Fixing taurus run

run.sh

@@ -37,11 +37,8 @@ then
 
  source /etc/profile
  echo "$PATH"
- module load eigen/3.2.0
- module load suitesparse/4.2.1-gnu-multimkl
- module load boost/1.60.0
- module load gcc/5.3.0
- module load openmpi/1.10.2-gnu
+ module load gcc/5.5.0
+ module load openmpi/3.0.0-gnu5.5
  module unload bullxmpi
 
  if [ x"$6" != x"" ]; then

src/Decomposition/CartDecomposition_ext.hpp

@@ -8,6 +8,11 @@
 #ifndef SRC_DECOMPOSITION_CARTDECOMPOSITION_EXT_HPP_
 #define SRC_DECOMPOSITION_CARTDECOMPOSITION_EXT_HPP_
 
+#include "memory/HeapMemory.hpp"
+#include "Decomposition/Distribution/ParMetisDistribution.hpp"
+#include "Space/Ghost.hpp"
+#include "Decomposition/nn_processor.hpp"
+
 template<unsigned int dim, typename T, typename Memory = HeapMemory, typename Distribution = ParMetisDistribution<dim, T>>
 class CartDecomposition;
 

src/Decomposition/Distribution/ParMetisDistribution.hpp

@@ -13,6 +13,7 @@
 #include "SubdomainGraphNodes.hpp"
 #include "parmetis_util.hpp"
 #include "Graph/ids.hpp"
+#include "Graph/CartesianGraphFactory.hpp"
 
 #define PARMETIS_DISTRIBUTION_ERROR 100002
 

src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp → src/Grid/tests/grid_dist_id_HDF5_chckpnt_restart_test.cpp

@@ -5,8 +5,8 @@
  *      Author: Yaroslav Zaluzhnyi
  */
 
-#ifndef SRC_GRID_GRID_DIST_ID_HDF5_CHCKPNT_RESTART_TEST_HPP_
-#define SRC_GRID_GRID_DIST_ID_HDF5_CHCKPNT_RESTART_TEST_HPP_
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
 
 #include "Grid/grid_dist_id.hpp"
 
@@ -147,4 +147,3 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
 
 BOOST_AUTO_TEST_SUITE_END()
 
-#endif /* SRC_GRID_GRID_DIST_ID_HDF5_CHCKPNT_RESTART_TEST_HPP_ */

src/Grid/grid_dist_id_unit_test.cpp → src/Grid/tests/grid_dist_id_unit_test.cpp

+
 #define BOOST_TEST_DYN_LINK
 #include <boost/test/unit_test.hpp>
 
 #include "Point_test.hpp"
-#include "grid_dist_id.hpp"
+#include "Grid/grid_dist_id.hpp"
 #include "data_type/aggregate.hpp"
+#include "grid_dist_id_unit_test_ext_dom.hpp"
+#include "grid_dist_id_unit_test_unb_ghost.hpp"
 
 extern void print_test_v(std::string test, size_t sz);
 
@@ -1665,9 +1668,6 @@ void Test_ghost_correction(Box<3,double> & domain, long int k, long int g_)
     BOOST_REQUIRE_EQUAL(is_inside,true);
 }
 
-#include "grid_dist_id_unit_test_ext_dom.hpp"
-#include "grid_dist_id_unit_test_unb_ghost.hpp"
-
 BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
 {
 	// Domain

src/Grid/grid_dist_id_unit_test_ext_dom.hpp → src/Grid/tests/grid_dist_id_unit_test_ext_dom.hpp

@@ -4,11 +4,10 @@
  *  Created on: Feb 24, 2016
  *      Author: i-bird
  */
-
-#ifndef SRC_GRID_GRID_DIST_ID_UNIT_TEST_EXT_DOM_HPP_
-#define SRC_GRID_GRID_DIST_ID_UNIT_TEST_EXT_DOM_HPP_
-
 #include "Decomposition/CartDecomposition_ext.hpp"
+#include "Grid/grid_dist_id.hpp"
+
+extern void print_test_v(std::string test, size_t sz);
 
 // Test duplicated topology
 
@@ -147,5 +146,3 @@ void Test3D_extended_grid(const Box<3,float> & domain, long int k)
 	}
 }
 
-
-#endif /* SRC_GRID_GRID_DIST_ID_UNIT_TEST_EXT_DOM_HPP_ */

src/Grid/grid_dist_id_unit_test_unb_ghost.hpp → src/Grid/tests/grid_dist_id_unit_test_unb_ghost.hpp

@@ -5,9 +5,6 @@
  *      Author: i-bird
  */
 
-#ifndef SRC_GRID_GRID_DIST_ID_UNIT_TEST_UNB_GHOST_HPP_
-#define SRC_GRID_GRID_DIST_ID_UNIT_TEST_UNB_GHOST_HPP_
-
 void Test3D_unb_ghost(const Box<3,float> & domain, long int k)
 {
 	long int big_step = k / 30;
@@ -267,4 +264,3 @@ void Test3D_unb_ghost_periodic(const Box<3,float> & domain, long int k)
 }
 
 
-#endif /* SRC_GRID_GRID_DIST_ID_UNIT_TEST_UNB_GHOST_HPP_ */

src/Grid/staggered_grid_dist_unit_test.hpp → src/Grid/tests/staggered_grid_dist_unit_test.cpp

@@ -5,10 +5,10 @@
  *      Author: i-bird
  */
 
-#ifndef SRC_GRID_STAGGERED_GRID_DIST_UNIT_TEST_HPP_
-#define SRC_GRID_STAGGERED_GRID_DIST_UNIT_TEST_HPP_
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
 
-#include "staggered_dist_grid.hpp"
+#include "Grid/staggered_dist_grid.hpp"
 #include "Point_test.hpp"
 
 BOOST_AUTO_TEST_SUITE( staggered_grid_dist_id_test )
@@ -55,4 +55,3 @@ BOOST_AUTO_TEST_CASE( staggered_grid_dist_unit_test)
 
 BOOST_AUTO_TEST_SUITE_END()
 
-#endif /* SRC_GRID_STAGGERED_GRID_DIST_UNIT_TEST_HPP_ */

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) $(PARMETIS_LIB) $(BOOST_UNIT_TEST_FRAMEWORK_LIB) $(BOOST_CHRONO_LIB) $(BOOST_TIMER_LIB) $(BOOST_SYSTEM_LIB) $(LIBIFCORE)
 
 noinst_PROGRAMS = pdata
-pdata_SOURCES = main.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 Grid/grid_dist_id_unit_test.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_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  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 = $(HDF5_CPPFLAGS) $(OPENMP_CFLAGS) $(AM_CXXFLAGS) $(LIBHILBERT_INCLUDE) $(PETSC_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) $(H5PART_INCLUDE) -DPARALLEL_IO  -Wno-unused-local-typedefs
 pdata_CFLAGS = $(CUDA_CFLAGS)
 pdata_LDADD = $(LINKLIBS) -lparmetis -lmetis

src/main.cpp

@@ -45,14 +45,12 @@ int main(int argc, char* argv[])
 #include "Decomposition/ORB_unit_test.hpp"
 #include "Decomposition/Distribution/metis_util_unit_test.hpp"
 #include "Decomposition/dec_optimizer_unit_test.hpp"
-#include "Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp"
 #include "Decomposition/Distribution/Distribution_unit_tests.hpp"
 #include "Grid/Iterators/grid_dist_id_iterators_unit_tests.hpp"
 //#include "DLB/DLB_unit_test.hpp"
 #include "Graph/dist_map_graph_unit_test.hpp"
 #include "Graph/DistGraphFactory.hpp"
 #include "Decomposition/nn_processor_unit_test.hpp"
-#include "Grid/staggered_grid_dist_unit_test.hpp"
 #include "Vector/se_class3_vector_unit_tests.hpp"
 #include "Vector/vector_dist_dlb_test.hpp"
 #include "Decomposition/Domain_NN_calculator_cart_unit_test.hpp"