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openfpm_pdata
Commit 49f7ef9c authored by incardon's avatar incardon
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merging with master

parents d0fb3919 34449ccd
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Showing with 98 additions and 36 deletions
CMakeLists.txt
View file @ 49f7ef9c
......@@ -7,6 +7,10 @@ endif ()
enable_testing()
if (POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake_modules/)
set(BOOST_INCLUDE ${Boost_INCLUDE_DIR} CACHE PATH "Include directory for BOOST")
......@@ -208,6 +212,7 @@ file(WRITE cuda_lib "${CUDA_cudart_static_LIBRARY} ${CUDA_cudadevrt_LIBRARY}")
file(WRITE cuda_include "-I${CUDA_INCLUDE_DIRS}")
file(WRITE mpi_include "-I${MPI_C_INCLUDE_DIRS}")
file(WRITE mpi_libs "${MPI_C_LINK_FLAGS} ${MPI_C_LIBRARIES}")
file(WRITE cuda_suppress_wr "${WARNING_SUPPRESSION_AND_OPTION_NVCC_TEXT}")
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/src/config/config_cmake.h.in ${CMAKE_CURRENT_SOURCE_DIR}/src/config/config.h)
......
Jenkinsfile_numerics_mpi
View file @ 49f7ef9c
......@@ -29,13 +29,16 @@ parallel (
stage ('run centos')
{
parallel (
"1" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 1 0 0 numerics"},
"2" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 2 0 0 numerics"},
"3" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 3 0 0 numerics"},
"4" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 4 0 0 numerics"}
)
timeout(30)
{
parallel (
"1" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 1 0 0 numerics"},
"2" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 2 0 0 numerics"},
"3" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 3 0 0 numerics"},
"4" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 4 0 0 numerics"}
)
sh "./success.sh 2 gin openfpm_numerics"
}
}
}
},
......@@ -70,9 +73,12 @@ parallel (
stage ('run mac')
{
sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 1 0 0 numerics"
sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 2 0 0 numerics"
sh "./success.sh 2 sbalzarini-mac-15 openfpm_numerics"
timeout(30)
{
sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 1 0 0 numerics"
sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 2 0 0 numerics"
sh "./success.sh 2 sbalzarini-mac-15 openfpm_numerics"
}
}
}
},
......@@ -104,13 +110,16 @@ parallel (
stage ('run ubuntu')
{
parallel (
"1" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 1 0 0 numerics"},
"2" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 2 0 0 numerics"},
"3" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 3 0 0 numerics"},
"4" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 4 0 0 numerics"}
)
sh "./success.sh 2 gin openfpm_numerics"
timeout(30)
{
parallel (
"1" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 1 0 0 numerics"},
"2" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 2 0 0 numerics"},
"3" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 3 0 0 numerics"},
"4" : {sh "cd openfpm_numerics && ./run.sh $WORKSPACE $NODE_NAME 4 0 0 numerics"}
)
sh "./success.sh 2 gin openfpm_numerics"
}
}
}
}
......
configure
View file @ 49f7ef9c
#!/bin/sh
#!/bin/bash
# configure script
#
#
......@@ -126,6 +126,8 @@ if [ ! -d "build" ]; then
mkdir build
fi
echo "/usr/local" > install_dir
##### Go over all options
for ac_option
do
......
example/Vector/1_gpu_first_step/main.cu
View file @ 49f7ef9c
......@@ -112,6 +112,9 @@
#define OPENMPI
//! \cond [using_openmpi] \endcond
//#define SCAN_WITH_CUB <------ MODERNGPU is broken on RTX use CUB library for scan
//#define EXTERNAL_SET_GPU <----- In case you want to distribute the GPUs differently from the default
#include "Vector/vector_dist.hpp"
//! \cond [kernel_translate_fill_prop] \endcond
......@@ -139,6 +142,20 @@ __global__ void translate_fill_prop(vector_type vd)
int main(int argc, char* argv[])
{
// OpenFPM GPU distribution
// OpenFPM by default select GPU 0 for process 0, gpu 1 for process 1 and so on ... . In case of multi-node is the same each node has
// has a group of processes and these group of processes are distributed across the available GPU on that node.
// If you want to override this behaviour use #define EXTERNAL_SET_GPU at the very beginning of the program and use
// cudaSetDevice to select the GPU for that particular process before openfpm_init
// Note: To get the process number do MPI_Init and and use the MPI_Comm_rank. VCluster is not available before openfpm_init
// A code snippet in case we want to skip GPU 0
// MPI_Init(&argc,&argv);
// int rank;
// MPI_Comm_rank(MPI_COMM_WORLD,&rank);
// cudaSetDevice(1+rank);
//! \cond [cpu_like_gpu] \endcond
// initialize the library
......
example/Vector/7_SPH_dlb/main.cpp
View file @ 49f7ef9c
......@@ -949,7 +949,7 @@ inline void sensor_pressure(Vector & vd,
}
// Get the position of the neighborhood particle q
Point<3,double> xq = vd.template getPos(q);
Point<3,double> xq = vd.getPos(q);
// Calculate the contribution of the particle to the pressure
// of the probe
......
example/Vector/7_SPH_dlb_gpu_opt/main.cu
View file @ 49f7ef9c
......@@ -40,11 +40,13 @@
#ifdef __NVCC__
#define PRINT_STACKTRACE
#define STOP_ON_ERROR
//#define STOP_ON_ERROR
#define OPENMPI
//#define SE_CLASS1
//#define USE_LOW_REGISTER_ITERATOR
//#define SCAN_WITH_CUB <------ In case you want to use CUB for scan operations
//#define EXTERNAL_SET_GPU <----- In case you want to distribute the GPUs differently from the default
#include "Vector/vector_dist.hpp"
#include <math.h>
......@@ -701,6 +703,20 @@ inline void sensor_pressure(Vector & vd,
int main(int argc, char* argv[])
{
// OpenFPM GPU distribution
// OpenFPM by default select GPU 0 for process 0, gpu 1 for process 1 and so on ... . In case of multi-node is the same each node has
// has a group of processes and these group of processes are distributed across the available GPU on that node.
// If you want to override this behaviour use #define EXTERNAL_SET_GPU at the very beginning of the program and use
// cudaSetDevice to select the GPU for that particular process before openfpm_init
// Note: To get the process number do MPI_Init and and use the MPI_Comm_rank. VCluster is not available before openfpm_init
// A code snippet in case we want to skip GPU 0
// MPI_Init(&argc,&argv);
// int rank;
// MPI_Comm_rank(MPI_COMM_WORLD,&rank);
// cudaSetDevice(1+rank);
// initialize the library
openfpm_init(&argc,&argv);
......
images/CMakeLists.txt
View file @ 49f7ef9c
......@@ -39,32 +39,32 @@ include_directories (${LIBHILBERT_INCLUDE_DIRS})
target_link_libraries(cart_dec ${Boost_LIBRARIES})
target_link_libraries(cart_dec -L${PARMETIS_ROOT}/lib parmetis)
target_link_libraries(cart_dec -L${METIS_ROOT}/lib metis)
target_link_libraries(cart_dec -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
#target_link_libraries(cart_dec ${HDF5_LIBRARIES})
#target_link_libraries(cart_dec -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
target_link_libraries(cart_dec ${HDF5_LIBRARIES})
target_link_libraries(cart_dec -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(cart_dec ${MPI_C_LIBRARIES})
target_link_libraries(metis_dec ${Boost_LIBRARIES})
target_link_libraries(metis_dec -L${PARMETIS_ROOT}/lib parmetis)
target_link_libraries(metis_dec -L${METIS_ROOT}/lib metis)
target_link_libraries(metis_dec -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
#target_link_libraries(metis_dec ${HDF5_LIBRARIES})
#target_link_libraries(metis_dec -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
target_link_libraries(metis_dec ${HDF5_LIBRARIES})
target_link_libraries(metis_dec -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(metis_dec ${MPI_C_LIBRARIES})
target_link_libraries(dom_box ${Boost_LIBRARIES})
target_link_libraries(dom_box -L${PARMETIS_ROOT}/lib parmetis)
target_link_libraries(dom_box -L${METIS_ROOT}/lib metis)
target_link_libraries(dom_box -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
#target_link_libraries(dom_box ${HDF5_LIBRARIES})
#target_link_libraries(dom_box -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
target_link_libraries(dom_box ${HDF5_LIBRARIES})
target_link_libraries(dom_box -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(dom_box ${MPI_C_LIBRARIES})
target_link_libraries(vector_dist ${Boost_LIBRARIES})
target_link_libraries(vector_dist -L${PARMETIS_ROOT}/lib parmetis)
target_link_libraries(vector_dist -L${METIS_ROOT}/lib metis)
target_link_libraries(vector_dist -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
#target_link_libraries(vector_dist ${HDF5_LIBRARIES})
#target_link_libraries(vector_dist -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
target_link_libraries(vector_dist ${HDF5_LIBRARIES})
target_link_libraries(vector_dist -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(vector_dist ${MPI_C_LIBRARIES})
......
install
View file @ 49f7ef9c
......@@ -434,7 +434,12 @@ else
echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $lin_alg_lib -ldl" >> example.mk
echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $lin_alg_lib" >> example.mk
fi
<<<<<<< HEAD
echo "INCLUDE_PATH_NVCC=-Xcompiler="-Wno-deprecated-declarations" $(cat openmp_flags) "$(cat cuda_options)" -I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/PARMETIS/include -I$i_dir/BOOST/include -I$i_dir/HDF5/include -I$i_dir/LIBHILBERT/include $lin_alg_inc" >> example.mk
=======
sup_cuda_wr=$(cat cuda_suppress_wr)
echo "INCLUDE_PATH_NVCC=-Xcompiler="-Wno-deprecated-declarations" $(cat openmp_flags) $sup_cuda_wr --expt-extended-lambda -I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/PARMETIS/include -I$i_dir/BOOST/include -I$i_dir/HDF5/include -I$i_dir/LIBHILBERT/include $lin_alg_inc" >> example.mk
>>>>>>> master
cp example.mk src/example.mk
cp example.mk example/example.mk
......
script/update_openfpm
View file @ 49f7ef9c
#! /bin/bash
source script/show_solutions
......@@ -46,7 +45,7 @@ function update_openfpm()
git stash -u
git submodule foreach 'git stash'
git pull origin master
git pull --no-edit origin master
else
#### New version require new version of CMAKE
......@@ -89,26 +88,33 @@ function update_openfpm()
if [ x"$1" == x"update" -a x"$force_up" == x"" ]; then
source $HOME/openfpm_vars
sh autogen.sh
./config.status
# Reconfigure
conf_command=$(cat config.log)
$conf_command
if [ $? -ne 0 ]; then
echo -e "Update summary\033[91;5;1m FAILED \033[0m"
return
fi
make
if [ $? -ne 0 ]; then
echo -e "Update summary\033[91;5;1m FAILED \033[0m"
return
else
echo -e "Update summary\033[92;5;1m SUCCEED \033[0m"
echo -e "To make the update active do: \033[1m make install \033[0m"
return
fi
else
#### Remove .deps for fresh install
./install $dir_prev_inst $for_opt
if [ $? -ne 0 ]; then
echo -e "Upgrade summary\033[91;5;1m FAILED \033[0m"
return
else
echo -e "Upgrade summary\033[92;5;1m SUCCEED \033[0m"
echo -e "To make the upgrade active do: \033[1m make install \033[0m"
rm force_upgrade
return
fi
fi
......
src/CMakeLists.txt
View file @ 49f7ef9c
......@@ -91,7 +91,7 @@ target_include_directories (pdata PUBLIC ${Boost_INCLUDE_DIRS})
target_link_libraries(pdata ${Boost_LIBRARIES})
target_link_libraries(pdata ${PARMETIS_LIBRARIES})
target_link_libraries(pdata -L${METIS_ROOT}/lib metis)
target_link_libraries(pdata -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
target_link_libraries(pdata ${HDF5_LIBRARIES})
target_link_libraries(pdata -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(pdata ${PETSC_LIBRARIES})
target_link_libraries(pdata ${Vc_LIBRARIES})
......
src/Vector/cuda/vector_dist_cuda_func_test.cu
View file @ 49f7ef9c
......@@ -11,6 +11,7 @@
#include "util/cuda/scan_cuda.cuh"
#include "util/cuda/moderngpu/kernel_scan.hxx"
#include "Vector/vector_dist.hpp"
#include "util/cuda/scan_ofp.cuh"
#define SUB_UNIT_FACTOR 1024
......
src/Vector/tests/vector_dist_cell_list_tests.cpp
View file @ 49f7ef9c
......@@ -1991,9 +1991,9 @@ void test_vector_dist_particle_NN_MP_iteration()
{
auto key = it.get();
vd.template getPosWrite(key)[0] = ud(eg);
vd.template getPosWrite(key)[1] = ud(eg);
vd.template getPosWrite(key)[2] = ud(eg);
vd.getPosWrite(key)[0] = ud(eg);
vd.getPosWrite(key)[1] = ud(eg);
vd.getPosWrite(key)[2] = ud(eg);
// Fill some properties randomly
......
src/Vector/vector_dist_comm.hpp
View file @ 49f7ef9c
......@@ -19,6 +19,7 @@
#include "Vector/util/vector_dist_funcs.hpp"
#include "cuda/vector_dist_comm_util_funcs.cuh"
#include "util/cuda/scan_ofp.cuh"
constexpr int NO_POSITION = 1;
constexpr int WITH_POSITION = 2;
......
update
View file @ 49f7ef9c
http://openfpm.mpi-cbg.de/upload/update_110
http://openfpm.mpi-cbg.de/upload/update_200
upgrade
View file @ 49f7ef9c
openfpm.mpi-cbg.de/upload/upgrade_110
openfpm.mpi-cbg.de/upload/upgrade_210
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