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  • mosaic/software/parallel-computing/openfpm/openfpm_pdata
  • argupta/openfpm_pdata
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.gitignore 0 → 100644
View file @ b9ccc50e
# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so
# Packages #
############
# it's better to unpack these files and commit the raw source
# git has its own built in compression methods
*.7z
*.dmg
*.gz
*.iso
*.jar
*.rar
*.tar
*.zip
# Logs and databases #
######################
*.log
*.sql
*.sqlite
*.xml
# OS generated files #
######################
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db
# CLion IDE-related
.idea/
cmake-build-debug/
cmake-build-release/
# Script-generated build folder
build/
###### Other
**/vtk/Makefile
**/src/Makefile
./Makefile
Makefile.in
Makefile
**/.deps
**/src/config
example.mk
src/pdata
.cproject
.project
.settings
**/*.vtk
!**/test_data/*.vtk
*.csv
*.h5
*.json
*.html
Makefile
/build
*CMake*
*cmake*
**/*cmake*
**/*CMake*
**/.gitignore
.gitignore
/doxygen/
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 ${DEFINE_HAVE_PARMETIS} CACHE INTERNAL "")
endif()
DoxygenLayout.xml 0 → 100644
View file @ b9ccc50e
<doxygenlayout version="1.0">
<!-- Generated by doxygen 1.8.6 -->
<!-- Navigation index tabs for HTML output -->
<navindex>
<tab type="mainpage" visible="yes" title=""/>
<tab type="pages" visible="yes" title="" intro=""/>
<tab type="modules" visible="yes" title="" intro=""/>
<tab type="namespaces" visible="yes" title="">
<tab type="namespacelist" visible="yes" title="" intro=""/>
<tab type="namespacemembers" visible="yes" title="" intro=""/>
</tab>
<tab type="classes" visible="yes" title="">
<tab type="classlist" visible="yes" title="" intro=""/>
<tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/>
<tab type="hierarchy" visible="yes" title="" intro=""/>
<tab type="classmembers" visible="yes" title="" intro=""/>
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<tab type="files" visible="yes" title="">
<tab type="filelist" visible="yes" title="" intro=""/>
<tab type="globals" visible="yes" title="" intro=""/>
</tab>
<tab type="examples" visible="yes" title="" intro=""/>
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<class>
<briefdescription visible="yes"/>
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</doxygenlayout>
Makefile.am deleted 100755 → 0
View file @ 665076bb
SUBDIRS = src
bin_PROGRAMS =
\ No newline at end of file
build_pdata.sh deleted 100644 → 0
View file @ 665076bb
#! /bin/bash
# Make a directory in /tmp/OpenFPM_data
echo "Directory: $1"
echo "Machine: $2"
mkdir /tmp/openfpm_pdata
mv * .[^.]* /tmp/openfpm_pdata
mv /tmp/openfpm_pdata OpenFPM_pdata
mkdir OpenFPM_pdata/src/config
git clone ssh://git@ppmcoremirror.dynu.com:2222/incardon/openfpm_vcluster.git OpenFPM_vcluster
git clone ssh://git@ppmcoremirror.dynu.com:2222/incardon/openfpm_devices.git OpenFPM_devices
git clone ssh://git@ppmcoremirror.dynu.com:2222/incardon/openfpm_data.git OpenFPM_data
cd OpenFPM_pdata
git checkout develop
cd ..
cd "$1/OpenFPM_pdata"
if [ "$2" == "gin" ]
then
echo "Compiling on gin\n"
module load gcc/4.9.2
module load openmpi/1.8.1
elif [ "$2" == "wetcluster" ]
then
echo "Compiling on wetcluster"
## produce the module path
export MODULEPATH="/sw/apps/modules/modulefiles:$MODULEPATH"
script="module load gcc/4.9.2\n
module load openmpi/1.8.1\n
module load boost/1.54.0\n
compile_options='--with-boost=/sw/apps/boost/1.54.0/'\n
\n
sh ./autogen.sh\n
sh ./configure \"\$compile_options\" CXX=mpic++\n
make\n
if [ \"\$?\" = "0" ]; then exit 1 ; fi\n
exit(0)\n"
echo $script | sed -r 's/\\n/\n/g' > compile_script
bsub -o output_compile.%J -K -n 1 -J compile sh ./compile_script
## 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; mpirun -np 2 ./src/pdata"
if [ $? -ne 0 ]; then 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; mpirun -np 3 ./src/pdata"
if [ $? -ne 0 ]; then 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; mpirun -np 4 ./src/pdata"
if [ $? -ne 0 ]; then 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; mpirun -np 5 ./src/pdata"
if [ $? -ne 0 ]; then 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; mpirun -np 6 ./src/pdata"
if [ $? -ne 0 ]; then exit 1 ; fi
bsub -o output_run6.%J -K -n 7 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 7 ./src/pdata"
if [ $? -ne 0 ]; then exit 1 ; fi
bsub -o output_run6.%J -K -n 8 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 8 ./src/pdata"
if [ $? -ne 0 ]; then exit 1 ; fi
bsub -o output_run6.%J -K -n 9 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 9 ./src/pdata"
if [ $? -ne 0 ]; then exit 1 ; fi
bsub -o output_run6.%J -K -n 10 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 10 ./src/pdata"
if [ $? -ne 0 ]; then exit 1 ; fi
bsub -o output_run6.%J -K -n 11 -R "span[hosts=1]" "module load openmpi/1.8.1 ; module load gcc/4.9.2; mpirun -np 11 ./src/pdata"
if [ $? -ne 0 ]; then 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; mpirun -np 12 ./src/vcluster"
if [ $? -ne 0 ]; then 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 [ "$2" == "taurus" ]
then
echo "Compiling on taurus"
echo "$PATH"
module load gcc/4.8.2
module load boost/1.55.0-gnu4.8
module load openmpi/1.8.7
module unload bullxmpi
sh ./autogen.sh
sh ./configure --enable-verbose CXX=mpic++
make
if [ $? -ne 0 ]; then exit 1 ; fi
# salloc --nodes=1 --ntasks-per-node=16 --time=00:05:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 16 src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
# salloc --nodes=2 --ntasks-per-node=16 --time=00:05:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 32 src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
# salloc --nodes=4 --ntasks-per-node=16 --time=00:05:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 64 src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
# salloc --nodes=8 --ntasks-per-node=16 --time=00:05:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 128 src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
# salloc --nodes=16 --ntasks-per-node=16 --time=00:5:00 --mem-per-cpu=1900 --partition=haswell bash -c "ulimit -s unlimited && mpirun -np 256 src/vcluster"
# if [ $? -ne 0 ]; then exit 1 ; fi
else
echo "Compiling general"
sh ./autogen.sh
sh ./configure CXX=mpic++
make
mpirun -np 2 ./src/pdata
mpirun -np 3 ./src/pdata
mpirun -np 4 ./src/pdata
fi
configure.ac deleted 100755 → 0
View file @ 665076bb
# -*- Autoconf -*-
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
AC_INIT(FULL-PACKAGE-NAME, VERSION, BUG-REPORT-ADDRESS)
AC_CANONICAL_SYSTEM
AC_CONFIG_SRCDIR([src/main.cpp])
AM_INIT_AUTOMAKE
AC_CONFIG_HEADER([src/config/config.h])
m4_ifdef([ACX_PTHREAD],,[m4_include([m4/acx_pthread.m4])])
m4_ifdef([AX_BOOST],,[m4_include([m4/ax_boost.m4])])
m4_ifdef([ACX_MPI],,[m4_include([m4/acx_mpi.m4])])
m4_ifdef([AX_OPENMP],,[m4_include([m4/ax_openmp.m4])])
m4_ifdef([AX_CUDA],,[m4_include([m4/ax_cuda.m4])])
CXXFLAGS+=" --std=c++11 -march=native -mtune=native "
NVCCFLAGS=" "
INCLUDES_PATH=" "
# Checks for programs.
AC_PROG_CXX
# Checks g++ flags
AC_CANONICAL_HOST
# Check target architetture
#AX_GCC_ARCHFLAG([], [CXXFLAGS="$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 memcheck
AC_MSG_CHECKING(whether to build with memcheck capabilities)
AC_ARG_ENABLE(memcheck,
AC_HELP_STRING(
[--enable-memcheck],
[enable memory check (def=no)]
),
memcheck="$enableval"
)
AC_MSG_RESULT($memcheck)
if test x"$memcheck" = x"yes"; then
AC_DEFINE([MEMLEAK_CHECK],[],[Memory check, corruption and leak])
fi
#########
####### include OpenFPM_devices include path
INCLUDES_PATH+="-I. -Isrc/config/ -I../../metis_install/include -I../../OpenFPM_IO/src -I../../OpenFPM_data/src -I../../OpenFPM_devices/src -I../../OpenFPM_vcluster/src/"
##### CHECK FOR BOOST ##############
AX_BOOST([1.52],[],[])
####### Checking for GPU support
AX_CUDA
## detect for NVCC
if test x"$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"$gpu_support" = x"yes"; then
AC_DEFINE([GPU],[],[GPU support])
fi
else
gpu_support=no
fi
# Set this conditional if cuda is wanted
AM_CONDITIONAL(BUILDCUDA, test ! x$NVCC = x"no")
###########################
# Define that there is MPI
AC_DEFINE([HAVE_MPI],[],[MPI Enabled])
AC_SUBST(NVCCFLAGS)
AC_SUBST(INCLUDES_PATH)
# Checks for typedefs, structures, and compiler characteristics.
# Checks for library functions.
AC_CONFIG_FILES([Makefile src/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"$debuger" = x"yes" ]; then
echo "* debug: yes *"
else
echo "* debug: no *"
fi
if [ test x"$gpu_support" = x"no" ]; then
echo "* gpu: no *"
else
echo "* gpu: yes *"
fi
echo "* *"
echo "***********************************"
ofpdoxygen.css 0 → 100644
View file @ b9ccc50e
This diff is collapsed.
src/.deps/pdata-HeapMemory.Po deleted 100644 → 0
View file @ 665076bb
pdata-HeapMemory.o: ../../OpenFPM_devices/src/memory/HeapMemory.cpp \
/usr/include/stdc-predef.h \
../../OpenFPM_devices/src/memory/HeapMemory.hpp ../src/config/config.h \
../../OpenFPM_devices/src/memory/memory.hpp \
/usr/lib/gcc/x86_64-redhat-linux/4.9.2/include/stddef.h \
/usr/include/c++/4.9.2/cstddef \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/c++config.h \
/usr/include/bits/wordsize.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/os_defines.h \
/usr/include/features.h /usr/include/sys/cdefs.h \
/usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cpu_defines.h \
/usr/include/c++/4.9.2/cstdint \
/usr/lib/gcc/x86_64-redhat-linux/4.9.2/include/stdint.h \
/usr/include/stdint.h /usr/include/bits/wchar.h \
/usr/include/c++/4.9.2/iostream /usr/include/c++/4.9.2/ostream \
/usr/include/c++/4.9.2/ios /usr/include/c++/4.9.2/iosfwd \
/usr/include/c++/4.9.2/bits/stringfwd.h \
/usr/include/c++/4.9.2/bits/memoryfwd.h \
/usr/include/c++/4.9.2/bits/postypes.h /usr/include/c++/4.9.2/cwchar \
/usr/include/wchar.h /usr/include/stdio.h \
/usr/lib/gcc/x86_64-redhat-linux/4.9.2/include/stdarg.h \
/usr/include/xlocale.h /usr/include/c++/4.9.2/exception \
/usr/include/c++/4.9.2/bits/atomic_lockfree_defines.h \
/usr/include/c++/4.9.2/bits/exception_ptr.h \
/usr/include/c++/4.9.2/bits/exception_defines.h \
/usr/include/c++/4.9.2/bits/nested_exception.h \
/usr/include/c++/4.9.2/bits/char_traits.h \
/usr/include/c++/4.9.2/bits/stl_algobase.h \
/usr/include/c++/4.9.2/bits/functexcept.h \
/usr/include/c++/4.9.2/bits/cpp_type_traits.h \
/usr/include/c++/4.9.2/ext/type_traits.h \
/usr/include/c++/4.9.2/ext/numeric_traits.h \
/usr/include/c++/4.9.2/bits/stl_pair.h \
/usr/include/c++/4.9.2/bits/move.h \
/usr/include/c++/4.9.2/bits/concept_check.h \
/usr/include/c++/4.9.2/type_traits \
/usr/include/c++/4.9.2/bits/stl_iterator_base_types.h \
/usr/include/c++/4.9.2/bits/stl_iterator_base_funcs.h \
/usr/include/c++/4.9.2/debug/debug.h \
/usr/include/c++/4.9.2/bits/stl_iterator.h \
/usr/include/c++/4.9.2/bits/ptr_traits.h \
/usr/include/c++/4.9.2/bits/predefined_ops.h \
/usr/include/c++/4.9.2/bits/localefwd.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/c++locale.h \
/usr/include/c++/4.9.2/clocale /usr/include/locale.h \
/usr/include/bits/locale.h /usr/include/c++/4.9.2/cctype \
/usr/include/ctype.h /usr/include/bits/types.h \
/usr/include/bits/typesizes.h /usr/include/endian.h \
/usr/include/bits/endian.h /usr/include/bits/byteswap.h \
/usr/include/bits/byteswap-16.h /usr/include/c++/4.9.2/bits/ios_base.h \
/usr/include/c++/4.9.2/ext/atomicity.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/gthr.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/gthr-default.h \
/usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
/usr/include/bits/sched.h /usr/include/bits/time.h \
/usr/include/bits/timex.h /usr/include/bits/pthreadtypes.h \
/usr/include/bits/setjmp.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/atomic_word.h \
/usr/include/c++/4.9.2/bits/locale_classes.h \
/usr/include/c++/4.9.2/string /usr/include/c++/4.9.2/bits/allocator.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/c++allocator.h \
/usr/include/c++/4.9.2/ext/new_allocator.h /usr/include/c++/4.9.2/new \
/usr/include/c++/4.9.2/bits/ostream_insert.h \
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src/Amr/grid_dist_amr_key.hpp 0 → 100644
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/*
* grid_dist_amr_key.hpp
*
* Created on: Sep 23, 2017
* Author: i-bird
*/
#ifndef SRC_AMR_GRID_DIST_AMR_KEY_HPP_
#define SRC_AMR_GRID_DIST_AMR_KEY_HPP_
/*! \brief Amr grid distributed key
*
* \tparam dim dimensionality
*
*/
template<unsigned int dim>
class grid_dist_amr_key
{
//! actual level
size_t lvl;
//! actual position in the distributed grid
grid_dist_key_dx<dim> key;
public:
/*! \constructor
*
* \param lvl level
* \param key distributed grid key
* \param offsets to move between levels
*
*/
inline grid_dist_amr_key(size_t lvl,
grid_dist_key_dx<dim> key)
:lvl(lvl),key(key)
{}
/*! \brief Return the grid key
*
* \return the distributed key
*
*/
inline const grid_dist_key_dx<dim> & getKey() const
{
return key;
}
/*! \brief Return the grid key (as reference)
*
* \return the distributed key
*
*/
inline grid_dist_key_dx<dim> & getKeyRef()
{
return key;
}
/*! \brief Return the level
*
* \return the level
*
*/
inline size_t getLvl() const
{
return lvl;
}
/*! \brief Return the level
*
* \param lvl level to set
*
*/
inline void setLvl(size_t lvl)
{
this->lvl = lvl;
}
/*! \brief Create a new key moving the old one
*
* \param s dimension id
* \param s number of steps
*
* \return new key
*
*/
inline grid_dist_amr_key<dim> moveSpace(size_t d,size_t s)
{
return grid_dist_amr_key<dim>(lvl,key.move(d,s));
}
};
#endif /* SRC_AMR_GRID_DIST_AMR_KEY_HPP_ */
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/*
* grid_amr_dist_key_iterator.hpp
*
* Created on: Sep 22, 2017
* Author: i-bird
*/
#ifndef SRC_AMR_GRID_DIST_AMR_KEY_ITERATOR_HPP_
#define SRC_AMR_GRID_DIST_AMR_KEY_ITERATOR_HPP_
#include "Vector/map_vector.hpp"
#include "Grid/Iterators/grid_dist_id_iterator.hpp"
#include "grid_dist_amr_key.hpp"
template<unsigned int dim, typename device_grid, typename device_sub_it, typename it_type = grid_dist_iterator<dim,device_grid,device_sub_it,FREE>>
class grid_dist_amr_key_iterator
{
//! Array of grid iterators
openfpm::vector<it_type> & git;
//! actual it type
struct actual_it
{
it_type & it;
};
//! Actual distributed grid iterator
it_type * a_it;
//! iterator pointer
size_t g_c;
/*! \brief from g_c increment g_c until you find a valid grid
*
*/
void selectValidGrid()
{
// When the grid has size 0 potentially all the other informations are garbage
while (g_c < git.size() && git.get(g_c).isNext() == false ) g_c++;
// get the next grid iterator
if (g_c < git.size())
{
a_it = &git.get(g_c);
}
}
public:
/*! \brief Constructor
*
* \param git vector of iterator
*
*/
grid_dist_amr_key_iterator(openfpm::vector<it_type> & git)
:git(git),g_c(0)
{
a_it = &git.get(0);
selectValidGrid();
}
//! Destructor
~grid_dist_amr_key_iterator()
{
}
/*! \brief Get the next element
*
* \return the next grid_key
*
*/
inline grid_dist_amr_key_iterator<dim,device_grid,device_sub_it,it_type> & operator++()
{
++(*a_it);
// check if a_it is at the end
if (a_it->isNext() == true)
{return *this;}
else
{
// switch to the new iterator
g_c++;
selectValidGrid();
}
return *this;
}
/*! \brief Is there a next point
*
* \return true is there is a next point
*
*/
inline bool isNext()
{
return g_c < git.size();
}
/*! \brief Return the actual AMR grid iterator point
*
*
*/
inline grid_dist_amr_key<dim> get()
{
return grid_dist_amr_key<dim>(g_c,a_it->get());
}
/*! \brief Return the actual global grid position in the AMR struct in global
* coordinates
*
*
*/
inline grid_key_dx<dim> getGKey()
{
return git.get(g_c).getGKey(a_it->get());
}
/*! \brief Return the level at which we are
*
*
*/
inline size_t getLvl() const
{
return g_c;
}
};
#endif /* SRC_AMR_GRID_DIST_AMR_KEY_ITERATOR_HPP_ */
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/*
* amr_base_gpu_unit_tests.cu
*
* Created on: Aug 28, 2019
* Author: i-bird
*/
/*
* amr_base_unit_test.cpp
*
* Created on: Oct 5, 2017
* Author: i-bird
*/
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include "Amr/grid_dist_amr.hpp"
#include "Point_test.hpp"
#include "Grid/tests/grid_dist_id_util_tests.hpp"
struct amr_launch_sparse
{
template<typename grid_type, typename ite_type>
__device__ void operator()(grid_type & grid, ite_type itg, float spacing, Point<3,float> center)
{
GRID_ID_3_GLOBAL(itg);
__shared__ bool is_block_empty;
if (threadIdx.x == 0 && threadIdx.y == 0 && threadIdx.z == 0)
{is_block_empty = true;}
grid.init();
int offset = 0;
grid_key_dx<3,int> blk;
bool out = grid.getInsertBlockOffset(itg,key,blk,offset);
auto blockId = grid.getBlockLinId(blk);
const float x = keyg.get(0)*spacing - center.get(0);
const float y = keyg.get(1)*spacing - center.get(1);
const float z = keyg.get(2)*spacing - center.get(2);
float radius = sqrt((float) (x*x + y*y + z*z));
bool is_active = radius < 0.4 && radius > 0.3;
if (is_active == true)
{is_block_empty = false;}
__syncthreads();
if (is_block_empty == false)
{
auto ec = grid.insertBlock(blockId);
if ( is_active == true)
{
ec.template get<0>()[offset] = x+y+z;
ec.template get<grid_type::pMask>()[offset] = 1;
}
}
__syncthreads();
grid.flush_block_insert();
}
};
BOOST_AUTO_TEST_SUITE( amr_grid_dist_id_test )
BOOST_AUTO_TEST_CASE( grid_dist_id_amr_gpu )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
Ghost<3,long int> g(1);
sgrid_dist_amr_gpu<3,float,aggregate<float>> amr_g(domain3,g);
size_t g_sz[3] = {4,4,4};
size_t n_lvl = 6;
amr_g.initLevels(n_lvl,g_sz);
for (size_t i = 0 ; i < amr_g.getNLvl() ; i++)
{
// Fill the AMR with something
size_t count = 0;
auto it = amr_g.getGridIteratorGPU(i);
it.setGPUInsertBuffer(1);
Point<3,float> center({0.5,0.5,0.5});
it.launch(amr_launch_sparse(),it.getSpacing(0),center);
amr_g.getDistGrid(i).template flush<smax_<0>>(FLUSH_ON_DEVICE);
amr_g.getDistGrid(i).template deviceToHost<0>();
auto it2 = amr_g.getDistGrid(i).getDomainIterator();
while (it2.isNext())
{
auto key = it2.get();
auto keyg = it2.getGKey(key);
count++;
++it2;
}
auto & v_cl = create_vcluster();
v_cl.sum(count);
v_cl.execute();
switch(i)
{
case 0:
BOOST_REQUIRE_EQUAL(count,0);
break;
case 1:
BOOST_REQUIRE_EQUAL(count,30);
break;
case 2:
BOOST_REQUIRE_EQUAL(count,282);
break;
case 3:
BOOST_REQUIRE_EQUAL(count,2192);
break;
case 4:
BOOST_REQUIRE_EQUAL(count,16890);
break;
case 5:
BOOST_REQUIRE_EQUAL(count,136992);
break;
}
}
// Iterate across all the levels initialized
/* auto it = amr_g.getDomainIterator();
size_t count = 0;
while (it.isNext())
{
count++;
++it;
}
Vcluster<> & v_cl = create_vcluster();
v_cl.sum(count);
v_cl.execute();
BOOST_REQUIRE_EQUAL(count,correct_result);
auto itc = amr_g.getDomainIteratorCells();
size_t count_c = 0;
while (itc.isNext())
{
count_c++;
++itc;
}
v_cl.sum(count_c);
v_cl.execute();
auto it_level = amr_g.getDomainIteratorCells(3);
while (it_level.isNext())
{
auto key = it_level.get();
amr_g.template get<0>(3,key);
++it_level;
}
BOOST_REQUIRE_EQUAL(count_c,correct_result_cell);*/
}
BOOST_AUTO_TEST_CASE( grid_dist_id_amr_gpu_link_test )
{
// To uncomment (It does not work when we run the full suite for some weird reason)
#if 0
auto & v_cl = create_vcluster();
// Domain
Box<2,float> domain({0.0,0.0},{1.0,1.0});
Ghost<2,long int> g(1);
sgrid_dist_amr_gpu<2,float,aggregate<float>> amr_g(domain,g);
size_t g_sz[2] = {17,17};
size_t n_lvl = 3;
amr_g.initLevels(n_lvl,g_sz);
grid_key_dx<2> start({5,5});
grid_key_dx<2> start_lvl_dw({9,9});
grid_key_dx<2> stop_lvl_dw({12,12});
grid_key_dx<2> start_lvl_dw2({19,19});
grid_key_dx<2> stop_lvl_dw2({23,23});
auto it = amr_g.getGridIterator(0,start,start);
auto it2 = amr_g.getGridIterator(1,start_lvl_dw,stop_lvl_dw);
auto it3 = amr_g.getGridIterator(2,start_lvl_dw2,stop_lvl_dw2);
// it.setGPUInsertBuffer(4);
auto & lvl_0 = amr_g.getDistGrid(0);
auto & lvl_1 = amr_g.getDistGrid(1);
auto & lvl_2 = amr_g.getDistGrid(2);
// Add points in level 0
while (it.isNext())
{
auto key = it.get_dist();
lvl_0.template insertFlush<0>(key) = 1.0;
++it;
}
while (it2.isNext())
{
auto key = it2.get_dist();
lvl_1.template insertFlush<0>(key) = 2.0;
++it2;
}
while (it3.isNext())
{
auto key = it3.get_dist();
lvl_2.template insertFlush<0>(key) = 3.0;
++it3;
}
amr_g.hostToDevice<0>();
amr_g.tagBoundaries<NNStar<2>>();
amr_g.construct_level_connections();
/////////////////////////////////////////////////////////////
auto & lvl_zero_d = amr_g.getDistGrid(0);
auto & lvl_one_d = amr_g.getDistGrid(1);
auto & lvl_two_d = amr_g.getDistGrid(2);
// For each local grid
for (int i = 0 ; i < lvl_zero_d.getN_loc_grid() ; i++)
{
// Check
auto & lvl_zero = lvl_zero_d.get_loc_grid(i);
auto & lvl_one = lvl_one_d.get_loc_grid(i);
auto & lvl_two = lvl_two_d.get_loc_grid(i);
auto & offs_dw_link = lvl_zero.getDownLinksOffsets();
auto & dw_links = lvl_zero.getDownLinks();
BOOST_REQUIRE_EQUAL(offs_dw_link.size(),1);
BOOST_REQUIRE_EQUAL(dw_links.size(),4);
auto & indexL0 = lvl_zero.private_get_blockMap().getIndexBuffer();
auto & indexL1 = lvl_one.private_get_blockMap().getIndexBuffer();
auto & indexL2 = lvl_two.private_get_blockMap().getIndexBuffer();
auto & dataL0 = lvl_zero.private_get_blockMap().getDataBuffer();
auto & dataL1 = lvl_one.private_get_blockMap().getDataBuffer();
auto & dataL2 = lvl_two.private_get_blockMap().getDataBuffer();
dw_links.template deviceToHost<0,1>();
BOOST_REQUIRE_EQUAL(dataL1.template get<0>(dw_links.template get<0>(0))[dw_links.template get<1>(0)],2);
BOOST_REQUIRE_EQUAL(dataL1.template get<0>(dw_links.template get<0>(1))[dw_links.template get<1>(1)],2);
BOOST_REQUIRE_EQUAL(dataL1.template get<0>(dw_links.template get<0>(2))[dw_links.template get<1>(2)],2);
BOOST_REQUIRE_EQUAL(dataL1.template get<0>(dw_links.template get<0>(3))[dw_links.template get<1>(3)],2);
auto & offs_dw_link_1 = lvl_one.getDownLinksOffsets();
auto & dw_links_1 = lvl_one.getDownLinks();
BOOST_REQUIRE_EQUAL(offs_dw_link_1.size(),12);
BOOST_REQUIRE_EQUAL(dw_links_1.size(),9);
dw_links_1.template deviceToHost<0,1>();
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(0))[dw_links_1.template get<1>(0)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(1))[dw_links_1.template get<1>(1)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(2))[dw_links_1.template get<1>(2)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(3))[dw_links_1.template get<1>(3)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(4))[dw_links_1.template get<1>(4)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(5))[dw_links_1.template get<1>(5)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(6))[dw_links_1.template get<1>(6)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(7))[dw_links_1.template get<1>(7)],3);
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(8))[dw_links_1.template get<1>(8)],3);
}
/////////////////////////////////////////////////////////////
#endif
}
BOOST_AUTO_TEST_CASE( grid_dist_id_amr_gpu_link_test_more_dense )
{
// To uncomment (It does not work when we run the full suite for some weird reason)
#if 0
auto & v_cl = create_vcluster();
// Domain
Box<2,float> domain({0.0,0.0},{1.0,1.0});
Ghost<2,long int> g(1);
sgrid_dist_amr_gpu<2,float,aggregate<float>> amr_g(domain,g);
size_t g_sz[2] = {17,17};
size_t n_lvl = 3;
amr_g.initLevels(n_lvl,g_sz);
grid_key_dx<2> start({1,1});
grid_key_dx<2> stop({15,15});
grid_key_dx<2> start_lvl_dw({2,2});
grid_key_dx<2> stop_lvl_dw({31,31});
grid_key_dx<2> start_lvl_dw2({4,4});
grid_key_dx<2> stop_lvl_dw2({63,63});
auto it = amr_g.getGridIterator(0,start,stop);
auto it2 = amr_g.getGridIterator(1,start_lvl_dw,stop_lvl_dw);
auto it3 = amr_g.getGridIterator(2,start_lvl_dw2,stop_lvl_dw2);
auto & lvl_0 = amr_g.getDistGrid(0);
auto & lvl_1 = amr_g.getDistGrid(1);
auto & lvl_2 = amr_g.getDistGrid(2);
// Add points in level 0
while (it.isNext())
{
auto key = it.get_dist();
lvl_0.template insertFlush<0>(key) = 1.0;
++it;
}
while (it2.isNext())
{
auto key = it2.get_dist();
lvl_1.template insertFlush<0>(key) = 2.0;
++it2;
}
while (it3.isNext())
{
auto key = it3.get_dist();
lvl_2.template insertFlush<0>(key) = 3.0;
++it3;
}
amr_g.hostToDevice<0>();
amr_g.ghost_get<0>(RUN_ON_DEVICE);
amr_g.tagBoundaries<NNStar<2>>();
amr_g.ghost_get<0>(RUN_ON_DEVICE);
amr_g.construct_level_connections();
amr_g.deviceToHost<0>();
amr_g.write("TESTOUT");
/////////////////////////////////////////////////////////////
auto & lvl_zero_d = amr_g.getDistGrid(0);
auto & lvl_one_d = amr_g.getDistGrid(1);
auto & lvl_two_d = amr_g.getDistGrid(2);
// For each local grid
size_t tot_dw_offs_12 = 0;
size_t tot_dw_lk_12 = 0;
size_t tot_dw_offs_23 = 0;
size_t tot_dw_lk_23 = 0;
size_t tot_up_offs_12 = 0;
size_t tot_up_lk_12 = 0;
size_t tot_up_offs_23 = 0;
size_t tot_up_lk_23 = 0;
for (int i = 0 ; i < lvl_zero_d.getN_loc_grid() ; i++)
{
// Check
auto & lvl_zero = lvl_zero_d.get_loc_grid(i);
auto & lvl_one = lvl_one_d.get_loc_grid(i);
auto & lvl_two = lvl_two_d.get_loc_grid(i);
auto & offs_dw_link = lvl_zero.getDownLinksOffsets();
auto & dw_links = lvl_zero.getDownLinks();
auto & offs_up_link = lvl_one.getUpLinksOffsets();
auto & up_links = lvl_one.getUpLinks();
tot_dw_offs_12 += offs_dw_link.size();
tot_dw_lk_12 += dw_links.size();
tot_up_offs_12 += offs_up_link.size();
tot_up_lk_12 += up_links.size();
auto & indexL0 = lvl_zero.private_get_blockMap().getIndexBuffer();
auto & indexL1 = lvl_one.private_get_blockMap().getIndexBuffer();
auto & indexL2 = lvl_two.private_get_blockMap().getIndexBuffer();
auto & dataL0 = lvl_zero.private_get_blockMap().getDataBuffer();
auto & dataL1 = lvl_one.private_get_blockMap().getDataBuffer();
auto & dataL2 = lvl_two.private_get_blockMap().getDataBuffer();
dw_links.template deviceToHost<0,1>();
up_links.template deviceToHost<0,1>();
for (int i = 0 ; i < dw_links.size(); i++)
{
BOOST_REQUIRE_EQUAL(dataL1.template get<0>(dw_links.template get<0>(i))[dw_links.template get<1>(i)],2);
}
for (int i = 0 ; i < up_links.size(); i++)
{
BOOST_REQUIRE_EQUAL(dataL0.template get<0>(up_links.template get<0>(i))[up_links.template get<1>(i)],1);
}
auto & offs_dw_link_1 = lvl_one.getDownLinksOffsets();
auto & dw_links_1 = lvl_one.getDownLinks();
auto & offs_up_link_1 = lvl_two.getUpLinksOffsets();
auto & up_links_1 = lvl_two.getUpLinks();
tot_dw_offs_23 += offs_dw_link_1.size();
tot_dw_lk_23 += dw_links_1.size();
tot_up_offs_23 += offs_up_link_1.size();
tot_up_lk_23 += up_links_1.size();
dw_links_1.template deviceToHost<0,1>();
up_links_1.template deviceToHost<0,1>();
for (int i = 0 ; i < dw_links_1.size(); i++)
{
BOOST_REQUIRE_EQUAL(dataL2.template get<0>(dw_links_1.template get<0>(i))[dw_links_1.template get<1>(i)],3);
}
for (int i = 0 ; i < up_links_1.size(); i++)
{
BOOST_REQUIRE_EQUAL(dataL1.template get<0>(up_links_1.template get<0>(i))[up_links_1.template get<1>(i)],2);
}
}
v_cl.sum(tot_dw_offs_12);
v_cl.sum(tot_dw_lk_12);
v_cl.sum(tot_dw_offs_23);
v_cl.sum(tot_dw_lk_23);
v_cl.sum(tot_up_offs_12);
v_cl.sum(tot_up_lk_12);
v_cl.sum(tot_up_offs_23);
v_cl.sum(tot_up_lk_23);
v_cl.execute();
BOOST_REQUIRE_EQUAL(tot_dw_offs_12,56);
BOOST_REQUIRE_EQUAL(tot_dw_lk_12,56*4);
BOOST_REQUIRE_EQUAL(tot_dw_offs_23,116);
BOOST_REQUIRE_EQUAL(tot_dw_lk_23,116*4);
BOOST_REQUIRE_EQUAL(tot_up_offs_12,116);
BOOST_REQUIRE_EQUAL(tot_up_lk_12,116);
BOOST_REQUIRE_EQUAL(tot_up_offs_23,236);
BOOST_REQUIRE_EQUAL(tot_up_lk_23,236);
/////////////////////////////////////////////////////////////
#endif
}
BOOST_AUTO_TEST_SUITE_END()
src/Amr/tests/amr_base_unit_tests.cpp 0 → 100644
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/*
* amr_base_unit_test.cpp
*
* Created on: Oct 5, 2017
* Author: i-bird
*/
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include "Grid/grid_dist_id.hpp"
#include "Point_test.hpp"
#include "Grid/tests/grid_dist_id_util_tests.hpp"
BOOST_AUTO_TEST_SUITE( amr_grid_dist_id_test )
BOOST_AUTO_TEST_CASE( grid_dist_id_amr )
{
// Domain
Box<2,float> domain2({0.0,0.0},{1.0,1.0});
size_t sz[2] = {100,100};
// Ghost
Ghost<2,long int> g(1);
// periodicity
periodicity<2> pr = {{PERIODIC,PERIODIC}};
openfpm::vector<Box<2,long int>> C_draw;
C_draw.add(Box<2,long int>({20,20},{50,24}));
C_draw.add(Box<2,long int>({51,20},{60,24}));
C_draw.add(Box<2,long int>({61,20},{70,24}));
C_draw.add(Box<2,long int>({20,25},{24,66}));
C_draw.add(Box<2,long int>({15,67},{49,85}));
C_draw.add(Box<2,long int>({50,76},{70,81}));
C_draw.add(Box<2,long int>({30,25},{34,37}));
C_draw.add(Box<2,long int>({50,66},{70,70}));
size_t volume_key = 0;
for (size_t i = 0 ; i < C_draw.size() ; i++)
{
volume_key += Box<2,long int>(C_draw.get(i)).getVolumeKey();
}
// Distributed grid with id decomposition
grid_dist_id<2,float,Point_test<float>> g_dist(sz,domain2,g,pr,C_draw);
// fill with gkey
auto git = g_dist.getDomainIterator();
grid_sm<2,void> gs(sz);
size_t count = 0;
while (git.isNext())
{
auto key = git.get();
auto gkey = git.getGKey(key);
g_dist.template get<0>(key) = gs.LinId(gkey);
count++;
++git;
}
Vcluster<> & vcl = create_vcluster();
vcl.sum(count);
vcl.execute();
BOOST_REQUIRE_EQUAL(count,volume_key);
g_dist.ghost_get<0>();
// Check it is correct
bool check = true;
size_t check_count = 0;
auto git2 = g_dist.getDomainGhostIterator();
while (git2.isNext())
{
auto key = git2.get();
auto gkey = git2.getGKey(key);
float value = g_dist.template get<0>(key);
// check if the point is inside or outside the domain
for (size_t k = 0; k < C_draw.size() ; k++)
{
if (Box<2,long int>(C_draw.get(k)).isInside(gkey.toPoint()) == true)
{
check &= value == gs.LinId(gkey);
// get the gdb_ext
auto & gdb_ext = g_dist.getLocalGridsInfo();
for (size_t s = 0 ; s < gdb_ext.size() ; s++)
{
Box<2,long int> bx = gdb_ext.get(s).Dbox;
bx += gdb_ext.get(s).origin;
if (bx.isInside(gkey.toPoint()))
{
check_count++;
break;
}
}
break;
}
}
++git2;
}
vcl.sum(check_count);
vcl.execute();
BOOST_REQUIRE_EQUAL(check,true);
BOOST_REQUIRE(check_count >= volume_key);
}
BOOST_AUTO_TEST_CASE( amr_grid_dist_id_iterator_test_use_2D)
{
// Domain
Box<2,float> domain({0.0,0.0},{1.0,1.0});
#ifdef TEST_COVERAGE_MODE
long int k = 256*256*create_vcluster().getProcessingUnits();
#else
long int k = 1024*1024*create_vcluster().getProcessingUnits();
#endif
k = std::pow(k, 1/2.);
long int big_step = k / 30;
big_step = (big_step == 0)?1:big_step;
long int small_step = 21;
print_test( "AMR Testing 2D full grid k<=",k);
// 2D test
for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
{
BOOST_TEST_CHECKPOINT( "AMR Testing 2D full grid k=" << k );
//! [Create and access a distributed grid]
// grid size
size_t sz[2];
sz[0] = k;
sz[1] = k;
// periodicity
periodicity<2> pr = {{PERIODIC,PERIODIC}};
// Ghost
Ghost<2,long int> g(1);
openfpm::vector<Box<2,long int>> bx_def;
bx_def.add(Box<2,long int>({0,0},{k-1,k-1}));
// Distributed grid with id decomposition
grid_dist_id<2, float, aggregate<double>> g_dist(sz,domain,g,pr,bx_def);
Test2D_core(g_dist,sz,k);
}
}
BOOST_AUTO_TEST_SUITE_END()
src/CMakeLists.txt 0 → 100644
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src/DLB/DLB.hpp 0 → 100644
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src/DLB/DLB_unit_test.hpp 0 → 100644
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/*
* DLB_unit_test.hpp
*
* Created on: Nov 24, 2015
* Author: Antonio Leo
*/
#ifndef DLB_UNIT_TEST_HPP_
#define DLB_UNIT_TEST_HPP_
#include "DLB.hpp"
BOOST_AUTO_TEST_SUITE (DLB_test)
BOOST_AUTO_TEST_CASE( DLB_test_use)
{
// Vcluster
Vcluster & vcl = *global_v_cluster;
// Initialize the global VCluster
init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
// Init DLB tool
DLB dlb(vcl);
// Init dlb parameters
dlb.setComputationCost(5);
dlb.setSimulationStartTime(0);
dlb.setSimulationEndTime(10);
// Time value of the "unbalanced" process
float t_high = 1;
for(float t = dlb.getSimulationStartTime();
t < dlb.getSimulationEndTime();
t++)
{
dlb.startIteration(0);
if(vcl.getProcessUnitID() == 0)
dlb.endIteration(1);
else{
dlb.endIteration(t_high++);
}
bool rebalance = dlb.rebalanceNeeded();
if(rebalance) {t_high = 1;}
if(t == 6)
BOOST_REQUIRE_EQUAL(rebalance,true);
}
}
BOOST_AUTO_TEST_SUITE_END()
#endif /* DLB_UNIT_TEST_HPP_ */