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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
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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
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color: #354C7B;
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box-shadow: 2px 2px 3px #999;
-webkit-box-shadow: 2px 2px 3px #999;
-moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444));
background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000);
}
div.classindex ul {
list-style: none;
padding-left: 0;
}
div.classindex span.ai {
display: inline-block;
}
div.groupHeader {
margin-left: 16px;
margin-top: 12px;
font-weight: bold;
}
div.groupText {
margin-left: 16px;
font-style: italic;
}
body {
background-color: white;
color: black;
margin: 0;
}
div.contents {
margin-top: 10px;
margin-left: 12px;
margin-right: 8px;
}
td.indexkey {
background-color: #EBEFF6;
font-weight: bold;
border: 1px solid #C4CFE5;
margin: 2px 0px 2px 0;
padding: 2px 10px;
white-space: nowrap;
vertical-align: top;
}
td.indexvalue {
background-color: #EBEFF6;
border: 1px solid #C4CFE5;
padding: 2px 10px;
margin: 2px 0px;
}
tr.memlist {
background-color: #EEF1F7;
}
p.formulaDsp {
text-align: center;
}
img.formulaDsp {
}
img.formulaInl {
vertical-align: middle;
}
div.center {
text-align: center;
margin-top: 0px;
margin-bottom: 0px;
padding: 0px;
}
div.center img {
border: 0px;
}
address.footer {
text-align: right;
padding-right: 12px;
}
img.footer {
border: 0px;
vertical-align: middle;
}
/* @group Code Colorization */
span.keyword {
color: #008000
}
span.keywordtype {
color: #604020
}
span.keywordflow {
color: #e08000
}
span.comment {
color: #800000
}
span.preprocessor {
color: #806020
}
span.stringliteral {
color: #002080
}
span.charliteral {
color: #008080
}
span.vhdldigit {
color: #ff00ff
}
span.vhdlchar {
color: #000000
}
span.vhdlkeyword {
color: #700070
}
span.vhdllogic {
color: #ff0000
}
blockquote {
background-color: #F7F8FB;
border-left: 2px solid #9CAFD4;
margin: 0 24px 0 4px;
padding: 0 12px 0 16px;
}
/* @end */
/*
.search {
color: #003399;
font-weight: bold;
}
form.search {
margin-bottom: 0px;
margin-top: 0px;
}
input.search {
font-size: 75%;
color: #000080;
font-weight: normal;
background-color: #e8eef2;
}
*/
td.tiny {
font-size: 75%;
}
.dirtab {
padding: 4px;
border-collapse: collapse;
border: 1px solid #A3B4D7;
}
th.dirtab {
background: #EBEFF6;
font-weight: bold;
}
hr {
height: 0px;
border: none;
border-top: 1px solid #4A6AAA;
}
hr.footer {
height: 1px;
}
/* @group Member Descriptions */
table.memberdecls {
border-spacing: 0px;
padding: 0px;
}
.memberdecls td, .fieldtable tr {
-webkit-transition-property: background-color, box-shadow;
-webkit-transition-duration: 0.5s;
-moz-transition-property: background-color, box-shadow;
-moz-transition-duration: 0.5s;
-ms-transition-property: background-color, box-shadow;
-ms-transition-duration: 0.5s;
-o-transition-property: background-color, box-shadow;
-o-transition-duration: 0.5s;
transition-property: background-color, box-shadow;
transition-duration: 0.5s;
}
.memberdecls td.glow, .fieldtable tr.glow {
background-color: cyan;
box-shadow: 0 0 15px cyan;
}
.mdescLeft, .mdescRight,
.memItemLeft, .memItemRight,
.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
background-color: #F9FAFC;
border: none;
margin: 4px;
padding: 1px 0 0 8px;
}
.mdescLeft, .mdescRight {
padding: 0px 8px 4px 8px;
color: #555;
}
.memSeparator {
border-bottom: 1px solid #DEE4F0;
line-height: 1px;
margin: 0px;
padding: 0px;
}
.memItemLeft, .memTemplItemLeft {
white-space: nowrap;
}
.memItemRight {
width: 100%;
}
.memTemplParams {
color: #4665A2;
white-space: nowrap;
font-size: 80%;
}
/* @end */
/* @group Member Details */
/* Styles for detailed member documentation */
.memtemplate {
font-size: 80%;
color: #4665A2;
font-weight: normal;
margin-left: 9px;
}
.memnav {
background-color: #EBEFF6;
border: 1px solid #A3B4D7;
text-align: center;
margin: 2px;
margin-right: 15px;
padding: 2px;
}
.mempage {
width: 100%;
}
.memitem {
padding: 0;
margin-bottom: 10px;
margin-right: 5px;
-webkit-transition: box-shadow 0.5s linear;
-moz-transition: box-shadow 0.5s linear;
-ms-transition: box-shadow 0.5s linear;
-o-transition: box-shadow 0.5s linear;
transition: box-shadow 0.5s linear;
display: table;
width: 100%;
}
.memitem.glow {
box-shadow: 0 0 15px cyan;
}
.memname {
font-weight: bold;
margin-left: 6px;
}
.memname td {
vertical-align: bottom;
}
.memproto, dl.reflist dt {
border-top: 1px solid #A8B8D9;
border-left: 1px solid #A8B8D9;
border-right: 1px solid #A8B8D9;
padding: 6px 0px 6px 0px;
color: #253555;
font-weight: bold;
text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
background-image:url('nav_f.png');
background-repeat:repeat-x;
background-color: #E2E8F2;
/* opera specific markup */
box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
border-top-right-radius: 4px;
border-top-left-radius: 4px;
/* firefox specific markup */
-moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
-moz-border-radius-topright: 4px;
-moz-border-radius-topleft: 4px;
/* webkit specific markup */
-webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-webkit-border-top-right-radius: 4px;
-webkit-border-top-left-radius: 4px;
}
.memdoc, dl.reflist dd {
border-bottom: 1px solid #A8B8D9;
border-left: 1px solid #A8B8D9;
border-right: 1px solid #A8B8D9;
padding: 6px 10px 2px 10px;
background-color: #FBFCFD;
border-top-width: 0;
background-image:url('nav_g.png');
background-repeat:repeat-x;
background-color: #FFFFFF;
/* opera specific markup */
border-bottom-left-radius: 4px;
border-bottom-right-radius: 4px;
box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
/* firefox specific markup */
-moz-border-radius-bottomleft: 4px;
-moz-border-radius-bottomright: 4px;
-moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
/* webkit specific markup */
-webkit-border-bottom-left-radius: 4px;
-webkit-border-bottom-right-radius: 4px;
-webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
}
dl.reflist dt {
padding: 5px;
}
dl.reflist dd {
margin: 0px 0px 10px 0px;
padding: 5px;
}
.paramkey {
text-align: right;
}
.paramtype {
white-space: nowrap;
}
.paramname {
color: #602020;
white-space: nowrap;
}
.paramname em {
font-style: normal;
}
.paramname code {
line-height: 14px;
}
.params, .retval, .exception, .tparams {
margin-left: 0px;
padding-left: 0px;
}
.params .paramname, .retval .paramname {
font-weight: bold;
vertical-align: top;
}
.params .paramtype {
font-style: italic;
vertical-align: top;
}
.params .paramdir {
font-family: "courier new",courier,monospace;
vertical-align: top;
}
table.mlabels {
border-spacing: 0px;
}
td.mlabels-left {
width: 100%;
padding: 0px;
}
td.mlabels-right {
vertical-align: bottom;
padding: 0px;
white-space: nowrap;
}
span.mlabels {
margin-left: 8px;
}
span.mlabel {
background-color: #728DC1;
border-top:1px solid #5373B4;
border-left:1px solid #5373B4;
border-right:1px solid #C4CFE5;
border-bottom:1px solid #C4CFE5;
text-shadow: none;
color: white;
margin-right: 4px;
padding: 2px 3px;
border-radius: 3px;
font-size: 7pt;
white-space: nowrap;
vertical-align: middle;
}
/* @end */
/* these are for tree view inside a (index) page */
div.directory {
margin: 10px 0px;
border-top: 1px solid #9CAFD4;
border-bottom: 1px solid #9CAFD4;
width: 100%;
}
.directory table {
border-collapse:collapse;
}
.directory td {
margin: 0px;
padding: 0px;
vertical-align: top;
}
.directory td.entry {
white-space: nowrap;
padding-right: 6px;
padding-top: 3px;
}
.directory td.entry a {
outline:none;
}
.directory td.entry a img {
border: none;
}
.directory td.desc {
width: 100%;
padding-left: 6px;
padding-right: 6px;
padding-top: 3px;
border-left: 1px solid rgba(0,0,0,0.05);
}
.directory tr.even {
padding-left: 6px;
background-color: #F7F8FB;
}
.directory img {
vertical-align: -30%;
}
.directory .levels {
white-space: nowrap;
width: 100%;
text-align: right;
font-size: 9pt;
}
.directory .levels span {
cursor: pointer;
padding-left: 2px;
padding-right: 2px;
color: #3D578C;
}
.arrow {
color: #9CAFD4;
-webkit-user-select: none;
-khtml-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
cursor: pointer;
font-size: 80%;
display: inline-block;
width: 16px;
height: 22px;
}
.icon {
font-family: Arial, Helvetica;
font-weight: bold;
font-size: 12px;
height: 14px;
width: 16px;
display: inline-block;
background-color: #728DC1;
color: white;
text-align: center;
border-radius: 4px;
margin-left: 2px;
margin-right: 2px;
}
.icona {
width: 24px;
height: 22px;
display: inline-block;
}
.iconfopen {
width: 24px;
height: 18px;
margin-bottom: 4px;
background-image:url('folderopen.png');
background-position: 0px -4px;
background-repeat: repeat-y;
vertical-align:top;
display: inline-block;
}
.iconfclosed {
width: 24px;
height: 18px;
margin-bottom: 4px;
background-image:url('folderclosed.png');
background-position: 0px -4px;
background-repeat: repeat-y;
vertical-align:top;
display: inline-block;
}
.icondoc {
width: 24px;
height: 18px;
margin-bottom: 4px;
background-image:url('doc.png');
background-position: 0px -4px;
background-repeat: repeat-y;
vertical-align:top;
display: inline-block;
}
table.directory {
font: 400 14px Roboto,sans-serif;
}
/* @end */
div.dynheader {
margin-top: 8px;
-webkit-touch-callout: none;
-webkit-user-select: none;
-khtml-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
address {
font-style: normal;
color: #2A3D61;
}
table.doxtable {
border-collapse:collapse;
margin-top: 4px;
margin-bottom: 4px;
}
table.doxtable td, table.doxtable th {
border: 1px solid #2D4068;
padding: 3px 7px 2px;
}
table.doxtable th {
background-color: #374F7F;
color: #FFFFFF;
font-size: 110%;
padding-bottom: 4px;
padding-top: 5px;
}
table.fieldtable {
/*width: 100%;*/
margin-bottom: 10px;
border: 1px solid #A8B8D9;
border-spacing: 0px;
-moz-border-radius: 4px;
-webkit-border-radius: 4px;
border-radius: 4px;
-moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
-webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
}
.fieldtable td, .fieldtable th {
padding: 3px 7px 2px;
}
.fieldtable td.fieldtype, .fieldtable td.fieldname {
white-space: nowrap;
border-right: 1px solid #A8B8D9;
border-bottom: 1px solid #A8B8D9;
vertical-align: top;
}
.fieldtable td.fieldname {
padding-top: 3px;
}
.fieldtable td.fielddoc {
border-bottom: 1px solid #A8B8D9;
/*width: 100%;*/
}
.fieldtable td.fielddoc p:first-child {
margin-top: 0px;
}
.fieldtable td.fielddoc p:last-child {
margin-bottom: 2px;
}
.fieldtable tr:last-child td {
border-bottom: none;
}
.fieldtable th {
background-image:url('nav_f.png');
background-repeat:repeat-x;
background-color: #E2E8F2;
font-size: 90%;
color: #253555;
padding-bottom: 4px;
padding-top: 5px;
text-align:left;
-moz-border-radius-topleft: 4px;
-moz-border-radius-topright: 4px;
-webkit-border-top-left-radius: 4px;
-webkit-border-top-right-radius: 4px;
border-top-left-radius: 4px;
border-top-right-radius: 4px;
border-bottom: 1px solid #A8B8D9;
}
.tabsearch {
top: 0px;
left: 10px;
height: 36px;
background-image: url('tab_b.png');
z-index: 101;
overflow: hidden;
font-size: 13px;
}
.navpath ul
{
font-size: 11px;
background-image:url('tab_b.png');
background-repeat:repeat-x;
background-position: 0 -5px;
height:30px;
line-height:30px;
color:#8AA0CC;
border:solid 1px #C2CDE4;
overflow:hidden;
margin:0px;
padding:0px;
}
.navpath li
{
list-style-type:none;
float:left;
padding-left:10px;
padding-right:15px;
background-image:url('bc_s.png');
background-repeat:no-repeat;
background-position:right;
color:#364D7C;
}
.navpath li.navelem a
{
height:32px;
display:block;
text-decoration: none;
outline: none;
color: #283A5D;
font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
text-decoration: none;
}
.navpath li.navelem a:hover
{
color:#6884BD;
}
.navpath li.footer
{
list-style-type:none;
float:right;
padding-left:10px;
padding-right:15px;
background-image:none;
background-repeat:no-repeat;
background-position:right;
color:#364D7C;
font-size: 8pt;
}
div.summary
{
float: right;
font-size: 8pt;
padding-right: 5px;
width: 50%;
text-align: right;
}
div.summary a
{
white-space: nowrap;
}
div.ingroups
{
font-size: 8pt;
width: 50%;
text-align: left;
}
div.ingroups a
{
white-space: nowrap;
}
div.header
{
background-image:url('nav_h.png');
background-repeat:repeat-x;
background-color: #F9FAFC;
margin: 0px;
border-bottom: 1px solid #C4CFE5;
}
div.headertitle
{
padding: 5px 5px 5px 10px;
}
dl
{
padding: 0 0 0 10px;
}
/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
dl.section
{
margin-left: 0px;
padding-left: 0px;
}
dl.note
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #D0C000;
}
dl.warning, dl.attention
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #FF0000;
}
dl.pre, dl.post, dl.invariant
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #00D000;
}
dl.deprecated
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #505050;
}
dl.todo
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #00C0E0;
}
dl.test
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #3030E0;
}
dl.bug
{
margin-left:-7px;
padding-left: 3px;
border-left:4px solid;
border-color: #C08050;
}
dl.section dd {
margin-bottom: 6px;
}
#projectlogo
{
text-align: center;
vertical-align: bottom;
border-collapse: separate;
}
#projectlogo img
{
border: 0px none;
}
#projectalign
{
vertical-align: middle;
}
#projectname
{
font: 300% Tahoma, Arial,sans-serif;
margin: 0px;
padding: 2px 0px;
}
#projectbrief
{
font: 120% Tahoma, Arial,sans-serif;
margin: 0px;
padding: 0px;
}
#projectnumber
{
font: 50% Tahoma, Arial,sans-serif;
margin: 0px;
padding: 0px;
}
#titlearea
{
padding: 0px;
margin: 0px;
width: 100%;
border-bottom: 1px solid #5373B4;
}
.image
{
text-align: center;
}
.dotgraph
{
text-align: center;
}
.mscgraph
{
text-align: center;
}
.diagraph
{
text-align: center;
}
.caption
{
font-weight: bold;
}
div.zoom
{
border: 1px solid #90A5CE;
}
dl.citelist {
margin-bottom:50px;
}
dl.citelist dt {
color:#334975;
float:left;
font-weight:bold;
margin-right:10px;
padding:5px;
}
dl.citelist dd {
margin:2px 0;
padding:5px 0;
}
div.toc {
padding: 14px 25px;
background-color: #F4F6FA;
border: 1px solid #D8DFEE;
border-radius: 7px 7px 7px 7px;
float: right;
height: auto;
margin: 0 20px 10px 10px;
width: 200px;
}
div.toc li {
background: url("bdwn.png") no-repeat scroll 0 5px transparent;
font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
margin-top: 5px;
padding-left: 10px;
padding-top: 2px;
}
div.toc h3 {
font: bold 12px/1.2 Arial,FreeSans,sans-serif;
color: #4665A2;
border-bottom: 0 none;
margin: 0;
}
div.toc ul {
list-style: none outside none;
border: medium none;
padding: 0px;
}
div.toc li.level1 {
margin-left: 0px;
}
div.toc li.level2 {
margin-left: 15px;
}
div.toc li.level3 {
margin-left: 30px;
}
div.toc li.level4 {
margin-left: 45px;
}
.inherit_header {
font-weight: bold;
color: gray;
cursor: pointer;
-webkit-touch-callout: none;
-webkit-user-select: none;
-khtml-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
.inherit_header td {
padding: 6px 0px 2px 5px;
}
.inherit {
display: none;
}
tr.heading h2 {
margin-top: 12px;
margin-bottom: 4px;
}
/* tooltip related style info */
.ttc {
position: absolute;
display: none;
}
#powerTip {
cursor: default;
white-space: nowrap;
background-color: white;
border: 1px solid gray;
border-radius: 4px 4px 4px 4px;
box-shadow: 1px 1px 7px gray;
display: none;
font-size: smaller;
max-width: 80%;
opacity: 0.9;
padding: 1ex 1em 1em;
position: absolute;
z-index: 2147483647;
}
#powerTip div.ttdoc {
color: grey;
font-style: italic;
}
#powerTip div.ttname a {
font-weight: bold;
}
#powerTip div.ttname {
font-weight: bold;
}
#powerTip div.ttdeci {
color: #006318;
}
#powerTip div {
margin: 0px;
padding: 0px;
font: 12px/16px Roboto,sans-serif;
}
#powerTip:before, #powerTip:after {
content: "";
position: absolute;
margin: 0px;
}
#powerTip.n:after, #powerTip.n:before,
#powerTip.s:after, #powerTip.s:before,
#powerTip.w:after, #powerTip.w:before,
#powerTip.e:after, #powerTip.e:before,
#powerTip.ne:after, #powerTip.ne:before,
#powerTip.se:after, #powerTip.se:before,
#powerTip.nw:after, #powerTip.nw:before,
#powerTip.sw:after, #powerTip.sw:before {
border: solid transparent;
content: " ";
height: 0;
width: 0;
position: absolute;
}
#powerTip.n:after, #powerTip.s:after,
#powerTip.w:after, #powerTip.e:after,
#powerTip.nw:after, #powerTip.ne:after,
#powerTip.sw:after, #powerTip.se:after {
border-color: rgba(255, 255, 255, 0);
}
#powerTip.n:before, #powerTip.s:before,
#powerTip.w:before, #powerTip.e:before,
#powerTip.nw:before, #powerTip.ne:before,
#powerTip.sw:before, #powerTip.se:before {
border-color: rgba(128, 128, 128, 0);
}
#powerTip.n:after, #powerTip.n:before,
#powerTip.ne:after, #powerTip.ne:before,
#powerTip.nw:after, #powerTip.nw:before {
top: 100%;
}
#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
border-top-color: #ffffff;
border-width: 10px;
margin: 0px -10px;
}
#powerTip.n:before {
border-top-color: #808080;
border-width: 11px;
margin: 0px -11px;
}
#powerTip.n:after, #powerTip.n:before {
left: 50%;
}
#powerTip.nw:after, #powerTip.nw:before {
right: 14px;
}
#powerTip.ne:after, #powerTip.ne:before {
left: 14px;
}
#powerTip.s:after, #powerTip.s:before,
#powerTip.se:after, #powerTip.se:before,
#powerTip.sw:after, #powerTip.sw:before {
bottom: 100%;
}
#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after {
border-bottom-color: #ffffff;
border-width: 10px;
margin: 0px -10px;
}
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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 \
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src/.deps/pdata-Memleak_check.Po deleted 100644 → 0
View file @ 665076bb
pdata-Memleak_check.o: ../../OpenFPM_data/src/Memleak_check.cpp \
/usr/include/stdc-predef.h ../src/config/config.h \
../../OpenFPM_data/src/Memleak_check.hpp /usr/include/c++/4.9.2/iostream \
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metis_util.hpp ../../metis_install/include/metis.h \
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../../OpenFPM_data/src/NN/CellList/CellList.hpp \
../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
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../../OpenFPM_data/src/NN/CellList/CellNNIterator.hpp \
../../OpenFPM_data/src/NN/CellList/CellListBal.hpp \
../../OpenFPM_data/src/NN/CellList/CellListMem.hpp \
../../OpenFPM_data/src/Space/Ghost.hpp ../../OpenFPM_IO/src/util.hpp \
unit_test_init_cleanup.hpp Decomposition/CartDecomposition_unit_test.hpp \
Decomposition/CartDecomposition.hpp Decomposition/ORB_unit_test.hpp \
Decomposition/ORB.hpp ../../OpenFPM_data/src/data_type/scalar.hpp \
Graph/CartesianGraphFactory_unit_test.hpp \
Graph/CartesianGraphFactory.hpp metis_util_unit_test.hpp metis_util.hpp \
dec_optimizer_unit_test.hpp dec_optimizer.hpp \
Grid/grid_dist_id_unit_test.hpp Grid/grid_dist_id.hpp \
Vector/vector_dist_unit_test.hpp Vector/vector_dist.hpp \
Vector/vector_dist_iterator.hpp Vector/vector_dist_key.hpp \
Vector/vector_dist_key.hpp \
../../OpenFPM_devices/src/memory/PreAllocHeapMemory.hpp \
../../OpenFPM_devices/src/memory/HeapMemory.hpp \
../../OpenFPM_IO/src/CSVWriter.hpp \
../../OpenFPM_IO/src/csv_multiarray.hpp
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Decomposition/CartDecomposition.hpp:
Decomposition/ORB_unit_test.hpp:
Decomposition/ORB.hpp:
../../OpenFPM_data/src/data_type/scalar.hpp:
Graph/CartesianGraphFactory_unit_test.hpp:
Graph/CartesianGraphFactory.hpp:
metis_util_unit_test.hpp:
metis_util.hpp:
dec_optimizer_unit_test.hpp:
dec_optimizer.hpp:
Grid/grid_dist_id_unit_test.hpp:
Grid/grid_dist_id.hpp:
Vector/vector_dist_unit_test.hpp:
Vector/vector_dist.hpp:
Vector/vector_dist_iterator.hpp:
Vector/vector_dist_key.hpp:
Vector/vector_dist_key.hpp:
../../OpenFPM_devices/src/memory/PreAllocHeapMemory.hpp:
../../OpenFPM_devices/src/memory/HeapMemory.hpp:
../../OpenFPM_IO/src/CSVWriter.hpp:
../../OpenFPM_IO/src/csv_multiarray.hpp:
src/Amr/grid_dist_amr.hpp 0 → 100644
View file @ b9ccc50e
/*
* grid_amr_dist.hpp
*
* Created on: Sep 21, 2017
* Author: i-bird
*/
#ifndef AMR_GRID_AMR_DIST_HPP_
#define AMR_GRID_AMR_DIST_HPP_
#define OPENFPM_DATA_ENABLE_IO_MODULE
#include "Grid/grid_dist_id.hpp"
#include "Amr/grid_dist_amr_key_iterator.hpp"
#ifdef __NVCC__
#include "SparseGridGpu/SparseGridGpu.hpp"
#endif
#define AMR_IMPL_TRIVIAL 1
#define AMR_IMPL_PATCHES 2
#define AMR_IMPL_OPENVDB 3
template<typename Decomposition, typename garray>
class Decomposition_encap
{
Decomposition & dec;
garray & gd_array;
public:
Decomposition_encap(Decomposition & dec, garray & gd_array)
:dec(dec),gd_array(gd_array)
{}
Decomposition & internal_dec() const
{
return dec;
}
/*! \brief Start decomposition
*
*/
void decompose()
{
dec.decompose();
for(size_t i = 0 ; i < gd_array.size() ; i++)
{
Ghost<Decomposition::dims,typename Decomposition::stype> gold = gd_array.get(i).getDecomposition().getGhost();
gd_array.get(i).getDecomposition() = dec.duplicate(gold);
}
}
/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
*
* \param ts number of time step from the previous load balancing
*
*/
void refine(size_t ts)
{
dec.refine();
for(size_t i = 0 ; i < gd_array.size() ; i++)
{
Ghost<Decomposition::dims,typename Decomposition::stype> gold = gd_array.get(i).getDecomposition().getGhost();
gd_array.get(i).getDecomposition() = dec.duplicate(gold);
}
}
/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
*
* \param ts number of time step from the previous load balancing
*
*/
void redecompose(size_t ts)
{
dec.redecompose();
for(size_t i = 0 ; i < gd_array.size() ; i++)
{
Ghost<Decomposition::dims,typename Decomposition::stype> gold = gd_array.get(i).getDecomposition().getGhost();
gd_array.get(i).getDecomposition() = dec.duplicate(gold);
}
}
auto getDistribution() -> decltype(dec.getDistribution())
{
return dec.getDistribution();
}
Decomposition_encap<Decomposition,garray> operator=(const Decomposition_encap<Decomposition,garray> & de) const
{
for(size_t i = 0 ; i < gd_array.size() ; i++)
{gd_array.get(i).getDecomposition() = de.gd_array.get(i).getDecomposition();}
return *this;
}
bool write(std::string output) const
{
return dec.write(output);
}
};
template<unsigned int dim,
typename St,
typename T,
unsigned int impl=AMR_IMPL_TRIVIAL ,
typename Decomposition = CartDecomposition<dim,St>,
typename Memory=HeapMemory ,
typename device_grid=grid_cpu<dim,T> >
class grid_dist_amr
{
};
/*! \brief AMR Adaptive Multi Resolution Grid
*
* \tparam dim Dimensionality
* \tparam St type of space
* \tparam T what each point of the grid store
* \tparam Decomposition type of decomposition
*
*/
template<unsigned int dim,
typename St,
typename T,
typename Decomposition,
typename Memory,
typename device_grid >
class grid_dist_amr<dim,St,T,AMR_IMPL_TRIVIAL,Decomposition,Memory,device_grid>
{
//! Simulation domain
Box<dim,St> domain;
//! Ghost integer
Ghost<dim,long int> g_int;
//! Boundary conditions of the structure
periodicity<dim> bc;
//! array of grids
//
openfpm::vector<grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>,
HeapMemory,
memory_traits_lin,
openfpm::grow_policy_identity,STD_VECTOR> gd_array;
//! Type of structure sub-grid iterator
typedef decltype(device_grid::type_of_subiterator()) device_sub_it;
//! Type of structure for the grid iterator
typedef decltype(device_grid::type_of_iterator()) device_it;
//! Domain iterator for each distributed grid
openfpm::vector<grid_dist_iterator<dim,device_grid,device_sub_it,FREE>> git;
//! Domain and ghost iterator for each distributed grid
openfpm::vector<grid_dist_iterator<dim,device_grid,device_it,FIXED>> git_g;
//! Iterator for each distributed grid
openfpm::vector<grid_dist_iterator_sub<dim,device_grid>> git_sub;
//! Moving offsets
openfpm::vector<openfpm::vector<offset_mv<dim>>> mv_off;
//! background level
T bck;
/*! \brief Initialize the others levels
*
* \param n_grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>lvl number of levels
* \param g_sz_lvl grid size on each level
*
*/
void initialize_other(size_t n_lvl, size_t (& g_sz_lvl)[dim])
{
for (size_t i = 0; i < n_lvl - 1 ; i++)
{
for (size_t j = 0 ; j < dim ; j++)
{
if (bc.bc[j] == NON_PERIODIC)
{g_sz_lvl[j] = (g_sz_lvl[j]-1)*2 + 1;}
else
{g_sz_lvl[j] = g_sz_lvl[j]*2;}
}
gd_array.add(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>(gd_array.get(0).getDecomposition(),g_sz_lvl,g_int));
gd_array.last().setBackgroundValue(bck);
gd_array.last().getDecomposition().free_geo_cell();
gd_array.last().getDecomposition().getDistribution().destroy_internal_graph();
gd_array.last().getDecomposition().free_fines();
}
recalculate_mvoff();
}
public:
/*! \brief Constructor
*
* \param domain Simulation domain
* \param g ghost extension
*
*/
grid_dist_amr(const Box<dim,St> & domain, const Ghost<dim,long int> & g)
:domain(domain),g_int(g)
{
// set boundary consitions to non periodic
for (size_t i = 0; i < dim ; i++)
{bc.bc[i] = NON_PERIODIC;}
}
/*! \brief Constructor
*
* \param domain Simulation domain
* \param g ghost extension
* \param bc boundary conditions
*
*/
grid_dist_amr(const Box<dim,St> & domain, const Ghost<dim,long int> & g, periodicity<dim> & bc)
:domain(domain),g_int(g),bc(bc)
{
}
/*! \brief Initialize the amr grid
*
* \param dec Decomposition (this parameter is useful in case we want to constrain the AMR to an external decomposition)
* \param n_lvl maximum number of levels (0 mean no additional levels)
* \param g_sz coarsest grid size on each direction
*
*/
void initLevels(const Decomposition & dec, size_t n_lvl,const size_t (& g_sz)[dim])
{
size_t g_sz_lvl[dim];
for (size_t i = 0; i < dim ; i++)
{g_sz_lvl[i] = g_sz[i];}
// Add the coarse level
gd_array.add(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>(dec,g_sz,g_int));
gd_array.last().setBackgroundValue(bck);
initialize_other(n_lvl,g_sz_lvl);
}
/*! \brief Initialize the amr grid
*
* \param dec Decomposition (this parameter is useful in case we want to constrain the AMR to an external decomposition)
* \param n_lvl maximum number of levels (0 mean no additional levels)
* \param g_sz coarsest grid size on each direction
*
*/
template<typename TT> void initLevels(const Decomposition_encap<Decomposition,TT> & dec, size_t n_lvl,const size_t (& g_sz)[dim])
{
initLevels(dec.internal_dec(),n_lvl,g_sz);
}
/*! \brief Recalculate the offset array for the moveLvlUp and moveLvlDw
*
*
*
*/
void recalculate_mvoff()
{
// Here we calculate the offset to move one level up and one level down
// in global coordinated moving one level up is multiply the coordinates by 2
// and moving one level down is dividing by 2. In local coordinates is the same
// with the exception that because of the decomposition you can have an offset
// look at the picture below
//
// (-1) (0)
// * | * * coarse level
// * |* * * * finer level
// |(0)(1)
//
// Line of the decomposition
//
// The coarse level point 0 in local coordinates converted to the finer level is not
// just 2*0 = 0 but is 2*(0) + 1 so a formula like 2*x+offset is required. here we calculate
// these offset. In the case of moving from finer to coarse is the same the formula is
// Integer_round(x+1)/2 - 1
//
mv_off.resize(gd_array.size());
for (size_t i = 1 ; i < gd_array.size() ; i++)
{
auto & g_box_c = gd_array.get(i-1).getLocalGridsInfo();
auto & g_box_f = gd_array.get(i).getLocalGridsInfo();
#ifdef SE_CLASS1
if (g_box_c.size() != g_box_f.size())
{
std::cerr << __FILE__ << ":" << __LINE__ << " error it seem that the AMR construction between level " <<
i << " and " << i-1 << " is inconsistent" << std::endl;
}
#endif
mv_off.get(i-1).resize(g_box_f.size());
mv_off.get(i).resize(g_box_f.size());
for (size_t j = 0 ; j < g_box_f.size() ; j++)
{
for (size_t s = 0 ; s < dim ; s++)
{
size_t d_orig_c = g_box_c.get(j).origin.get(s);
size_t d_orig_f = g_box_f.get(j).origin.get(s);
mv_off.get(i-1).get(j).dw.get(s) = d_orig_c*2 - d_orig_f;
mv_off.get(i).get(j).up.get(s) = d_orig_c*2 - d_orig_f;
}
}
}
}
/*! \brief Initialize the amr grid
*
* \param n_lvl maximum number of levels (0 mean no additional levels)
* \param g_sz coarsest grid size on each direction
* \param opt options
*
*/
void initLevels(size_t n_lvl,const size_t (& g_sz)[dim], size_t opt = 0)
{
size_t g_sz_lvl[dim];
for (size_t i = 0; i < dim ; i++)
{g_sz_lvl[i] = g_sz[i];}
// Add the coarse level
gd_array.add(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>(g_sz,domain,g_int,bc,opt));
initialize_other(n_lvl,g_sz_lvl);
}
/*! \brief Add the computation cost on the decomposition using a resolution function
*
*
* \param md Model to use
* \param ts It is an optional parameter approximately should be the number of ghost get between two
* rebalancing at first decomposition this number can be ignored (default = 1) because not used
*
*/
template <typename Model>inline void addComputationCosts(Model md=Model(), size_t ts = 1)
{
gd_array.get(0).addComputationCosts(md,ts);
}
/*! \brief Get the object that store the information about the decomposition
*
* \return the decomposition object
*
*/
Decomposition_encap<Decomposition,decltype(gd_array)> getDecomposition()
{
Decomposition_encap<Decomposition,decltype(gd_array)> tmp(gd_array.get(0).getDecomposition(),gd_array);
return tmp;
}
/*! \brief Get the underlying grid level
*
* \param lvl level
*
* \return the grid level
*
*/
grid_dist_id<dim,St,T,Decomposition,Memory,device_grid> & getLevel(size_t lvl)
{
return gd_array.get(lvl);
}
grid_dist_amr_key_iterator<dim,device_grid,
decltype(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>::type_of_subiterator()),
decltype(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>::type_of_subiterator()) >
getDomainIteratorCells()
{
git_sub.clear();
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
grid_key_dx<dim> start;
grid_key_dx<dim> stop;
for (size_t j = 0 ; j < dim ; j++)
{
start.set_d(j,0);
if (bc.bc[j] == NON_PERIODIC)
{stop.set_d(j,getGridInfoVoid(i).size(j) - 2);}
else
{stop.set_d(j,getGridInfoVoid(i).size(j) - 1);}
}
git_sub.add(gd_array.get(i).getSubDomainIterator(start,stop));
}
return grid_dist_amr_key_iterator<dim,device_grid,
decltype(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>::type_of_subiterator()),
decltype(grid_dist_id<dim,St,T,Decomposition,Memory,device_grid>::type_of_subiterator())>(git_sub);
}
grid_dist_iterator_sub<dim,device_grid> getDomainIteratorCells(size_t lvl)
{
grid_key_dx<dim> start;
grid_key_dx<dim> stop;
for (size_t j = 0 ; j < dim ; j++)
{
start.set_d(j,0);
if (bc.bc[j] == NON_PERIODIC)
{stop.set_d(j,getGridInfoVoid(lvl).size(j) - 2);}
else
{stop.set_d(j,getGridInfoVoid(lvl).size(j) - 1);}
}
return gd_array.get(lvl).getSubDomainIterator(start,stop);
}
/*! \brief Get an iterator to the grid
*
* \return an iterator to the grid
*
*/
auto getGridGhostIterator(size_t lvl) -> decltype(gd_array.get(lvl).getGridGhostIterator(grid_key_dx<dim>(),grid_key_dx<dim>()))
{
grid_key_dx<dim> key_start;
grid_key_dx<dim> key_stop;
for (size_t i = 0 ; i < dim ; i++)
{
key_start.set_d(i,g_int.getLow(i));
key_stop.set_d(i,g_int.getHigh(i) + getGridInfoVoid(lvl).size(i) -1);
}
return gd_array.get(lvl).getGridGhostIterator(key_start,key_stop);
}
/*! \brief Get an iterator to the grid
*
* \return an iterator to the grid
*
*/
auto getGridIterator(size_t lvl) -> decltype(gd_array.get(lvl).getGridIterator())
{
return gd_array.get(lvl).getGridIterator();
}
/*! \brief Get an iterator to the grid
*
* \return an iterator to the grid
*
*/
auto getGridIterator(size_t lvl, grid_key_dx<dim> & start, grid_key_dx<dim> & stop) -> decltype(gd_array.get(lvl).getGridIterator(start,stop))
{
return gd_array.get(lvl).getGridIterator(start,stop);
}
#ifdef __NVCC__
/*! \brief Get an iterator to the grid
*
* \return an iterator to the grid
*
*/
auto getGridIteratorGPU(size_t lvl) -> decltype(gd_array.get(lvl).getGridIteratorGPU())
{
return gd_array.get(lvl).getGridIteratorGPU();
}
#endif
/*! \brief Get an iterator to the grid
*
* \return an iterator to the grid
*
*/
auto getGridIteratorCells(size_t lvl) -> decltype(gd_array.get(lvl).getGridIterator())
{
grid_key_dx<dim> start;
grid_key_dx<dim> stop;
for (size_t j = 0 ; j < dim ; j++)
{
start.set_d(j,0);
if (bc.bc[j] == NON_PERIODIC)
{stop.set_d(j,getGridInfoVoid(lvl).size(j) - 2);}
else
{stop.set_d(j,getGridInfoVoid(lvl).size(j) - 1);}
}
return gd_array.get(lvl).getGridIterator(start,stop);
}
/*! \brief return an iterator over the level lvl
*
* \param lvl level
*
* \return an iterator over the level lvl selected
*
*/
grid_dist_iterator<dim,device_grid,decltype(device_grid::type_of_subiterator()),FREE>
getDomainIterator(size_t lvl) const
{
return gd_array.get(lvl).getDomainIterator();
}
/*! \brief return an iterator over the level lvl
*
* \param lvl level
*
* \return an iterator over the level lvl selected
*
*/
grid_dist_iterator<dim,device_grid,
decltype(device_grid::type_of_iterator()),
FIXED>
getDomainGhostIterator(size_t lvl) const
{
return gd_array.get(lvl).getDomainGhostIterator();
}
/*! \brief Get domain iterator
*
* \return an iterator over all the grid levels
*
*/
grid_dist_amr_key_iterator<dim,device_grid, decltype(device_grid::type_of_subiterator())>
getDomainIterator()
{
git.clear();
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
git.add(gd_array.get(i).getDomainIterator());
}
return grid_dist_amr_key_iterator<dim,device_grid,decltype(device_grid::type_of_subiterator())>(git);
}
/*! \brief Get domain iterator
*
* \return an iterator over all the grid levels
*
*/
grid_dist_amr_key_iterator<dim,device_grid, decltype(device_grid::type_of_iterator()),
grid_dist_iterator<dim,device_grid,decltype(device_grid::type_of_iterator()),FIXED>>
getDomainGhostIterator()
{
git_g.clear();
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
git_g.add(gd_array.get(i).getDomainGhostIterator());
}
return grid_dist_amr_key_iterator<dim,device_grid,decltype(device_grid::type_of_iterator()),
grid_dist_iterator<dim,device_grid,decltype(device_grid::type_of_iterator()),FIXED>>(git_g);
}
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
* \param v1 grid_key that identify the element in the grid
*
* \return the selected element
*
*/
template <unsigned int p>inline auto get(const grid_dist_amr_key<dim> & v1) const -> decltype(gd_array.get(v1.getLvl()).template get<p>(v1.getKey()))
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(v1.getLvl()).template get<p>(v1.getKey());
}
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
* \param v1 grid_key that identify the element in the grid
*
* \return the selected element
*
*/
template <unsigned int p>inline auto get(const grid_dist_amr_key<dim> & v1) -> decltype(gd_array.get(v1.getLvl()).template get<p>(v1.getKey()))
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(v1.getLvl()).template get<p>(v1.getKey());
}
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
* \param v1 grid_key that identify the element in the grid
*
* \return the selected element
*
*/
template <unsigned int p>inline auto get(size_t lvl, const grid_dist_key_dx<dim> & v1) const -> decltype(gd_array.get(lvl).template get<p>(v1))
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(lvl).template get<p>(v1);
}
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
* \param v1 grid_key that identify the element in the grid
*
* \return the selected element
*
*/
template <unsigned int p>inline auto get(size_t lvl, const grid_dist_key_dx<dim> & v1) -> decltype(gd_array.get(lvl).template get<p>(v1))
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(lvl).template get<p>(v1);
}
//////////////////// Insert functions
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
* \param v1 grid_key that identify the element in the grid
*
* \return the selected element
*
*/
template <unsigned int p>
inline auto insert(const grid_dist_amr_key<dim> & v1)
-> decltype(gd_array.get(v1.getLvl()).template insert<p>(v1.getKey()))
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(v1.getLvl()).template insert<p>(v1.getKey());
}
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
* \param v1 grid_key that identify the element in the grid
*
* \return the selected element
*
*/
template <unsigned int p>inline auto insert(size_t lvl, const grid_dist_key_dx<dim> & v1)
-> decltype(gd_array.get(lvl).template insert<p>(v1))
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(lvl).template insert<p>(v1);
}
//////////////////////////////////////
/*! \brief Get the internal distributed grid
*
* \param lvl level
*
* \return the internal distributed grid
*
*/
grid_dist_id<dim,St,T,Decomposition,Memory,device_grid> & getDistGrid(size_t lvl)
{
return gd_array.get(lvl);
}
//////////////////// Remove functions
/*! \brief Remove a grid point (this function make sense only in case of
* sparse grid)
*
* \param v1 grid_key that identify the element in the AMR grid to eleminate
*
*/
inline void remove(const grid_dist_amr_key<dim> & v1)
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(v1.getLvl()).remove(v1.getKey());
}
/*! \brief Remove a grid point (this function make sense only in case of
* sparse grid)
*
* \param v1 grid_key that identify the element in the AMR grid to eleminate
*
*/
void remove(size_t lvl, const grid_dist_key_dx<dim> & v1)
{
#ifdef SE_CLASS2
check_valid(this,8);
#endif
return gd_array.get(lvl).remove(v1);
}
/*! \brief construct level connections for padding particles
*
*
*/
void construct_level_connections()
{
for (int lvl = 0 ; lvl < gd_array.size() ; lvl++)
{
if (lvl == 0)
{
gd_array.get(lvl).construct_link_dw(gd_array.get(lvl+1),mv_off.get(lvl));
}
else if (lvl == gd_array.size() - 1)
{gd_array.get(lvl).construct_link_up(gd_array.get(lvl-1),mv_off.get(lvl));}
else
{
gd_array.get(lvl).construct_link_dw(gd_array.get(lvl+1),mv_off.get(lvl));
gd_array.get(lvl).construct_link_up(gd_array.get(lvl-1),mv_off.get(lvl));
}
}
}
/*! \brief construct level connections for padding particles
*
* \tparam stencil_type type of stencil
*
*/
template<typename stencil_type>
void tagBoundaries()
{
for (int lvl = 0 ; lvl < gd_array.size() ; lvl++)
{
gd_array.get(lvl).template tagBoundaries<stencil_type>();
}
}
//////////////////////////////////////
/*! \brief It synchronize the ghost parts
*
* \tparam prp... Properties to synchronize
*
*/
template<int... prp> void ghost_get(size_t opt = 0)
{
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
gd_array.get(i).template ghost_get<prp...>(opt);
}
}
/*! \brief It move all the grid parts that do not belong to the local processor to the respective processor
*
*/
void map(size_t opt = 0)
{
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
gd_array.get(i).map();
}
recalculate_mvoff();
}
/*! \brief Apply the ghost put
*
* \tparam prp... Properties to apply ghost put
*
*/
template<template<typename,typename> class op,int... prp> void ghost_put()
{
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
gd_array.get(i).template ghost_put<op,prp...>();
}
}
/*! \brief Return the number of inserted points on a particular level
*
* \return the number of inserted points
*
*/
size_t size_inserted(size_t lvl)
{
return gd_array.get(lvl).size_local_inserted();
}
/*! \brief set the background value
*
* You can use this function make sense in case of sparse in case of dense
* it does nothing
*
*/
void setBackgroundValue(T & bv)
{
for (size_t i = 0 ; i < getNLvl() ; i++)
{gd_array.get(i).setBackgroundValue(bv);}
meta_copy<T>::meta_copy_(bv,bck);
}
/*! \brief delete all the points in the grid
*
* In case of sparse grid in delete all the inserted points, in case
* of dense it does nothing
*
*/
void clear()
{
for (size_t i = 0 ; i < getNLvl() ; i++)
{gd_array.get(i).clear();}
}
/*! \brief Get an object containing the grid informations for a specific level
*
* \param lvl level
*
* \return an information object about this grid
*
*/
const grid_sm<dim,void> & getGridInfoVoid(size_t lvl) const
{
return gd_array.get(lvl).getGridInfoVoid();
}
/*! \brief Return the maximum number of levels in the AMR struct
*
* \return the number of levels
*
*/
size_t getNLvl()
{
return gd_array.size();
}
/*! \brief Move down (to finer level) the key
*
* \param key multi-resolution AMR key
*
*/
void moveLvlDw(grid_dist_amr_key<dim> & key)
{
#ifdef SE_CLASS1
if (key.getLvl() >= getNLvl() - 1)
{std::cerr << __FILE__ << ":" << __LINE__ << " error: we are already at the last level, we cannot go one level down" << std::endl;}
#endif
auto & key_ref = key.getKeyRef().getKeyRef();
size_t lvl = key.getLvl();
for (size_t i = 0 ; i < dim ; i++)
{
key_ref.set_d(i,(key_ref.get(i) << 1) + mv_off.get(key.getLvl()).get(key.getKeyRef().getSub()).dw.get(i) );
}
key.setLvl(lvl+1);
}
/*! \brief Move down (to finer level) the key
*
* \param lvl level
* \param key multi-resolution AMR key
*
*/
grid_dist_key_dx<dim> moveDw(int lvl, const grid_dist_key_dx<dim> & key)
{
#ifdef SE_CLASS1
if (lvl >= getNLvl() - 1)
{std::cerr << __FILE__ << ":" << __LINE__ << " error: we are already at the last level, we cannot go one level down" << std::endl;}
#endif
grid_dist_key_dx<dim> out;
for (size_t i = 0 ; i < dim ; i++)
{
out.getKeyRef().set_d(i,(key.getKeyRef().get(i) << 1) + mv_off.get(lvl).get(key.getSub()).dw.get(i) );
}
out.setSub(key.getSub());
return out;
}
/*! \brief From a distributed key it return a AMR key that contain also the grid level
*
* \param lvl level
* \param key distributed key
*
*/
inline grid_dist_amr_key<dim> getAMRKey(size_t lvl, grid_dist_key_dx<dim> key)
{
return grid_dist_amr_key<dim>(lvl,key);
}
/*! \brief Move up (to coarser level) the key
*
* \param key multi-resolution AMR key
*
*/
void moveLvlUp(grid_dist_amr_key<dim> & key)
{
#ifdef SE_CLASS1
if (key.getLvl() == 0)
{std::cerr << __FILE__ << ":" << __LINE__ << " error: we are already at the top level, we cannot go one level up" << std::endl;}
#endif
auto & key_ref = key.getKeyRef().getKeyRef();
size_t lvl = key.getLvl();
for (size_t i = 0 ; i < dim ; i++)
{
key_ref.set_d(i,(key_ref.get(i) - mv_off.get(key.getLvl()).get(key.getKeyRef().getSub()).up.get(i)) >> 1);
}
key.setLvl(lvl-1);
}
/*! \brief Move up (to coarser level) the key
*
* \param lvl level
* \param key multi-resolution AMR key
*
*/
grid_dist_key_dx<dim> moveUp(int lvl, const grid_dist_key_dx<dim> & key)
{
#ifdef SE_CLASS1
if (lvl == 0)
{std::cerr << __FILE__ << ":" << __LINE__ << " error: we are already at the top level, we cannot go one level up" << std::endl;}
#endif
grid_dist_key_dx<dim> out;
for (size_t i = 0 ; i < dim ; i++)
{
out.getKeyRef().set_d(i,(key.getKeyRef().get(i) - mv_off.get(lvl).get(key.getSub()).up.get(i)) >> 1);
}
out.setSub(key.getSub());
return out;
}
/*! \brief Get the position on the grid in global coordinates
*
* \param v1 amr key
*
* \return the position in global coordinates
*
*/
grid_key_dx<dim> getGKey(const grid_dist_amr_key<dim> & v1)
{
return gd_array.get(v1.getLvl()).getGKey(v1.getKey());
}
/*! \brief Get the position on the grid in global coordinates
*
* \param lvl level
* \param v1 point in the level
*
* \return the position in global coordinates
*
*/
grid_key_dx<dim> getGKey(int lvl, const grid_dist_key_dx<dim> & v1)
{
return gd_array.get(lvl).getGKey(v1);
}
/*! \brief Get the the position of the point
*
* \param v1 AMR point
*
* \return the position in global coordinates
*
*/
Point<dim,St> getPos(const grid_dist_amr_key<dim> & v1)
{
return gd_array.get(v1.getLvl()).getPos(v1.getKey());
}
/*! \brief Get the the position of the point
*
* \param v1 AMR point
*
* \return the position in global coordinates
*
*/
Point<dim,St> getPos(int lvl, const grid_dist_key_dx<dim> & v1)
{
return gd_array.get(lvl).getPos(v1);
}
/*! \brief return the spacing for the grid in the level lvl
*
* \param lvl level
*
* \return return the spacing
*
*/
Point<dim,St> getSpacing(size_t lvl)
{
return gd_array.get(lvl).getSpacing();
}
/* \brief Check if a point exist
*
* \param v1 point to checl
*
*/
bool existPoint(const grid_dist_amr_key<dim> & v1)
{
return gd_array.get(v1.getLvl()).existPoint(v1.getKey());
}
/* \brief Check if a point exist
*
* \param v1 point to checl
*
*/
bool existPoint(int lvl, const grid_dist_key_dx<dim> & v1)
{
return gd_array.get(lvl).existPoint(v1);
}
/*! \brief Write on vtk file
*
* \param output filename output
*
*/
bool write(std::string output, size_t opt = VTK_WRITER | FORMAT_ASCII )
{
bool ret = true;
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
ret &= gd_array.get(i).write(output + "_" + std::to_string(i),opt);
}
return ret;
}
#ifdef __NVCC__
/*! \brief Move the memory from the device to host memory
*
*/
template<unsigned int ... prp> void deviceToHost()
{
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
gd_array.get(i).template deviceToHost<prp ...>();
}
}
/*! \brief Move the memory from the device to host memory
*
*/
template<unsigned int ... prp> void hostToDevice()
{
for (size_t i = 0 ; i < gd_array.size() ; i++)
{
gd_array.get(i).template hostToDevice<prp ...>();
}
}
#endif
};
template<unsigned int dim, typename St, typename T>
using sgrid_dist_amr = grid_dist_amr<dim,St,T,AMR_IMPL_TRIVIAL,CartDecomposition<dim,St>,HeapMemory,sgrid_cpu<dim,T,HeapMemory>>;
#ifdef __NVCC__
template<unsigned int dim, typename St, typename T, unsigned int blockEdgeSize = 8>
using sgrid_dist_amr_gpu = grid_dist_amr<dim,St,T,AMR_IMPL_TRIVIAL,CartDecomposition<dim,St,CudaMemory,memory_traits_inte>,CudaMemory,SparseGridGpu<dim,T,blockEdgeSize,IntPow<blockEdgeSize,dim>::value >>;
#endif
#endif /* AMR_GRID_AMR_DIST_HPP_ */
src/Amr/grid_dist_amr_key.hpp 0 → 100644
View file @ b9ccc50e
/*
* 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_ */
src/Amr/grid_dist_amr_key_iterator.hpp 0 → 100644
View file @ b9ccc50e
/*
* 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_ */
src/Amr/grid_dist_amr_unit_tests.cpp 0 → 100644
View file @ b9ccc50e
/*
* grid_dist_amr_dist_unit_tests.cpp
*
* Created on: Sep 21, 2017
* Author: i-bird
*/
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include "grid_dist_amr.hpp"
BOOST_AUTO_TEST_SUITE( grid_dist_amr_test )
/*! \brief Coarsest levels of the grid
*
* \param domain Simulation domain
* \param coars_g coarsest grid resolution
* \param n_lvl number of levels
*
*/
template<typename grid_amr>
void Test3D_amr_create_levels(grid_amr & amr_g, Box<3,float> & domain, size_t coars_g, size_t n_lvl)
{
size_t g_sz[3] = {coars_g,coars_g,coars_g};
size_t tot_c = (coars_g - 1)*(coars_g - 1)*(coars_g - 1);
size_t correct_result = 0;
size_t correct_result_cell = 0;
size_t fact = 1;
for (size_t i = 0 ; i < n_lvl ; i++)
{
correct_result += coars_g*coars_g*coars_g;
correct_result_cell += tot_c*fact;
coars_g = 2*(coars_g - 1) + 1;
fact *= 8;
}
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.getGridIterator(i);
while (it.isNext())
{
auto key = it.get_dist();
auto akey = amr_g.getAMRKey(i,key);
amr_g.template insert<0>(akey) = 3.0;
amr_g.template insert<1>(akey)[0] = 3.0;
amr_g.template insert<1>(akey)[1] = 3.0;
amr_g.template insert<1>(akey)[2] = 3.0;
amr_g.template insert<2>(akey)[0] = 3;
amr_g.template insert<2>(akey)[1] = 3;
amr_g.template insert<2>(akey)[2] = 3;
count++;
++it;
}
}
// 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);
}
template<unsigned int dim>
inline bool gr_is_inside(const grid_key_dx<dim> & key, const size_t (& sz)[dim])
{
for (size_t i = 0 ; i < dim ; i++)
{
if (key.get(i) >= (long int)sz[i] || key.get(i) < 0)
{
return false;
}
}
return true;
}
template <typename grid>
void Test3D_amr_child_parent_get_no_periodic(grid & amr_g, Box<3,float> & domain, size_t coars_g, size_t n_lvl)
{
const int x = 0;
const int y = 1;
const int z = 2;
size_t g_sz[3] = {coars_g,coars_g,coars_g};
size_t tot = coars_g*coars_g*coars_g;
size_t correct_result = 0;
size_t fact = 1;
for (size_t i = 0 ; i < n_lvl ; i++)
{
correct_result += tot*fact;
fact *= 8;
}
amr_g.initLevels(n_lvl,g_sz);
//////// Add something /////
for (size_t i = 0 ; i < amr_g.getNLvl() ; i++)
{
// Fill the AMR with something
size_t count = 0;
auto it = amr_g.getGridIterator(i);
while (it.isNext())
{
auto key = it.get_dist();
auto akey = amr_g.getAMRKey(i,key);
amr_g.template insert<0>(akey) = 3.0;
count++;
++it;
}
}
////////////////////////////
std::string test = amr_g.getSpacing(0).toString();
// Iterate across all the levels initialized
auto it = amr_g.getDomainIterator();
while (it.isNext())
{
auto key = it.get();
auto gkey = it.getGKey();
amr_g.template insert<0>(key) = gkey.get(0);
amr_g.template insert<1>(key) = gkey.get(1);
amr_g.template insert<2>(key) = gkey.get(2);
amr_g.template insert<3>(key)[0] = gkey.get(0);
amr_g.template insert<3>(key)[1] = gkey.get(1);
amr_g.template insert<3>(key)[2] = gkey.get(2);
amr_g.template insert<3>(key)[3] = gkey.get(0);
++it;
}
amr_g.template ghost_get<0,1,2,3>();
// now we check that move space work
auto it2 = amr_g.getDomainIterator();
bool match = true;
while (it2.isNext())
{
auto key = it2.get();
auto gkey = it2.getGKey();
auto key_px = key.moveSpace(x,1);
auto key_gpx = amr_g.getGKey(key_px);
auto key_mx = key.moveSpace(x,-1);
auto key_gmx = amr_g.getGKey(key_mx);
auto key_py = key.moveSpace(y,1);
auto key_gpy = amr_g.getGKey(key_py);
auto key_my = key.moveSpace(y,-1);
auto key_gmy = amr_g.getGKey(key_my);
auto key_pz = key.moveSpace(z,1);
auto key_gpz = amr_g.getGKey(key_pz);
auto key_mz = key.moveSpace(z,-1);
auto key_gmz = amr_g.getGKey(key_mz);
if (gr_is_inside(key_gpx,amr_g.getGridInfoVoid(it2.getLvl()).getSize()) == true)
{
match &= amr_g.template get<0>(key_px) == gkey.get(0) + 1;
match &= amr_g.template get<1>(key_px) == gkey.get(1);
match &= amr_g.template get<2>(key_px) == gkey.get(2);
match &= amr_g.template get<3>(key_px)[0] == gkey.get(0) + 1;
match &= amr_g.template get<3>(key_px)[1] == gkey.get(1);
match &= amr_g.template get<3>(key_px)[2] == gkey.get(2);
match &= amr_g.template get<3>(key_px)[3] == gkey.get(0) + 1;
}
if (gr_is_inside(key_gmx,amr_g.getGridInfoVoid(it2.getLvl()).getSize()) == true)
{
match &= amr_g.template get<0>(key_mx) == gkey.get(0) - 1;
match &= amr_g.template get<1>(key_mx) == gkey.get(1);
match &= amr_g.template get<2>(key_mx) == gkey.get(2);
match &= amr_g.template get<3>(key_mx)[0] == gkey.get(0) - 1;
match &= amr_g.template get<3>(key_mx)[1] == gkey.get(1);
match &= amr_g.template get<3>(key_mx)[2] == gkey.get(2);
match &= amr_g.template get<3>(key_mx)[3] == gkey.get(0) - 1;
}
if (gr_is_inside(key_gpy,amr_g.getGridInfoVoid(it2.getLvl()).getSize()) == true)
{
match &= amr_g.template get<0>(key_py) == gkey.get(0);
match &= amr_g.template get<1>(key_py) == gkey.get(1) + 1;
match &= amr_g.template get<2>(key_py) == gkey.get(2);
match &= amr_g.template get<3>(key_py)[0] == gkey.get(0);
match &= amr_g.template get<3>(key_py)[1] == gkey.get(1) + 1;
match &= amr_g.template get<3>(key_py)[2] == gkey.get(2);
match &= amr_g.template get<3>(key_py)[3] == gkey.get(0);
}
if (gr_is_inside(key_gmy,amr_g.getGridInfoVoid(it2.getLvl()).getSize()) == true)
{
match &= amr_g.template get<0>(key_my) == gkey.get(0);
match &= amr_g.template get<1>(key_my) == gkey.get(1) - 1;
match &= amr_g.template get<2>(key_my) == gkey.get(2);
match &= amr_g.template get<3>(key_my)[0] == gkey.get(0);
match &= amr_g.template get<3>(key_my)[1] == gkey.get(1) - 1;
match &= amr_g.template get<3>(key_my)[2] == gkey.get(2);
match &= amr_g.template get<3>(key_my)[3] == gkey.get(0);
}
if (gr_is_inside(key_gpz,amr_g.getGridInfoVoid(it2.getLvl()).getSize()) == true)
{
match &= amr_g.template get<0>(key_pz) == gkey.get(0);
match &= amr_g.template get<1>(key_pz) == gkey.get(1);
match &= amr_g.template get<2>(key_pz) == gkey.get(2) + 1;
match &= amr_g.template get<3>(key_pz)[0] == gkey.get(0);
match &= amr_g.template get<3>(key_pz)[1] == gkey.get(1);
match &= amr_g.template get<3>(key_pz)[2] == gkey.get(2) + 1;
match &= amr_g.template get<3>(key_pz)[3] == gkey.get(0);
}
if (gr_is_inside(key_gmz,amr_g.getGridInfoVoid(it2.getLvl()).getSize()) == true)
{
match &= amr_g.template get<0>(key_mz) == gkey.get(0);
match &= amr_g.template get<1>(key_mz) == gkey.get(1);
match &= amr_g.template get<2>(key_mz) == gkey.get(2) - 1;
match &= amr_g.template get<3>(key_mz)[0] == gkey.get(0);
match &= amr_g.template get<3>(key_mz)[1] == gkey.get(1);
match &= amr_g.template get<3>(key_mz)[2] == gkey.get(2) - 1;
match &= amr_g.template get<3>(key_mz)[3] == gkey.get(0);
}
// Test to go to all the levels down
size_t lvl = it2.getLvl();
if (lvl < amr_g.getNLvl() - 1)
{
auto key_l1 = key;
amr_g.moveLvlDw(key_l1);
auto key_gl1 = amr_g.getGKey(key_l1);
for (size_t s = 0 ; s < 3 ; s++)
{
match &= key_gl1.get(s) >> 1 == gkey.get(s);
match &= amr_g.template get<0>(key_l1) == key_gl1.get(0);
match &= amr_g.template get<1>(key_l1) == key_gl1.get(1);
match &= amr_g.template get<2>(key_l1) == key_gl1.get(2);
}
}
if (lvl != 0)
{
auto key_l1 = key;
amr_g.moveLvlUp(key_l1);
auto key_gl1 = amr_g.getGKey(key_l1);
for (size_t s = 0 ; s < 3 ; s++)
{
match &= gkey.get(s) >> 1 == key_gl1.get(s);
match &= amr_g.template get<0>(key_l1) == key_gl1.get(0);
match &= amr_g.template get<1>(key_l1) == key_gl1.get(1);
match &= amr_g.template get<2>(key_l1) == key_gl1.get(2);
}
}
++it2;
}
BOOST_REQUIRE_EQUAL(match,true);
}
template <typename grid>
void Test3D_amr_child_parent_get_periodic(grid & amr_g, Box<3,float> & domain, size_t coars_g, size_t n_lvl)
{
const int x = 0;
const int y = 1;
const int z = 2;
size_t g_sz[3] = {coars_g,coars_g,coars_g};
size_t tot = coars_g*coars_g*coars_g;
size_t correct_result = 0;
size_t fact = 1;
for (size_t i = 0 ; i < n_lvl ; i++)
{
correct_result += tot*fact;
fact *= 8;
}
amr_g.initLevels(n_lvl,g_sz);
//////// Add something /////
for (size_t i = 0 ; i < amr_g.getNLvl() ; i++)
{
// Fill the AMR with something
size_t count = 0;
auto it = amr_g.getGridIterator(i);
while (it.isNext())
{
auto key = it.get_dist();
auto akey = amr_g.getAMRKey(i,key);
amr_g.template insert<0>(akey) = 3.0;
count++;
++it;
}
}
////////////////////////////
std::string test = amr_g.getSpacing(0).toString();
// Iterate across all the levels initialized
auto it = amr_g.getDomainIterator();
while (it.isNext())
{
auto key = it.get();
auto gkey = it.getGKey();
amr_g.template insert<0>(key) = gkey.get(0);
amr_g.template insert<1>(key) = gkey.get(1);
amr_g.template insert<2>(key) = gkey.get(2);
++it;
}
amr_g.template ghost_get<0,1,2>();
// now we check that move space work
auto it2 = amr_g.getDomainIterator();
bool match = true;
while (it2.isNext())
{
auto key = it2.get();
auto gkey = it2.getGKey();
auto key_px = key.moveSpace(x,1);
auto key_mx = key.moveSpace(x,-1);
auto key_py = key.moveSpace(y,1);
auto key_my = key.moveSpace(y,-1);
auto key_pz = key.moveSpace(z,1);
auto key_mz = key.moveSpace(z,-1);
match &= amr_g.template get<0>(key_px) == openfpm::math::positive_modulo(gkey.get(0) + 1,amr_g.getGridInfoVoid(it2.getLvl()).size(0));
match &= amr_g.template get<1>(key_px) == gkey.get(1);
match &= amr_g.template get<2>(key_px) == gkey.get(2);
match &= amr_g.template get<0>(key_mx) == openfpm::math::positive_modulo(gkey.get(0) - 1,amr_g.getGridInfoVoid(it2.getLvl()).size(0));
match &= amr_g.template get<1>(key_mx) == gkey.get(1);
match &= amr_g.template get<2>(key_mx) == gkey.get(2);
match &= amr_g.template get<0>(key_py) == gkey.get(0);
match &= amr_g.template get<1>(key_py) == openfpm::math::positive_modulo(gkey.get(1) + 1,amr_g.getGridInfoVoid(it2.getLvl()).size(1));
match &= amr_g.template get<2>(key_py) == gkey.get(2);
match &= amr_g.template get<0>(key_my) == gkey.get(0);
match &= amr_g.template get<1>(key_my) == openfpm::math::positive_modulo(gkey.get(1) - 1,amr_g.getGridInfoVoid(it2.getLvl()).size(1));
match &= amr_g.template get<2>(key_my) == gkey.get(2);
match &= amr_g.template get<0>(key_pz) == gkey.get(0);
match &= amr_g.template get<1>(key_pz) == gkey.get(1);
match &= amr_g.template get<2>(key_pz) == openfpm::math::positive_modulo(gkey.get(2) + 1,amr_g.getGridInfoVoid(it2.getLvl()).size(2));
match &= amr_g.template get<0>(key_mz) == gkey.get(0);
match &= amr_g.template get<1>(key_mz) == gkey.get(1);
match &= amr_g.template get<2>(key_mz) == openfpm::math::positive_modulo(gkey.get(2) - 1,amr_g.getGridInfoVoid(it2.getLvl()).size(2));
// Test to go to all the levels down
size_t lvl = it2.getLvl();
if (lvl < amr_g.getNLvl() - 1)
{
auto key_l1 = key;
amr_g.moveLvlDw(key_l1);
auto key_gl1 = amr_g.getGKey(key_l1);
for (size_t s = 0 ; s < 3 ; s++)
{
match &= key_gl1.get(s) >> 1 == gkey.get(s);
match &= amr_g.template get<0>(key_l1) == key_gl1.get(0);
match &= amr_g.template get<1>(key_l1) == key_gl1.get(1);
match &= amr_g.template get<2>(key_l1) == key_gl1.get(2);
}
}
if (lvl != 0)
{
auto key_l1 = key;
amr_g.moveLvlUp(key_l1);
auto key_gl1 = amr_g.getGKey(key_l1);
for (size_t s = 0 ; s < 3 ; s++)
{
match &= gkey.get(s) >> 1 == key_gl1.get(s);
match &= amr_g.template get<0>(key_l1) == key_gl1.get(0);
match &= amr_g.template get<1>(key_l1) == key_gl1.get(1);
match &= amr_g.template get<2>(key_l1) == key_gl1.get(2);
}
}
++it2;
}
BOOST_REQUIRE_EQUAL(match,true);
}
template <typename grid>
void Test3D_amr_ghost_it(grid & amr_g, Box<3,float> & domain, size_t coars_g, size_t n_lvl)
{
size_t g_sz[3] = {coars_g,coars_g,coars_g};
size_t tot = coars_g*coars_g*coars_g;
size_t correct_result = 0;
size_t fact = 1;
for (size_t i = 0 ; i < n_lvl ; i++)
{
correct_result += tot*fact;
fact *= 8;
}
amr_g.initLevels(n_lvl,g_sz);
//////// Add something /////
for (size_t i = 0 ; i < amr_g.getNLvl() ; i++)
{
// Fill the AMR with something
size_t count = 0;
auto it = amr_g.getGridGhostIterator(i);
while (it.isNext())
{
auto key = it.get_dist();
auto gkey = it.get();
auto akey = amr_g.getAMRKey(i,key);
amr_g.template insert<0>(akey) = gkey.get(0);
amr_g.template insert<1>(akey) = gkey.get(1);
amr_g.template insert<2>(akey) = gkey.get(2);
if (gkey.get(0) == -1 || gkey.get(0) == (long int)amr_g.getGridInfoVoid(i).size(0) ||
gkey.get(1) == -1 || gkey.get(1) == (long int)amr_g.getGridInfoVoid(i).size(1) ||
gkey.get(2) == -1 || gkey.get(2) == (long int)amr_g.getGridInfoVoid(i).size(2))
{count++;}
++it;
}
size_t tot = (amr_g.getGridInfoVoid(i).size(0) + 2)*
(amr_g.getGridInfoVoid(i).size(1) + 2)*
(amr_g.getGridInfoVoid(i).size(2) + 2) - amr_g.getGridInfoVoid(i).size();
auto & v_cl = create_vcluster();
if (v_cl.size() == 1)
{
v_cl.sum(count);
v_cl.execute();
BOOST_REQUIRE_EQUAL(tot,count);
}
bool match = true;
auto it2 = amr_g.getDomainIterator(i);
while (it2.isNext())
{
auto key = it2.get();
// move -x
auto key_m1 = key.move(0,-1);
auto key_gm1 = it2.getGKey(key_m1);
match &= amr_g.template get<0>(i,key_m1) == key_gm1.get(0);
// move +x
auto key_p1 = key.move(0,1);
auto key_gp1 = it2.getGKey(key_p1);
match &= amr_g.template get<0>(i,key_p1) == key_gp1.get(0);
// move -y
key_m1 = key.move(1,-1);
key_gm1 = it2.getGKey(key_m1);
match &= amr_g.template get<1>(i,key_m1) == key_gm1.get(1);
// move +y
key_p1 = key.move(1,1);
key_gp1 = it2.getGKey(key_p1);
match &= amr_g.template get<1>(i,key_p1) == key_gp1.get(1);
// move -z
key_m1 = key.move(2,-1);
key_gm1 = it2.getGKey(key_m1);
match &= amr_g.template get<2>(i,key_m1) == key_gm1.get(2);
// move +z
key_p1 = key.move(2,1);
key_gp1 = it2.getGKey(key_p1);
match &= amr_g.template get<2>(i,key_p1) == key_gp1.get(2);
++it2;
}
BOOST_REQUIRE_EQUAL(match,true);
}
}
template <typename grid>
void Test3D_amr_domain_ghost_it(grid & amr_g, Box<3,float> & domain, size_t coars_g, size_t n_lvl)
{
size_t g_sz[3] = {coars_g,coars_g,coars_g};
size_t tot = coars_g*coars_g*coars_g;
size_t correct_result = 0;
size_t fact = 1;
for (size_t i = 0 ; i < n_lvl ; i++)
{
correct_result += tot*fact;
fact *= 8;
}
amr_g.initLevels(n_lvl,g_sz);
size_t total_all_level = 0;
//////// Add something /////
for (size_t i = 0 ; i < amr_g.getNLvl() ; i++)
{
// Fill the AMR with something
size_t count = 0;
auto it = amr_g.getGridGhostIterator(i);
while (it.isNext())
{
auto key = it.get_dist();
auto gkey = it.get();
auto akey = amr_g.getAMRKey(i,key);
amr_g.template insert<0>(akey) = gkey.get(0);
amr_g.template insert<1>(akey) = gkey.get(1);
amr_g.template insert<2>(akey) = gkey.get(2);
count++;
++it;
}
size_t tot = (amr_g.getGridInfoVoid(i).size(0) + 2)*
(amr_g.getGridInfoVoid(i).size(1) + 2)*
(amr_g.getGridInfoVoid(i).size(2) + 2);
auto & v_cl = create_vcluster();
if (v_cl.size() == 1)
{
v_cl.sum(count);
v_cl.execute();
BOOST_REQUIRE_EQUAL(tot,count);
}
size_t amr_cnt = 0;
bool match = true;
auto it2 = amr_g.getDomainGhostIterator(i);
while (it2.isNext())
{
auto key = it2.get();
auto key_g = it2.getGKey(key);
match &= amr_g.template get<0>(i,key) == key_g.get(0);
total_all_level++;
amr_cnt++;
++it2;
}
BOOST_REQUIRE_EQUAL(amr_cnt,count);
BOOST_REQUIRE_EQUAL(match,true);
}
// test the total iterator
size_t gtot_count = 0;
auto tot_it = amr_g.getDomainGhostIterator();
while (tot_it.isNext())
{
gtot_count++;
++tot_it;
}
BOOST_REQUIRE_EQUAL(gtot_count,total_all_level);
}
template<typename grid_amr>
void Test3D_ghost_put(grid_amr & g_dist_amr, long int k)
{
size_t sz[3] = {(size_t)k,(size_t)k,(size_t)k};
g_dist_amr.initLevels(4,sz);
// Grid sm
grid_sm<3,void> info(sz);
size_t count = 0;
for (size_t i = 0 ; i < g_dist_amr.getNLvl() ; i++)
{
auto dom = g_dist_amr.getGridIterator(i);
while (dom.isNext())
{
auto key = dom.get_dist();
g_dist_amr.template insert<0>(i,key) = -6.0;
// Count the points
count++;
++dom;
}
}
// Set to zero the full grid
{
auto dom = g_dist_amr.getDomainIterator();
while (dom.isNext())
{
auto key = dom.get();
g_dist_amr.template insert<0>(key.moveSpace(0,1)) += 1.0;
g_dist_amr.template insert<0>(key.moveSpace(0,-1)) += 1.0;
g_dist_amr.template insert<0>(key.moveSpace(1,1)) += 1.0;
g_dist_amr.template insert<0>(key.moveSpace(1,-1)) += 1.0;
g_dist_amr.template insert<0>(key.moveSpace(2,1)) += 1.0;
g_dist_amr.template insert<0>(key.moveSpace(2,-1)) += 1.0;
++dom;
}
}
bool correct = true;
// Domain + Ghost iterator
auto dom_gi = g_dist_amr.getDomainIterator();
while (dom_gi.isNext())
{
auto key = dom_gi.get();
correct &= (g_dist_amr.template get<0>(key) == 0);
++dom_gi;
}
g_dist_amr.template ghost_put<add_,0>();
if (count != 0)
{BOOST_REQUIRE_EQUAL(correct, false);}
// sync the ghosts
g_dist_amr.template ghost_get<0>();
correct = true;
// Domain + Ghost iterator
auto dom_gi2 = g_dist_amr.getDomainIterator();
while (dom_gi2.isNext())
{
auto key = dom_gi2.get();
correct &= (g_dist_amr.template get<0>(key) == 0);
++dom_gi2;
}
BOOST_REQUIRE_EQUAL(correct, true);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_get_child_test_nop )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
long int k = 16*16*16*create_vcluster().getProcessingUnits();
k = std::pow(k, 1/3.);
Ghost<3,long int> g(1);
grid_dist_amr<3,float,aggregate<long int,long int,long int, long int[4]>> amr_g(domain3,g);
Test3D_amr_child_parent_get_no_periodic(amr_g,domain3,k,4);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_get_child_test_p )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
long int k = 16*16*16*create_vcluster().getProcessingUnits();
k = std::pow(k, 1/3.);
periodicity<3> bc = {PERIODIC,PERIODIC,PERIODIC};
Ghost<3,long int> g(1);
grid_dist_amr<3,float,aggregate<long int,long int,long int>> amr_g(domain3,g,bc);
Test3D_amr_child_parent_get_periodic(amr_g,domain3,k,4);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_test )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
long int k = 16*16*16*create_vcluster().getProcessingUnits();
k = std::pow(k, 1/3.);
Ghost<3,long int> g(0);
grid_dist_amr<3,float,aggregate<float,float[3],int[3]>> amr_g(domain3,g);
Test3D_amr_create_levels(amr_g,domain3,k,4);
sgrid_dist_amr<3,float,aggregate<float,float[3],int[3]>> amr_g2(domain3,g);
Test3D_amr_create_levels(amr_g2,domain3,k,4);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_ghost_it_test )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
long int k = 16*16*16*create_vcluster().getProcessingUnits();
k = std::pow(k, 1/3.);
Ghost<3,long int> g(1);
grid_dist_amr<3,float,aggregate<long int,long int,long int>> amr_g(domain3,g);
Test3D_amr_ghost_it(amr_g,domain3,k,4);
sgrid_dist_amr<3,float,aggregate<long int,long int,long int>> amr_g2(domain3,g);
Test3D_amr_ghost_it(amr_g2,domain3,k,4);
for (size_t i = 0 ; i < amr_g2.getNLvl() ; i++)
{BOOST_REQUIRE(amr_g2.size_inserted(i) != 0ul);}
amr_g2.clear();
for (size_t i = 0 ; i < amr_g2.getNLvl() ; i++)
{BOOST_REQUIRE_EQUAL(amr_g2.size_inserted(i),0ul);}
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_domain_ghost_it_test )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
long int k = 16*16*16*create_vcluster().getProcessingUnits();
k = std::pow(k, 1/3.);
Ghost<3,long int> g(1);
grid_dist_amr<3,float,aggregate<long int,long int,long int>> amr_g(domain3,g);
Test3D_amr_domain_ghost_it(amr_g,domain3,k,4);
sgrid_dist_amr<3,float,aggregate<long int,long int,long int>> amr_g2(domain3,g);
Test3D_amr_domain_ghost_it(amr_g2,domain3,k,4);
for (size_t i = 0 ; i < amr_g2.getNLvl() ; i++)
{BOOST_REQUIRE(amr_g2.size_inserted(i) != 0ul);}
amr_g2.clear();
for (size_t i = 0 ; i < amr_g2.getNLvl() ; i++)
{BOOST_REQUIRE_EQUAL(amr_g2.size_inserted(i),0ul);}
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_get_child_test_low_res )
{
// Domain
Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
long int k = 2;
Ghost<3,long int> g(1);
grid_dist_amr<3,float,aggregate<long int,long int,long int,long int[4]>> amr_g(domain3,g);
Test3D_amr_child_parent_get_no_periodic(amr_g,domain3,k,4);
sgrid_dist_amr<3,float,aggregate<long int,long int,long int, long int [4]>> amr_g2(domain3,g);
Test3D_amr_child_parent_get_no_periodic(amr_g2,domain3,k,4);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_test_background_value )
{
// 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<3,float,aggregate<long int,long int,long int>> amr_g2(domain3,g);
size_t g_sz[3] = {4,4,4};
amr_g2.initLevels(4,g_sz);
aggregate<long int,long int,long int> bck;
bck.get<0>() = -57;
bck.get<1>() = -90;
bck.get<2>() = -123;
amr_g2.setBackgroundValue(bck);
// Get a non existent point to check that
// the background value work
grid_dist_key_dx<3> key(0,grid_key_dx<3>({0,0,0}));
long int bck0 = amr_g2.get<0>(2,key);
BOOST_REQUIRE_EQUAL(bck0,-57);
long int bck1 = amr_g2.get<1>(2,key);
BOOST_REQUIRE_EQUAL(bck1,-90);
long int bck2 = amr_g2.get<2>(2,key);
BOOST_REQUIRE_EQUAL(bck2,-123);
// Now we insert that point and we check the subsequent point
amr_g2.insert<0>(2,key) = 5;
grid_dist_key_dx<3> key2(0,grid_key_dx<3>({1,0,0}));
bck0 = amr_g2.get<0>(2,key2);
BOOST_REQUIRE_EQUAL(bck0,-57);
bck1 = amr_g2.get<1>(2,key2);
BOOST_REQUIRE_EQUAL(bck1,-90);
bck2 = amr_g2.get<2>(2,key2);
BOOST_REQUIRE_EQUAL(bck2,-123);
auto & g_dist_lvl2 = amr_g2.getDistGrid(2);
g_dist_lvl2.get_loc_grid(0).internal_clear_cache();
bck0 = amr_g2.get<0>(2,key2);
BOOST_REQUIRE_EQUAL(bck0,-57);
bck1 = amr_g2.get<1>(2,key2);
BOOST_REQUIRE_EQUAL(bck1,-90);
bck2 = amr_g2.get<2>(2,key2);
BOOST_REQUIRE_EQUAL(bck2,-123);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_get_domain_ghost_check )
{
// Test grid periodic
Box<3,float> domain({0.0,0.0,0.0},{1.0,1.0,1.0});
Vcluster<> & v_cl = create_vcluster();
if ( v_cl.getProcessingUnits() > 32 )
{return;}
long int k = 13;
BOOST_TEST_CHECKPOINT( "Testing grid periodic k<=" << k );
// Ghost
Ghost<3,long int> g(1);
// periodicity
periodicity<3> pr = {{PERIODIC,PERIODIC,PERIODIC}};
// Distributed grid with id decomposition
grid_dist_amr<3, float, aggregate<long int>> g_dist(domain,g,pr);
Test3D_ghost_put(g_dist,k);
// Distributed grid with id decomposition
sgrid_dist_amr<3, float, aggregate<long int>> sg_dist(domain,g,pr);
Test3D_ghost_put(sg_dist,k);
}
BOOST_AUTO_TEST_CASE( grid_dist_amr_ghost_put_create )
{
// Test grid periodic
Box<3,float> domain({0.0,0.0,0.0},{1.0,1.0,1.0});
Vcluster<> & v_cl = create_vcluster();
if ( v_cl.getProcessingUnits() > 32 )
{return;}
long int k = 13;
BOOST_TEST_CHECKPOINT( "Testing grid periodic k<=" << k );
// Ghost
Ghost<3,long int> g(1);
// periodicity
periodicity<3> pr = {{PERIODIC,PERIODIC,PERIODIC}};
// Distributed grid with id decomposition
grid_dist_amr<3, float, aggregate<long int>> g_dist(domain,g,pr);
Test3D_ghost_put(g_dist,k);
// Distributed grid with id decomposition
sgrid_dist_amr<3, float, aggregate<long int>> sg_dist(domain,g,pr);
Test3D_ghost_put(sg_dist,k);
}
BOOST_AUTO_TEST_SUITE_END()
src/Amr/tests/amr_base_gpu_unit_tests.cu 0 → 100644
View file @ b9ccc50e
/*
* 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
View file @ b9ccc50e
/*
* 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
View file @ b9ccc50e
cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
########################### Executables
if(NOT CUDA_ON_BACKEND STREQUAL "None")
set(CUDA_SOURCES
Grid/tests/sgrid_dist_id_gpu_unit_tests.cu
Vector/cuda/vector_dist_gpu_MP_tests.cu
Vector/cuda/vector_dist_cuda_func_test.cu
Decomposition/cuda/decomposition_cuda_tests.cu
Vector/cuda/vector_dist_gpu_unit_tests.cu
Decomposition/cuda/Domain_icells_cart_unit_test.cu
Amr/tests/amr_base_gpu_unit_tests.cu
Grid/tests/grid_dist_id_unit_test.cu)
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
add_definitions("-DBOOST_MPL_CFG_HAS_TYPEOF")
endif()
if (CUDA_ON_BACKEND STREQUAL "OpenMP" OR CUDA_ON_BACKEND STREQUAL "SEQUENTIAL")
set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS "-D__NVCC__ -DCUDART_VERSION=11000")
set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX)
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
add_definitions("-x c++")
endif()
endif()
if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND )
list(APPEND HIP_HIPCC_FLAGS ${CMAKE_CXX_FLAGS_DEBUG})
if (CMAKE_BUILD_TYPE STREQUAL "Debug")
list(APPEND HIP_HIPCC_FLAGS -O0)
endif()
list(APPEND HIP_HIPCC_FLAGS -D__NVCC__ -D__HIP__ -DCUDART_VERSION=11000 -D__CUDACC__ -D__CUDACC_VER_MAJOR__=11 -D__CUDACC_VER_MINOR__=0 -D__CUDACC_VER_BUILD__=0 --std=c++17)
set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX)
#set(CMAKE_CXX_COMPILER ${HIP_HIPCC_EXECUTABLE})
hip_add_executable(pdata ${CUDA_SOURCES} ${OPENFPM_INIT_FILE} main.cpp
Amr/grid_dist_amr_unit_tests.cpp
Amr/tests/amr_base_unit_tests.cpp
Debug/debug_test.cpp
Grid/tests/grid_dist_id_HDF5_chckpnt_restart_test.cpp
Grid/tests/grid_dist_id_unit_test.cpp
Grid/tests/sgrid_dist_id_unit_tests.cpp
Grid/tests/grid_dist_id_dlb_unit_test.cpp
Grid/tests/staggered_grid_dist_unit_test.cpp
Vector/tests/vector_dist_cell_list_tests.cpp
Vector/tests/vector_dist_complex_prp_unit_test.cpp
Vector/tests/vector_dist_HDF5_chckpnt_restart_test.cpp
Vector/tests/vector_dist_MP_unit_tests.cpp
Vector/tests/vector_dist_NN_tests.cpp
Vector/tests/vector_dist_unit_test.cpp
pdata_performance.cpp
Decomposition/tests/CartDecomposition_unit_test.cpp
Decomposition/tests/shift_vect_converter_tests.cpp
Vector/performance/vector_dist_performance_util.cpp
lib/pdata.cpp)
hip_add_library(ofpm_pdata STATIC lib/pdata.cpp)
hip_add_library(ofpm_pdata_dl SHARED lib/pdata.cpp)
else()
add_executable(pdata ${OPENFPM_INIT_FILE} ${CUDA_SOURCES} main.cpp
Amr/grid_dist_amr_unit_tests.cpp
Amr/tests/amr_base_unit_tests.cpp
Debug/debug_test.cpp
Grid/tests/grid_dist_id_HDF5_chckpnt_restart_test.cpp
Grid/tests/grid_dist_id_unit_test.cpp
Grid/tests/sgrid_dist_id_unit_tests.cpp
Grid/tests/grid_dist_id_dlb_unit_test.cpp
Grid/tests/staggered_grid_dist_unit_test.cpp
Vector/tests/vector_dist_cell_list_tests.cpp
Vector/tests/vector_dist_complex_prp_unit_test.cpp
Vector/tests/vector_dist_HDF5_chckpnt_restart_test.cpp
Vector/tests/vector_dist_MP_unit_tests.cpp
Vector/tests/vector_dist_NN_tests.cpp
Vector/tests/vector_dist_unit_test.cpp
pdata_performance.cpp
Decomposition/tests/CartDecomposition_unit_test.cpp
Decomposition/tests/shift_vect_converter_tests.cpp
Vector/performance/vector_dist_performance_util.cpp
lib/pdata.cpp)
add_library(ofpm_pdata STATIC lib/pdata.cpp)
add_library(ofpm_pdata_dl SHARED lib/pdata.cpp)
add_library(ofpm_pdata_python SHARED lib/pdata_python.cpp)
set_property(TARGET pdata PROPERTY CUDA_ARCHITECTURES OFF)
set_property(TARGET ofpm_pdata PROPERTY CUDA_ARCHITECTURES OFF)
set_property(TARGET ofpm_pdata_dl PROPERTY CUDA_ARCHITECTURES OFF)
set_property(TARGET ofpm_pdata_python PROPERTY CUDA_ARCHITECTURES OFF)
endif()
add_dependencies(pdata ofpmmemory)
add_dependencies(pdata vcluster)
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
target_compile_options(pdata PRIVATE "-Wno-undefined-var-template")
target_compile_options(pdata PRIVATE "-Wno-macro-redefined")
endif()
if ( CMAKE_COMPILER_IS_GNUCC )
#target_compile_options(pdata PRIVATE "-Wno-deprecated-declarations")
#target_compile_options(pdata PRIVATE "-Wno-undefined-var-template")
#target_compile_options(pdata PRIVATE "-Wno-macro-redefined")
#target_compile_options(pdata PRIVATE "-fsanitize=address")
#target_link_options(pdata PRIVATE "-fsanitize=address")
if (TEST_COVERAGE)
target_compile_options(pdata PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fprofile-arcs -ftest-coverage>)
endif()
endif()
if (CMAKE_CUDA_COMPILER_ID STREQUAL "Clang")
add_definitions(-D__STRICT_ANSI__)
endif()
if (ENABLE_ASAN)
target_compile_options(pdata PUBLIC $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer -g" >)
target_compile_options(pdata PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer -g >)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer")
add_definitions(-DENABLE_ASAN)
endif()
add_test(NAME pdata_3_proc COMMAND mpirun -np 3 ./pdata)
add_test(NAME pdata_4_proc COMMAND mpirun -np 4 ./pdata)
###########################
if (CUDA_FOUND)
target_include_directories (pdata PUBLIC ${MPI_C_INCLUDE_DIRS})
if (TEST_COVERAGE)
target_compile_options(pdata PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fprofile-arcs -ftest-coverage" >)
endif()
endif()
if(TEST_PERFORMANCE AND ENABLE_NUMERICS)
target_include_directories (pdata PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_numerics/src/)
endif()
target_include_directories (pdata PUBLIC ${PARMETIS_ROOT}/include)
target_include_directories (pdata PUBLIC ${METIS_ROOT}/include)
target_include_directories (pdata PUBLIC ${HDF5_ROOT}/include)
target_include_directories (pdata PUBLIC ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
target_include_directories (pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories (pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_devices/src/)
target_include_directories (pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_vcluster/src/)
target_include_directories (pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/)
target_include_directories (pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_io/src/)
target_include_directories (pdata PRIVATE ${CMAKE_BINARY_DIR}/config)
target_include_directories (pdata PUBLIC ${PETSC_INCLUDES})
target_include_directories (pdata PUBLIC ${LIBHILBERT_INCLUDE_DIRS})
target_include_directories (pdata PUBLIC ${ALPAKA_ROOT}/include)
target_include_directories (pdata PUBLIC ${Vc_INCLUDE_DIR})
target_include_directories (pdata PUBLIC ${Boost_INCLUDE_DIRS})
target_include_directories (pdata PUBLIC ${MPI_C_INCLUDE_DIRS})
#target_include_directories (isolation_pdata PUBLIC ${PARMETIS_ROOT}/include)
#target_include_directories (isolation_pdata PUBLIC ${METIS_ROOT}/include)
#target_include_directories (isolation_pdata PUBLIC ${CUDA_INCLUDE_DIRS})
#target_include_directories (isolation_pdata PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
#target_include_directories (isolation_pdata PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../openfpm_devices/src/)
#target_include_directories (isolation_pdata PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../openfpm_vcluster/src/)
#target_include_directories (isolation_pdata PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../openfpm_data/src/)
#target_include_directories (isolation_pdata PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../openfpm_io/src/)
#target_include_directories (isolation_pdata PUBLIC ${CMAKE_BINARY_DIR}/config)
#target_include_directories (isolation_pdata PUBLIC ${PETSC_INCLUDES})
#target_include_directories (isolation_pdata PUBLIC ${HDF5_ROOT}/include)
#target_include_directories (isolation_pdata PUBLIC ${LIBHILBERT_INCLUDE_DIRS})
#target_include_directories (isolation_pdata PUBLIC ${Vc_INCLUDE_DIR})
#target_include_directories (isolation_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 ${HDF5_LIBRARIES})
target_link_libraries(pdata -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(pdata ${PETSC_LIBRARIES})
target_link_libraries(pdata ${Vc_LIBRARIES})
target_link_libraries(pdata ${alpaka_LIBRARIES})
target_link_libraries(pdata ${MPI_C_LIBRARIES})
target_link_libraries(pdata ${MPI_CXX_LIBRARIES})
target_link_libraries(pdata vcluster)
target_link_libraries(pdata ofpmmemory)
if (OpenMP_FOUND)
target_link_libraries(pdata OpenMP::OpenMP_CXX)
endif()
#target_link_libraries(isolation_pdata ${Boost_LIBRARIES})
#target_link_libraries(isolation_pdata ${PARMETIS_LIBRARIES})
#target_link_libraries(isolation_pdata -L${METIS_ROOT}/lib metis)
#target_link_libraries(isolation_pdata ${HDF5_LIBRARIES})
#target_link_libraries(isolation_pdata -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
#target_link_libraries(isolation_pdata ${PETSC_LIBRARIES})
#target_link_libraries(isolation_pdata ${Vc_LIBRARIES})
if (TEST_PERFORMANCE)
target_link_libraries(pdata ${Boost_FILESYSTEM_LIBRARY})
target_link_libraries(pdata ${Boost_SYSTEM_LIBRARY})
endif()
if (TEST_COVERAGE)
target_link_libraries(pdata -lgcov --coverage)
get_target_property(PDATA_SOURCES pdata SOURCES)
get_target_property(MEM_SOURCES mem SOURCES)
get_target_property(DATA_SOURCES mem_map SOURCES)
get_target_property(VCLUSTER_SOURCES vcluster_test SOURCES)
get_target_property(IO_SOURCES io SOURCES)
get_target_property(NUMERIC_SOURCES numerics SOURCES)
get_target_property(PDATA_INCLUDES pdata INCLUDE_DIRECTORIES)
get_target_property(NUMERIC_INCLUDES numerics INCLUDE_DIRECTORIES)
get_target_property(PDATA_LIBS pdata LINK_LIBRARIES)
get_target_property(NUMERIC_LIBS numerics LINK_LIBRARIES)
list(TRANSFORM MEM_SOURCES PREPEND "../../openfpm_devices/src/")
list(TRANSFORM DATA_SOURCES PREPEND "../../openfpm_data/src/")
list(TRANSFORM VCLUSTER_SOURCES PREPEND "../../openfpm_vcluster/src/")
list(TRANSFORM IO_SOURCES PREPEND "../../openfpm_io/src/")
list(TRANSFORM NUMERIC_SOURCES PREPEND "../../openfpm_numerics/src/")
set(PDATA_FULL_SOURCES ${PDATA_SOURCES} ${MEM_SOURCES} ${DATA_SOURCES} ${VCLUSTER_SOURCES} ${IO_SOURCES} ${NUMERIC_SOURCES})
set(PDATA_FULL_SOURCES_CU ${PDATA_SOURCES} ${MEM_SOURCES} ${DATA_SOURCES} ${VCLUSTER_SOURCES} ${IO_SOURCES} ${NUMERIC_SOURCES})
list(FILTER PDATA_FULL_SOURCES_CU INCLUDE REGEX ^.*\.cu)
### Test coverage are done in SEQUENTIAL
if (NOT CUDA_ON_BACKEND STREQUAL "SEQUENTIAL")
message(FATAL_ERROR "Error test coverage must be done with CUDA_ON_BACKEND=SEQUENTIAL backend")
endif()
set_source_files_properties(${PDATA_FULL_SOURCES_CU} PROPERTIES COMPILE_FLAGS "-D__NVCC__ -DCUDART_VERSION=11000")
set_source_files_properties(${PDATA_FULL_SOURCES_CU} PROPERTIES LANGUAGE CXX)
add_definitions("-x c++")
add_executable(pdata_full ${PDATA_FULL_SOURCES})
target_compile_definitions(pdata_full PUBLIC NO_INIT_AND_MAIN)
target_compile_options(pdata_full PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fprofile-arcs -ftest-coverage>)
target_link_options(pdata_full PUBLIC -fprofile-arcs -ftest-coverage)
target_link_options(pdata_full PUBLIC -fprofile-arcs -ftest-coverage)
if (ENABLE_ASAN)
target_compile_options(pdata_full PUBLIC $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer -g" >)
target_compile_options(pdata_full PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer -g >)
endif()
target_link_libraries(pdata_full -lgcov --coverage)
target_link_libraries(pdata_full ${PDATA_LIBS})
target_link_libraries(pdata_full ${NUMERIC_LIBS})
target_link_libraries(pdata_full Boost::thread)
target_include_directories(pdata_full PUBLIC ${PDATA_INCLUDES})
target_include_directories(pdata_full PUBLIC ${NUMERIC_INCLUDES})
endif()
target_include_directories (ofpm_pdata PUBLIC ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
target_include_directories (ofpm_pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories (ofpm_pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/)
target_include_directories (ofpm_pdata PRIVATE ${CMAKE_BINARY_DIR}/config)
target_include_directories (ofpm_pdata PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_devices/src/)
target_include_directories (ofpm_pdata PUBLIC ${Boost_INCLUDE_DIRS})
target_include_directories (ofpm_pdata_dl PUBLIC ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
target_include_directories (ofpm_pdata_dl PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories (ofpm_pdata_dl PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/)
target_include_directories (ofpm_pdata_dl PRIVATE ${CMAKE_BINARY_DIR}/config)
target_include_directories (ofpm_pdata_dl PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_devices/src/)
target_include_directories (ofpm_pdata_dl PUBLIC ${Boost_INCLUDE_DIRS})
target_compile_definitions(pdata PRIVATE ${MPI_VENDOR})
if(PETSC_FOUND)
target_link_libraries(pdata ${PETSC_LIBRARIES})
endif()
# Request that particles be built with -std=c++17
# As this is a public compile feature anything that links to particles
# will also build with -std=c++17
target_compile_features(pdata PUBLIC cxx_std_17)
target_link_libraries(pdata ${MPI_C_LIBRARIES})
target_link_libraries(pdata m)
target_link_libraries(pdata c)
if (NOT APPLE)
target_link_libraries(pdata rt)
endif ()
install(FILES Decomposition/CartDecomposition.hpp
Decomposition/Domain_icells_cart.hpp
Decomposition/shift_vect_converter.hpp
Decomposition/CartDecomposition_ext.hpp
Decomposition/common.hpp
Decomposition/Decomposition.hpp
Decomposition/ie_ghost.hpp
Decomposition/Domain_NN_calculator_cart.hpp
Decomposition/nn_processor.hpp Decomposition/ie_loc_ghost.hpp
Decomposition/ORB.hpp
Decomposition/dec_optimizer.hpp
DESTINATION openfpm_pdata/include/Decomposition/
COMPONENT OpenFPM)
install(FILES Decomposition/Distribution/metis_util.hpp
Decomposition/Distribution/SpaceDistribution.hpp
Decomposition/Distribution/parmetis_dist_util.hpp
Decomposition/Distribution/parmetis_util.hpp
Decomposition/Distribution/MetisDistribution.hpp
Decomposition/Distribution/ParMetisDistribution.hpp
Decomposition/Distribution/DistParMetisDistribution.hpp
Decomposition/Distribution/BoxDistribution.hpp
DESTINATION openfpm_pdata/include/Decomposition/Distribution
COMPONENT OpenFPM)
install(FILES Decomposition/cuda/ie_ghost_gpu.cuh
Decomposition/cuda/CartDecomposition_gpu.cuh
DESTINATION openfpm_pdata/include/Decomposition/cuda
COMPONENT OpenFPM)
install(FILES Grid/grid_dist_id.hpp
Grid/grid_dist_id_comm.hpp
Grid/grid_dist_util.hpp
Grid/grid_dist_key.hpp
Grid/staggered_dist_grid.hpp
Grid/staggered_dist_grid_util.hpp
Grid/staggered_dist_grid_copy.hpp
DESTINATION openfpm_pdata/include/Grid/
COMPONENT OpenFPM)
install(FILES Grid/cuda/grid_dist_id_kernels.cuh
Grid/cuda/grid_dist_id_iterator_gpu.cuh
DESTINATION openfpm_pdata/include/Grid/cuda/
COMPONENT OpenFPM)
install(FILES Amr/grid_dist_amr_key_iterator.hpp
Amr/grid_dist_amr_key.hpp
Amr/grid_dist_amr.hpp
DESTINATION openfpm_pdata/include/Amr/
COMPONENT OpenFPM)
install(FILES Grid/Iterators/grid_dist_id_iterator_util.hpp
Grid/Iterators/grid_dist_id_iterator_dec.hpp
Grid/Iterators/grid_dist_id_iterator_dec_skin.hpp
Grid/Iterators/grid_dist_id_iterator_sub.hpp
Grid/Iterators/grid_dist_id_iterator.hpp
DESTINATION openfpm_pdata/include/Grid/Iterators
COMPONENT OpenFPM)
install(FILES Vector/se_class3_vector.hpp
Vector/vector_dist_multiphase_functions.hpp
Vector/vector_dist_comm.hpp Vector/vector_dist.hpp
Vector/vector_dist_ofb.hpp
Vector/vector_dist_key.hpp
Vector/vector_dist_kernel.hpp
Vector/vector_dist_subset.hpp
DESTINATION openfpm_pdata/include/Vector
COMPONENT OpenFPM)
install(FILES util/common_pdata.hpp
DESTINATION openfpm_pdata/include/util
COMPONENT OpenFPM)
install(FILES Vector/Iterators/vector_dist_iterator.hpp
DESTINATION openfpm_pdata/include/Vector/Iterators/
COMPONENT OpenFPM)
install(FILES Vector/util/vector_dist_funcs.hpp
DESTINATION openfpm_pdata/include/Vector/util
COMPONENT OpenFPM)
install(FILES Vector/cuda/vector_dist_comm_util_funcs.cuh
Vector/cuda/vector_dist_cuda_funcs.cuh
Vector/cuda/vector_dist_operators_list_ker.hpp
DESTINATION openfpm_pdata/include/Vector/cuda
COMPONENT OpenFPM)
install(FILES Graph/ids.hpp Graph/dist_map_graph.hpp
Graph/DistGraphFactory.hpp
DESTINATION openfpm_pdata/include/Graph
COMPONENT OpenFPM)
install(FILES SubdomainGraphNodes.hpp
DESTINATION openfpm_pdata/include/ )
install(FILES DLB/DLB.hpp DLB/LB_Model.hpp
DESTINATION openfpm_pdata/include/DLB
COMPONENT OpenFPM)
install(FILES ${CMAKE_BINARY_DIR}/config/config.h
DESTINATION openfpm_pdata/include/config
COMPONENT OpenFPM)
install(FILES lib/pdata.hpp
DESTINATION openfpm_pdata/include/lib
COMPONENT OpenFPM)
install(FILES Debug/debug.hpp
DESTINATION openfpm_pdata/include/Debug
COMPONENT OpenFPM)
install(TARGETS ofpm_pdata EXPORT ofpm_pdata_config DESTINATION openfpm_pdata/lib COMPONENT OpenFPM)
install(TARGETS ofpm_pdata_dl EXPORT ofpm_pdata_dl_config DESTINATION openfpm_pdata/lib COMPONENT OpenFPM)
########## Create openfpmConfig.cmake + openfpmConfigVersion.cmake
set(DOBC $ENV{DISABLE_OPENFPM_BINARY_CONFIG})
if(NOT DOBC EQUAL 1)
add_library(binary_config INTERFACE)
add_library(binary_config_ INTERFACE)
add_library(binary_config_shared INTERFACE)
add_library(binary_config_static INTERFACE)
target_include_directories(
binary_config_
INTERFACE
${CMAKE_INSTALL_PREFIX}/openfpm_pdata/include
${CMAKE_INSTALL_PREFIX}/openfpm_data/include
${CMAKE_INSTALL_PREFIX}/openfpm_pdata/include/config
${CMAKE_INSTALL_PREFIX}/openfpm_io/include
${CMAKE_INSTALL_PREFIX}/openfpm_vcluster/include
${CMAKE_INSTALL_PREFIX}/openfpm_devices/include
${PARMETIS_ROOT}/include
${METIS_ROOT}/include
${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES}
${PETSC_INCLUDES}
${HDF5_ROOT}/include
${LIBHILBERT_INCLUDE_DIRS}
${Vc_INCLUDE_DIR}
${Boost_INCLUDE_DIRS}
${MPI_C_INCLUDE_DIRS})
if (ENABLE_NUMERICS)
target_include_directories(
binary_config_
INTERFACE
${CMAKE_INSTALL_PREFIX}/openfpm_numerics/include)
endif()
if (CUDA_ON_CPU)
target_compile_definitions(binary_config_ INTERFACE CUDA_ON_CPU)
endif()
target_compile_options(binary_config_ INTERFACE $<$<COMPILE_LANGUAGE:CUDA>: ${WARNING_SUPPRESSION_AND_OPTION_NVCC} >)
target_link_libraries(binary_config_ INTERFACE Boost::context)
target_link_libraries(binary_config_ INTERFACE Boost::fiber)
target_link_libraries(binary_config_ INTERFACE Boost::filesystem)
target_link_libraries(binary_config_ INTERFACE Boost::iostreams)
target_link_libraries(binary_config_ INTERFACE Boost::program_options)
target_link_libraries(binary_config_ INTERFACE ${PARMETIS_LIBRARIES})
target_link_libraries(binary_config_ INTERFACE -L${METIS_ROOT}/lib metis)
target_link_libraries(binary_config_ INTERFACE ${HDF5_LIBRARIES})
target_link_libraries(binary_config_ INTERFACE -L${LIBHILBERT_LIBRARY_DIRS} ${LIBHILBERT_LIBRARIES})
target_link_libraries(binary_config_ INTERFACE ${PETSC_LIBRARIES})
target_link_libraries(binary_config_ INTERFACE ${Vc_LIBRARIES})
target_link_libraries(binary_config_ INTERFACE ${alpaka_LIBRARIES})
target_link_libraries(binary_config_ INTERFACE ${MPI_C_LIBRARIES})
# Not OK before CMake 3.13
#target_link_libraries(binary_config INTERFACE $<INSTALL_PREFIX>/openfpm_vcluster/lib/$<TARGET_FILE_NAME:openfpm::vcluster> )
#target_link_libraries(binary_config INTERFACE $<INSTALL_PREFIX>/openfpm_devices/lib/$<TARGET_FILE_NAME:openfpm::ofpmmemory> )
target_link_libraries(binary_config_static INTERFACE ${CMAKE_INSTALL_PREFIX}/openfpm_vcluster/lib/libvcluster.a )
target_link_libraries(binary_config_static INTERFACE ${CMAKE_INSTALL_PREFIX}/openfpm_devices/lib/libofpmmemory.a )
target_link_libraries(binary_config_static INTERFACE ${CMAKE_INSTALL_PREFIX}/openfpm_pdata/lib/libofpm_pdata.a )
target_link_libraries(binary_config_shared INTERFACE ${CMAKE_INSTALL_PREFIX}/openfpm_vcluster/lib/libvcluster_dl.so )
target_link_libraries(binary_config_shared INTERFACE ${CMAKE_INSTALL_PREFIX}/openfpm_devices/lib/libofpmmemory_dl.so )
target_link_libraries(binary_config_shared INTERFACE ${CMAKE_INSTALL_PREFIX}/openfpm_pdata/lib/libofpm_pdata_dl.so )
target_link_libraries(binary_config_ INTERFACE ${CUDA_LIBRARIES} )
# Does not work before Cmake 3.13
#install(TARGETS binary_config vcluster ofpmmemory EXPORT openfpm_config CONFIGURATIONS)
install(TARGETS binary_config EXPORT openfpm_config CONFIGURATIONS)
install(TARGETS binary_config_ EXPORT openfpm_config CONFIGURATIONS)
install(TARGETS binary_config_static EXPORT openfpm_config CONFIGURATIONS)
install(TARGETS binary_config_shared EXPORT openfpm_config CONFIGURATIONS)
include(CMakePackageConfigHelpers)
write_basic_package_version_file(
"${CMAKE_CURRENT_BINARY_DIR}/openfpm_cmake/openfpmConfigVersion.cmake"
VERSION ${openfpm_VERSION}
COMPATIBILITY AnyNewerVersion)
install(EXPORT openfpm_config
DESTINATION cmake/
NAMESPACE openfpm::
FILE openfpmConfig.cmake)
install(
FILES
"${CMAKE_CURRENT_BINARY_DIR}/openfpm_cmake/openfpmConfigVersion.cmake"
DESTINATION
cmake/)
install(
FILES
"${CMAKE_CURRENT_SOURCE_DIR}/cmake/openfpmConfig-Vars.cmake"
DESTINATION
cmake/)
endif()
src/DLB/DLB.hpp 0 → 100644
View file @ b9ccc50e
/*
* DLB.hpp
*
* Created on: Nov 20, 2015
* Author: Antonio Leo
*/
#ifndef SRC_DECOMPOSITION_DLB_HPP_
#define SRC_DECOMPOSITION_DLB_HPP_
//! Time structure for statistical purposes
struct Times
{
//! starting time of the simulation (0)
size_t simulationStartTime = 0;
//! End iteration of the simulation
size_t simulationEndTime;
//! integration time
double timeStep = 0.1;
//! Interval between teo rebalance
//! Start time
size_t iterationStartTime;
//! End time
size_t iterationEndTime;
};
/*! Class that implements the two heuristics to determine when a re-balance of the distribution is needed.
*
* Used heuristics are: SAR and Un-balance Threshold (Default)\n
*
* To chose the heuristic use the method setHeuristic(Heuristic)
*
* In the SAR heuristic the following formula is applied:\n
* \f$W_{n} = \frac{\sum_{j=1}^{n} (T_{max}(j) - T_{avg}(j)) + C} {n}\f$
*
* \f$T_{max}(j)\f$ – wall-clock time of bottleneck process in time step j\n
* \f$T_{avg}(j)\f$ – average wall-clock time for time step j over all processes\n
* \f$C\f$ – cost of re-decomposing the problem\n
* \f$n\f$ – number of time steps since last re-decomposition\n
* \n
* For small n, load balance is good and W decreases since C is amortized over an increasing number of time steps.
* As the accumulated idle time starts to dominate, W starts to rise. At this point, C has been fully amortized.
* Re-decompose when \f$W_{n} > W_{n-1}\f$\n
*
* In the Un-balance Threshold heuristic the re-balance is triggered when the un-balance level exceeds a certain level.
* Levels can be chosen in the ThresholdLevel type.
*/
class DLB
{
public:
//! Type of DLB heuristics
enum Heuristic
{
SAR_HEURISTIC, UNBALANCE_THRLD
};
//! Level of un-balance needed to trigger the re-balance
enum ThresholdLevel
{
THRLD_LOW = 5, THRLD_MEDIUM = 7, THRLD_HIGH = 10
};
private:
//! Runtime virtual cluster machine
Vcluster<> & v_cl;
//! Structure that will contain all the timings
Times timeInfo;
//! Wn for SAR heuristic
float w_n = -1;
//! Computation cost for SAR heuristic
float c_c = 5;
//! Number of time-steps since the previous DLB
size_t n_ts = 1;
//! Idle time accumulated so far, needed for SAR heuristic
float i_time = 0;
//! Vector to collect all timings
openfpm::vector<long> times;
//! Type of the heuristic to use
Heuristic heuristic = UNBALANCE_THRLD;
//! Un-balance value
float unbalance = -1;
//! Threshold value
ThresholdLevel thl = THRLD_MEDIUM;
/*! \brief Function that gather times informations and decides if a rebalance is needed it uses the SAR heuristic
*
* \return true if re-balance is needed
*
*/
inline bool SAR()
{
long t = timeInfo.iterationEndTime - timeInfo.iterationStartTime;
float t_max = t, t_avg = t;
// Exchange time informations through processors
v_cl.max(t_max);
v_cl.sum(t_avg);
v_cl.execute();
t_avg /= v_cl.getProcessingUnits();
// add idle time to vector
i_time += t_max - t_avg;
// Compute Wn
float nw_n = (i_time + c_c) / n_ts;
if (w_n == -1)
w_n = nw_n;
if (nw_n > w_n)
{
i_time = 0;
n_ts = 1;
w_n = nw_n;
return true;
}
else
{
++n_ts;
w_n = nw_n;
return false;
}
}
/*! \brief Check if the un-balance has exceeded the threshold
*
* \return true if re-balance is needed, false otherwise
*/
bool unbalanceThreshold()
{
if (unbalance == -1)
{
std::cerr << "Error: Un-balance value must be set before checking DLB.";
return false;
}
if (unbalance > thl)
{
return true;
}
return false;
}
public:
/*! \brief Constructor for DLB class
*
* \param v_cl virtual cluster object
*/
DLB(Vcluster<> & v_cl) :
v_cl(v_cl)
{
}
/*! \brief Set the heuristic to use (default: un-balance threshold)
*
* \param h
*/
void setHeurisitc(Heuristic h)
{
heuristic = h;
}
/*! \brief Get the heuristic
*
* Indicate which heuristic model is used to calculate when a rebalance
* is needed
*
* \return the Heuristic used by DLB
*
*/
Heuristic getHeurisitc()
{
return heuristic;
}
/*! \brief check if a re-balance is needed using the selected heuristic
*
* \return true if the rebalance is needed
*
*/
bool rebalanceNeeded()
{
if (heuristic == SAR_HEURISTIC)
{
return SAR();
}
else
{
return unbalanceThreshold();
}
}
/*! \brief Set start time for the simulation
*
* \param t time when the whole simulation starts
*/
void setSimulationStartTime(size_t t)
{
timeInfo.simulationStartTime = t;
}
/*! \brief Get start time for the simulation
*
* \return the start point of the simulation
*
*/
size_t getSimulationStartTime()
{
return timeInfo.simulationStartTime;
}
/*! \brief Set end time for the simulation
*
* \param t time when the whole simulation ends
*/
void setSimulationEndTime(size_t t)
{
timeInfo.simulationEndTime = t;
}
/*! \brief Get end time for the simulation
*
* \return the end time of the simulation
*
*/
size_t getSimulationEndTime()
{
return timeInfo.simulationEndTime;
}
/*! \brief Set start time for the single iteration
*
*/
void startIteration()
{
timeInfo.iterationStartTime = clock();
}
/*! \brief Set start time for the single iteration
*
* \param t time when the one iteration starts
*/
void startIteration(size_t t)
{
timeInfo.iterationStartTime = t;
}
/*! \brief Set end time for the single iteration
*
* \param time when one iteration is completed
*
*/
void endIteration()
{
timeInfo.iterationEndTime = clock();
}
/*! \brief Set the end time when the previous rebalance has been performed
*
* \param t time when one iteration ends
*/
void endIteration(size_t t)
{
timeInfo.iterationEndTime = t;
}
/*! \brief Set delta time step for one iteration (Computation time)
*
* \param t timestep
*/
void setTimeStep(double t)
{
timeInfo.timeStep = t;
}
/*! \brief Set time step for the single iteration
*
* \param computation value of the computation cost (default: 5)
*/
void setComputationCost(size_t computation)
{
c_c = computation;
}
/*! \brief Get how many time-steps have passed since the last re-balancing
*
* \return number of timesteos
*
*/
size_t getNTimeStepSinceDLB()
{
return n_ts;
}
/*! \brief Set un-balance value
*
* \param u unbalance
*/
void setUnbalance(float u)
{
unbalance = u;
}
/*! \brief threshold of umbalance to start a rebalance
*
* \param t threshold level
*/
void setThresholdLevel(ThresholdLevel t)
{
thl = t;
}
};
#endif /* SRC_DECOMPOSITION_DLB_HPP_ */
src/DLB/DLB_unit_test.hpp 0 → 100644
View file @ b9ccc50e
/*
* 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_ */