Commit 52f0f1c5 authored by incardon's avatar incardon

Latest modules

parent d490c151
Pipeline #1837 passed with stages
in 30 minutes and 9 seconds
openfpm_data @ 0083a00b
Subproject commit 58f3b70f264af944182ff2182e168d68f196b7e8
Subproject commit 0083a00b0bf82127a828c52ff3c1e922c18e19cf
......@@ -2,8 +2,8 @@
# check if the directory $1/MPI exist
rm -rf openmpi-3.1.3
rm openmpi-3.1.3.tar.gz
wget http://ppmcore.mpi-cbg.de/upload/openmpi-3.1.3.tar.gz
tar -xvf openmpi-3.1.3.tar.gz
rm -rf openmpi-4.0.2
rm openmpi-4.0.2.tar.gz
wget http://ppmcore.mpi-cbg.de/upload/openmpi-4.0.2.tar.gz
tar -xvf openmpi-4.0.2.tar.gz
......@@ -37,9 +37,9 @@ else
fi
### 1.8.19 does not compile on CYGWIN
wget http://ppmcore.mpi-cbg.de/upload/hdf5-1.8.19.tar.gz
tar -xf hdf5-1.8.19.tar.gz
cd hdf5-1.8.19
wget http://ppmcore.mpi-cbg.de/upload/hdf5-1.10.6.tar.gz
tar -xf hdf5-1.10.6.tar.gz
cd hdf5-1.10.6
if [ x"$platform" != x"cygwin" ]; then
CC=mpicc ./configure --with-zlib=$1/ZLIB --enable-parallel --prefix=$1/HDF5
......@@ -54,4 +54,4 @@ if [ $? -ne 0 ]; then
echo "HDF5 error installing"
exit 0
fi
echo 1 > $1/HDF5/version
echo 2 > $1/HDF5/version
......@@ -8,7 +8,7 @@ if [ -d "$1/MPI" ]; then
fi
./script/download_MPI.sh
cd openmpi-3.1.3
cd openmpi-4.0.2
if [ x"$3" == x"1" ]; then
echo "Installing MPI with GPU support"
......@@ -25,5 +25,5 @@ make -j $2
make install
# Mark the installation
echo 4 > $1/MPI/version
echo 5 > $1/MPI/version
......@@ -19,7 +19,7 @@ source script/solve_python
discover_os
function test_configure_options() {
cd petsc-3.10.2
cd petsc-3.12.3
$python_command ./configure COPTFLAGS="-O3 -g" CXXOPTFLAGS="-O3 -g" FOPTFLAGS="-O3 -g" $ldflags_petsc --with-cxx-dialect=C++11 $petsc_openmp --with-mpi-dir=$mpi_dir $configure_options2 --with-debugging=0
error=$?
cd ..
......@@ -49,14 +49,14 @@ fi
#### Download and uncompress petsc
rm petsc-lite-3.10.2.tar.gz
rm -rf petsc-3.10.2
wget http://ppmcore.mpi-cbg.de/upload/petsc-lite-3.10.2.tar.gz
rm petsc-lite-3.12.3.tar.gz
rm -rf petsc-3.12.3
wget http://ppmcore.mpi-cbg.de/upload/petsc-lite-3.12.3.tar.gz
if [ $? -ne 0 ]; then
echo -e "\033[91;5;1m FAILED! Installation requires an Internet connection \033[0m"
exit 1
fi
tar -xf petsc-lite-3.10.2.tar.gz
tar -xf petsc-lite-3.12.3.tar.gz
####
......@@ -114,15 +114,15 @@ configure_options="$configure_options --download-scalapack --download-mumps"
configure_options="$configure_options --download-superlu_dist"
configure_options="$configure_options --download-hypre"
rm petsc-lite-3.10.2.tar.gz
rm -rf petsc-3.10.2
wget http://ppmcore.mpi-cbg.de/upload/petsc-lite-3.10.2.tar.gz
rm petsc-lite-3.12.3.tar.gz
rm -rf petsc-3.12.3
wget http://ppmcore.mpi-cbg.de/upload/petsc-lite-3.12.3.tar.gz
if [ $? -ne 0 ]; then
echo -e "\033[91;5;1m FAILED! Installation requires an Internet connection \033[0m"
exit 1
fi
tar -xf petsc-lite-3.10.2.tar.gz
cd petsc-3.10.2
tar -xf petsc-lite-3.12.3.tar.gz
cd petsc-3.12.3
if [ x"$CXX" != x"icpc" ]; then
......@@ -158,7 +158,7 @@ if [ ! "$(ls -A $1/PETSC)" ]; then
rm -rf $1/PETSC
else
#Mark the installation
echo 2 > $1/PETSC/version
echo 3 > $1/PETSC/version
exit 0
fi
......@@ -308,33 +308,6 @@ if [ x"$MPI_valid" == x"yes" ]; then
fi
fi
#### Detect a potential dangerous situation ###
#### In which g++ is different from mpic++ ###
output_mpi=$(mpic++ --version)
output_gcc=$($dgc_compiler --version)
if [ x"$output_mpi" != x"$output_gcc" ]; then
echo -e "\033[91;5;1m MPI dangerous installation \033[0m"
echo -e "Performing a \033[1m \"mpic++ --version\" \033[0m, we detect that your installed mpic++ does not wrap the standard command g++"
echo "In general we strongly disencourage to override the default compiler(s), this configuration not only is not supported by OpenFPM, but can lead potentialy to several problems at system level. For the following reasons"
echo -e "\033[1m 1) All system wide dependencies become potentially useless \033[0m"
echo -e "\033[1m 2) A package maneger (apt-get or brew) installing a packege from source can potentialy generate incompatible system packages \033[0m"
echo -e "\033[1m 3) It is not easy to discover which compiler has been used to compile one dependency \033[0m"
echo -e "For just the time of the installation the installer will realign mpic++ to g++, unfortunately this could be not enough to ensure that all the dependencies has been compiled with the same compiler"
echo -e "\033[1m Installation will resume in 20 seconds \033[0m"
export OMPI_CXX=g++
sleep 20
fi
output_mpi=$(mpic++ --version)
output_gcc=$($dgc_compiler --version)
if [ x"$output_mpi" != x"$output_gcc" ]; then
echo -e "\033[91;5;1m MPI dangerous installation \033[0m"
echo -e "\033[1m The realign operation failed the installation will continue \033[0m"
sleep 10
fi
fi
}
......
......@@ -76,10 +76,10 @@ function remove_old()
## Check the installed version of the dependencies
if [ -d $1/BOOST ]; then
is_update=$(cat $1/BOOST/include/boost/version.hpp | grep "#define BOOST_VERSION 106800")
is_update=$(cat $1/BOOST/include/boost/version.hpp | grep "#define BOOST_VERSION 107200")
if [ x"$is_update" == x"" ]; then
echo -e "\033[1;34;5m --------------------------------------------------------------------------- \033[0m"
echo -e "\033[1;34;5m Boost has been updated to 1.68, the component will be updated automatically \033[0m"
echo -e "\033[1;34;5m Boost has been updated to 1.72, the component will be updated automatically \033[0m"
echo -e "\033[1;34;5m --------------------------------------------------------------------------- \033[0m"
sleep 5
rm -rf $1/BOOST/include
......@@ -143,9 +143,9 @@ function remove_old()
if [ -d $1/PETSC ]; then
version=$(cat $1/PETSC/version)
if [ x"$version" != x"2" ]; then
if [ x"$version" != x"3" ]; then
echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
echo -e "\033[1;34;5m PETSC has been updated to version 3.10.2, the component will be updated automatically \033[0m"
echo -e "\033[1;34;5m PETSC has been updated to version 3.12.3, the component will be updated automatically \033[0m"
echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
sleep 5
rm -rf $1/PETSC
......@@ -158,7 +158,7 @@ function remove_old()
if [ -d $1/HDF5 ]; then
version=$(cat $1/HDF5/version)
if [ x"$version" != x"1" ]; then
if [ x"$version" != x"2" ]; then
echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
echo -e "\033[1;34;5m HDF5 has been updated to version 1.10.6, the component will be updated automatically \033[0m"
echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
......@@ -169,7 +169,7 @@ function remove_old()
if [ -d $1/MPI ]; then
version=$(cat $1/MPI/version)
if [ x"$version" != x"4" ]; then
if [ x"$version" != x"5" ]; then
echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
echo -e "\033[1;34;5m MPI has been updated to version 4.0.2, the component will be updated automatically \033[0m"
echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
......
......@@ -758,11 +758,11 @@ public:
* \tparam prp... Properties to synchronize
*
*/
template<int... prp> void ghost_get()
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...>();
gd_array.get(i).template ghost_get<prp...>(opt);
}
}
......
......@@ -376,8 +376,9 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_amr_gpu_link_test_more_dense )
}
amr_g.hostToDevice<0>();
amr_g.ghost_get<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");
......
......@@ -2688,7 +2688,12 @@ public:
{
for (int i = 0 ; i < loc_grid.size() ; i++)
{
loc_grid.get(i).template tagBoundaries<stencil_type>(v_cl.getmgpuContext());
// we limit to the domain subset for tagging
Box_check<dim,unsigned int> chk(gdb_ext.get(i).Dbox);
loc_grid.get(i).template tagBoundaries<stencil_type>(v_cl.getmgpuContext(),chk);
}
}
......
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