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  • mosaic/software/parallel-computing/openfpm/openfpm_pdata
  • argupta/openfpm_pdata
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.gitignore
View file @ b9ccc50e
......@@ -25,6 +25,7 @@
*.log
*.sql
*.sqlite
*.xml
# OS generated files #
######################
......@@ -36,40 +37,42 @@
ehthumbs.db
Thumbs.db
# CLion IDE-related
.idea/
cmake-build-debug/
cmake-build-release/
# Script-generated build folder
build/
###### Other
AUTHORS
COPYING
INSTALL
NEWS
README
**/vtk/Makefile
**/src/Makefile
./Makefile
Makefile.in
config.status
configure
numerics
Makefile
**/.deps
**/src/config
aclocal.m4
**/autom4te.cache
example.mk
src/pdata
vtk/cart_dec
vtk/dom_box
vtk/metis_dec
.autotools
.cproject
.project
.settings
ar-lib
compile
config.guess
config.sub
depcomp
install-sh
missing
install_dir
**/*.vtk
!**/test_data/*.vtk
*.csv
*.h5
*.json
*.html
Makefile
/build
*CMake*
*cmake*
**/*cmake*
**/*CMake*
**/.gitignore
.gitignore
/doxygen/
.gitmodules deleted 100644 → 0
View file @ 42321812
[submodule "openfpm_vcluster"]
path = openfpm_vcluster
url = ssh://git@ppmcore.mpi-cbg.de/incardon/openfpm_vcluster.git
[submodule "openfpm_devices"]
path = openfpm_devices
url = ssh://git@ppmcore.mpi-cbg.de/incardon/openfpm_devices.git
[submodule "openfpm_io"]
path = openfpm_io
url = ssh://git@ppmcore.mpi-cbg.de/incardon/openfpm_io.git
[submodule "openfpm_data"]
path = openfpm_data
url = ssh://git@ppmcore.mpi-cbg.de/incardon/openfpm_data.git
[submodule "openfpm_numerics"]
path = openfpm_numerics
url = ssh://git@ppmcore.mpi-cbg.de/incardon/openfpm_numerics.git
CHANGELOG.md deleted 100644 → 0
View file @ 42321812
# Change Log
All notable changes to this project will be documented in this file.
## [0.4.0] -
### Added
- Grid with periodic boundary conditions
- VTK Writer for distributed grid, now is the default writer
### Fixed
- GPU compilation
### Changed
## [0.3.0] - 16-04-2016
### Added
- Molacular Dynamic example
- addUpdateCell list for more optimal update of the cell list instead of recreate the CellList
### Fixed
- Nothing to report
### Changed
- Eliminated global_v_cluster, init_global_v_cluster, delete_global_v_cluster,
substituted by
create_vcluster, openfpm_init, openfpm_finalize
- CartDecomposition parameter for the distributed structures is now optional
- template getPos<0>(), substituted by getPos()
## [0.2.1] - 01-04-2016
### Changed
- GoogleChart name function changed: AddPointGraph to AddLinesGraph and AddColumsGraph to AddHistGraph
## [0.2.0] - 2016-03-25
### Added
- Added Load Balancing and Dynamic Load Balancing on Beta
- PSE 1D example with multiple precision
- Plot example for GoogleChart plotting
- Distributed data structure now support 128bit floating point precision (on Beta)
### Fixed
- Detection 32 bit system and report as an error
- Bug in rounding off for periodic boundary condition
### Changed
- Nothing to report
## [0.1.0] - 2016-02-05
### Added
- PSE 1D example
- Cell list example
- Verlet list example
- Kickstart for OpenFPM_numeric
- Automated dependency installation for SUITESPRASE EIGEN OPENBLAS(LAPACK)
### Fixed
- CRITICAL BUG in periodic bondary condition
- BOOST auto updated to 1.60
- Compilation with multiple .cpp files
### Changed
- Nothing to report
CMakeLists.txt 0 → 100644
View file @ b9ccc50e
cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
project(openfpm_pdata LANGUAGES C CXX)
if (POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
set(openfpm_VERSION 5.0.0)
if (METIS_FOUND)
set(DEFINE_HAVE_METIS "#define HAVE_METIS 1")
else()
message( FATAL_ERROR "Metis is required in order to install OpenFPM" )
endif()
if (PARMETIS_FOUND)
set(DEFINE_HAVE_PARMETIS "#define HAVE_PARMETIS 1")
else()
message( FATAL_ERROR "ParMetis is required in order to install OpenFPM")
endif()
add_subdirectory (src)
file(READ ${CMAKE_CURRENT_SOURCE_DIR}/src/cmake/openfpmConfig-configure.cmake CMAKE_OPENFPM_CONFIG_VARS)
set(CMAKE_OPENFPM_CONFIG_VARS "${CMAKE_OPENFPM_CONFIG_VARS}\nmessage(STATUS \"Found OpenFPM version ${openfpm_VERSION} (\$\{CMAKE_CURRENT_LIST_FILE\})\")")
set(CMAKE_OPENFPM_CONFIG_VARS "${CMAKE_OPENFPM_CONFIG_VARS}\nset(OPENFPM_CUDA_ON_BACKEND \"${CUDA_ON_BACKEND}\")")
file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/src/cmake/openfpmConfig-Vars.cmake "${CMAKE_OPENFPM_CONFIG_VARS}")
get_directory_property(hasParent PARENT_DIRECTORY)
if(hasParent)
set(DEFINE_HAVE_METIS ${DEFINE_HAVE_METIS} CACHE INTERNAL "")
set(DEFINE_HAVE_PARMETIS ${DEFINE_HAVE_PARMETIS} CACHE INTERNAL "")
endif()
Makefile.am deleted 100644 → 0
View file @ 42321812
SUBDIRS = src images openfpm_data openfpm_io openfpm_devices openfpm_vcluster openfpm_numerics
bin_PROGRAMS =
autogen.sh deleted 100644 → 0
View file @ 42321812
This diff is collapsed.
build_pdata.sh deleted 100644 → 0
View file @ 42321812
#! /bin/bash
# Make a directory in /tmp/OpenFPM_pdata
echo "Directory: $1"
echo "Machine: $2"
mkdir src/config
git submodule init
if [ $? -ne 0 ]; then
echo -e "Configure\033[91;5;1m FAILED \033[0m"
exit 1
fi
git submodule update
if [ $? -ne 0 ]; then
echo -e "Configure\033[91;5;1m FAILED \033[0m"
exit 1
fi
mkdir openfpm_numerics/src/config
# pull from all the projects
cd openfpm_data
git checkout develop
mkdir src/config
git pull origin develop
if [ $? -ne 0 ]; then
echo -e "Configure\033[91;5;1m FAILED \033[0m"
exit 1
fi
cd ..
cd openfpm_devices
mkdir src/config
git pull origin master
if [ $? -ne 0 ]; then
echo -e "Configure\033[91;5;1m FAILED \033[0m"
exit 1
fi
cd ..
cd openfpm_vcluster
mkdir src/config
git pull origin master
if [ $? -ne 0 ]; then
echo -e "Configure\033[91;5;1m FAILED \033[0m"
exit 1
fi
cd ..
cd openfpm_io
mkdir src/config
git pull origin master
if [ $? -ne 0 ]; then
echo -e "Configure\033[91;5;1m FAILED \033[0m"
exit 1
fi
cd ..
if [ "$2" == "gin" ]
then
echo "Compiling on gin\n"
source ~/.bashrc
module load gcc/4.9.2
./install -s -c "--prefix=/home/jenkins/openfpm_install"
make
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
make install
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 2 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 3 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 4 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 5 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 6 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 7 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 8 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 9 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 10 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 11 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 12 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
elif [ "$2" == "wetcluster" ]
then
echo "Compiling on wetcluster"
## produce the module path
source ~/.bashrc
module load gcc/4.9.2
module load openmpi/1.8.1
module load boost/1.54.0
sh ./autogen.sh
./install -s -c "--with-boost=/sw/apps/boost/1.54.0/ CXX=mpic++"
make
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
## Run on the cluster
bsub -o output_run2.%J -K -n 2 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 2 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run3.%J -K -n 3 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 3 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run4.%J -K -n 4 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 4 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run5.%J -K -n 5 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 5 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run6.%J -K -n 6 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 6 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run7.%J -K -n 7 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 7 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run8.%J -K -n 8 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 8 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run9.%J -K -n 9 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 9 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run10.%J -K -n 10 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 10 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run11.%J -K -n 11 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 11 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
bsub -o output_run12.%J -K -n 12 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; module load boost/1.54.0; mpirun -np 12 ./src/pdata"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
# bsub -o output_run32.%J -K -n 32 "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 32 ./src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
# bsub -o output_run32.%J -K -n 64 "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 64 ./src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
# bsub -o output_run32.%J -K -n 128 "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 128 ./src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
elif [ "$2" == "taurus" ]
then
echo "Compiling on taurus"
source /etc/profile
echo "$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 unload bullxmpi
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/incard/PARMETIS/lib:/home/incard/METIS/lib:/home/incard/HDF5/lib"
./install -s -c"CXX=mpic++ --with-boost=/sw/taurus/libraries/boost/1.60.0"
make
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
salloc --nodes=1 --ntasks-per-node=24 --time=00:5:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 24 src/pdata --report_level=no"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
salloc --nodes=2 --ntasks-per-node=24 --time=00:5:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 48 src/pdata --report_level=no"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
salloc --nodes=4 --ntasks-per-node=24 --time=00:5:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 96 src/pdata --report_level=no"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
salloc --nodes=8 --ntasks-per-node=24 --time=00:5:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 192 src/pdata --report_level=no"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
salloc --nodes=10 --ntasks-per-node=24 --time=00:5:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 240 src/pdata --report_level=no"
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
else
echo "Compiling general"
source ~/.bashrc
./install -s
make
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 1 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 2 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 3 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
mpirun -np 4 ./src/pdata
if [ $? -ne 0 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
exit 1 ;
fi
fi
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Info:\", \"color\": \"#00FF00\", \"text\":\"$2 completed succeffuly the openfpm_pdata test \" }] }" https://hooks.slack.com/services/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
configure.ac deleted 100644 → 0
View file @ 42321812
# -*- Autoconf -*-
# Process this file with autoconf to produce a configure script.
## Take all the options with the exception of --enable-install-req
AC_PREREQ(2.59)
AC_INIT(FULL-PACKAGE-NAME, VERSION, BUG-REPORT-ADDRESS)
AC_CANONICAL_SYSTEM
AC_CONFIG_SRCDIR([src/main.cpp])
AC_CONFIG_SUBDIRS([openfpm_data openfpm_devices openfpm_vcluster openfpm_io openfpm_numerics])
#### Adding --with-pdata option and openfpm_pdata to prefix folder
if test "$prefix" = "NONE"; then
prefix=/usr/local
fi
base=$prefix
prefix="$prefix/openfpm_pdata"
echo "Installation dir is: $prefix"
ac_configure_args="$ac_configure_args --with-pdata=../../src"
########################
AM_INIT_AUTOMAKE([subdir-objects])
AC_CONFIG_HEADER([src/config/config.h])
m4_ifdef([ACX_PTHREAD],,[m4_include([m4/acx_pthread.m4])])
m4_ifdef([ACX_MPI],,[m4_include([m4/acx_mpi.m4])])
m4_ifdef([AX_OPENMP],,[m4_include([m4/ax_openmp.m4])])
m4_ifdef([AX_CUDA],,[m4_include([m4/ax_cuda.m4])])
m4_ifdef([IMMDX_LIB_METIS],,[m4_include([m4/immdx_lib_metis.m4])])
m4_ifdef([IMMDX_LIB_PARMETIS],,[m4_include([m4/immdx_lib_parmetis.m4])])
m4_ifdef([AX_BOOST_BASE],,[m4_include([m4/ax_boost_base.m4])])
m4_ifdef([AX_BOOST_IOSTREAMS],,[m4_include([m4/ax_boost_iostreams.m4])])
m4_ifdef([AX_BOOST_PROGRAM_OPTIONS],,[m4_include([m4/ax_boost_program_options.m4])])
m4_ifdef([AX_BOOST_UNIT_TEST_FRAMEWORK],,[m4_include([m4/ax_boost_unit_test_framework.m4])])
m4_ifdef([AX_BLAS],,[m4_include([m4/ax_blas.m4])])
m4_ifdef([AX_LAPACK],,[m4_include([m4/ax_lapack.m4])])
m4_ifdef([AX_SUITESPARSE],,[m4_include([m4/ax_suitesparse.m4])])
m4_ifdef([AX_EIGEN],,[m4_include([m4/ax_eigen.m4])])
m4_ifdef([AX_LIB_HDF5],,[m4_include([m4/ax_lib_hdf5.m4])]])
case $host_os in
*darwin*|*macosx*)
CXXFLAGS+=" --std=c++11 "
AC_DEFINE([HAVE_OSX],[],[We have OSX])
;;
*cygwin*)
# Do something specific for cygwin
CXXFLAGS+=" --std=gnu++11 "
;;
*)
#Default Case
CXXFLAGS+=" --std=c++11 "
;;
esac
NVCCFLAGS=" "
INCLUDES_PATH=" "
# Create a file with the install base folder
echo "$base" > install_dir
# Needed for build library
AC_PROG_RANLIB
AM_PROG_AR
# Checks for programs.
AC_PROG_CXX
# Checks g++ flags
AC_CANONICAL_HOST
# Check that the compiler support mpi
AC_LANG_PUSH([C++])
AC_CHECK_HEADER(mpi.h,[],[echo "mpi.h not found"
exit 200])
AC_LANG_POP([C++])
# Check target architetture
#AX_GCC_ARCHFLAG([], [CXXFLAGS="$CXXFLAGS $ax_cv_gcc_archflag"], [])
###### Check for debug compilation
AC_MSG_CHECKING(whether to build with debug information)
debuger=no
AC_ARG_ENABLE(debug,
AC_HELP_STRING(
[--enable-debug],
[enable debug data generation (def=no)]
),
debuger="$enableval"
)
AC_MSG_RESULT($debuger)
if test x"$debuger" = x"yes"; then
AC_DEFINE([DEBUG_MODE],[],[Debug])
AC_DEFINE([DEBUG],[],[Debug])
CXXFLAGS="$CXXFLAGS -g3 -Wall -O0 "
NVCCFLAGS+="$NVCCFLAGS -g -O0 "
else
CXXFLAGS="$CXXFLAGS -Wall -O3 -g3 -funroll-loops "
NVCCFLAGS+="$NVCCFLAGS -O3 "
fi
#########
## Check for Metis
IMMDX_LIB_METIS([],[echo "Cannot detect metis, use the --with-metis option if it is not installed in the default location"
exit 201])
#########
## Check for HDF5
AX_LIB_HDF5([parallel])
if test x"$with_hdf5" = x"no"; then
echo "Cannot detect hdf5, use the --with-hdf5 option if it is not installed in the default location"
exit 207
fi
########
## Enable scan coverty
AC_MSG_CHECKING(whether to build for scan coverty compilation)
AC_ARG_ENABLE(scan-coverty,
AC_HELP_STRING(
[--enable-scan-coverty],
[enable scan-coverty compilation (def=no)]
),
scancoverty="$enableval"
)
AC_MSG_RESULT($scancoverty)
if test x"$scancoverty" = x"yes"; then
AC_DEFINE([COVERTY_SCAN],[],[Compile for coverty scan])
fi
## Check for parMetis
IMMDX_LIB_PARMETIS([],[echo "Cannot detect parmetis, use the --with-parmetis option if it is not installed in the default location"
exit 208])
####### include OpenFPM_devices include path
INCLUDES_PATH+="-I. -Iconfig/ -I../openfpm_io/src -I../openfpm_data/src -I../openfpm_devices/src -I../openfpm_vcluster/src/"
###### Check for se-class1
AC_MSG_CHECKING(whether to build with security enhancement class1)
se_class1=no
AC_ARG_ENABLE(se-class1,
AC_HELP_STRING(
[--enable-se-class1],
[enable security enhancement class1]
),
se_class1="$enableval"
)
AC_MSG_RESULT($se_class1)
if test x"$se_class1" = x"yes"; then
AC_DEFINE([SE_CLASS1],[],[Security enhancement class 1])
fi
###### Check for se-class 2
AC_MSG_CHECKING(whether to build with security enhancement class 2)
se_class2=no
AC_ARG_ENABLE(se-class2,
AC_HELP_STRING(
[--enable-se-class2],
[enable security enhancement class 2]
),
se_class2="$enableval"
)
AC_MSG_RESULT($se_class2)
if test x"$se_class2" = x"yes"; then
AC_DEFINE([SE_CLASS2],[],[Security enhancement class 2])
fi
###### Check for se-class 3
AC_MSG_CHECKING(whether to build with security enhancement class 3)
se_class3=no
AC_ARG_ENABLE(se-class3,
AC_HELP_STRING(
[--enable-se-class3],
[enable security enhancement class 3]
),
se_class3="$enableval"
)
AC_MSG_RESULT($se_class3)
if test x"$se_class3" = x"yes"; then
AC_DEFINE([SE_CLASS3],[],[Security enhancement class 3])
fi
###### Check for action on error
action_on_e=continue
AC_ARG_WITH([action-on-error],
AS_HELP_STRING([--with-action-on-error=stop,throw,continue],
[specify the action to do in case of error]),
[action_on_e="$withval"],
[action_on_e=continue])
if test x"$action_on_e" = x"stop"; then
AC_DEFINE([STOP_ON_ERROR],[],[If an error occur stop the program])
fi
if test x"$action_on_e" = x"throw"; then
AC_DEFINE([THROW_ON_ERROR],[],[when an error accur continue but avoid unsafe operation])
fi
##### CHECK FOR BOOST ##############
AX_BOOST_BASE([1.52],[],[echo "boost not found"
exit 202])
AX_BOOST_UNIT_TEST_FRAMEWORK
AX_BOOST_PROGRAM_OPTIONS
AX_BOOST_IOSTREAMS
if test x"$ax_cv_boost_unit_test_framework" = x"no"; then
echo "Notify boost unit test framework not usable"
exit 202
fi
if test x"$ax_cv_boost_iostreams" = x"no"; then
echo "Notify boost iostream not usable"
exit 202
fi
if test x"$ax_cv_boost_programs_options" = x"no"; then
echo "Notify boost program options not usable"
exit 202
fi
### Unfortunately a lot of linux distros install a pretty old MPI in the system wide folder,
### override such MPI with the installed one is extremely difficult and tricky, because we want
### to include "some" system library but exclude mpi. One possibility is to give specifically
### the wanted libmpi.so directly to the linker. But this is not possible because this lib is
### given by mpic++ in the form -L/path/to/mpi -lmpi, the other is completely eliminate every
### -L with a system default library
###
# eliminate any /usr/lib and and /usr/include from $BOOST_LIB and $BOOST_INCLUDE
BOOST_LDFLAGS=$(echo "$BOOST_LDFLAGS" | sed -e 's/ -L\/usr\/lib64[ \b]//g' | sed -e 's/ -L\/usr\/lib[ \b]//g')
BOOST_CPPFLAGS=$(echo "$BOOST_CPPFLAGS" | sed -e 's/-I\/usr\/include[ \b]//g')
AC_SUBST(BOOST_LDFLAGS)
AC_SUBST(BOOST_CPPFLAGS)
###### Checking for OpenBLAS
AX_BLAS([],[echo "blas not found"
exit 204])
AX_LAPACK([],[echo "lapack not found"
exit 204])
###### Checking for SUITESPARSE
AX_SUITESPARSE([],[echo "suitesparse not found"
exit 205])
###### Checking for EIGEN
AX_EIGEN([],[echo "eigen not found"
exit 206])
###### RT runtime lib
AC_CHECK_LIB(rt, clock_gettime, [AC_DEFINE([HAVE_CLOCK_GETTIME],[],[Have clock time])
OPT_LIBS="$OPT_LIBS -lrt"
])
####### Checking for GPU support
AX_CUDA
## detect for NVCC
if test x"$NVCC_EXIST" = x"yes"; then
AC_MSG_CHECKING(whether to build with GPU support)
gpu_support=yes
AC_ARG_ENABLE(gpu,
AC_HELP_STRING(
[--enable-gpu],
[enable gpu support]
),
gpu_support="$enableval"
)
AC_MSG_RESULT($gpu_support)
if test x"$gpu_support" = x"yes"; then
AC_DEFINE([GPU],[],[GPU support])
else
CUDA_LIBS=""
CUDA_CFLAGS=""
fi
else
gpu_support=no
fi
if test x$gpu_support = x"no"; then
CUDA_LIBS=""
CUDA_CFLAGS=""
fi
# Set this conditional if cuda is wanted
AM_CONDITIONAL(BUILDCUDA, test ! x$NVCC = x"no")
###########################
# Define that there is MPI
AC_DEFINE([HAVE_MPI],[],[MPI Enabled])
AC_SUBST(NVCCFLAGS)
AC_SUBST(INCLUDES_PATH)
AC_SUBST(OPT_LIBS)
# Checks for typedefs, structures, and compiler characteristics.
# Checks for library functions.
AC_CONFIG_FILES([Makefile src/Makefile images/Makefile ])
AC_OUTPUT
echo ""
echo "***********************************"
echo "* *"
if [ test x"$profiler" = x"yes" ]; then
echo "* profiler: yes *"
else
echo "* profiler: no *"
fi
if [ test x"$memcheck" = x"yes" ]; then
echo "* memcheck: yes *"
else
echo "* memcheck: no *"
fi
if [ test x"$debuger" = x"yes" ]; then
echo "* debug: yes *"
else
echo "* debug: no *"
fi
if [ test x"$se_class1" = x"yes" ]; then
echo "* se-class1: yes *"
else
echo "* se-class1: no *"
fi
if [ test x"$se_class2" = x"yes" ]; then
echo "* se-class2: yes *"
else
echo "* se-class2: no *"
fi
if [ test x"$se_class3" = x"yes" ]; then
echo "* se-class3: yes *"
else
echo "* se-class3: no *"
fi
if [ test x"$gpu_support" = x"no" ]; then
echo "* gpu: no *"
else
echo "* gpu: yes *"
fi
echo "* *"
echo "***********************************"
example/Grid/0_simple/Makefile deleted 100644 → 0
View file @ 42321812
include ../../example.mk
CC=mpic++
LDIR =
OBJ = main.o
%.o: %.cpp
$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
grid: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
all: grid
.PHONY: clean all
clean:
rm -f *.o *~ core grid
example/Grid/0_simple/config.cfg deleted 100644 → 0
View file @ 42321812
[pack]
files = main.cpp Makefile
example/Grid/0_simple/main.cpp deleted 100644 → 0
View file @ 42321812
#include "Grid/grid_dist_id.hpp"
#include "data_type/aggregate.hpp"
#include "Decomposition/CartDecomposition.hpp"
/*
* ### WIKI 1 ###
*
* ## Simple example
*
* This example show several basic functionalities of the distributed grid
*
* ### WIKI END ###
*
*/
int main(int argc, char* argv[])
{
//
// ### WIKI 2 ###
//
// Initialize the library and several objects
//
openfpm_init(&argc,&argv);
//
// ### WIKI 3 ###
//
// Create
// * A 3D box that define the domain
// * an array of 3 unsigned integer that will define the size of the grid on each dimension
// * A Ghost object that will define the extension of the ghost part for each sub-domain in physical units
Box<3,float> domain({0.0,0.0,0.0},{1.0,1.0,1.0});
size_t sz[3];
sz[0] = 100;
sz[1] = 100;
sz[2] = 100;
// Ghost
Ghost<3,float> g(0.01);
//
// ### WIKI 4 ###
//
// Create a distributed grid in 3D (1° template parameter) space in with float precision (2° template parameter)
// each grid point contain a vector of dimension 3 (float[3]),
// using a CartesianDecomposition strategy (4° parameter) (the parameter 1° and 2° inside CartDecomposition must match 1° and 2°
// of grid_dist_id)
//
// Constructor parameters:
//
// * sz: size of the grid on each dimension
// * domain: where the grid is defined
// * g: ghost extension
//
grid_dist_id<3, float, aggregate<float[3]>> g_dist(sz,domain,g);
// ### WIKI 5 ###
//
// Get an iterator that go through the points of the grid (No ghost)
//
auto dom = g_dist.getDomainIterator();
// ### WIKI END ###
size_t count = 0;
// Iterate over all the points
while (dom.isNext())
{
//
// ### WIKI 6 ###
//
// Get the local grid key, the local grid key store internally the sub-domain id (each sub-domain contain a grid)
// and the local grid point id identified by 2 integers in 2D 3 integer in 3D and so on. These two distinct elements are
// available with key.getSub() and key.getKey()
//
auto key = dom.get();
//
// ### WIKI 7 ###
//
// Here we convert the local grid position, into global position, key_g contain 3 integers that identify the position
// of the grid point in global coordinates
//
//
auto key_g = g_dist.getGKey(key);
//
// ### WIKI 8 ###
//
// we write on the grid point of position (i,j,k) the value i*i + j*j + k*k on the component [0] of the vector
g_dist.template get<0>(key)[0] = key_g.get(0)*key_g.get(0) + key_g.get(1)*key_g.get(1) + key_g.get(2)*key_g.get(2);
// ### WIKI END ###
// Count the points
count++;
//
// ### WIKI 9 ###
//
// next point
++dom;
// ### WIKI END ###
}
//
// ### WIKI 10 ###
//
// Each sub-domain has an extended part, that is materially contained from another processor that in general is not synchronized
// ghost_get<0> synchronize the property 0 (the vector) in the ghost part
//
//
g_dist.template ghost_get<0>();
//
// ### WIKI 11 ###
//
// count contain the number of points the local processor contain, if we are interested to count the total number across the processor
// we can use the function add, to sum across processors. First we have to get an instance of Vcluster, queue an operation of add with
// the variable count and finally execute. All the operation are asynchronous, execute work like a barrier and ensure that all the
// queued operations are executed
//
Vcluster & vcl = g_dist.getVC();
vcl.sum(count);
vcl.execute();
// only master output
if (vcl.getProcessUnitID() == 0)
std::cout << "Number of points: " << count << "\n";
//
// ### WIKI 12 ###
//
// Finally we want a nice output to visualize the information stored by the distributed grid
//
g_dist.write("output");
//
// ### WIKI 13 ###
//
// For debugging purpose and demonstration we output the decomposition
//
g_dist.getDecomposition().write("out_dec");
//
// ### WIKI 14 ###
//
// Deinitialize the library
//
openfpm_finalize();
}
example/Grid/1_stencil/Makefile deleted 100644 → 0
View file @ 42321812
include ../../example.mk
CC=mpic++
LDIR =
OBJ = main.o
%.o: %.cpp
$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
stencil: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
all: stencil
.PHONY: clean all
clean:
rm -f *.o *~ core stencil
example/Grid/1_stencil/config.cfg deleted 100644 → 0
View file @ 42321812
[pack]
files = main.cpp Makefile
example/Grid/1_stencil/main.cpp deleted 100644 → 0
View file @ 42321812
#include "Grid/grid_dist_id.hpp"
#include "data_type/aggregate.hpp"
#include "Decomposition/CartDecomposition.hpp"
/*
* ### WIKI 1 ###
*
* ## Simple example
*
* This example show how to move grid_key in order to create a Laplacian stencil,
* be careful, the function move are convenient, but not the fastest implementation
*
* ### WIKI END ###
*
*/
/*
*
* ### WIKI 2 ###
*
* Define some convenient constants and types
*
*/
constexpr size_t x = 0;
constexpr size_t y = 1;
constexpr size_t z = 2;
constexpr size_t A = 0;
constexpr size_t B = 0;
typedef aggregate<float[3],float[3]> grid_point;
int main(int argc, char* argv[])
{
//
// ### WIKI 3 ###
//
// Initialize the library and several objects
//
openfpm_init(&argc,&argv);
//
// ### WIKI 4 ###
//
// Create several object needed later, in particular
// * A 3D box that define the domain
// * an array of 3 unsigned integer that define the size of the grid on each dimension
// * A Ghost object that will define the extension of the ghost part for each sub-domain in physical units
Box<3,float> domain({0.0,0.0,0.0},{1.0,1.0,1.0});
size_t sz[3];
sz[0] = 100;
sz[1] = 100;
sz[2] = 100;
// Ghost
Ghost<3,float> g(0.03);
//
// ### WIKI 4 ###
//
// Create a distributed grid in 3D (1° template parameter) space in with float precision (2° template parameter)
// each grid point contain a vector of dimension 3 (float[3]),
// using a CartesianDecomposition strategy (4° parameter) (the parameter 1° and 2° inside CartDecomposition must match 1° and 2°
// of grid_dist_id)
//
// Constructor parameters:
//
// * sz: size of the grid on each dimension
// * domain: where the grid is defined
// * g: ghost extension
//
grid_dist_id<3, float, grid_point> g_dist(sz,domain,g);
// ### WIKI 5 ###
//
// Get an iterator that go throught the point of the domain (No ghost)
//
auto dom = g_dist.getDomainIterator();
// ### WIKI END ###
while (dom.isNext())
{
//
// ### WIKI 6 ###
//
// Get the local grid key, the local grid key store internally the sub-domain id (each sub-domain contain a grid)
// and the local grid point id identified by 2 integers in 2D 3 integer in 3D and so on. These two distinct elements are
// available with key.getSub() and key.getKey()
//
auto key = dom.get();
//
// ### WIKI 7 ###
//
// Here we convert the local grid position, into global position, key_g contain 3 integers that identify the position
// of the grid point in global coordinates
//
//
auto key_g = g_dist.getGKey(key);
//
// ### WIKI 8 ###
//
// we write on the grid point of position (i,j,k) the value i*i + j*j + k*k on the component [0] of the vector
g_dist.template get<0>(key)[0] = key_g.get(0)*key_g.get(0) + key_g.get(1)*key_g.get(1) + key_g.get(2)*key_g.get(2);
//
// ### WIKI 9 ###
//
// next point
++dom;
// ### WIKI END ###
}
//
// ### WIKI 10 ###
//
// Each sub-domain has an extended part, that is materially contained from another processor that in general is not synchronized
// ghost_get<0> synchronize the property 0 (the vector) in the ghost part
//
//
g_dist.template ghost_get<0>();
//
// ### WIKI 11 ###
//
// Get again another iterator, iterate across all the domain points, calculating a Laplace stencil
//
//
auto dom2 = g_dist.getDomainIterator();
while (dom2.isNext())
{
auto key = dom2.get();
// Laplace stencil
g_dist.template get<B>(key)[1] = g_dist.template get<A>(key.move(x,1))[0] + g_dist.template get<A>(key.move(x,-1))[0] +
g_dist.template get<A>(key.move(y,1))[0] + g_dist.template get<A>(key.move(y,-1))[0] +
g_dist.template get<A>(key.move(z,1))[0] + g_dist.template get<A>(key.move(z,-1))[0] -
6*g_dist.template get<A>(key)[0];
++dom2;
}
//
// ### WIKI 12 ###
//
// Finally we want a nice output to visualize the information stored by the distributed grid
//
g_dist.write("output");
//
// ### WIKI 14 ###
//
// Deinitialize the library
//
openfpm_finalize();
}
example/Grid/Makefile deleted 100644 → 0
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SUBDIRS := $(wildcard */.)
all clean:
for dir in $(SUBDIRS); do \
$(MAKE) -C $$dir $@; \
done
clean: $(SUBDIRS)
.PHONY: all clean $(SUBDIRS)
example/Makefile deleted 100644 → 0
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SUBDIRS := $(wildcard */.)
all clean:
for dir in $(SUBDIRS); do \
$(MAKE) -C $$dir $@; \
done
clean: $(SUBDIRS)
.PHONY: all clean $(SUBDIRS)
example/Numerics/Agent_sim/main.cpp deleted 100644 → 0
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/*
* ### WIKI 1 ###
*
* ## Simple example
*
* In this example show an agent based simulation
*
* ### WIKI END ###
*
*/
#include "Vector/vector_dist.hpp"
#include "Decomposition/CartDecomposition.hpp"
#include "PSE/Kernels.hpp"
#include "Plot/util.hpp"
#include "Plot/GoogleChart.hpp"
#include "data_type/aggregate.hpp"
#include <cmath>
struct animal
{
typedef boost::fusion::vector<float[2], size_t, size_t, long int> type;
//! Attributes name
struct attributes
{
static const std::string name[];
};
//! type of the positional field
typedef float s_type;
//! The data
type data;
//! position property id in boost::fusion::vector
static const unsigned int pos = 0;
//! genre of animal property id in boost::fusion::vector
static const unsigned int genre = 1;
//! state property id in boost::fusion::vector
static const unsigned int status = 2;
//! alive time property id in boost::fusion::vector
static const unsigned int time_a = 3;
//! total number of properties boost::fusion::vector
static const unsigned int max_prop = 4;
animal()
{
}
inline animal(const animal & p)
{
boost::fusion::at_c<0>(data)[0] = boost::fusion::at_c<0>(p.data)[0];
boost::fusion::at_c<0>(data)[1] = boost::fusion::at_c<0>(p.data)[1];
//boost::fusion::at_c<0>(data)[2] = boost::fusion::at_c<0>(p.data)[2];
boost::fusion::at_c<1>(data) = boost::fusion::at_c<1>(p.data);
boost::fusion::at_c<2>(data) = boost::fusion::at_c<2>(p.data);
boost::fusion::at_c<3>(data) = boost::fusion::at_c<3>(p.data);
}
template<unsigned int id> inline auto get() -> decltype(boost::fusion::at_c < id > (data))
{
return boost::fusion::at_c<id>(data);
}
template<unsigned int id> inline auto get() const -> const decltype(boost::fusion::at_c < id > (data))
{
return boost::fusion::at_c<id>(data);
}
template<unsigned int dim, typename Mem> inline animal(const encapc<dim, animal, Mem> & p)
{
this->operator=(p);
}
template<unsigned int dim, typename Mem> inline animal & operator=(const encapc<dim, animal, Mem> & p)
{
boost::fusion::at_c<0>(data)[0] = p.template get<0>()[0];
boost::fusion::at_c<0>(data)[1] = p.template get<0>()[1];
//boost::fusion::at_c<0>(data)[2] = p.template get<0>()[2];
boost::fusion::at_c<1>(data) = p.template get<1>();
boost::fusion::at_c<2>(data) = p.template get<2>();
boost::fusion::at_c<3>(data) = p.template get<3>();
return *this;
}
static bool noPointers()
{
return true;
}
};
const std::string animal::attributes::name[] = { "pos", "genre", "status", "time_a", "j_repr" };
int main(int argc, char* argv[])
{
init_global_v_cluster(&argc,&argv);
Vcluster & v_cl = *global_v_cluster;
//time the animal stays alive without eating
size_t PRED_TIME_A = 14;
size_t PREY_TIME_A = 7;
size_t PREDATOR = 1, PREY = 0;
size_t ALIVE = 1, DEAD = 0;
// Predators reproducing probability
float PRED_REPR = 0.2;
// Predators eating probability
float PRED_EAT = 0.6;
// Prey reproducing probability
float PREY_REPR = 0.5;
// set the seed
// create the random generator engine
std::srand(v_cl.getProcessUnitID());
unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
std::default_random_engine eg(seed);
std::uniform_real_distribution<float> ud(0.0f, 1.0f);
std::uniform_real_distribution<float> md(-1.0f, 1.0f);
std::uniform_real_distribution<float> uc(0.0f, 0.7f);
std::uniform_real_distribution<float> lc(0.3f, 1.0f);
size_t k = 100000;
Box<2, float> box( { 0.0, 0.0 }, { 1.0, 1.0 });
// Grid info
grid_sm<2, void> info( { 8, 8 });
// Boundary conditions
size_t bc[2] = { PERIODIC, PERIODIC };
// factor
float factor = pow(global_v_cluster->getProcessingUnits() / 2.0f, 1.0f / 3.0f);
// interaction radius
float r_cut = 0.01 / factor;
// ghost
Ghost<2, float> ghost(r_cut);
// Distributed vector
vector_dist<2, float, animal, CartDecomposition<2, float, HeapMemory, ParMetisDistribution<2, float>>> vd(k,box,bc,ghost);
// Init DLB tool
DLB dlb(v_cl);
// Set unbalance threshold
dlb.setHeurisitc(DLB::Heuristic::UNBALANCE_THRLD);
dlb.setThresholdLevel(DLB::ThresholdLevel::THRLD_MEDIUM);
auto it = vd.getIterator();
while (it.isNext())
{
auto key = it.get();
if(ud(eg) < 0.7 )
{
vd.template getPos<animal::pos>(key)[0] = lc(eg);
vd.template getPos<animal::pos>(key)[1] = lc(eg);
vd.template getProp<animal::genre>(key) = PREY;
vd.template getProp<animal::status>(key) = ALIVE;
vd.template getProp<animal::time_a>(key) = PREY_TIME_A;
}
else
{
vd.template getPos<animal::pos>(key)[0] = uc(eg);
vd.template getPos<animal::pos>(key)[1] = uc(eg);
vd.template getProp<animal::genre>(key) = PREDATOR;
vd.template getProp<animal::status>(key) = ALIVE;
vd.template getProp<animal::time_a>(key) = PRED_TIME_A;
}
++it;
}
vd.map();
vd.addComputationCosts();
vd.getDecomposition().rebalance(dlb);
vd.map();
//vd.getDecomposition().getDistribution().write("parmetis_prey_predators_" + std::to_string(0) + ".vtk");
//vd.write("particles_", 0, NO_GHOST);
// 100 step random walk
for (size_t j = 0; j < 100; j++)
{
size_t prey = 0, predators = 0;
auto it = vd.getDomainIterator();
while (it.isNext())
{
auto key = it.get();
vd.template getPos<animal::pos>(key)[0] += 0.01 * md(eg);
vd.template getPos<animal::pos>(key)[1] += 0.01 * md(eg);
if(vd.template getProp<animal::genre>(key) == PREY)
prey++;
else
predators++;
++it;
}
vd.map();
/////// Interactions ///
// get ghosts
vd.ghost_get<0>();
// vector of dead animals
openfpm::vector<size_t> deads;
openfpm::vector<vect_dist_key_dx> reps_prey;
openfpm::vector<vect_dist_key_dx> reps_pred;
// get the cell list with a cutoff radius
bool error = false;
auto NN = vd.getCellList(0.01/factor);
// iterate across the domain particle
auto it2 = vd.getDomainIterator();
while (it2.isNext())
{
auto p = it2.get();
Point<2,float> xp = vd.getPos<0>(p);
size_t gp = vd.getProp<animal::genre>(p);
size_t sp = vd.getProp<animal::status>(p);
if(sp == ALIVE)
{
if(gp == PREY)
{
if( prey < k/1.5 && ud(eg) < PREY_REPR )
reps_prey.add(p);
vd.getProp<animal::time_a>(p)--;
if(vd.getProp<animal::time_a>(p) <= 0)
{
vd.getProp<animal::status>(p) = DEAD;
prey--;
}
}
else if(gp == PREDATOR)
{
vd.getProp<animal::time_a>(p)--;
if(vd.getProp<animal::time_a>(p) <= 0)
{
vd.getProp<animal::status>(p) = DEAD;
}
else
{
auto Np = NN.getIterator(NN.getCell(xp));
while (Np.isNext())
{
auto q = Np.get();
size_t gq = vd.getProp<animal::genre>(q);
size_t sq = vd.getProp<animal::status>(q);
Point<2,float> xq = vd.getPos<0>(q);
Point<2,float> f = (xp - xq);
float distance = f.norm();
if (distance < 2*r_cut*sqrt(2) && gq == PREY && sq == ALIVE)
{
if( ud(eg) < PRED_EAT )
{
vd.getProp<animal::status>(q) = DEAD;
vd.getProp<animal::time_a>(p) = PRED_TIME_A;
if( ud(eg) < PRED_REPR )
reps_pred.add(p);
}
}
++Np;
}
}
}
}
++it2;
}
vd.deleteGhost();
// Replicate
for (size_t i = 0 ; i < reps_prey.size() ; i++)
{
vd.add();
vd.getLastPos<animal::pos>()[0] = vd.getPos<0>(reps_prey.get(i))[0];
vd.getLastPos<animal::pos>()[1] = vd.getPos<0>(reps_prey.get(i))[1];
vd.getLastProp<animal::genre>() = PREY;
vd.getLastProp<animal::status>() = ALIVE;
vd.getLastProp<animal::time_a>() = PREY_TIME_A;
}
for (size_t i = 0 ; i < reps_pred.size() ; i++)
{
vd.add();
vd.getLastPos<animal::pos>()[0] = vd.getPos<0>(reps_pred.get(i))[0];
vd.getLastPos<animal::pos>()[1] = vd.getPos<0>(reps_pred.get(i))[1];
vd.getLastProp<animal::genre>() = PREDATOR;
vd.getLastProp<animal::status>() = ALIVE;
vd.getLastProp<animal::time_a>() = PRED_TIME_A;
}
auto it3 = vd.getDomainIterator();
while (it3.isNext())
{
auto key = it3.get();
if(vd.getProp<animal::status>(key.getKey()) == DEAD)
{
deads.add(key.getKey());
}
++it3;
}
deads.sort();
vd.remove(deads, 0);
deads.resize(0);
vd.deleteGhost();
////////////////////////
vd.addComputationCosts();
vd.getDecomposition().rebalance(dlb);
vd.map();
}
//
// ### WIKI 10 ###
//
// Deinitialize the library
//
delete_global_v_cluster();
}
example/Numerics/Makefile deleted 100644 → 0
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SUBDIRS := $(wildcard */.)
all clean:
for dir in $(SUBDIRS); do \
$(MAKE) -C $$dir $@; \
done
clean: $(SUBDIRS)
.PHONY: all clean $(SUBDIRS)
example/Numerics/PSE/0_Derivative_approx_1D/Makefile deleted 100644 → 0
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include ../../../example.mk
CC=mpic++
LDIR =
OBJ = main.o
%.o: %.cpp
$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
pse_1d: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
all: pse_1d
.PHONY: clean all
clean:
rm -f *.o *~ core pse_1d
example/Numerics/PSE/0_Derivative_approx_1D/config.cfg deleted 100644 → 0
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[pack]
files = main.cpp Makefile