-mpi-compilers - Turns on MPI compiling mode and sets the MPI C++
+dnl                       compiler = mpicxx, mpic++ or mpiCC,
+dnl                       the MPI C compiler = mpicc and 
+dnl                       the MPI Fortran compiler = mpif77
+dnl --with-mpi-incdir - specify include directory for MPI 
+dnl --with-mpi-libs    - specify MPI libraries
+dnl --with-mpi-libdir  - specify location of MPI libraries
+dnl
+dnl If any of these options are set, HAVE_MPI will be defined for both
+dnl Autoconf and Automake, and HAVE_MPI will be defined in the
+dnl generated config.h file
+dnl
+dnl
+dnl @author Mike Heroux <maherou@sandia.gov>
+dnl Modified 12/26/2007 by Jim Willenbring to skip the Fortran compiler
+dnl check if Fortran is not enabled.
+dnl
+AC_DEFUN([TAC_ARG_CONFIG_MPI],
+[
+
+AC_ARG_ENABLE(mpi,
+[AC_HELP_STRING([--enable-mpi],[MPI support])],
+[HAVE_PKG_MPI=$enableval],
+[HAVE_PKG_MPI=yes]
+)
+
+AC_ARG_WITH(mpi-compilers,
+[AC_HELP_STRING([--with-mpi-compilers=PATH],
+[use MPI compilers mpicc, mpif77, and mpicxx, mpic++ or mpiCC in the specified path or in the default path if no path is specified. Enables MPI])],
+[
+  if test X${withval} != Xno; then
+    HAVE_PKG_MPI=yes
+    if test X${withval} = Xyes; then
+      # Check for mpicxx, if it does not exist, check for mpic++, if it does 
+      # not exist, use mpiCC instead.
+      AC_CHECK_PROG(MPI_TEMP_CXX, mpicxx, mpicxx, no)
+      if test X${MPI_TEMP_CXX} = Xno; then
+	AC_CHECK_PROG(MPI_CXX, mpic++, mpic++, mpiCC)
+      else 
+	MPI_CXX=${MPI_TEMP_CXX}
+      fi
+      MPI_CC=mpicc
+      MPI_F77=mpif77
+      MPI_F90=mpif90
+    else
+      if test -f ${withval}/mpicxx; then
+        MPI_CXX=${withval}/mpicxx
+      elif test -f ${withval}/mpic++; then
+	MPI_CXX=${withval}/mpic++
+      else
+        MPI_CXX=${withval}/mpiCC
+      fi
+      MPI_CC=${withval}/mpicc
+      MPI_F77=${withval}/mpif77
+      MPI_F90=${withval}/mpif90
+    fi
+  fi
+],
+[
+  HAVE_PKG_MPI=yes
+  # Check for mpicxx, if it does not exist, check for mpic++, if it does 
+  # not exist, use mpiCC instead.
+  AC_CHECK_PROG(MPI_TEMP_CXX, mpicxx, mpicxx, no)
+  if test X${MPI_TEMP_CXX} = Xno; then
+    AC_CHECK_PROG(MPI_CXX, mpic++, mpic++, mpiCC)
+  else 
+    MPI_CXX=${MPI_TEMP_CXX}
+  fi
+  MPI_CC=mpicc
+  MPI_F77=mpif77
+  MPI_F90=mpif90
+]
+)
+
+AC_ARG_WITH(mpi,
+[AC_HELP_STRING([--with-mpi=MPIROOT],[use MPI root directory (enables MPI)])],
+[
+  HAVE_PKG_MPI=yes
+  MPI_DIR=${withval}
+  AC_MSG_CHECKING(MPI directory)
+  AC_MSG_RESULT([${MPI_DIR}])
+]
+)
+
+#AC_ARG_WITH(mpi-include,
+#[AC_HELP_STRING([--with-mpi-include],[Obsolete.  Use --with-mpi-incdir=DIR instead.  Do not prefix DIR with '-I'.])],
+#[AC_MSG_ERROR([--with-mpi-include is an obsolte option.   Use --with-mpi-incdir=DIR instead.  Do not prefix DIR with '-I'.  For example '--with-mpi-incdir=/usr/lam_path/include'.])]
+#)
+
+AC_ARG_WITH(mpi-libs,
+[AC_HELP_STRING([--with-mpi-libs="LIBS"],[MPI libraries @<:@"-lmpi"@:>@])],
+[
+  MPI_LIBS=${withval}
+  AC_MSG_CHECKING(user-defined MPI libraries)
+  AC_MSG_RESULT([${MPI_LIBS}])
+]
+)
+
+AC_ARG_WITH(mpi-incdir,
+[AC_HELP_STRING([--with-mpi-incdir=DIR],[MPI include directory @<:@MPIROOT/include@:>@  Do not use -I])],
+[
+  MPI_INC=${withval}
+  AC_MSG_CHECKING(user-defined MPI includes)
+  AC_MSG_RESULT([${MPI_INC}])
+]
+)
+
+AC_ARG_WITH(mpi-libdir,
+[AC_HELP_STRING([--with-mpi-libdir=DIR],[MPI library directory @<:@MPIROOT/lib@:>@  Do not use -L])],
+[
+  MPI_LIBDIR=${withval}
+  AC_MSG_CHECKING(user-defined MPI library directory)
+  AC_MSG_RESULT([${MPI_LIBDIR}])
+]
+)
+
+AC_MSG_CHECKING(whether we are using MPI)
+AC_MSG_RESULT([${HAVE_PKG_MPI}])
+
+if test "X${HAVE_PKG_MPI}" = "Xyes"; then
+   AC_DEFINE(HAVE_MPI,,[define if we want to use MPI])
+fi
+
+dnl Define Automake version of HAVE_MPI if appropriate
+
+AM_CONDITIONAL(HAVE_MPI, [test "X${HAVE_PKG_MPI}" = "Xyes"])
+
+
+dnl
+dnl --------------------------------------------------------------------
+dnl Check for MPI compilers (must be done *before* AC_PROG_CXX,
+dnl AC_PROG_CC and AC_PROG_F77)
+dnl 
+dnl --------------------------------------------------------------------
+
+if test "X$ac_cv_use_zoltan_cppdriver" = "Xyes"; then
+
+if test -n "${MPI_CXX}"; then
+  if test -f ${MPI_CXX}; then
+    MPI_CXX_EXISTS=yes
+  else
+    AC_CHECK_PROG(MPI_CXX_EXISTS, ${MPI_CXX}, yes, no)
+  fi
+
+  if test "X${MPI_CXX_EXISTS}" = "Xyes"; then
+    CXX=${MPI_CXX}
+  else
+    echo "-----"
+    echo "Cannot find MPI C++ compiler ${MPI_CXX}."
+    echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH"
+    echo "or specify a C++ compiler using CXX=<compiler>"
+    echo "Do not use --with-mpi-compilers if using CXX=<compiler>"
+    echo "-----"
+    AC_MSG_ERROR([MPI C++ compiler (${MPI_CXX}) not found.])
+  fi
+fi
+
+fi dnl ac_cv_use_zoltan_cppdriver
+
+if test -n "${MPI_CC}"; then
+  if test -f ${MPI_CC}; then
+    MPI_CC_EXISTS=yes
+  else
+    AC_CHECK_PROG(MPI_CC_EXISTS, ${MPI_CC}, yes, no)
+  fi
+
+  if test "X${MPI_CC_EXISTS}" = "Xyes"; then
+    CC=${MPI_CC}
+  else
+    echo "-----"
+    echo "Cannot find MPI C compiler ${MPI_CC}."
+    echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH"
+    echo "or specify a C compiler using CC=<compiler>"
+    echo "Do not use --with-mpi-compilers if using CC=<compiler>"
+    echo "-----"
+    AC_MSG_ERROR([MPI C compiler (${MPI_CC}) not found.])
+  fi
+fi
+
+if test "X$ac_cv_use_fortran" = "Xyes"; then
+
+if test -n "${MPI_F77}"; then
+  if test -f ${MPI_F77}; then
+    MPI_F77_EXISTS=yes
+  else
+    AC_CHECK_PROG(MPI_F77_EXISTS, ${MPI_F77}, yes, no)
+  fi
+
+  if test "X${MPI_F77_EXISTS}" = "Xyes"; then
+    F77=${MPI_F77}
+  else
+    echo "-----"
+    echo "Cannot find MPI Fortran compiler ${MPI_F77}."
+    echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH"
+    echo "or specify a Fortran 77 compiler using F77=<compiler>"
+    echo "Do not use --with-mpi-compilers if using F77=<compiler>"
+    echo "-----"
+    AC_MSG_ERROR([MPI Fortran 77 compiler (${MPI_F77}) not found.])
+  fi
+fi
+
+if test "X$ac_cv_use_fortran90" = "Xyes"; then
+
+if test -n "${MPI_F90}"; then
+  if test -f ${MPI_F90}; then
+    MPI_F90_EXISTS=yes
+  else
+    AC_CHECK_PROG(MPI_F90_EXISTS, ${MPI_F90}, yes, no)
+  fi
+
+  if test "X${MPI_F90_EXISTS}" = "Xyes"; then
+    FC=${MPI_F90}
+  else
+    echo "-----"
+    echo "Cannot find MPI Fortran compiler ${MPI_F90}."
+    echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH"
+    echo "or specify a Fortran compiler using FC=<compiler>"
+    echo "Do not use --with-mpi-compilers if using FC=<compiler>"
+    echo "-----"
+    AC_MSG_ERROR([MPI Fortran compiler (${MPI_F90}) not found.])
+  fi
+fi
+
+fi dnl ac_cv_use_fortran90
+
+fi dnl ac_cv_use_fortran
+])

thirdParty/Zoltan/config/tac_arg_enable_export-makefiles.m4

@@ -0,0 +1,76 @@
+dnl Enables export makefile specific code
+dnl 
+dnl The following AM_CONDITIONALS are set for makefiles to access:
+dnl USING_EXPORT_MAKEFILES
+dnl USING_PERL via TAC_ARG_WITH_PERL
+dnl USING_GNUMAKE
+dnl
+dnl The following AC_DEFINES are set:
+dnl HAVE_EXPORT_MAKEFILES
+dnl 
+dnl the following variables are set:
+dnl PERL_EXE for the perl executable via TAC_ARG_WITH_PERL
+dnl 
+dnl This file was based on tac_arg_enable_feature.m4 by Mike Heroux
+dnl @author Roger Pawlowski <rppawlo@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_ENABLE_EXPORT_MAKEFILES],
+[
+AC_ARG_ENABLE(export-makefiles,
+AC_HELP_STRING([--enable-export-makefiles],[Creates export makefiles in the install (prefix) directory.  This option requires perl to be set in your path or defined with --with-perl=<perl executable>. Note that the export makefiles are always created and used in the build directory, but will not be installable without this option to change the paths. (default is $1)]),
+ac_cv_use_export_makefiles=$enableval, 
+ac_cv_use_export_makefiles=$1)
+
+AC_MSG_CHECKING(whether to build export makefiles)
+
+if test "X$ac_cv_use_export_makefiles" != "Xno"; then
+
+  AC_MSG_RESULT(yes)
+  AC_DEFINE([HAVE_EXPORT_MAKEFILES],,[Define if you want to build export makefiles.])
+
+else
+
+  AC_MSG_RESULT(no)
+
+fi
+
+AM_CONDITIONAL(USING_EXPORT_MAKEFILES, test X${ac_cv_use_export_makefiles} = Xyes)
+
+# Check for perl to run scripts (Required dependency)
+TAC_ARG_WITH_PERL
+
+if test "X$HAVE_PERL" != "Xyes" && 
+   test "X$ac_cv_use_export_makefiles" != "Xno"; then
+  AC_MSG_RESULT(no)
+  AC_MSG_ERROR([Failed to find the perl executable.  The flag --enable-export-makefiles requires perl to be either in your path or explicitly defined by the flag --with-perl=<executable>.  If you do not require the export makefiles to be installed via 'make install', you can disable the export makefiles with --disable-export-makefiles.])
+fi
+
+# Check for using gnumake to clean up link lines via 
+# gnumake's "shell" command. Optional dependency.
+AC_DEFUN([TAC_ARG_WITH_GNUMAKE],
+[
+AC_ARG_WITH(gnumake,
+AC_HELP_STRING([--with-gnumake],[Gnu's make has special functions we can use to eliminate redundant paths in the build and link lines. Enable this if you use gnu-make to build Trilinos. This requires that perl is in your path or that you have specified the perl executable with --with-perl=<perl executable>.  Configure will check for the existence of the perl executable and quit with an error if it is not found. (default is no)]),
+ac_cv_use_gnumake=$withval, ac_cv_use_gnumake=no)
+
+AC_MSG_CHECKING(whether gnumake specific code should be enabled)
+
+if test "X$ac_cv_use_gnumake" != "Xno"; then
+  AC_MSG_RESULT(yes)  
+  AC_DEFINE([HAVE_GNUMAKE],,[Define if you are using gnumake - this will shorten your link lines.])
+else
+  AC_MSG_RESULT(no)
+fi
+AM_CONDITIONAL(USING_GNUMAKE, test "X$ac_cv_use_gnumake" = "Xyes")
+])
+
+TAC_ARG_WITH_GNUMAKE
+
+if test "X$HAVE_PERL" != "Xyes" && 
+   test "X$ac_cv_use_gnumake" != "Xno"; then
+  AC_MSG_RESULT(no)
+  AC_MSG_ERROR([The flag --with-gnumake requires perl to be in your path.  The perl executable can alternatively be explicitly defined by the flag --with-perl=<executable>.])
+fi
+
+])
+

thirdParty/Zoltan/config/tac_arg_enable_feature.m4

@@ -0,0 +1,40 @@
+dnl @synopsis TAC_ARG_ENABLE_FEATURE(FEATURE_NAME, FEATURE_DESCRIPTION, HAVE_NAME, DEFAULT_VAL)
+dnl
+dnl Test for --enable-${FEATURE_NAME} and set to DEFAULT_VAL value if feature not specified.
+dnl Also calls AC_DEFINE to define HAVE_${HAVE_NAME} if value is not equal to "no"
+dnl 
+dnl Use this macro to help defining whether or not optional 
+dnl features* should compiled.  For example:
+dnl
+dnl TAC_ARG_ENABLE_FEATURE(epetra, [Configure and build epetra], EPETRA, yes)
+dnl 
+dnl will test for --enable-epetra when configure is run.  If it is defined 
+dnl and not set to "no" or not defined (default is "yes") then HAVE_EPETRA will
+dnl be defined, if --enable-epetra is defined to be "no", HAVE_EPETRA will not
+dnl be defined.
+dnl
+dnl *NOTE: epetra, aztecoo, komplex, ifpack, and other software found in
+dnl subdirectories of Trilinos/packages are "packages" in their own right.
+dnl However, these packages are also "features" of the larger package
+dnl "Trilinos".  Therefore, when configuring from the Trilinos directory,
+dnl it is appropriate to refer to these software packages as "features".
+dnl
+dnl This file was based on tac_arg_with_package.m4 by Mike Heroux
+dnl @author James Willenbring <jmwille@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_ENABLE_FEATURE],
+[
+AC_ARG_ENABLE([$1],
+AC_HELP_STRING([--enable-$1],[$2 (default is [$4])]),
+ac_cv_use_$1=$enableval, ac_cv_use_$1=$4)
+
+AC_MSG_CHECKING(whether to use [$1])
+
+if test "X$ac_cv_use_$1" != "Xno"; then
+  AC_MSG_RESULT(yes)  
+  AC_DEFINE([HAVE_$3],,[Define if want to build $1])
+else
+  AC_MSG_RESULT(no)
+fi
+])
+

thirdParty/Zoltan/config/tac_arg_enable_feature_sub.m4

@@ -0,0 +1,52 @@
+dnl @synopsis TAC_ARG_ENABLE_FEATURE_SUB(FEATURE_NAME, SUB_FEATURE_NAME, FEATURE_DESCRIPTION, HAVE_NAME, DEFAULT_VAL)
+dnl
+dnl This hack gets around the fact that TAC_ARG_ENABLE_FEATURE does not support underscores
+dnl in its feature names.  TAC_ARG_ENABLE_FEATURE_SUB allows exactly one underscore.  Not great,
+dnl but arguably better than supporting no underscores.
+dnl
+dnl TAC_ARG_ENABLE_FEATURE(feature-sub, [Configure and build feature-sub], FEATURE_SUB, yes) 
+dnl   fails because tac_arg_enable_feature tests for ac_cv_use_feature-sub which gets 
+dnl   rejected because the `-' is not allowed in variables.  (AC_ARG_ENABLE sets ac_cv_use_feature_sub
+dnl   to avoid this problem.)  Use:
+dnl 
+dnl TAC_ARG_ENABLE_FEATURE(feature, sub, [Configure and build feature-sub], FEATURE_SUB, yes) 
+dnl   instead.
+dnl
+dnl Test for --enable-${FEATURE_NAME} and set to DEFAULT_VAL value if feature not specified.
+dnl Also calls AC_DEFINE to define HAVE_${HAVE_NAME} if value is not equal to "no"
+dnl 
+dnl Use this macro to help defining whether or not optional 
+dnl features* should compiled.  For example:
+dnl
+dnl TAC_ARG_ENABLE_FEATURE(epetra, [Configure and build epetra], EPETRA, yes)
+dnl 
+dnl will test for --enable-epetra when configure is run.  If it is defined 
+dnl and not set to "no" or not defined (default is "yes") then HAVE_EPETRA will
+dnl be defined, if --enable-epetra is defined to be "no", HAVE_EPETRA will not
+dnl be defined.
+dnl
+dnl *NOTE: epetra, aztecoo, komplex, ifpack, and other software found in
+dnl subdirectories of Trilinos/packages are "packages" in their own right.
+dnl However, these packages are also "features" of the larger package
+dnl "Trilinos".  Therefore, when configuring from the Trilinos directory,
+dnl it is appropriate to refer to these software packages as "features".
+dnl
+dnl This file was based on tac_arg_enable_package.m4 by Jim Willenbring
+dnl @author Ken Stanley <ksstanl@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_ENABLE_FEATURE_SUB],
+[
+AC_ARG_ENABLE([$1-$2],
+AC_HELP_STRING([--enable-$1-$2],[$3 (default is [$5])]),
+ac_cv_use_$1_$2=$enableval, ac_cv_use_$1_$2=$5)
+
+AC_MSG_CHECKING(whether to use [$1-$2])
+
+if test "X$ac_cv_use_$1_$2" != "Xno"; then
+  AC_MSG_RESULT(yes)  
+  AC_DEFINE([HAVE_$4],,[Define if want to build $1-$2])
+else
+  AC_MSG_RESULT(no)
+fi
+])
+

thirdParty/Zoltan/config/tac_arg_enable_feature_sub_check.m4

@@ -0,0 +1,54 @@
+dnl @synopsis TAC_ARG_ENABLE_FEATURE_SUB_CHECK(FEATURE_NAME, SUB_FEATURE_NAME, FEATURE_DESCRIPTION, HAVE_NAME)
+dnl
+dnl This hack gets around the fact that TAC_ARG_ENABLE_FEATURE does not support underscores
+dnl in its feature names.  TAC_ARG_ENABLE_FEATURE_SUB_CHECK allows exactly one underscore.  Not great,
+dnl but arguably better than supporting no underscores.
+dnl
+dnl TAC_ARG_ENABLE_FEATURE(feature-sub, [Configure and build feature-sub], FEATURE_SUB, yes) 
+dnl   fails because tac_arg_enable_feature tests for ac_cv_use_feature-sub which gets 
+dnl   rejected because the `-' is not allowed in variables.  (AC_ARG_ENABLE sets ac_cv_use_feature_sub
+dnl   to avoid this problem.)  Use:
+dnl 
+dnl TAC_ARG_ENABLE_FEATURE_SUB_CHECK(feature, sub, [Configure and build feature-sub], FEATURE_SUB) 
+dnl   instead.
+dnl
+dnl This macro will test for --enable-${FEATURE_NAME}-${SUB_FEATURE_NAME} when configure is run.  
+dnl If it is defined and not set to "no" or not defined and --disable-${SUB_FEATURE_NAME} is not
+dnl specified then HAVE_${HAVE_NAME} will be defined.
+dnl
+dnl *NOTE: This macro is designed for the use-case when there is an individual Trilinos package 
+dnl offering fine-grained control of a Trilinos option.  This way, the individual package 
+dnl option is enabled, as long as the Trilinos option is not disabled.  If the Trilinos option is
+dnl disabled, then the user must enable each packages option individually.  For instance:
+dnl
+dnl --disable-tests --enable-teuchos-tests
+dnl
+dnl *NOTE: epetra, aztecoo, komplex, ifpack, and other software found in
+dnl subdirectories of Trilinos/packages are "packages" in their own right.
+dnl However, these packages are also "features" of the larger package
+dnl "Trilinos".  Therefore, when configuring from the Trilinos directory,
+dnl it is appropriate to refer to these software packages as "features".
+dnl
+dnl This file was based on tac_arg_enable_package.m4 by Jim Willenbring
+dnl and tac_arg_enable_package_sub.m4 by Ken Stanley.
+dnl
+dnl @author Heidi Thornquist <hkthorn@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_ENABLE_FEATURE_SUB_CHECK],
+[
+AC_ARG_ENABLE([$2],, ac_cv_use_$2=$enableval, ac_cv_use_$2=yes)
+
+AC_ARG_ENABLE([$1-$2],
+AC_HELP_STRING([--enable-$1-$2],[$3 (default is yes if --disable-$2 is not specified)]),
+ac_cv_use_$1_$2=$enableval, ac_cv_use_$1_$2=${ac_cv_use_$2})
+
+AC_MSG_CHECKING(whether to use [$1-$2])
+
+if test "X$ac_cv_use_$1_$2" != "Xno"; then
+  AC_MSG_RESULT(yes)  
+  AC_DEFINE([HAVE_$4],,[Define if want to build $1-$2])
+else
+  AC_MSG_RESULT(no)
+fi
+])
+

thirdParty/Zoltan/config/tac_arg_enable_option.m4

@@ -0,0 +1,30 @@
+dnl @synopsis TAC_ARG_ENABLE_OPTION(FEATURE_NAME, FEATURE_DESCRIPTION, HAVE_NAME, DEFAULT_VAL)
+dnl
+dnl Test for --enable-${FEATURE_NAME} and set to DEFAULT_VAL value if feature not specified.
+dnl Also calls AC_DEFINE to define HAVE_${HAVE_NAME} if value is not equal to "no"
+dnl
+dnl Use this macro to facilitate definition of options in a package.  For example:
+dnl 
+dnl TAC_ARG_ENABLE_OPTION(threads, [enable shared memory threads], THREADS, no)
+dnl 
+dnl will test for --enable-threads when configure is run.  If it is defined (and not set to "no")
+dnl then HAVE_THREADS will be defined, Otherwise HAVE_THREADS will not be defined.
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_ENABLE_OPTION],
+[
+AC_ARG_ENABLE([$1],
+AC_HELP_STRING([--enable-$1],[$2 (default is [$4])]),
+ac_cv_use_$1=$enableval, ac_cv_use_$1=$4)
+
+AC_MSG_CHECKING(whether to use [$1])
+
+if test "X$ac_cv_use_$1" != "Xno"; then
+  AC_MSG_RESULT(yes)
+  AC_DEFINE([HAVE_$3],1,[Define if want to build with $1 enabled])
+else
+  AC_MSG_RESULT(no)
+fi
+])
+

thirdParty/Zoltan/config/tac_arg_with_3pl_sub.m4

@@ -0,0 +1,17 @@
+dnl @synopsis TAC_ARG_WITH_3PL_SUB( VALUE_NAME, VALUE_SUB_NAME, VALUE_DESCRIPTION)
+dnl
+dnl Test for --with-${VALUE_NAME}-${VALUE_SUB_NAME} and set to no if value not specified.
+dnl 
+dnl Use this macro to set variables, such as library names and include paths, which
+dnl include an underscore.
+dnl
+dnl This file was based on tac_arg_with_sub.m4 by Ken Stanley
+dnl @author Jim Willenbring <jmwille@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_3PL_SUB],
+[
+AC_ARG_WITH([$1-$2],
+AC_HELP_STRING([--with-$1-$2],[$3]),
+tac_with_$1_$2=$withval, tac_with_$1_$2=no)
+])
+

thirdParty/Zoltan/config/tac_arg_with_ar.m4

@@ -0,0 +1,39 @@
+dnl @synopsis TAC_ARG_WITH_AR
+dnl
+dnl Test for --with-ar="ar_program ar_flags".
+dnl Default is "ar cru"
+dnl 
+dnl Generates an Automake conditional USE_ALTERNATE_AR that can be tested.  
+dnl Generates the user-specified archiver command in @ALTERNATE_AR@.
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_AR],
+[
+AC_ARG_WITH(ar,
+AC_HELP_STRING([--with-ar], [override archiver command (default is "ar cru")]),
+[
+AC_MSG_CHECKING(user-defined archiver)
+AC_MSG_RESULT([${withval}])
+USE_ALTERNATE_AR=yes
+ALTERNATE_AR="${withval}"
+]
+)
+
+if test -n "${SPECIAL_AR}" && test "X${USE_ALTERNATE_AR}" != "Xyes";
+then
+  USE_ALTERNATE_AR=yes
+  ALTERNATE_AR="${SPECIAL_AR}"
+fi
+
+AC_MSG_CHECKING(for special archiver command)
+if test "X${USE_ALTERNATE_AR}" = "Xyes"; then
+   AC_MSG_RESULT([${ALTERNATE_AR}])
+   AM_CONDITIONAL(USE_ALTERNATE_AR, true)
+else
+   AC_MSG_RESULT([none])
+   AM_CONDITIONAL(USE_ALTERNATE_AR, false)
+fi
+AC_SUBST(ALTERNATE_AR)
+])
+

thirdParty/Zoltan/config/tac_arg_with_flags.m4

@@ -0,0 +1,31 @@
+dnl @synopsis TAC_ARG_WITH_FLAGS(lcase_name, UCASE_NAME)
+dnl
+dnl Test for --with-lcase_name="compiler/loader flags".  if defined, prepend 
+dnl flags to standard UCASE_NAME definition.
+dnl
+dnl Use this macro to facilitate additional special flags that should be
+dnl passed on to the preprocessor/compilers/loader.
+dnl
+dnl Example use
+dnl 
+dnl TAC_ARG_WITH_FLAGS(cxxflags, CXXFLAGS)
+dnl 
+dnl tests for --with-cxxflags and pre-pends to CXXFLAGS
+dnl 
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_FLAGS],
+[
+AC_MSG_CHECKING([whether additional [$2] flags should be added])
+AC_ARG_WITH($1,
+AC_HELP_STRING([--with-$1], 
+[additional [$2] flags to be added: will prepend to [$2]]),
+[
+$2="${withval} ${$2}"
+AC_MSG_RESULT([$2 = ${$2}])
+],
+AC_MSG_RESULT(no)
+)
+])
+

thirdParty/Zoltan/config/tac_arg_with_incdirs.m4

@@ -0,0 +1,27 @@
+dnl @synopsis TAC_ARG_WITH_INCDIRS
+dnl
+dnl Test for --with-incdirs="-Iincdir1 -Iincdir2".  if defined, prepend 
+dnl "-Iincdir1 -Iincdir2" to CPPFLAGS
+dnl
+dnl Use this macro to facilitate addition of directories to include file search path.
+dnl 
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_INCDIRS],
+[
+AC_MSG_CHECKING([whether additional include search paths defined])
+AC_ARG_WITH(incdirs,
+AC_HELP_STRING([--with-incdirs], 
+[additional directories containing include files: will prepend to search here for includes, use -Idir format]),
+[
+CPPFLAGS="${withval} ${CPPFLAGS}"
+CFLAGS="${withval} ${CFLAGS}"
+FCFLAGS="${withval} ${FCFLAGS}"
+FFLAGS="${withval} ${FFLAGS}"
+AC_MSG_RESULT([${withval}])
+],
+AC_MSG_RESULT(no)
+)
+])
+

thirdParty/Zoltan/config/tac_arg_with_libdirs.m4

@@ -0,0 +1,24 @@
+dnl @synopsis TAC_ARG_WITH_LIBDIRS
+dnl
+dnl Test for --with-libdirs="-Llibdir1 -Llibdir2".  if defined, 
+dnl prepend "-Llibdir1 -Llibdir2" to LDFLAGS
+dnl
+dnl Use this macro to facilitate addition of directories to library search path.
+dnl 
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_LIBDIRS],
+[
+AC_MSG_CHECKING([whether additional library search paths defined])
+AC_ARG_WITH(libdirs,
+AC_HELP_STRING([--with-libdirs], 
+[OBSOLETE use --with-ldflags instead.  (ex. --with-ldflags="-L<DIR> -L<DIR2>")]),
+[
+LDFLAGS="${withval} ${LDFLAGS}"
+AC_MSG_RESULT([${withval}])
+],
+AC_MSG_RESULT(no)
+)
+])
+

thirdParty/Zoltan/config/tac_arg_with_libs.m4

@@ -0,0 +1,30 @@
+dnl @synopsis TAC_ARG_WITH_LIBS
+dnl
+dnl Test for --with-libs="name(s)".
+dnl 
+dnl Prepends the specified name(s) to the list of libraries to link 
+dnl with.  
+dnl
+dnl Example use
+dnl
+dnl TAC_ARG_WITH_LIBS
+dnl 
+dnl tests for --with-libs and pre-pends to LIBS
+dnl
+dnl @author Jim Willenbring <jmwille@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_LIBS],
+[
+AC_MSG_CHECKING([whether additional libraries are needed])
+AC_ARG_WITH(libs,
+AC_HELP_STRING([--with-libs], 
+[List additional libraries here.  For example, --with-libs=-lsuperlu
+or --with-libs=/path/libsuperlu.a]),
+[
+LIBS="${withval} ${LIBS}"
+AC_MSG_RESULT([LIBS = ${LIBS}])
+],
+AC_MSG_RESULT(no)
+)
+]
+)

thirdParty/Zoltan/config/tac_arg_with_package.m4

@@ -0,0 +1,32 @@
+dnl @synopsis TAC_ARG_WITH_PACKAGE(FEATURE_NAME, FEATURE_DESCRIPTION, HAVE_NAME, DEFAULT_VAL)
+dnl
+dnl Test for --with-${FEATURE_NAME} and set to DEFAULT_VAL value if feature not specified.
+dnl Also calls AC_DEFINE to define HAVE_${HAVE_NAME} if value is not equal to "no"
+dnl 
+dnl Use this macro to help defining whether or not interfaces for optional 
+dnl package should compiled.  For example:
+dnl
+dnl TAC_ARG_WITH_PACKAGE(zoltan, [Enable Zoltan interface support], ZOLTAN, no)
+dnl 
+dnl will test for --with-zoltan when configure is run.  If it is defined 
+dnl (and not set to "no") then HAVE_ZOLTAN will be defined, 
+dnl Otherwise HAVE_ZOLTAN will not be defined.
+dnl
+dnl @author Mike Heroux <mheroux@cs.sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_PACKAGE],
+[
+AC_ARG_WITH([$1],
+AC_HELP_STRING([--with-$1],[$2 (default is [$4])]),
+ac_cv_use_$1=$withval, ac_cv_use_$1=$4)
+
+AC_MSG_CHECKING(whether to use [$1])
+
+if test "X$ac_cv_use_$1" != "Xno"; then
+  AC_MSG_RESULT(yes)  
+  AC_DEFINE([HAVE_$3],,[Define if want to build with $1 enabled])
+else
+  AC_MSG_RESULT(no)
+fi
+])
+

thirdParty/Zoltan/config/tac_arg_with_perl.m4

@@ -0,0 +1,34 @@
+dnl @synopsis TAC_ARG_WITH_PERL(DEFAULT_VAL)
+dnl
+dnl Test for --enable-gnumake and set to DEFAULT_VAL value if feature not specified.
+dnl Calls AC_DEFINE to define HAVE_GNUMAKE if value is not equal to "no"
+dnl Calls AM_CONDITIONAL to define USING_GNUMAKE to true/false.
+dnl 
+dnl This file was based on tac_arg_with_ar.m4 by Mike Heroux
+dnl @author Roger Pawlowski <rppawlo@sandia.gov>
+dnl
+AC_DEFUN([TAC_ARG_WITH_PERL],
+[
+
+AC_ARG_WITH(perl,
+AC_HELP_STRING([--with-perl], [supply a perl executable.  For example --with-perl=/usr/bin/perl.]),
+[
+AC_MSG_CHECKING(for user supplied perl executable)
+AC_MSG_RESULT([${withval}])
+USER_SPECIFIED_PERL=yes
+PERL_EXE="${withval}"
+],
+[
+USER_SPECIFIED_PERL=no
+])
+
+if test "X${USER_SPECIFIED_PERL}" = "Xyes"; then
+  AC_CHECK_FILE(${PERL_EXE}, [HAVE_PERL=yes], [HAVE_PERL=no])
+  AC_SUBST(PERL_EXE, ${PERL_EXE})
+else
+  AC_CHECK_PROG(HAVE_PERL, perl, yes, no)
+  AC_SUBST(PERL_EXE, perl)
+fi
+AM_CONDITIONAL(USING_PERL, test X${HAVE_PERL} = Xyes)
+])
+

thirdParty/Zoltan/config/token-replace.pl

@@ -0,0 +1,43 @@
+#!/usr/bin/perl -w
+#
+# This perl script replaces a string with another string
+# on a token basis.  Here it is allowed for file_in and
+# file_out to be the same file.
+#
+use strict;
+#
+my $g_use_msg =
+  "Use: token-replace.pl find_token replacement_token file_in file_out\n";
+if( scalar(@ARGV) < 4 ) {
+  print STDERR $g_use_msg;
+  exit(-1);
+}
+#
+my $find_token         = shift;
+my $replacement_token  = shift;
+my $file_in_name       = shift;
+my $file_out_name      = shift;
+#
+#print "file_in_name = $file_in_name\n";
+if($file_in_name=~/CVS/) {
+#  print "Do not replace in CVS\n";
+  exit;
+}
+open FILE_IN, "<$file_in_name" || die "The file $file_in_name could not be opended for input\n";
+my @file_in_array = <FILE_IN>;
+close FILE_IN;
+#
+my $match_str = '([^\w\d_]|^)' . $find_token . '([^\w\d_]|$)';
+#print $match_str . "\n";
+#
+my @file_out_array;
+my $did_replacement = 0;
+foreach(@file_in_array) {
+  $did_replacement = 1 if $_=~s/$match_str/$1$replacement_token$2/g;
+  push @file_out_array, $_;
+}
+if($did_replacement || $file_out_name ne $file_in_name) {
+  open FILE_OUT, ">$file_out_name" || die "The file $file_out_name could not be opended for output\n";
+  print FILE_OUT @file_out_array;
+  close FILE_OUT;
+}

thirdParty/Zoltan/config/wk_fc_get_vendor.m4

@@ -0,0 +1,104 @@
+dnl Determine F90 vendor and version string.
+AC_DEFUN([WK_FC_GET_VENDOR],
+[AC_CACHE_CHECK([the compiler ID],
+[wk_cv_prog_f90_version_string],
+[$FC -version >conftest.log 2>&1
+$FC -V >>conftest.log 2>&1
+$FC --version >>conftest.log 2>&1
+
+wk_grep_f90_NAG=`grep NAG conftest.log | head -1`
+wk_grep_f90_Compaq=`grep Compaq conftest.log | head -1`
+wk_grep_f90_Digital=`grep DIGITAL conftest.log | head -1`
+wk_grep_f90_SGI=`grep MIPS conftest.log | head -1`
+wk_grep_f90_Intel=`grep 'Intel(R)' conftest.log | head -1`
+wk_grep_f90_Sun=`grep 'Sun' conftest.log | head -1`
+wk_grep_f90_Lahey=`grep 'Lahey' conftest.log | head -1`
+wk_grep_f90_PGI=`grep 'pgf' conftest.log | head -1`
+wk_grep_f90_G95=`grep -i 'g95' conftest.log | grep -i 'gcc' | head -1`
+wk_grep_f90_GFORTRAN=`grep -i 'GNU Fortran' conftest.log | head -1`
+wk_grep_f90_Absoft=`grep -i 'Absoft' conftest.log | head -1`
+ 
+if test -n "$wk_grep_f90_NAG"; then
+  wk_cv_prog_f90_type="NAG"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_NAG
+  wk_cv_prog_f90_version=[`echo $wk_cv_prog_f90_version_string | sed -e 's/.* Release \([0-9][0-9]*\.[0-9][0-9]*.*$\)/\1/'`]
+  wk_cv_prog_f90_major_version=[`echo $wk_cv_prog_f90_version | sed -e 's/\([0-9][0-9]*\)\..*/\1/'`]
+elif test -n "$wk_grep_f90_Compaq"; then
+  wk_cv_prog_f90_type="Compaq"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_Compaq
+elif test -n "$wk_grep_f90_Digital"; then
+  wk_cv_prog_f90_type="DEC"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_Digital
+elif test -n "$wk_grep_f90_SGI"; then
+  wk_cv_prog_f90_type="SGI"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_SGI
+elif test -n "$wk_grep_f90_Intel"; then
+  wk_cv_prog_f90_type="Intel"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_Intel
+  wk_cv_prog_f90_version=[`echo $wk_cv_prog_f90_version_string | sed -e 's/.* Version \([0-9][0-9]*\.[0-9][0-9]*\) .*/\1/'`]
+  wk_cv_prog_f90_major_version=[`echo $wk_cv_prog_f90_version | sed -e 's/\([0-9][0-9]*\)\..*/\1/'`]
+elif test -n "$wk_grep_f90_Sun"; then
+  wk_cv_prog_f90_type="Sun"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_Sun
+  wk_cv_prog_f90_version=[`echo $wk_cv_prog_f90_version_string | sed -e 's/.* Fortran 95 \([0-9][0-9]*\.[0-9][0-9]*\) .*/\1/'`]
+  wk_cv_prog_f90_major_version=[`echo $wk_cv_prog_f90_version | sed -e 's/\([0-9][0-9]*\)\..*/\1/'`]
+elif test -n "$wk_grep_f90_Lahey"; then
+  wk_cv_prog_f90_type="Lahey"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_Lahey
+elif test -n "$wk_grep_f90_PGI"; then
+  wk_cv_prog_f90_type="PGI"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_PGI
+elif test -n "$wk_grep_f90_G95"; then
+  wk_cv_prog_f90_type="G95"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_G95
+elif test -n "$wk_grep_f90_GFORTRAN"; then
+  wk_cv_prog_f90_type="GNU"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_GFORTRAN
+  wk_cv_prog_f90_version=[`echo $wk_cv_prog_f90_version_string | sed -e 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/'`]
+  wk_cv_prog_f90_major_version=[`echo $wk_cv_prog_f90_version | sed -e 's/\([0-9][0-9]*\)\..*/\1/'`]
+elif test -n "$wk_grep_f90_Absoft"; then
+  wk_cv_prog_f90_type="Absoft"
+  wk_cv_prog_f90_version_string=$wk_grep_f90_Absoft
+else
+  wk_cv_prog_f90_type="unknown"
+  wk_cv_prog_f90_version_string="unknown"
+fi
+
+rm -f conftest.log
+
+])  dnl end AC_CACHE_CHECK
+
+dnl Vendor-specific variables:
+AC_CACHE_CHECK([the compiler vendor], [wk_cv_prog_f90_type])
+
+if test -n "$wk_cv_prog_f90_version"; then
+  AC_CACHE_CHECK([the compiler version], [wk_cv_prog_f90_version])
+else
+  wk_cv_prog_f90_version=$wk_cv_prog_f90_version_string
+fi
+
+if test -n "$wk_cv_prog_f90_major_version"; then
+  AC_CACHE_CHECK([the compiler major version], [wk_cv_prog_f90_major_version])
+else
+  wk_cv_prog_f90_major_version=$wk_cv_prog_f90_version
+fi
+
+FC_VERSION_STRING=$wk_cv_prog_f90_version_string
+FC_VENDOR=$wk_cv_prog_f90_type
+FC_VERSION=$wk_cv_prog_f90_version
+FC_MAJOR_VERSION=$wk_cv_prog_f90_major_version
+AC_SUBST(FC_VERSION_STRING)
+AC_SUBST(FC_VENDOR)
+AC_SUBST(FC_VERSION)
+AC_SUBST(FC_MAJOR_VERSION)
+
+dnl Module names: (all compilers apparently have converged to '.mod')
+dnl The perl scripts need a quoted version of this
+FC_MODNAME='$(1:.o=.mod)'
+FC_MODNAME_Q='\$(1:.o=.mod)'
+AC_SUBST(FC_MODNAME)
+AC_SUBST(FC_MODNAME_Q)
+
+])  dnl end AC_DEFUN
+
+

thirdParty/Zoltan/config/zac_arg_config_mpi.m4

@@ -0,0 +1,279 @@
+dnl @synopsis ZAC_ARG_CONFIG_MPI
+dnl
+dnl Test a variety of MPI options:
+dnl --enable-mpi       - Turns MPI compiling mode on
+dnl --with-mpi         - specify root directory of MPI
+dnl --with-mpi-compilers - Turns on MPI compiling mode and sets the MPI C++
+dnl                       compiler C, and Fortran
+dnl --with-mpi-incdir - specify include directory for MPI 
+dnl --with-mpi-libs    - specify MPI libraries
+dnl --with-mpi-libdir  - specify location of MPI libraries
+dnl
+dnl If any of these options are set, HAVE_MPI will be defined for both
+dnl Autoconf and Automake, and HAVE_MPI will be defined in the
+dnl generated config.h file
+dnl
+dnl if --disable-mpi, then Zoltan will build serial MPI.
+dnl
+dnl --enable-mpi and --with-mpi-compilers are the default.
+dnl
+dnl --without-mpi is actually a user error, but we'll interpret it as --disable-mpi
+dnl
+dnl If CC, CXX, F77 and/or F90/FTN/FC have been set by the user, and MPI compilers
+dnl are desired, these will be assumed to be the MPI compilers.
+dnl
+dnl This was adapted from the Trilinos TAC_ARG_CONFIG_MPI.
+dnl
+AC_DEFUN([ZAC_ARG_CONFIG_MPI],
+[
+
+HAVE_PKG_MPI=unset
+SEEK_MPI_COMPILERS=unset
+MPI_COMPILER_PATH=unset
+
+AC_ARG_ENABLE(mpi,
+[AC_HELP_STRING([--enable-mpi],[enable MPI support])],
+[
+  if test X${enableval} = Xno; then
+    HAVE_PKG_MPI=no
+  else
+    HAVE_PKG_MPI=yes
+  fi
+]
+)
+
+AC_ARG_WITH(mpi,
+[AC_HELP_STRING([--with-mpi=MPIROOT],[the MPI root directory (above bin,lib,include), enables MPI])],
+[
+  if test X${withval} = Xno; then
+    HAVE_PKG_MPI=no
+  else
+    HAVE_PKG_MPI=yes
+    if test X${withval} != Xyes; then
+      MPI_DIR=${withval}
+    fi
+  fi
+]
+)
+
+AC_ARG_WITH(mpi-compilers,
+[AC_HELP_STRING([--with-mpi-compilers={yes/no/path}],[Find MPI compilers/Don't use MPI compilers/Find MPI compilers in path])],
+[
+  HAVE_PKG_MPI=yes
+  if test X${withval} = Xno; then
+    SEEK_MPI_COMPILERS=no
+  else
+    SEEK_MPI_COMPILERS=yes
+    if test X${withval} != Xyes; then
+      MPI_COMPILER_PATH=${withval}
+    fi
+  fi
+],
+[
+  if test X${HAVE_PKG_MPI} != Xno; then
+    SEEK_MPI_COMPILERS=yes
+    HAVE_PKG_MPI=yes
+  fi
+]
+)
+
+dnl Using MPI is the default
+
+if test X${HAVE_PKG_MPI} = unset ; then
+  HAVE_PKG_MPI=yes
+fi
+
+if test X${SEEK_MPI_COMPILERS} = Xyes; then
+
+  if test X${MPI_COMPILER_PATH} != Xunset ; then
+#    MPI_SEEK_PATH=$MPI_COMPILER_PATH$PATH_SEPARATOR$PATH
+    MPI_SEEK_PATH=$MPI_COMPILER_PATH
+  elif test -n "${MPI_DIR}" ; then
+#    MPI_SEEK_PATH=$MPI_DIR/bin$PATH_SEPARATOR$PATH
+    MPI_SEEK_PATH=$MPI_DIR/bin
+  else
+    MPI_SEEK_PATH=$PATH
+  fi
+
+  dnl Find C MPI compiler if MPI_CC is not already defined
+
+  if test -z "${MPI_CC}"; then
+    if test -f "${CC}"; then
+
+      MPI_CC=${CC}
+
+    else
+
+      if test -n "${CC}" ; then
+        MPI_CC_CANDIDATE=${CC}
+      else
+        MPI_CC_CANDIDATE=mpicc
+      fi
+
+      AC_PATH_PROG(MPI_CC, ${MPI_CC_CANDIDATE}, [notFound], [PATH = ${MPI_SEEK_PATH}])
+  
+      if test "${MPI_CC}" != "notFound" ; then
+        CC=${MPI_CC}
+      else
+        echo "-----"
+        echo "Cannot find MPI C compiler in " ${MPI_SEEK_PATH}
+        echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH,"
+        echo "or specify a path to top mpi directory (above bin) with --with-mpi=PATH,"
+        echo "or specify a C compiler using CC=<compiler>"
+        echo "or --disable-mpi"
+        echo "-----"
+        AC_MSG_ERROR([MPI C compiler not found.])
+      fi
+    fi
+  fi
+
+  if test "X$ac_cv_use_zoltan_cppdriver" = "Xyes"; then
+    dnl Find C++ MPI compiler if MPI_CXX is not already defined
+  
+    if test -z "${MPI_CXX}"; then
+
+      if test -f "${CXX}"; then
+  
+        MPI_CXX=${CXX}
+  
+      else
+  
+        if test -n "${CXX}" ; then
+          MPI_CXX_CANDIDATES=${CXX}
+        else
+          MPI_CXX_CANDIDATES="[mpicxx mpic++ mpiCC]"
+        fi
+  
+        AC_PATH_PROGS(MPI_CXX, ${MPI_CXX_CANDIDATES}, [notFound], [PATH = ${MPI_SEEK_PATH}])
+    
+        if test "${MPI_CXX}" != "notFound" ; then
+          CXX=${MPI_CXX}
+        else
+          echo "-----"
+          echo "Cannot find MPI C++ compiler in " ${MPI_SEEK_PATH}
+          echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH,"
+          echo "or specify a path to top mpi directory (above bin) with --with-mpi=PATH,"
+          echo "or specify a C++ compiler using CXX=<compiler>"
+          echo "or --disable-mpi"
+          echo "-----"
+          AC_MSG_ERROR([MPI C++ compiler not found.])
+        fi
+      fi
+    fi
+  fi
+
+#  if test "X$ac_cv_use_fortran" = "Xyes"; then
+#    dnl Find a Fortran 77 MPI compiler if MPI_F77 is not already defined
+#  
+#    if test -z "${MPI_F77}"; then
+#      MPI_F77_CANDIDATE=mpif77
+#      if test -n "${F77}"; then
+#        MPI_F77_CANDIDATE=${F77}
+#      fi
+#  
+#      AC_PATH_PROG(MPI_F77, ${MPI_F77_CANDIDATE}, [notFound], [PATH = ${MPI_SEEK_PATH}])
+#  
+#      if test "${MPI_F77}" != "notFound" ; then
+#        F77=${MPI_F77}
+#      else
+#        echo "-----"
+#        echo "Cannot find MPI Fortan 77 compiler."
+#        echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH,"
+#        echo "or specify a path to top mpi directory (above bin) with --with-mpi=PATH,"
+#        echo "or specify a fortran 77 compiler using F77=<compiler>"
+#        echo "-----"
+#        AC_MSG_ERROR([MPI C compiler not found.])
+#      fi
+#    fi
+#  fi
+
+  if test "X$ac_cv_use_fortran90" = "Xyes"; then
+    dnl Find a Fortran 90 MPI compiler if MPI_F90 is not already defined
+  
+    if test -z "${MPI_FC}"; then
+
+      if test -f "${FC}"; then
+
+        MPI_FC=${FC}
+
+      else
+        MPI_FC_CANDIDATES=""
+    
+        if test -n "${FC}"; then
+          MPI_FC_CANDIDATES=${FC}
+        elif test -n "${FTN}"; then
+          MPI_FC_CANDIDATES=${FTN}
+        elif test -n "${F90}"; then
+          MPI_FC_CANDIDATES=${F90}
+        fi
+
+        if test -n "${MPI_FC_CANDIDATES}" && test -f ${MPI_FC_CANDIDATES} ; then
+          MPI_FC=${MPI_FC_CANDIDATES}
+        else
+          if test -z "${MPI_FC_CANDIDATES}"; then
+            MPI_FC_CANDIDATES="[mpif90 mpif77]"
+          fi
+
+          AC_PATH_PROGS(MPI_FC, ${MPI_FC_CANDIDATES}, [notFound], [PATH = ${MPI_SEEK_PATH}])
+
+          if test "${MPI_FC}" != "notFound" ; then
+            FC=${MPI_FC}
+          else
+            echo "-----"
+            echo "Cannot find MPI Fortran 90 compiler in " ${MPI_SEEK_PATH}
+            echo "Specify a path to all mpi compilers with --with-mpi-compilers=PATH,"
+            echo "or specify a path to top mpi directory (above bin) with --with-mpi=PATH,"
+            echo "or specify a fortran 90 compiler using FC=<compiler>"
+            echo "-----"
+            AC_MSG_ERROR([MPI C compiler not found.])
+          fi
+        fi
+      fi
+    fi
+  fi
+fi
+
+#AC_ARG_WITH(mpi-include,
+#[AC_HELP_STRING([--with-mpi-include],[Obsolete.  Use --with-mpi-incdir=DIR instead.  Do not prefix DIR with '-I'.])],
+#[AC_MSG_ERROR([--with-mpi-include is an obsolte option.   Use --with-mpi-incdir=DIR instead.  Do not prefix DIR with '-I'.  For example '--with-mpi-incdir=/usr/lam_path/include'.])]
+#)
+
+AC_ARG_WITH(mpi-libs,
+[AC_HELP_STRING([--with-mpi-libs="LIBS"],[MPI libraries @<:@"-lmpi"@:>@])],
+[
+  MPI_LIBS=${withval}
+  AC_MSG_CHECKING(user-defined MPI libraries)
+  AC_MSG_RESULT([${MPI_LIBS}])
+]
+)
+
+AC_ARG_WITH(mpi-incdir,
+[AC_HELP_STRING([--with-mpi-incdir=DIR],[MPI include directory @<:@MPIROOT/include@:>@  Do not use -I])],
+[
+  MPI_INC=${withval}
+  AC_MSG_CHECKING(user-defined MPI includes)
+  AC_MSG_RESULT([${MPI_INC}])
+]
+)
+
+AC_ARG_WITH(mpi-libdir,
+[AC_HELP_STRING([--with-mpi-libdir=DIR],[MPI library directory @<:@MPIROOT/lib@:>@  Do not use -L])],
+[
+  MPI_LIBDIR=${withval}
+  AC_MSG_CHECKING(user-defined MPI library directory)
+  AC_MSG_RESULT([${MPI_LIBDIR}])
+]
+)
+
+AC_MSG_CHECKING(whether we are using MPI)
+AC_MSG_RESULT([${HAVE_PKG_MPI}])
+
+if test "X${HAVE_PKG_MPI}" = "Xyes"; then
+   AC_DEFINE(HAVE_MPI,,[define if we want to use MPI])
+fi
+
+dnl Define Automake version of HAVE_MPI if appropriate
+
+AM_CONDITIONAL(HAVE_MPI, [test "X${HAVE_PKG_MPI}" = "Xyes"])
+
+])

thirdParty/Zoltan/config/zac_arg_with_id.m4

@@ -0,0 +1,39 @@
+dnl @synopsis ZAC_ARG_WITH_ID
+dnl
+dnl Test for "--with-id-type="
+dnl Default is "unsigned int".  Can also be "long", "llong" or "int".
+dnl 
+dnl Generates config.h macro.
+dnl
+AC_DEFUN([ZAC_ARG_WITH_ID],
+[
+AC_MSG_CHECKING([data type for ZOLTAN_ID_TYPE])
+zoltan_id_type="unset"
+AC_ARG_WITH(id-type,
+AC_HELP_STRING([--with-id-type], [Zoltan global ID type: uint (default), ulong, or ullong]),
+[
+if test "X$withval" == "Xuint" ; then
+  AC_DEFINE([UNSIGNED_INT_GLOBAL_IDS],[1],[define if ZOLTAN_ID_TYPE is unsigned int])
+  zoltan_id_type="unsigned int"
+else
+  if test "X$withval" == "Xulong" ; then
+    AC_DEFINE([UNSIGNED_LONG_GLOBAL_IDS],[1],[define if ZOLTAN_ID_TYPE is unsigned long])
+    zoltan_id_type="unsigned long"
+  else
+    if test "X$withval" == "Xullong" ; then
+      AC_DEFINE([UNSIGNED_LONG_LONG_GLOBAL_IDS],[1],[define if ZOLTAN_ID_TYPE is unsigned long long])
+      zoltan_id_type="unsigned long long"
+    else
+       AC_MSG_ERROR([Valid global ID types for Zoltan are uint, ulong, and ullong])
+    fi
+  fi
+fi
+],
+[
+AC_DEFINE([UNSIGNED_INT_GLOBAL_IDS],[1],[define if ZOLTAN_ID_TYPE is unsigned int])
+zoltan_id_type="unsigned int"
+]
+)
+AC_MSG_RESULT([typedef $zoltan_id_type ZOLTAN_ID_TYPE])
+]
+)

thirdParty/Zoltan/configure.ac

@@ -0,0 +1,463 @@
+# @HEADER
+#
+########################################################################
+#
+#  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+#                  Copyright 2012 Sandia Corporation
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Questions? Contact Karen Devine	kddevin@sandia.gov
+#                    Erik Boman	        egboman@sandia.gov
+#
+########################################################################
+#
+# @HEADER
+# ------------------------------------------------------------------------
+# Process this file with autoconf to produce a configure script.
+# ------------------------------------------------------------------------
+
+# ------------------------------------------------------------------------
+# Initialization 
+# ------------------------------------------------------------------------
+
+
+
+# This must be the first line in configure.ac.
+# Optional 3rd argument is email address for bugs.
+
+AC_INIT(Zoltan, 3.6, lriesen@sandia.gov)
+
+echo "----------------------------------------"
+echo "Running Zoltan Configure Script"
+echo "----------------------------------------"
+
+# This is to protect against accidentally specifying the wrong
+# directory with --srcdir.  Any file in that directory will do,
+# preferably one that is unlikely to be removed or renamed.
+
+AC_CONFIG_SRCDIR([src/include/zoltan.h])
+
+# Specify directory for auxillary build tools (e.g., install-sh,
+# config.sub, config.guess) and M4 files.
+
+AC_CONFIG_AUX_DIR(config)
+
+#
+# We don't want people to configure in the source directory.  Some
+# things may break.
+#
+
+if test -e configure.ac ; then
+  echo "You are trying to run configure in the source directory.  This is not allowed.  Please run configure from a separate build directory."
+  exit
+fi
+
+# Configure should create src/Zoltan_config.h from src/Zoltan_config.h.in
+AM_CONFIG_HEADER(src/include/Zoltan_config.h:src/include/Zoltan_config.h.in)
+
+# Allow users to specify their own "install" command.  If none is specified,
+# the default is install-sh found in the config subdirectory.
+                                                                                
+AC_ARG_WITH(install,
+ [AC_HELP_STRING([--with-install=INSTALL_PROGRAM],
+ [Use the installation program INSTALL_PROGRAM rather the default that is provided.  For example --with-install="/path/install -p"])],
+ [
+   INSTALL=$withval
+   INSTALL_PROGRAM=$withval
+   INSTALL_SCRIPT=$withval
+   INSTALL_DATA="$withval -m 644"
+ ],)
+                                                                                
+# AM_MAINTAINER_MODE turns off maintainer-only makefile targets by
+# default, and changes configure to understand a
+# --enable-maintainer-mode option. --enable-maintainer-mode turns the
+# maintainer-only targets back on. The maintainer-only makefile
+# targets permit end users to clean automatically-generated files such
+# as configure, which means they have to have autoconf and automake
+# installed to repair the damage. AM_MAINTAINER_MODE makes it a bit
+# harder for users to shoot themselves in the foot.
+
+AM_MAINTAINER_MODE
+
+# Define $build, $host, $target, etc
+
+AC_CANONICAL_TARGET
+
+# Note in header file and Makefile conditional what the host OS is
+  
+AM_CONDITIONAL(HOST_CYGWIN, false)
+AM_CONDITIONAL(HOST_LINUX, false)
+AM_CONDITIONAL(HOST_SOLARIS, false)
+
+case $host_os in
+  cygwin)
+    AM_CONDITIONAL(HOST_CYGWIN, true)
+    AC_DEFINE(HOST_CYGWIN,1,[software host will be cygwin])
+    ;;
+  linux*)
+    AM_CONDITIONAL(HOST_LINUX, true)
+    AC_DEFINE(HOST_LINUX,1,[software host will be linux])
+    ;;
+  solaris*)
+    AM_CONDITIONAL(HOST_SOLARIS, true)
+    AC_DEFINE(HOST_SOLARIS,1,[software host will be solaris])
+    ;;
+esac
+
+# Use automake
+
+#  - Required version of automake.
+AM_INIT_AUTOMAKE(1.9.6 no-define tar-ustar)
+
+# Specify required version of autoconf.
+
+AC_PREREQ(2.59)
+
+#TAC_ARG_ENABLE_OPTION(fortran, [enable Fortran support], FORTRAN_SUPPORT, no)
+#This option is not currently available
+TAC_ARG_ENABLE_OPTION(f90interface, [enable Fortran 90 interface (automatically enables Fortran support)], F90INTERFACE, no)
+AM_CONDITIONAL(BUILD_ZOLTAN_F90_INTERFACE, [test "X$ac_cv_use_f90interface" != "Xno"])
+#AM_CONDITIONAL(USE_FORTRAN, [test "X$ac_cv_use_fortran" != "Xno"])
+
+if test "X$ac_cv_use_f90interface" = "Xyes"; then
+  ac_cv_use_fortran=yes
+else
+  ac_cv_use_fortran=no
+fi
+
+if test "X$ac_cv_use_fortran" = "Xyes"; then
+  ac_cv_use_fortran90=yes
+#  AX_F90_MODULE_FLAG
+#  if test "X$ax_cv_f90_modflag" = "Xunknown" ; then
+#    AC_MSG_ERROR([unable to find f90 modules extension])
+#  else
+#    FCFLAGS="$ax_cv_f90_modflag../ $ax_cv_f90_modflag. ${FCFLAGS}"
+#  fi
+else
+  ac_cv_use_fortran90=no
+fi
+
+TAC_ARG_ENABLE_FEATURE_SUB(zoltan, cppdriver, [Enable Zoltan's C++ driver], ZOLTAN_CPPDRIVER, yes)
+AM_CONDITIONAL(HAVE_ZOLTAN_CPPDRIVER, [test "X$ac_cv_use_zoltan_cppdriver" != "Xno"])
+
+#This can be removed after we retire the old build system
+#AC_DEFINE([TRILINOS_CONFIG_H],,[Define when using the autotools to build Zoltan])
+
+# ------------------------------------------------------------------------
+# Check to see if MPI enabled and if any special configuration done
+# ------------------------------------------------------------------------
+
+# We may want to handle this differently because Zoltan requires MPI
+#TAC_ARG_CONFIG_MPI
+
+ZAC_ARG_CONFIG_MPI
+
+#  #np# - can eliminate compiler checks below if your package does not use the
+#         language corresponding to the check.  Please note that if you use
+#	  F77_FUNC to determine Fortran name mangling, you should not remove
+#	  the Fortran compiler check or the check for Fortran flags.  Doing
+#	  so will prevent the detection of the proper name mangling in some
+#	  cases.
+
+AC_ARG_ENABLE(mpi-recv-limit,
+ AS_HELP_STRING([--enable-mpi-recv-limit],[Set to the limit on the number of simultaneous MPI posted receives, if any; default is --enable-mpi-recv-limit=10]),
+ [ AC_MSG_NOTICE(Building Zoltan to observe a limit of $enable_mpi_recv_limit simultaneously posted MPI receives)
+   AC_SUBST(MPI_RECV_LIMIT_FLAG, "-DMPI_RECV_LIMIT=$enable_mpi_recv_limit")
+ ]
+ )
+
+# ------------------------------------------------------------------------
+# Checks for programs
+# ------------------------------------------------------------------------
+
+AM_PROG_CC_C_O(cc gcc)
+#Conditional only?
+#if test "X$ac_cv_use_zoltan_cppdriver" = "Xyes"; then
+AC_PROG_CXX(CC g++ c++ cxx)
+#fi
+
+if test "X$ac_cv_use_fortran90" = "Xyes"; then
+AC_PROG_FC(FC gfortran f90 xlf90 f95)
+fi
+
+if test "X$ac_cv_use_fortran" = "Xyes"; then
+AC_PROG_FC(FC gfortran f90 xlf90 f95)
+fi
+
+AC_PROG_RANLIB
+
+# Check if --with-flags present, prepend any specs to FLAGS
+
+TAC_ARG_WITH_FLAGS(ccflags, CCFLAGS)
+#if test "X$ac_cv_use_zoltan_cppdriver" = "Xyes"; then
+TAC_ARG_WITH_FLAGS(cxxflags, CXXFLAGS)
+CXXFLAGS="-DMPICH_IGNORE_CXX_SEEK  ${CXXFLAGS}"
+#fi
+TAC_ARG_WITH_FLAGS(cflags, CFLAGS)
+TAC_ARG_WITH_FLAGS(fcflags, FCFLAGS)
+#TAC_ARG_WITH_FLAGS(fflags, FFLAGS)
+TAC_ARG_WITH_LIBS
+TAC_ARG_WITH_FLAGS(ldflags, LDFLAGS)
+
+# ------------------------------------------------------------------------
+# Alternate archiver
+# ------------------------------------------------------------------------
+
+TAC_ARG_WITH_AR
+
+# ------------------------------------------------------------------------
+# MPI link check
+# ------------------------------------------------------------------------
+TAC_ARG_CHECK_MPI
+
+# ------------------------------------------------------------------------
+# Checks for Makefile.export related systems
+# ------------------------------------------------------------------------
+# Add this later
+TAC_ARG_ENABLE_EXPORT_MAKEFILES(yes)
+
+# ------------------------------------------------------------------------
+# Checks for special package flags 
+# ------------------------------------------------------------------------
+
+ZAC_ARG_WITH_ID()
+
+TAC_ARG_ENABLE_OPTION(gzip, [enable zlib support for driver], GZIP, no)
+if test "X$ac_cv_use_gzip" != "Xno"; then
+   LIBS="-lz ${LIBS}"
+fi
+AM_CONDITIONAL(BUILD_GZIP, [test "X$ac_cv_use_gzip" != "Xno"])
+
+TAC_ARG_WITH_PACKAGE(parmetis, [Enable Parmetis support.], PARMETIS, no)
+AM_CONDITIONAL(BUILD_PARMETIS, [test "X$ac_cv_use_parmetis" != "Xno"])
+TAC_ARG_WITH_3PL_SUB(parmetis, libdir, [Specify where the Parmetis library is located.  Ex. /path/to/library])
+if test "X$tac_with_parmetis_libdir" != "Xno"; then
+  LIBS="-L${tac_with_parmetis_libdir} -lparmetis -lmetis ${LIBS}"
+fi
+
+TAC_ARG_WITH_3PL_SUB(parmetis, incdir, [Specify where the Parmetis header files are located.  Ex. /path/to/headers])
+# It was necessary to move the parmetis include directories before the scotch
+# include directories.
+#if test "X$tac_with_parmetis_incdir" != "Xno"; then
+#  CPPFLAGS="-I${tac_with_parmetis_incdir}  ${CPPFLAGS}"
+#fi
+
+
+TAC_ARG_WITH_PACKAGE(scotch, [Enable Scotch support.], SCOTCH, no)
+AM_CONDITIONAL(BUILD_SCOTCH, [test "X$ac_cv_use_scotch" != "Xno"])
+TAC_ARG_WITH_3PL_SUB(scotch, libdir, [Specify where the Scotch library is located.  Ex. /path/to/library])
+if test "X$tac_with_scotch_libdir" != "Xno"; then
+  LIBS="-L${tac_with_scotch_libdir} -lptscotch  -lptscotcherr -lptscotcherrexit -lscotch -lscotcherr -lscotcherrexit ${LIBS}"
+fi
+TAC_ARG_WITH_3PL_SUB(scotch, incdir, [Specify where the Scotch header files are located.  Ex. /path/to/headers])
+if test "X$tac_with_scotch_incdir" != "Xno"; then
+  CPPFLAGS="-I${tac_with_scotch_incdir}  ${CPPFLAGS}"
+fi
+# The parmetis include directories need to be before the Scotch include
+# directories.
+if test "X$tac_with_parmetis_incdir" != "Xno"; then
+  CPPFLAGS="-I${tac_with_parmetis_incdir}  ${CPPFLAGS}"
+fi
+
+TAC_ARG_WITH_PACKAGE(patoh, [Enable Patoh support.], PATOH, no)
+TAC_ARG_WITH_3PL_SUB(patoh, libdir, [Specify where the Patoh library is located.  Ex. /path/to/library])
+if test "X$tac_with_patoh_libdir" != "Xno"; then
+  LIBS="-L${tac_with_patoh_libdir} -lpatoh ${LIBS}"
+fi
+TAC_ARG_WITH_3PL_SUB(patoh, incdir, [Specify where the Patoh header files are located.  Ex. /path/to/headers])
+if test "X$tac_with_patoh_incdir" != "Xno"; then
+  CPPFLAGS="-I${tac_with_patoh_incdir}  ${CPPFLAGS}"
+fi
+
+#TAC_ARG_WITH_PACKAGE(drum, [Enable Drum support.  Library name as well as library and include paths must be specified using LDFLAGS and CPPFLAGS.], DRUM, no)
+#TAC_ARG_WITH_3PL_SUB(drum, libdir, [Specify where the Drum library is located.  Ex. /path/to/library])
+#if test "X$tac_with_drum_libdir" != "Xno"; then
+#  LIBS="-L${tac_with_drum_libdir} ${LIBS}"
+#fi
+#TAC_ARG_WITH_3PL_SUB(drum, incdir, [Specify where the Drum header files are located.  Ex. /path/to/headers])
+#if test "X$tac_with_drum_incdir" != "Xno"; then
+#  CPPFLAGS="-I${tac_with_drum_incdir}  ${CPPFLAGS}"
+#fi
+
+TAC_ARG_WITH_PACKAGE(nemesis_exodus, [Enable Nemesis/Exodus support for the Zdrive test executable.  Library and include paths must be specified using LDFLAGS and CFLAGS.], NEMESIS_EXODUS, no)
+#I am not sure if we can do this.  We may not be able to get things in the right
+#order. JW.
+if test "X$ac_cv_use_nemesis_exodus" != "Xno"; then
+  LIBS="-lnemIc -lexoIIv2c -lnetcdf ${LIBS}"
+fi
+
+LIBS="${LIBS} -lm"
+
+#TAC_ARG_WITH_PACKAGE(parkway, [Enable Parkway support.], PARKWAY, no)
+#TAC_ARG_WITH_3PL_SUB(parkway, libdir, [Specify where the Parkway library is located.  Ex. /path/to/library])
+#if test "X$tac_with_parkway_libdir" != "Xno"; then
+#  LIBS="-L${tac_with_parkway_libdir} -lparkway -lpmpich++ -lstdc++ ${LIBS}"
+#fi
+#TAC_ARG_WITH_3PL_SUB(parkway, incdir, [Specify where the Parkway header files are located.  Ex. /path/to/headers])
+#if test "X$tac_with_parkway_incdir" != "Xno"; then
+#  CPPFLAGS="-I${tac_with_parkway_incdir}  ${CPPFLAGS}"
+#fi
+
+# ------------------------------------------------------------------------
+# Checks if tests and examples should be built
+# ------------------------------------------------------------------------
+
+
+TAC_ARG_ENABLE_FEATURE(tests, [Make tests for all Trilinos packages buildable with 'make tests'], TESTS, yes)
+TAC_ARG_ENABLE_FEATURE_SUB_CHECK( zoltan, tests, [Make Zoltan tests buildable with 'make tests'], ZOLTAN_TESTS)
+AM_CONDITIONAL(BUILD_TESTS, test "X$ac_cv_use_zoltan_tests" != "Xno")
+
+TAC_ARG_ENABLE_FEATURE(examples, [Make examples for all Trilinos packages buildable with 'make examples'], EXAMPLES, yes)
+TAC_ARG_ENABLE_FEATURE_SUB_CHECK( zoltan, examples, [Make Zoltan examples buildable with 'make examples'], ZOLTAN_EXAMPLES)
+AM_CONDITIONAL(BUILD_EXAMPLES, test "X$ac_cv_use_zoltan_examples" != "Xno")
+
+#We now build tests and examples through separate make targets, rather than
+#during "make".  We still need to conditionally include the test and example
+#in SUBDIRS, even though SUB_TEST and SUB_EXAMPLE will never be
+#defined, so that the tests and examples are included in the distribution
+#tarball.
+AM_CONDITIONAL(SUB_TEST, test "X$ac_cv_use_sub_test" = "Xyes")
+AM_CONDITIONAL(SUB_EXAMPLE, test "X$ac_cv_use_sub_example" = "Xyes")
+
+#TAC_ARG_ENABLE_FEATURE(libcheck, [Check for some third-party libraries.  (Cannot be disabled unless tests and examples are also disabled.)], LIBCHECK, yes)
+
+# ------------------------------------------------------------------------
+# Specify other directories 
+# ------------------------------------------------------------------------
+
+# enable use of --with-libdirs="-Llibdir1 -Llibdir2 ..." to prepend to LDFLAGS
+TAC_ARG_WITH_LIBDIRS
+# enable use of --with-incdirs="-Iincdir1 -Iincdir2 ..." to prepend to CPPFLAGS
+TAC_ARG_WITH_INCDIRS
+
+# ------------------------------------------------------------------------
+# Checks for libraries
+# ------------------------------------------------------------------------
+
+ax_cv_f90_modulecase="lower"
+FC_VENDOR="none"
+
+# Define F77_FUNC that will be used to link with Fortran subroutines.
+if test "X$ac_cv_use_fortran" != "Xno"; then
+  AC_FC_WRAPPERS
+  AC_FC_SRCEXT(f)
+  AC_FC_SRCEXT(f90)
+  # Determine compile-line flag for F90 modules (e.g., -M).
+  AX_F90_MODULE_FLAG
+  if test "X$ax_cv_f90_modflag" = "Xunknown" ; then
+    AC_MSG_ERROR([unable to find f90 modules extension])
+  else
+    FCFLAGS="$ax_cv_f90_modflag../ $ax_cv_f90_modflag. ${FCFLAGS}"
+  fi
+  # Determine case (upper or lower) of F90 module files. 
+  AX_F90_MODULE_CASE
+  echo "KDDKDD " $ax_cv_f90_modulecase 
+
+  WK_FC_GET_VENDOR()
+  echo "KDDKDD " $FC_VENDOR
+  if test "$FC_VENDOR" = "PGI"; then
+    FCFLAGS="-DPGI ${FCFLAGS}"
+    CFLAGS="-DPGI ${CFLAGS}"
+  fi
+  if test "$FC_VENDOR" = "Lahey"; then
+    FCFLAGS="-DFUJITSU ${FCFLAGS}"
+    CFLAGS="-DFUJITSU ${CFLAGS}"
+  fi
+fi
+AM_CONDITIONAL(F90_MODULE_LOWERCASE, [test "X$ax_cv_f90_modulecase" != "Xupper"])
+AM_CONDITIONAL(NAG_F90_COMPILER, [test "X$FC_VENDOR" == "XNAG"])
+
+# If tests, examples and libcheck are disabled, we don't have to check
+# for these libraries.
+
+#if test "X$ac_cv_use_new_package_examples" != "Xno" || test "X$ac_cv_use_libcheck" != "Xno"; then
+#if test "X$ac_cv_use_zoltan_tests" != "Xno" || test "X$ac_cv_use_zoltan_examples" != "Xno" || test "X$ac_cv_use_libcheck" != "Xno"; then
+# checks for libraries now
+dnl Replace `main' with a function in -lm:
+#AC_SEARCH_LIBS(pow,[m],,AC_MSG_ERROR(Cannot find math library))
+#AC_SEARCH_LIBS(sqrt,[m],,AC_MSG_ERROR(Cannot find math library))
+#fi
+# end of the list of libraries that don't need to be checked for if
+# tests and examples are disabled.
+
+# ------------------------------------------------------------------------
+# Checks for linker characteristics
+# ------------------------------------------------------------------------
+
+# Determine libraries needed for linking with Fortran
+#AC_FC_LIBRARY_LDFLAGS
+if test "X$ac_cv_use_fortran" = "Xyes"; then
+AC_FC_LIBRARY_LDFLAGS
+fi
+
+# ------------------------------------------------------------------------
+# Zoltan may be built via autotools, cmake, or our native makefile
+# ------------------------------------------------------------------------
+
+CPPFLAGS="-DAUTOTOOLS_BUILD  ${CPPFLAGS}"
+
+# ------------------------------------------------------------------------
+# Perform substitutions in output files
+# ------------------------------------------------------------------------
+
+AC_SUBST(ac_aux_dir)
+
+# ------------------------------------------------------------------------
+# Output files
+# ------------------------------------------------------------------------
+#
+AC_CONFIG_FILES([
+		Makefile
+		src/Makefile
+		src/driver/Makefile
+		src/fdriver/Makefile
+		Makefile.export.zoltan
+		example/Makefile
+		example/C/Makefile
+		example/CPP/Makefile
+		siMPI/Makefile
+		siMPI/pyMPI/Makefile
+		siMPI/pyMPI/siMPI/Makefile
+		])
+#		test/Large_Data/Makefile
+#		example/lib/Makefile
+#		example/C/Makefile
+#		example/C/sparse_matrix/Makefile
+#		example/CPP/Makefile
+#		Utilities/Makefile
+
+AC_OUTPUT()
+
+echo "---------------------------------------------"
+echo "Finished Running Zoltan Configure Script"
+echo "---------------------------------------------"
+

thirdParty/Zoltan/doc/NEA_docs/developer_html/dev_hybrid.html

@@ -0,0 +1,515 @@
+<!-------- @HEADER
+ !
+ ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ !
+ !  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+ !                  Copyright 2012 Sandia Corporation
+ !
+ ! Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+ ! the U.S. Government retains certain rights in this software.
+ !
+ ! Redistribution and use in source and binary forms, with or without
+ ! modification, are permitted provided that the following conditions are
+ ! met:
+ !
+ ! 1. Redistributions of source code must retain the above copyright
+ ! notice, this list of conditions and the following disclaimer.
+ !
+ ! 2. Redistributions in binary form must reproduce the above copyright
+ ! notice, this list of conditions and the following disclaimer in the
+ ! documentation and/or other materials provided with the distribution.
+ !
+ ! 3. Neither the name of the Corporation nor the names of the
+ ! contributors may be used to endorse or promote products derived from
+ ! this software without specific prior written permission.
+ !
+ ! THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+ ! EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ ! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ ! PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+ ! CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ ! EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ ! PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ ! PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ ! LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ ! NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ ! SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ !
+ ! Questions? Contact Karen Devine	kddevin@sandia.gov
+ !                    Erik Boman	egboman@sandia.gov
+ !
+ ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ !
+ ! @HEADER
+-------> 
+<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
+<html>
+<head>
+  <meta http-equiv="Content-Type"
+ content="text/html; charset=iso-8859-1">
+  <meta name="GENERATOR"
+ content="Mozilla/4.76 [en] (X11; U; Linux 2.4.2-2smp i686) [Netscape]">
+  <meta name="sandia.approved" content="SAND99-1377">
+  <meta name="author" content="nick aase, neaase@sandia.gov">
+  <title>Zoltan Developer's Guide: Hybrid Partitioning</title>
+</head>
+<body bgcolor="#ffffff">
+<div align="right"><b><i><a href="dev.html">Zoltan Developer's Guide</a>&nbsp;
+|&nbsp; <a href="dev_reftree.html">Next(NEANEA CHANGE ME)</a>&nbsp; |&nbsp; <a
+ href="dev_parmetis.html">Previous(NEANEA CHANGE ME)</a></i></b></div>
+<h2>
+<a name="Hybrid Partitioning"></a>Appendix: Hybrid Partitioning</h2>
+Hybrid partitioning is an amalgam of Zoltan's native parallel hypergraph
+partitioner (<a href="dev_phg.html">PHG</a>) and it Recursive Coordinate
+Bisection algortihm (<a href="dev_rcb.html">RCB</a>). Hybrid partitioning can
+be useful when a user is looking to strike a happy medium of both efficiency
+and fidelity in their work. Traditional Zoltan-PHG is well suited to minimize
+the number of cut hyperedges in the system, but it is comparatively slow due
+to the multiple layers of coarsening it goes through and the standard matching
+methods used to calculate new vertices for the coarser hypergraph.
+
+
+<p>
+Hypergraph partitioning is a useful partitioning and
+load balancing method when connectivity data is available. It can be
+viewed as a more sophisticated alternative to
+the traditional graph partitioning.
+<p>A hypergraph consists of vertices and hyperedges. A hyperedge
+connects
+one or more vertices. A graph is a special case of a hypergraph where
+each edge has size two (two vertices). The hypergraph model is well
+suited to parallel computing, where vertices correspond to data objects
+and hyperedges represent the communication requirements. The basic
+partitioning problem is to partition the vertices into <i>k</i>
+approximately equal sets such that the number of cut hyperedges is
+minimized. Most partitioners (including Zoltan-PHG) allows a more
+general
+model where both vertices and hyperedges can be assigned weights.
+It has been
+shown that the hypergraph model gives a more accurate representation
+of communication cost (volume) than the graph model. In particular,
+for sparse matrix-vector multiplication, the hypergraph model
+<strong>exactly</strong> represents communication volume. Sparse
+matrices can be partitioned either along rows or columns;
+in the row-net model the columns are vertices and each row corresponds
+to an hyperedge, while in the column-net model the roles of vertices
+and hyperedges are reversed. </p>
+<p>Zoltan contains a native parallel hypergraph partitioner, called PHG
+(Parallel HyperGraph partitioner). In addition, Zoltan provides
+access to <a href="http://bmi.osu.edu/%7Eumit/software.htm">PaToH</a>,
+a serial hypergraph partitioner.
+Note that PaToH is not part of Zoltan and should be obtained
+separately from the <a href="http://bmi.osu.edu/%7Eumit/software.htm">
+PaToH web site</a>.
+Zoltan-PHG is a fully parallel multilevel hypergraph partitioner. For
+further technical description, see <a
+ href="ug_refs.html#hypergraph-ipdps06">[Devine et al, 2006]</a>.<br>
+</p>
+<h4>Algorithm:</h4>
+The algorithm used is multilevel hypergraph partitioning. For
+coarsening, several versions of inner product (heavy connectivity)
+matching are available.
+The refinement is based on Fiduccia-Mattheysis (FM) but in parallel it
+is only an approximation.
+
+<h4>Parallel implementation:</h4>
+A novel feature of our parallel implementation is that we use a 2D
+distribution of the hypergraph. That is, each processor owns partial
+data about some vertices and some hyperedges. The processors are
+logically organized in a 2D grid as well. Most communication is limited
+to either a processor row or column. This design should allow for
+good scalability on large number of processors.<br>
+
+<h4>Data structures:</h4>
+The hypergraph is the most important data structure. This is stored as
+a compressed sparse matrix. Note that in parallel, each processor owns
+a local part of the global hypergraph
+(a submatrix of the whole matrix).
+The hypergraph data type is <i>struct HGraph</i>, and contains
+information like number of vertices, hyperedges, pins, compressed
+storage of all pins, optional vertex and edge weights, pointers
+to relevant communicators, and more. One cryptic notation needs an
+explanation: The arrays <i>hindex, hvertex</i> are used to
+look up vertex info given a hyperedge, and <i>vindex, vedge</i> are
+used to look up hyperedge info given a vertex. Essentially,
+we store the hypergraph as a sparse matrix in both CSR and CSC formats.
+This doubles the memory cost but gives better performance.
+The data on each processor is stored using local indexing, starting at zero.
+In order to get the global vertex or edge number, use the macros 
+<i>VTX_LNO_TO_GNO</i> and <i>EDGE_LNO_TO_GNO</i>. These macros will 
+look up the correct offsets (using the dist_x and dist_y arrays). 
+Note that <i>phg->nVtx</i> is always the local number of vertices, 
+which may be zero on some processors.
+
+<h4>Parameters:</h4>
+In the User's Guide, only the most essential parameters have been
+documented. There are several other parameters, intended for developers
+and perhaps expert "power" users. We give a more complete list of all
+parameters below. Note that these parameters <span
+ style="font-style: italic;">may change in future versions!<br>
+</span>
+For a precise list of parameters in a particular version of Zoltan, look at the source code (phg.c). 
+<table nosave="" width="100%">
+  <tbody>
+    <tr>
+      <td valign="top"><b>Method String:</b></td>
+      <td><b>HYPERGRAPH</b></td>
+    </tr>
+    <tr>
+      <td><b>Parameters:</b></td>
+      <td><br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">HYPERGRAPH_PACKAGE</span><br>
+      </td>
+      <td style="vertical-align: top;">PHG (parallel) or PaToH (serial)<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp; <span
+ style="font-style: italic;">CHECK_HYPERGRAPH</span><br>
+      </td>
+      <td style="vertical-align: top;">Check if input data is valid.
+(Slows performance;intended for debugging.)<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><span style="font-style: italic;">&nbsp;&nbsp;&nbsp;
+PHG_OUTPUT_LEVEL</span><br>
+      </td>
+      <td style="vertical-align: top;">Level of verbosity; 0 is silent.<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_FINAL_OUTPUT</span><br>
+      </td>
+      <td style="vertical-align: top;">Print stats about final
+partition? (0/1)<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_NPROC_VERTEX</span><br>
+      </td>
+      <td style="vertical-align: top;">Desired number of processes in
+the vertex direction (for 2D internal layout) </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_NPROC_HEDGE</span><br>
+      </td>
+      <td style="vertical-align: top;">Desired number of processes in
+the hyperedge direction (for 2D internal layout) </td>
+    </tr>
+    <tr>
+      <td valign="top"><i>&nbsp;&nbsp;&nbsp; PHG_COARSENING_METHOD</i></td>
+      <td>The method to use in matching/coarsening; currently these are
+available.&nbsp; <br>
+      <span style="font-style: italic;">agg</span> - agglomerative inner product
+matching (a.k.a. heavy connectivity matching) <br>
+      <span style="font-style: italic;">ipm</span> - inner product
+matching (a.k.a. heavy connectivity matching) <br>
+      <span style="font-style: italic;">c-ipm</span> -&nbsp; column
+ipm;&nbsp; faster method based on ipm within processor columns <br>
+      <span style="font-style: italic;">a-ipm </span>- alternate
+between fast method (l-ipm ) and ipm <br>
+      <span style="font-style: italic;">l-ipm </span>-&nbsp; local ipm
+on each processor. Fastest option&nbsp; but often gives poor quality. <br>
+      <i>h-ipm - </i>hybrid ipm that&nbsp; uses partial c-ipm followed
+by ipm on each level <br>
+      <i><br>
+      </i></td>
+    </tr>
+    <tr>
+      <td>&nbsp;&nbsp;&nbsp; <span style="font-style: italic;">PHG_COARSENING_LIMIT</span><br>
+      </td>
+      <td>Number of vertices at which to stop coarsening.<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_VERTEX_VISIT_ORDER</span><br>
+      </td>
+      <td style="vertical-align: top;">Ordering of vertices in greedy
+matching scheme:<br>
+0 - random<br>
+1 - natural order (as given by the query functions)<br>
+2 - increasing vertex weights<br>
+3 - increasing vertex degree<br>
+4 - increasing vertex degree, weighted by pins<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_EDGE_SCALING</span><br>
+      </td>
+      <td style="vertical-align: top;">Scale edge weights by some
+function of size of the hyperedges:<br>
+0 - no scaling<br>
+1 - scale by 1/(size-1)&nbsp;&nbsp;&nbsp;&nbsp; [absorption scaling]<br>
+2 - scale by 2/((size*size-1)) [clique scaling]<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_VERTEX_SCALING</span><br>
+      </td>
+      <td style="vertical-align: top;">Variations in "inner product"
+similarity metric (for matching):<br>
+0 - Euclidean inner product: &lt;x,y&gt;<br>
+1 - cosine similarity: &lt;x,y&gt;/(|x|*|y|)<br>
+2 - &lt;x,y&gt;/(|x|^2 * |y|^2)<br>
+3 - scale by sqrt of vertex weights<br>
+4 - scale by vertex weights<br>
+      </td>
+    </tr>
+    <tr>
+      <td valign="top">&nbsp;&nbsp;&nbsp; <i>PHG_COARSEPARTITION_METHOD</i></td>
+      <td>Method to partition the coarsest (smallest) hypergraph;
+typically done in serial:<br>
+      <span style="font-style: italic;">random</span> - random<br>
+      <span style="font-style: italic;">linear</span> - linear
+(natural) order<br>
+      <span style="font-style: italic;">greedy </span>- greedy method
+based on minimizing cuts<br>
+      <span style="font-style: italic;">auto </span>- automatically
+select from the above methods (in parallel, the processes will do
+different methods)<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp;&nbsp; <span
+ style="font-style: italic;">PHG_REFINEMENT_METHOD</span><br>
+      </td>
+      <td style="vertical-align: top;">Refinement algorithm:<br>
+&nbsp;<span style="font-style: italic;">fm </span>- two-way
+approximate&nbsp; FM<br>
+      <span style="font-style: italic;">none</span> - no refinement<br>
+      </td>
+    </tr>
+    <tr>
+      <td>&nbsp;&nbsp;&nbsp; <i>PHG_REFINEMENT_LOOP_LIMIT</i></td>
+      <td>Loop limit in FM refinement. Higher number means more
+refinement. <br>
+      </td>
+    </tr>
+    <tr nosave="" valign="top">
+      <td>&nbsp;&nbsp;&nbsp; <span style="font-style: italic;">PHG_REFINEMENT_MAX_NEG_MOVE</span><br>
+      </td>
+      <td nosave="">Maximum number of negative moves allowed in FM.<br>
+      </td>
+    </tr>
+    <tr nosave="" valign="top">
+      <td>&nbsp;&nbsp; <span style="font-style: italic;">PHG_BAL_TOL_ADJUSTMENT</span><br>
+      </td>
+      <td nosave="">Controls how the balance tolerance is adjusted at
+each level of bisection.<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp; <span
+ style="font-style: italic;">PHG_RANDOMIZE_INPUT</span><br>
+      </td>
+      <td style="vertical-align: top;">Randomize layout of vertices and
+hyperedges in internal parallel 2D layout? (0/1)<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp; <a
+ name="PHG_EDGE_WEIGHT_OPERATION"></a><span style="font-style: italic;">PHG_EDGE_WEIGHT_OPERATION</span>
+      </td>
+      <td style="vertical-align: top;">Operation to be applied to edge
+weights supplied by different processes for the same hyperedge:<br>
+      <i>add</i> - the hyperedge weight will be the sum of the supplied
+weights<br>
+      <i>max</i> - the hyperedge weight will be the maximum of the
+supplied weights<br>
+      <i>error</i> - if the hyperedge weights are not equal, Zoltan
+will flag an error, otherwise the hyperedge weight will be the value
+returned by the processes<br>
+      </td>
+    </tr>
+    <tr nosave="" valign="top">
+      <td>&nbsp;&nbsp; <span style="font-style: italic;">EDGE_SIZE_THRESHOLD</span><br>
+      </td>
+      <td nosave="">Ignore hyperedges greater than this fraction times
+number of vertices.<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp; <span
+ style="font-style: italic;">PATOH_ALLOC_POOL0</span><br>
+      </td>
+      <td style="vertical-align: top;">Memory allocation for PaToH; see
+the PaToH manual for details.<br>
+      </td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;">&nbsp;&nbsp; <span
+ style="font-style: italic;">PATOH_ALLOC_POOL1</span><br>
+      </td>
+      <td style="vertical-align: top;">Memory allocation for PaToH; see
+the PaToH manual for details.</td>
+    </tr>
+    <tr>
+      <td valign="top"><b>Default values:</b></td>
+      <td><br>
+      </td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><i>HYPERGRAPH_PACKAGE = PHG<br>
+      </i></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">CHECK_HYPERGRAPH</span>
+= 0<br>
+      </td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_OUTPUT_LEVEL=0</span></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_FINAL_OUTPUT=0</span></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><i>PHG_REDUCTION_METHOD=ipm</i></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_REDUCTION_LIMIT=100</span></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_VERTEX_VISIT_ORDER=0</span></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_EDGE_SCALING=0</span></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_VERTEX_SCALING=0</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><i>PHG_COARSEPARTITION_METHOD=greedy</i></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">PHG_REFINEMENT_METHOD=fm</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><i>PHG_REFINEMENT_LOOP_LIMIT=10</i></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">PHG_REFINEMENT_MAX_NEG_MOVE=100</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">PHG_BAL_TOL_ADJUSTMENT=0.7</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">PHG_RANDOMIZE_INPUT=0</span></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><span style="font-style: italic;">PHG_EDGE_WEIGHT_OPERATION=max</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">EDGE_SIZE_THRESHOLD=0.25</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">PATOH_ALLOC_POOL0=0</span></td>
+    </tr>
+    <tr>
+      <td style="vertical-align: top;"><br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">PATOH_ALLOC_POOL1=0</span></td>
+    </tr>
+    <tr>
+      <td valign="top"><b>Required Query Functions:</b></td>
+      <td><br>
+      </td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><b><a href="../ug_html/ug_query_lb.html#ZOLTAN_NUM_OBJ_FN">ZOLTAN_NUM_OBJ_FN</a></b></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><b><a href="../ug_html/ug_query_lb.html#ZOLTAN_OBJ_LIST_FN">ZOLTAN_OBJ_LIST_FN</a></b>
+or <b><a href="../ug_html/ug_query_lb.html#ZOLTAN_FIRST_OBJ_FN">ZOLTAN_FIRST_OBJ_FN</a></b>/<b><a
+ href="../ug_html/ug_query_lb.html#ZOLTAN_NEXT_OBJ_FN">ZOLTAN_NEXT_OBJ_FN</a></b>
+pair</td>
+    </tr>
+    <tr nosave="" valign="top">
+      <td><br>
+      </td>
+      <td nosave=""> <b><a href="../ug_html/ug_query_lb.html#ZOLTAN_HG_SIZE_CS_FN">ZOLTAN_HG_SIZE_CS_FN</a></b>
+      <br>
+      <b><a href="../ug_html/ug_query_lb.html#ZOLTAN_HG_CS_FN">ZOLTAN_HG_CS_FN</a></b>
+      </td>
+    </tr>
+    <tr>
+      <td valign="top"><b>Optional Query Functions:</b></td>
+      <td><br>
+      </td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><b><a href="../ug_html/ug_query_lb.html#ZOLTAN_HG_SIZE_EDGE_WTS_FN">ZOLTAN_HG_SIZE_EDGE_WTS_FN</a></b></td>
+    </tr>
+    <tr>
+      <td><br>
+      </td>
+      <td><b><a href="../ug_html/ug_query_lb.html#ZOLTAN_HG_EDGE_WTS_FN">ZOLTAN_HG_EDGE_WTS_FN</a></b></td>
+    </tr>
+  </tbody>
+</table>
+<p>
+It is possible to provide the graph query functions instead of the
+hypergraph queries, though this is not recommended. If only graph query
+functions are registered, Zoltan will automatically create a hypergraph
+from the graph, but some information (specifically, edge weights) will
+be lost. </p>
+<hr width="100%">[<a href="ug.html">Table of Contents</a>&nbsp; | <a
+ href="dev_reftree.html">Next:&nbsp;
+Refinement Tree Partitioning(NEANEA CHANGE ME)</a>&nbsp; |&nbsp; <a
+ href="dev_parmetis.html">Previous:&nbsp;
+ParMetis(NEANEA CHANGE ME)</a>&nbsp; |&nbsp; <a href="http://www.sandia.gov/general/privacy-security/index.html">Privacy and Security</a>]
+</body>
+</html>

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