Starting porting the project to cmake.

CMakeLists.txt

+#Libtnl
+
+#Je potreba prenest vsechny Cmakelisty
+#PrelozVse
+#configDirectory.h.in - podle nej se vytvori hlavickovy soubor s informacemi o umisteni konfiguracnich souboru
+#src/dummy.cpp
+#src/core/config.h
+#src/core/tnlFieldCUDA2D.h
+#src/debug/parse.cc - zmena na include tnlDebugParser.h misto
+#src/debug/tnlDebugScanner.l	a jeho projeti skrz sflex++
+
+#tests/matrix-formats-test.cpp
+#tests/sparse-matrix-benchmark.cpp
+#tools/src/mdiff-err-norms.cpp
+#tools/src/tnlcurve2gnuplot.cpp
+#tools/src/tnl-grid-view.cpp
+#tools/src/tnl/matrix-convert.cpp
+
+project(libtnl)
+
+cmake_minimum_required(VERSION 2.8)
+FIND_PACKAGE(CUDA)
+#Najdem CPPUNIT tohle by bylo hezci mit mimo, aby slo jen volat find_package(cppunit), ale to bych to zase ztratil
+FIND_PATH(CPPUNIT_INCLUDE_DIR cppunit/TestCase.h
+  /usr/local/include
+  /usr/include
+)
+
+# With Win32, important to have both
+IF(WIN32)
+  FIND_LIBRARY(CPPUNIT_LIBRARY cppunit
+               ${CPPUNIT_INCLUDE_DIR}/../lib
+               /usr/local/lib
+               /usr/lib)
+  FIND_LIBRARY(CPPUNIT_DEBUG_LIBRARY cppunitd
+               ${CPPUNIT_INCLUDE_DIR}/../lib
+               /usr/local/lib
+               /usr/lib)
+ELSE(WIN32)
+  # On unix system, debug and release have the same name
+  FIND_LIBRARY(CPPUNIT_LIBRARY cppunit
+               ${CPPUNIT_INCLUDE_DIR}/../lib
+               /usr/local/lib
+               /usr/lib)
+  FIND_LIBRARY(CPPUNIT_DEBUG_LIBRARY cppunit
+               ${CPPUNIT_INCLUDE_DIR}/../lib
+               /usr/local/lib
+               /usr/lib)
+ENDIF(WIN32)
+
+IF(CPPUNIT_INCLUDE_DIR)
+  IF(CPPUNIT_LIBRARY)
+    SET(CPPUNIT_FOUND "YES")
+    SET(CPPUNIT_LIBRARIES ${CPPUNIT_LIBRARY} ${CMAKE_DL_LIBS})
+    SET(CPPUNIT_DEBUG_LIBRARIES ${CPPUNIT_DEBUG_LIBRARY}
+${CMAKE_DL_LIBS})
+  ENDIF(CPPUNIT_LIBRARY)
+ENDIF(CPPUNIT_INCLUDE_DIR)
+
+
+
+#-------------------------Skutecny zacatek-----------------------------
+
+ENABLE_TESTING()	#zapneme moznost testovani
+# set (BUILD_CUDA)
+# set (BUILD_MPI)
+
+#Nastaveni kam davat vysledne soubory pro debug/release verzi
+IF( CMAKE_BUILD_TYPE STREQUAL "Debug")
+	set (LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/lib)
+	set (EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/bin)
+	set(debugExt -dbg)
+else()
+	set (LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Release/lib)
+	set (EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Release/bin)
+	set (addAlsoSubdirs TRUE)
+endif()
+
+if (BUILD_MPI)		#Pokud to ma byt za pouziti MPI nastavime si koncovku -mpi, a spravne prekladace
+  set(mpiExt -mpi)
+  SET(CMAKE_C_COMPILER mpicc)
+  SET(CMAKE_CXX_COMPILER mpicxx)
+endif()
+
+
+set (Config_Directory \"${EXECUTABLE_OUTPUT_PATH}/config/\")
+configure_file ("configDirectory.h.in"  "${PROJECT_BINARY_DIR}/headers/configDirectory.h" )
+
+#Nastavime cesty k hlavickovym souborum a knihovnam
+INCLUDE_DIRECTORIES(src)
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/headers)
+LINK_DIRECTORIES(${LIBRARY_OUTPUT_PATH})
+
+#Pokracujeme dalsimi podadresari
+add_subdirectory (src)
+add_subdirectory (tests)
+add_subdirectory (tools)
+

buildAll

+#!/bin/bash
+#Pokud nemam potrebne adresare (Debug, Release), tak si je vytvorim
+if [ ! -d Debug ];
+then
+   mkdir Debug
+fi
+if [ ! -d Release ];
+then
+   mkdir Release
+fi
+
+cd Debug
+cmake .. -DCMAKE_BUILD_TYPE=Debug
+make
+cd ../Release
+cmake ..
+make
\ No newline at end of file

configDirectory.h.in

+#define CONFIG_DIRECTORY @Config_Directory@
\ No newline at end of file

src/CMakeLists.txt

+INCLUDE_DIRECTORIES( config core debug diff matrix mesh solver )
+
+add_subdirectory( config )
+add_subdirectory( core )
+add_subdirectory( debug )
+add_subdirectory( diff )
+add_subdirectory( matrix )
+add_subdirectory( mesh )
+add_subdirectory( solver )
+
+# Build the main library
+set( libtnl_0_1_la_LIBADD
+     libtnlconfig${mpiExt}${debugExt}-0.1
+     libtnlcore${mpiExt}${debugExt}-0.1
+     libtnldebug${mpiExt}${debugExt}-0.1
+     libtnldiff${mpiExt}${debugExt}-0.1 
+     libtnlmatrix${mpiExt}${debugExt}-0.1
+     libtnlmesh${mpiExt}${debugExt}-0.1
+     libtnlsolver${mpiExt}${debugExt}-0.1
+    )
+
+ADD_LIBRARY( libtnl${mpiExt}${debugExt}-0.1 SHARED )
+target_link_libraries( libtnl${mpiExt}${debugExt}-0.1 ${libtnl_0_1_la_LIBADD} )
+if (BUILD_MPI)
+  target_link_libraries(libtnl${mpiExt}${debugExt}-0.1 mpi)
+endif()

src/config/CMakeLists.txt

+set( EXTRA_DIST tnlConfigDescriptionParser.y 
+	             tnlConfigDescriptionScanner.l 
+	             FlexLexer.h
+    )
+
+set( headers tnlConfigDescription.h     	    
+ 		     tnlConfigDescriptionParser.h 
+		     tnlConfigDescriptionParserbase.h 
+		     tnlConfigDescriptionParser.ih 
+		     tnlConfigDescriptionScanner.h 
+		     tnlParameterContainer.h 
+    )
+set( sources tnlConfigDescription.cpp 
+        	 tnlConfigDescriptionScanner.cpp 
+        	 tnlConfigDescriptionParser.cpp 
+        	 tnlParameterContainer.cpp 
+        	 parse.cc
+    )
+
+set( libmconfigincludedir ${TNL_INCLUDE_DIR}/config )
+set( libmconfiginclude_HEADERS ${headers} )
+
+ADD_LIBRARY( libtnlconfig${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers} )
+
+if( BUILD_MPI )
+  target_link_libraries( libtnlcore${mpiExt}${debugExt}-0.1 mpi )
+endif()
+

src/core/CMakeLists.txt

+set (headers tnlAssert.h  
+    	     tnlCurve.h 
+    	     tnlCudaSupport.h
+		     tnlDataElement.h 
+		     tnlFlopsCounter.h 
+		     tnlList.h 
+		     tnlLongVectorBase.h 
+		     tnlLongVectorHost.h 
+		     tnlLongVectorCUDA.h  
+		     tnlLogger.h 
+		     tnlObject.h 
+		     tnlStack.h 
+		     tnlString.h 
+		     tnlReal.h 
+		     tnlRealTester.h 
+		     tnlTimerCPU.h  
+		     tnlTimerRT.h  
+		     tnlVector.h 
+		     tnl-cuda-kernels.h  
+		     tnlCUDAKernelsTester.h
+			 tnlCudaSupport.h
+		     compress-file.h 
+		     mfilename.h 
+		     mfuncs.h 
+		     mpi-supp.h 
+		     param-types.h
+    )
+set( sources tnlCudaSupport.cpp 
+             tnlFlopsCounter.cpp 
+             tnlLogger.cpp 
+        	 tnlObject.cpp 
+        	 tnlString.cpp 
+        	 tnlTimerCPU.cpp  
+        	 tnlTimerRT.cpp   
+        	 mfilename.cpp 
+        	 mpi-supp.cpp 
+    )
+
+set (libmcoreincludedir ${TNL_INCLUDE_DIR}/core )
+set (libmcoreinclude_HEADERS ${headers} )
+
+if (BUILD_CUDA)
+  CUDA_ADD_LIBRARY(libtnlcore${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers} debug.h tnlLongVectorCUDA.cu tnl-cuda-kernels.cu )
+else()
+  ADD_LIBRARY(libtnlcore${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers} debug.h)
+endif()
+if (BUILD_MPI)
+  target_link_libraries(libtnlcore${mpiExt}${debugExt}-0.1 mpi)
+endif()
+

src/debug/CMakeLists.txt

+set (EXTRA_DIST tnlDebugParser.y 
+	         tnlDebugScanner.l 
+             create-tnl-debug-parser
+     )      
+set (sources tnlDebug.cpp 
+          tnlDebugGroup.cpp 
+          tnlDebugStructure.cpp 
+	      tnlDebugParser.cpp 
+	      tnlDebugScanner.cpp 
+	      parse.cc
+	)
+set (headers tnlDbgDataElement.h 
+	      tnlDebugEntry.h 
+	      tnlDebugGroup.h 
+	      tnlDebugParserbase.h 
+	      tnlDebugParser.h 
+       tnlDebug.h 
+    tnlDebugScanner.h 
+  tnlDebugStructure.h
+	)
+
+ADD_LIBRARY(libtnldebug${mpiExt}${debugExt}-0.1 SHARED ${sources})	#Mozna jeste prekladaci ${OPTIMISECXXFLAGS}
+
+add_executable ( tnl-debug-test tnl-debug-test.cpp)
+target_link_libraries ( tnl-debug-test  libtnldebug-0.1) 
\ No newline at end of file

src/diff/CMakeLists.txt

+set (headers 
+   mdiff-debug.h 
+   drawGrid1D.h 
+   drawGrid2D.h 
+   drawGrid3D.h 
+   tnlExplicitSolver.h 
+   tnlGrid1D.h 
+   tnlGrid2D.h 
+   tnlGrid3D.h 
+   tnlGridCUDA1D.h 
+   tnlGridCUDA2D.h 
+   tnlGridCUDA3D.h 
+   tnlGridCUDA2DTester.h 
+   tnlGridSystem1D.h 
+   tnlEulerSolver.h 
+   tnlMersonSolver.h 
+   tnlMersonSolverCUDA.h 
+   tnlMersonSolverCUDA.cu.h 
+   tnlMPIMesh2D.h 
+   tnlMPIMesh3D.h 
+   tnlNonlinearRungeKuttaSolver.h 
+   curve-ident.h 
+   norms.h
+	)
+set (sources )
+
+set (libtnldiffincludedir ${TNL_INCLUDE_DIR}/diff)
+set (libtnldiffinclude_HEADERS ${headers})
+
+if (BUILD_CUDA)
+  CUDA_ADD_LIBRARY(libtnldiff${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers} tnlMersonSolverCUDA.cu ../dummy.cpp)
+  CUDA_ADD_LIBRARY(libdiff-tests${debugExt} SHARED tnlMersonSolverCUDATester.h tnlMersonSolverCUDATester.cu ../dummy.cpp)
+else()
+  ADD_LIBRARY(libtnldiff${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers} ../dummy.cpp)	#${OPTIMISECXXFLAGS}
+  ADD_LIBRARY(libdiff-tests${debugExt} SHARED ../dummy.cpp)
+endif()
+if (BUILD_MPI)
+  target_link_libraries(libtnldiff-0.1 mpi)
+endif()
\ No newline at end of file

src/matrix/CMakeLists.txt

+set (headers 
+     tnlMatrix.h 
+	  tnlCSRMatrixOld.h 
+	  tnlCoalescedCSRMatrix.h 
+	  tnlCoalescedCSRMatrixCUDA.h 
+	  tnlCoalescedFastCSRMatrix.h 
+	  tnlCoalescedFastCSRMatrixCUDA.h 
+	  tnlEllpackMatrix.h 
+	  tnlEllpackMatrixCUDA.h 
+	  tnlCSRMatrix.h 
+	  tnlCSRMatrixTester.h 
+	  tnlFastCSRMatrix.h 
+	  tnlFullMatrix.h 
+	  tnlBaseMatrix.h 
+	  tnlCoalescedCSRMatrixTester.h 
+	  tnlEllpackMatrixTester.h 
+	  tnlMatrixSolver.h 
+	  tnlPETSCMatrix.h 
+	  tnlPETSCSolver.h 
+	  tnlSORSolver.h 
+	  tnlCGSolver.h 
+	  tnlBICGSolver.h 
+	  tnlBICGStabSolver.h 
+	  tnlGMRESSolver.h  
+	  tnlPreconditioner.h 
+	  tnlILUPreconditioner.h 
+	  tnlPETSCPreconditioner.h
+	)
+set (sources tnlBaseMatrix.cpp)
+
+set (libtnlmatrixincludedir  ${TNL_INCLUDE_DIR}/matrix)
+set (libtnlmatrixinclude_HEADERS ${headers})
+
+if (BUILD_CUDA)
+  set (cudaAdd tnlCoalescedCSRMatrixCUDA.cu
+	    tnlCoalescedFastCSRMatrixCUDA.cu
+	    tnlEllpackMatrixCUDA.cu
+	    tnlCoalescedCSRMatrixCUDA.cu.h
+	    tnlCoalescedFastCSRMatrixCUDA.cu.h
+	    tnlEllpackMatrixCUDA.cu.h 
+  )
+  CUDA_ADD_LIBRARY(libtnlmatrix${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers} ${cudaAdd}) # ${OPTIMISECXXFLAGS}
+else()
+  ADD_LIBRARY(libtnlmatrix${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers}) # ${OPTIMISECXXFLAGS}
+endif()
+if (BUILD_MPI)
+  target_link_libraries(libtnlmatrix${mpiExt}${debugExt}-0.1 mpi)
+endif()
+

src/mesh/CMakeLists.txt

+set( headers tnlDistributedGrid.h
+             tnlGrid.h  
+   )
+set( sources )
+
+set( libtnlmeshincludedir ${TNL_INCLUDE_DIR}/mesh )
+set( libtnlmeshinclude_HEADERS ${headers} )
+
+ADD_LIBRARY(libtnlmesh${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers})	#${OPTIMISECXXFLAGS}
+
+if (BUILD_MPI)
+  target_link_libraries(libtnldiff-0.1 mpi)
+endif()
\ No newline at end of file

src/solver/CMakeLists.txt

+set( headers tnlBICGSolver.h
+             tnlBICGStabSolver.h
+             tnlCGSolver.h
+             tnlEulerSolver.h
+             tnlExplicitSolver.h
+             tnlGMRESSolver.h
+             tnlILUPreconditioner.h
+             tnlMatrixSolver.h
+             tnlMersonSolver.h
+             tnlPETSCSolver.h
+             tnlPreconditioner.h
+             tnlSORSolver.h
+   )
+set( sources )
+
+set( libtnlsolverincludedir ${TNL_INCLUDE_DIR}/mesh )
+set( libtnlsolverinclude_HEADERS ${headers} )
+
+ADD_LIBRARY(libtnlsolver${mpiExt}${debugExt}-0.1 SHARED ${sources} ${headers})    #${OPTIMISECXXFLAGS}
+
+if( BUILD_MPI )
+  target_link_libraries( libtnlsolver-0.1 mpi )
+endif()
+
+

src/solver/tnlILUPreconditioner.cpp

-/***************************************************************************
-                          tnlILUPreconditioner.cpp  -  description
-                             -------------------
-    begin                : 2007/02/01
-    copyright            : (C) 2007 by Tomas Oberhuber
-    email                : tomas.oberhuber@fjfi.cvut.cz
- ***************************************************************************/
-
-/***************************************************************************
- *                                                                         *
- *   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 of the License, or     *
- *   (at your option) any later version.                                   *
- *                                                                         *
- ***************************************************************************/
-
-#include <assert.h>
-#include <math.h>
-#include "tnlILUPreconditioner.h"
-#include "mfuncs.h"
-
-#ifdef ILU_DEBUG
-#include <iomanip>
-#include <fstream>
-//--------------------------------------------------------------------------
-void WriteFullMatrix( ostream& o_str, const m_real* M, const m_int N )
-{
-   m_int i, j;
-   for( i = 0; i < N; i ++ )
-   {
-      for( j = 0; j < N; j ++ )
-      {
-         const m_real& v = M[ i * N + j ];
-         if( v == 0.0 ) o_str << setw( 10 ) << ".";
-         else o_str << setprecision( 6 ) << setw( 10 ) << v;
-      }
-      o_str << endl;
-   }
-}
-#endif
-//--------------------------------------------------------------------------
-tnlILUPreconditioner :: tnlILUPreconditioner( const m_int _size, 
-                                          const m_int initial_size,
-                                          const m_int segment_size,
-                                          const m_int init_row_elements )
-: size( _size )
-{
-#ifdef ILU_DEBUG
-   full_M = new m_real[ size * size ];
-   ilu_check = new m_real[ size * size ];
-#endif
-   y = new m_real[ size ];
-   M = new tnlCSRMatrix( size, initial_size, segment_size, init_row_elements );
-}
-//--------------------------------------------------------------------------  
-tnlILUPreconditioner :: ~tnlILUPreconditioner()
-{
-   if( M ) delete M;
-   if( y ) delete[] y;
-#ifdef ILU_DEBUG
-   if( full_M ) delete[] full_M;
-   if( ilu_check ) delete[] ilu_check;
-#endif
-}
-//--------------------------------------------------------------------------  
-const tnlCSRMatrix* tnlILUPreconditioner :: getVector() const
-{
-   return M;
-}
-//--------------------------------------------------------------------------  
-m_int tnlILUPreconditioner :: Init( const tnlCSRMatrix& A, const m_real& threshold )
-{
-   dbgFunctionName( "tnlILUPreconditioner", "Init" );
-   assert( A. Size() == M -> Size() );
-   int non_zero_elements( 0 );
-#ifdef CSR_MATRIX_TUNING
-   M -> ResetStatistics();
-#endif
-   m_int i, j, k;
-   const tnlCSRMatrixElement *A_data;
-   const tnlCSRMatrixRowInfo *A_rows_info;
-   A. getVector( A_data, A_rows_info );
-   
-#ifdef ILU_DEBUG
-   // 1. Copy data of A to full_M
-   bzero( full_M, size * size * sizeof( m_real ) );
-   for( i = 0; i < size; i ++ )
-      for( j = A_rows_info[ i ]. first; j < A_rows_info[ i ]. last; j ++ )
-      {
-         m_int col = A_data[ j ]. column;
-         if( col != -1 )
-            full_M[ i * size + col ] = A_data[ j ]. value;
-      }
-#endif
-
-   M -> Reset();
-   tnlCSRMatrixElement* M_data;
-   const tnlCSRMatrixRowInfo *M_rows_info;
-   // 2. Processing IKJ version of ILU factorisation
-   // For i = 0, ... , N
-   for( i = 0; i < size; i ++ )
-   {
-      // y = a_i*  - i-th row
-      bzero( y, size * sizeof( m_real ) );
-      m_real y_norm( 0.0 );
-      const m_int a_row_beg = A_rows_info[ i ]. first;
-      const m_int a_row_end = A_rows_info[ i ]. last;
-      for( k = a_row_beg; k < a_row_end; k ++ )
-      {
-         const m_int col = A_data[ k ]. column;
-         const m_real& a_ik = A_data[ k ]. value;
-         if( col == -1 ) break;
-         y[ col ] = a_ik;
-         y_norm += a_ik * a_ik;
-      }
-      // get 2-norm of the i-th row for the dropping rule on y_k
-      y_norm = sqrt( y_norm );
-      const m_real threshold_i = y_norm * threshold;
-      M -> Data( M_data, M_rows_info );
-      for( k = 0; k < i; k ++ )
-      {
-         const m_real& m_kk = ( *M )( k, k );
-         if( m_kk != 0.0 )
-            y[ k ] /= m_kk;
-         if( fabs( y[ k ] ) < threshold_i ) y[ k ] = 0.0;
-         if( y[ k ] != 0.0 )
-         {
-            const m_int row_beg = M_rows_info[ k ]. diagonal + 1;
-            const m_int row_end = M_rows_info[ k ]. last;
-            m_int col;
-            for( j = row_beg;
-                 j < row_end && ( col = M_data[ j ]. column ) != -1;
-                 j ++ )
-               y[ col ] -= y[ k ] * M_data[ j ]. value;
-         }
-      }
-      for( j = 0; j < size; j ++ )
-      {
-         if( i == j || fabs( y[ j ] ) > threshold_i )
-         {
-             M -> Set( i, j , y[ j ] );
-             non_zero_elements ++;
-         }
-         if( i == j && ( *M )( i, i ) == 0.0 )
-         {
-            cerr << endl << "Zero pivot appears at line " << i << "!" << endl;
-            M -> Set( i, i, 1.0 );
-            abort();
-            //return 0;
-         }
-      }
-     cout << "Computing ILUT ... " << 100.0 * ( m_real ) ( i + 1 ) / ( m_real ) ( size ) << "%    \r" << flush; 
-      dbgExpr( i );
-      //dbgExpr( * M );
-   }
-   cout << non_zero_elements / size << " elems. per line in average " <<  endl;
-   //dbgExpr( * M );
-
-#ifdef ILU_DEBUG
-   fstream file;
-   /*file. open( "orig_full_M2", ios :: out );
-   WriteFullMatrix( file, full_M, size );
-   file. close();*/
-   
-   /*file. open( "M", ios :: out );
-   file << *M << endl;
-   file. close();*/
-
-   for( i = 0; i < size; i ++ )
-   {
-cout << "LU: " << ( m_real ) i / ( m_real ) size * 100.0 << " % done   \r" << flush;
-      // y = a_i*  - i-th row
-      bzero( y, size * sizeof( m_real ) );
-      m_real y_norm( 0.0 );
-      for( k = 0; k < size; k ++ )
-      {
-         const m_real& m_ik = full_M[ i * size + k ];
-         y[ k ] = m_ik;
-         y_norm += m_ik * m_ik;
-         //cout << i << ", " << k << " <- " << y[ k ] << endl;
-      }
-      // get 2-norm of the i-th row for the dropping rule on y_k
-      y_norm = sqrt( y_norm );
-      const m_real threshold_i = y_norm * threshold;
-      for( k = 0; k < i; k ++ )
-      {
-         const m_real& m_kk = full_M[ k * size + k ];
-         if( m_kk != 0.0 )
-            y[ k ] /= m_kk;
-         if( fabs( y[ k ] ) < threshold_i )
-            y[ k ] = 0.0;
-         if( y[ k ] != 0.0 )
-            for( j = k + 1; j < size; j ++ )
-               y[ j ] -= y[ k ] * full_M[ k * size + j ];
-      }
-      for( j = 0; j < size; j ++ )
-      {
-         if( i == j || fabs( y[ j ] ) > threshold_i )
-            full_M[ i * size + j ] = y[ j ];
-         else
-            full_M[ i * size + j  ] = 0.0;
-      }
-      if( full_M[ i * size + i ] == 0.0 )
-         cerr << endl << "FULL MATRIX ILU CHECK: Zero pivot appears at line " << i << "!" << endl;
-   }
-   /*file. open( "full_M", ios :: out );
-   WriteFullMatrix( file, full_M, size );
-   file. close();*/
-
-   cout << endl;
-   cout << "Checking if M == full M..." << endl;
-   for( i = 0; i < size; i ++ )
-      for( j = 0; j < size; j ++ )
-         if( full_M[ i * size + j ] != ( *M )( i, j ) )
-         {
-            cerr << "M != full M at " << i << ", " << j << " : " <<
-            fabs( full_M[ i * size + j ] - ( *M )( i, j ) ) << endl;
-            break;
-         }
-   
-   /*cout << "Checking  if LU = A" << endl;
-   // check whether L U == A
-   for( i = 0; i < size; i ++ )
-      for( j = 0; j < size; j ++ )
-      {
-         cout << i << " : " << j << "     \r" << flush;
-         m_int l = Min( i, j );
-         m_real sum( 0.0 );
-         for( k = 0; k <= l; k ++ )
-            if( k < i )
-               sum += full_M[ i * size + k ] * full_M[ k * size + j ];
-            else
-               sum += full_M[ i * size + j ];  // L has 1 on diagonal
-         if( fabs( sum ) < 1.0e-15 ) sum = 0.0;
-         ilu_check[ i * size + j ] = sum;
-      }
-   cout << endl;
-   m_real ilu_diff( 0.0 );
-   for( i = 0; i < size; i ++ )
-      for( j = 0; j < size; j ++ )
-         ilu_diff = Max( ilu_diff, fabs( ilu_check[ i * size +j ] - A( i, j ) ) );
-   cout << "ILU Max. error is " << ilu_diff << endl;*/
-#endif
-
-#ifdef CSR_MATRIX_TUNING
-   M -> PrintStatistics();
-#endif
-   return 1;  
-   
-     
-   /*
-   // For i = 1 ... n - 1
-   for( i = 1; i < size; i ++ )
-   {
-      // For k = 0 ... i - 1 and for ( i, k ) non-zero
-      //  = take non-zero entries at the i-th row before the diagonal entry
-      m_int i_th_row_beg = M_row_ind[ i ];
-      m_int i_th_row_end = M_row_ind[ i + 1 ];
-      m_int k_ind;
-      for( k_ind = i_th_row_beg; k_ind < i_th_row_end; k_ind ++ )
-      {
-         k = M_data[ k_ind ]. column;
-         if( k == -1 ) break;
-         // a_ik := a_ik / a_kk
-         M_data[ k_ind ]. value /= M_data[ M_diag_ind[ k ] ]. value;
-         const m_real& a_ik = M_data[ k_ind ]. value;
-
-         // For j = k + 1 ... n - 1 and for ( i, j ) non-zero
-         // = take non-zero entries at the i-th row behind the diagonal entry
-         m_int j_ind;
-         for( j_ind = k_ind + 1; j_ind < i_th_row_end; j_ind ++ )
-         {
-            j = M_data[ j_ind ]. column;
-            if( j == -1 ) break;
-            // a_ij :=  a_ij - a_ik * a_kj
-            M_data[ j_ind ]. value -= a_ik * ( *M )( k, j );
-         }
-      }
-   }*/
-
-}
-//--------------------------------------------------------------------------     
-void tnlILUPreconditioner :: Solve( const m_real* b, m_real* x ) const
-{
-   dbgFunctionName( "tnlILUPreconditioner", "Solve" );
-   const m_int size = M -> Size();
-   const tnlCSRMatrixElement* M_data;
-   const tnlCSRMatrixRowInfo *M_rows_info;
-   M -> Data( M_data, M_rows_info );
-   m_int i, j;
-   
-   dbgCout( "Solving Ly = b" );
-   // L is unit lower triangular
-   for( i = 0; i < size; i ++ )
-   {
-      y[ i ] = b[ i ];
-      const m_int i_row_beg = M_rows_info[ i ]. first;
-      const m_int i_row_end = M_rows_info[ i ]. diagonal;
-      m_int col;
-      for( j = i_row_beg;
-           j < i_row_end && ( col = M_data[ j ]. column ) != -1;
-           j ++ )
-         y[ i ] -= y[ M_data[ j ]. column ] * M_data[ j ]. value;
-      //for( j = 0; j < i; j ++ )
-      //   y[ i ] -= y[ j ] * ( * M )( i, j );
-   }
-   
-   dbgCout( "Solving Ux = y" );
-   for( i = size - 1; i >=0 ; i -- )
-   {
-      x[ i ] = y[ i ];
-      const m_int i_row_beg = M_rows_info[ i ]. diagonal;
-      assert( i_row_beg != -1 );
-      const m_int i_row_end = M_rows_info[ i ]. last;
-      m_int col;
-      for( j = i_row_beg + 1;
-           j < i_row_end && ( col = M_data[ j ]. column ) != -1;
-           j ++ )
-         x[ i ] -= x[ col ] * M_data[ j ]. value;
-      
-      assert( M_data[ i_row_beg ]. value != 0.0 );
-      x[ i ] /= M_data[ i_row_beg ]. value;
-      //for( j = i + 1; j < size; j ++ )
-      //   x[ i ] -= x[ j ] * ( *M )( i, j );
-      //x[ i ] /= ( *M )( i, i );
-   }
-#ifdef ILU_DEBUG
-   /*for( i = 0; i < size; i ++ )
-   {
-      y[ i ] = b[ i ];
-      for( j = 0; j < i; j ++ )
-         y[ i ] -= y[ j ] * full_M[ i * size + j ];
-   }
-   
-   dbgCout( "Solving Ux = y" );
-   for( i = size - 1; i >=0 ; i -- )
-   {
-      x[ i ] = y[ i ];
-      for( j = i + 1; j < size; j ++ )
-         x[ i ] -= x[ j ] * full_M[ i * size + j ];
-      x[ i ] /= full_M[ i * size + i ];
-   }*/
-#endif
-}
-

src/solver/tnlPETSCSolver.cpp

-/***************************************************************************
-                          tnlPETSCSolver.cpp  -  description
-                             -------------------
-    begin                : 2008/05/12
-    copyright            : (C) 2008 by Tomas Oberhuber
-    email                : tomas.oberhuber@fjfi.cvut.cz
- ***************************************************************************/
-
-/***************************************************************************
- *                                                                         *
- *   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 of the License, or     *
- *   (at your option) any later version.                                   *
- *                                                                         *
- ***************************************************************************/
-
-#include "tnlPETSCSolver.h"
-
-//--------------------------------------------------------------------------
-#ifdef HAVE_PETSC
-/*PetscErrorCode PETSCSolverMonitorCallback( KSP petsc_solver, PetscInt iter, PetscReal rnorm, void* ctx )
-{
-   cout << "*" << flush;
-}*/
-#endif
-

tests/CMakeLists.txt

+file(COPY matrix-market DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
+file(COPY florida-matrix-market DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
+file(COPY tnl-sparse-matrix-check.cfg.desc DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
+
+set (tnl_sparse_matrix_check_SOURCES tnl-sparse-matrix-check.cpp tnl-sparse-matrix-check.h)
+set (matrix_formats_test_SOURCES matrix-formats-test.cpp matrix-formats-test.h)
+set (sparse_matrix_benchmark_SOURCES sparse-matrix-benchmark.cpp sparse-matrix-benchmark.h)
+#sparse_matrix_benchmark_CXXFLAGS = $(OPTIMISECXXFLAGS)
+
+add_executable (tnl_sparse_matrix_check${mpiExt}${debugExt} ${tnl_sparse_matrix_check_SOURCES})
+target_link_libraries (tnl_sparse_matrix_check${mpiExt}${debugExt} libtnl${mpiExt}${debugExt}-0.1 
+    libtnlcore${mpiExt}${debugExt}-0.1 libtnlmatrix${mpiExt}${debugExt}-0.1)
+
+add_executable (matrix_formats_test${mpiExt}${debugExt} ${matrix_formats_test_SOURCES})
+target_link_libraries (matrix_formats_test${mpiExt}${debugExt} libtnl${mpiExt}${debugExt}-0.1 
+    libtnlcore${mpiExt}${debugExt}-0.1 libtnlmatrix${mpiExt}${debugExt}-0.1)
+
+add_executable (sparse_matrix_benchmark${mpiExt}${debugExt} ${sparse_matrix_benchmark_SOURCES})
+target_link_libraries (sparse_matrix_benchmark${mpiExt}${debugExt} libtnl${mpiExt}${debugExt}-0.1 
+    libtnlcore${mpiExt}${debugExt}-0.1 libtnlmatrix${mpiExt}${debugExt}-0.1)
\ No newline at end of file

tools/CMakeLists.txt

+add_subdirectory (src)
+add_subdirectory (share)
\ No newline at end of file

tools/share/CMakeLists.txt

+file(COPY mdiff-err-norms.cfg.desc DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
+file(COPY mgrid-view.cfg.desc DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
+file(COPY tnlcurve2gnuplot.cfg.desc DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
+file(COPY tnl-matrix-convert.cfg.desc DESTINATION ${EXECUTABLE_OUTPUT_PATH}/config)
\ No newline at end of file

tools/src/CMakeLists.txt

+set(common read-file.h)
+set(tnlerrnormssources mdiff-err-norms.cpp 
+                     tnl-err-norms.h
+                     compare-objects.h
+                     ${common}
+)
+
+set(tnlgridviewsources tnl-grid-view.cpp
+                     tnl-grid-view.h
+                     ${common}
+)
+                     
+set(tnlcurve2gnuplotsources tnlcurve2gnuplot.cpp
+                          ${common} 
+)
+
+set(tnlfunctionsbenchmarksources functions-benchmark.cpp
+                               functions-benchmark.h
+)
+
+set(tnlmatrixconvertsources tnl-matrix-convert.cpp
+                          tnl-matrix-convert.h      
+)
+
+if (BUILD_CUDA)
+    set(tnlfunctionsbenchmarksources  ${tnlfunctionsbenchmarksources}
+			functions-benchmark-cuda.cu 
+			functions-benchmark-cuda.cu.h 
+    )
+    CUDA_ADD_EXECUTABLE(tnl-functions-benchmark ${tnlfunctionsbenchmarksources})
+	target_link_libraries (tnl-functions-benchmark libtnl${mpiExt}${debugExt}-0.1)
+else (BUILD_CUDA)
+    ADD_EXECUTABLE(nl-functions-benchmark ${tnlfunctionsbenchmarksources})
+	target_link_libraries (nl-functions-benchmark libtnl${mpiExt}${debugExt}-0.1 )
+endif(BUILD_CUDA)
+
+ADD_EXECUTABLE(tnl-err-norms ${tnlerrnormssources})
+target_link_libraries (tnl-err-norms libtnl${mpiExt}${debugExt}-0.1 )
+ADD_EXECUTABLE(tnlgrid-view ${tnlgridviewsources})
+target_link_libraries (tnlgrid-view libtnl${mpiExt}${debugExt}-0.1 )
+ADD_EXECUTABLE(tnlcurve2gnuplot ${tnlcurve2gnuplotsources})
+target_link_libraries (tnlcurve2gnuplot libtnl${mpiExt}${debugExt}-0.1 )
+ADD_EXECUTABLE(tnl-matrix-convert ${tnlmatrixconvertsources})
+target_link_libraries (tnl-matrix-convert libtnl${mpiExt}${debugExt}-0.1 )