In situ visualization starting point

example/Vector/7_SPH_dlb_opt/main.cpp

@@ -209,10 +209,10 @@
  */
 
 // A constant to indicate boundary particles
-#define BOUNDARY 1
+#define BOUNDARY 0
 
 // A constant to indicate fluid particles
-#define FLUID 0
+#define FLUID 1
 
 // initial spacing between particles dp in the formulas
 const double dp = 0.0085;
@@ -1130,7 +1130,6 @@ int main(int argc, char* argv[])
 		{
 			vd.deleteGhost();
 			vd.write_frame("Geometry",write,VTK_WRITER | FORMAT_BINARY);
-                        vd.getDecomposition().write("dec" + std::to_string(write));
 			vd.ghost_get<type,rho,Pressure,velocity>(SKIP_LABELLING);
 			write++;
 

m4/ax_petsc_lib.m4

@@ -104,8 +104,8 @@ AC_DEFUN([AX_LIB_PETSC], [
                         old_LDFLAGS=$LDFLAGS
 			AX_OPENMP([CFLAGS="$OPENMP_CFLAGS"
 				   LDFLAGS="$OPENMP_LDFLAGS"],[])
-                        CFLAGS="$CFLAGS -I$with_petsc/include $HDF5_INCLUDE $METIS_INCLUDE "
-                        LDFLAGS="$LDFLAGS -L$with_petsc/lib $HDF5_LDFLAGS  $HDF5_LIBS $METIS_LIB -lmetis $SUITESPARSE_LIBS"
+                        CFLAGS="$CFLAGS -I$with_petsc/include $HDF5_INCLUDE $METIS_INCLUDE -fPIC "
+                        LDFLAGS="$LDFLAGS -L$with_petsc/lib $HDF5_LDFLAGS  $HDF5_LIBS $METIS_LIB -lmetis -shared  $SUITESPARSE_LIBS"
 			CC=$CXX
 
                         AC_LANG_SAVE

openfpm_data @ b2db24e3

-Subproject commit 5f0029a65ad864efbfafedfb0818f8160cb1fc53
+Subproject commit b2db24e3ada717cc30bfcd70bea43616bcdff920

script/detect_gcc

@@ -6,7 +6,7 @@ function haveProg() {
 
 function gpp_clang()
 {
-    if [ x"$dgc_compiler" == x"g++" ]; then
+    if [ x"$possible_solutions_command" == x"g++" ]; then
         CXX=g++
         CC=gcc
         F77=gfortran

script/install_HDF5.sh

@@ -6,10 +6,6 @@ discover_os
 
 # check if the directory $1/HDF5 exist
 
-if [ -d "$1/HDF5" ]; then
-  echo "HDF5 is already installed"
-  exit 0
-fi
 
 if [ ! -d "$1/ZLIB"  -a x"$platform" != x"cygwin" ]; then
   rm zlib-1.2.11.tar.gz
@@ -36,6 +32,11 @@ else
   echo "ZLIB is already installed"
 fi
 
+if [ -d "$1/HDF5" ]; then
+  echo "HDF5 is already installed"
+  exit 0
+fi
+
 ### 1.8.19 does not compile on CYGWIN
 wget http://ppmcore.mpi-cbg.de/upload/hdf5-1.8.19.tar.gz
 tar -xf hdf5-1.8.19.tar.gz

script/install_SUITESPARSE.sh

@@ -22,10 +22,14 @@ fi
 cd SuiteSparse
 
 if [ x"$CXX" == x"icpc" ]; then
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/$1/OPENBLAS/lib"
     STS_LIB="-shared-intel -lrt -lifcore"
 fi
 
+if [ x"$CXX" == x"g++" ]; then
+    OPT_GPP=" -shared -fPIC "
+fi
+
+
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1/OPENBLAS/lib"
 
 if [ x"$platform" == x"cygwin" ]; then
@@ -34,7 +38,7 @@ if [ x"$platform" == x"cygwin" ]; then
 fi
 
 echo "Compiling SuiteSparse without CUDA (old variable $CUDA)"
-LDLIBS="$STS_LIB -lm" LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1/OPENBLAS/lib"  make -j $2 "CUDA=no" "BLAS=-L$1/OPENBLAS/lib -lopenblas -pthread" "LAPACK="
+LDLIBS="$STS_LIB -lm" LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1/OPENBLAS/lib"  make "AUTOCC=no" "CXX=$CXX" "CC=$CC" "CPPFLAGS=$OPT_GPP"  -j $2 "CUDA=no" "BLAS=-L$1/OPENBLAS/lib -lopenblas -pthread" "LAPACK="
 if [ $? != 0 ]; then
   echo "Failed to compile SuiteSparse"
   exit 1

src/Decomposition/Distribution/parmetis_dist_util.hpp

@@ -182,7 +182,7 @@ public:
 			v_cl(v_cl), nc(nc)
 	{
 		// TODO Move into VCluster
-		MPI_Comm_dup(MPI_COMM_WORLD, &comm);
+		MPI_Comm_dup(v_cl.getMPIComm(), &comm);
 
 		// Nullify Mg
 		Mg.nvtxs = NULL;

src/Decomposition/Distribution/parmetis_util.hpp

@@ -224,7 +224,7 @@ public:
 #endif
 
 		// TODO Move into VCluster
-		MPI_Comm_dup(MPI_COMM_WORLD, &comm);
+		MPI_Comm_dup(v_cl.getMPIComm(), &comm);
 
 		// Nullify Mg
 		Mg.nvtxs = NULL;

src/Makefile.am

-LINKLIBS = $(HDF5_LDFLAGS)  $(HDF5_LIBS) $(OPENMP_LDFLAGS) $(LIBHILBERT_LIB)  $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS) $(PETSC_LIB) $(SUITESPARSE_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)  $(PARMETIS_LIB) $(BOOST_UNIT_TEST_FRAMEWORK_LIB) $(BOOST_CHRONO_LIB) $(BOOST_TIMER_LIB) $(BOOST_SYSTEM_LIB) $(LIBIFCORE)
+LINKLIBS = $(HDF5_LDFLAGS)  $(HDF5_LIBS) $(OPENMP_LDFLAGS) $(LIBHILBERT_LIB) $(PARMETIS_LIB)  $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS) $(PETSC_LIB) $(SUITESPARSE_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(BOOST_UNIT_TEST_FRAMEWORK_LIB) $(BOOST_CHRONO_LIB) $(BOOST_TIMER_LIB) $(BOOST_SYSTEM_LIB) $(LIBIFCORE)
 
 noinst_PROGRAMS = pdata
 pdata_SOURCES = main.cpp Grid/tests/grid_dist_id_HDF5_chckpnt_restart_test.cpp Grid/tests/grid_dist_id_unit_test.cpp Grid/tests/staggered_grid_dist_unit_test.cpp Vector/tests/vector_dist_cell_list_tests.cpp Vector/tests/vector_dist_complex_prp_unit_test.cpp Vector/tests/vector_dist_HDF5_chckpnt_restart_test.cpp Vector/tests/vector_dist_MP_unit_tests.cpp Vector/tests/vector_dist_NN_tests.cpp Vector/tests/vector_dist_unit_test.cpp  pdata_performance.cpp Decomposition/tests/CartDecomposition_unit_test.cpp Decomposition/tests/shift_vect_converter_tests.cpp Vector/performance/vector_dist_performance_util.cpp  lib/pdata.cpp test_multiple_o.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-pdata_CXXFLAGS = $(BOOST_CPPFLAGS) $(HDF5_CPPFLAGS) $(OPENMP_CFLAGS) $(AM_CXXFLAGS) $(LIBHILBERT_INCLUDE) $(PETSC_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(H5PART_INCLUDE) -DPARALLEL_IO  -Wno-unused-local-typedefs
+pdata_CXXFLAGS = $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) $(HDF5_CPPFLAGS) $(OPENMP_CFLAGS) $(AM_CXXFLAGS) $(LIBHILBERT_INCLUDE) $(PETSC_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(H5PART_INCLUDE) -DPARALLEL_IO  -Wno-unused-local-typedefs
 pdata_CFLAGS = $(CUDA_CFLAGS)
 pdata_LDADD = $(LINKLIBS) -lparmetis -lmetis
 nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/shift_vect_converter.hpp Decomposition/CartDecomposition_ext.hpp  Decomposition/common.hpp Decomposition/Decomposition.hpp  Decomposition/ie_ghost.hpp \

src/unit_test_init_cleanup.hpp

@@ -19,7 +19,7 @@ struct ut_start
     {
     	BOOST_TEST_MESSAGE("Initialize global VCluster");
 
-    	openfpm_init(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
+    	openfpm_init(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv,init_options::in_situ_visualization);
 
 #ifdef PERFORMANCE_TEST
     	test_dir = getenv("OPENFPM_PERFORMANCE_TEST_DIR");