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Sbalzarini Lab
S
Software
P
Parallel Computing
OpenFPM
openfpm_pdata
Commits
d6289937
Commit
d6289937
authored
Mar 12, 2018
by
incardon
Browse files
Fixing taurus run
parent
2f275c11
Changes
10
Hide whitespace changes
Inline
Side-by-side
run.sh
View file @
d6289937
...
...
@@ -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
View file @
d6289937
...
...
@@ -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
View file @
d6289937
...
...
@@ -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.
h
pp
→
src/Grid/
tests/
grid_dist_id_HDF5_chckpnt_restart_test.
c
pp
View file @
d6289937
...
...
@@ -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
View file @
d6289937
#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
View file @
d6289937
...
...
@@ -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
View file @
d6289937
...
...
@@ -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.
h
pp
→
src/Grid/
tests/
staggered_grid_dist_unit_test.
c
pp
View file @
d6289937
...
...
@@ -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
View file @
d6289937
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
View file @
d6289937
...
...
@@ -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"
...
...
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