diff --git a/package/petsc/3.6.2/install.sh b/package/petsc/3.6.2/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..43a556683d4d17691ee2908205bf588577a7523c --- /dev/null +++ b/package/petsc/3.6.2/install.sh @@ -0,0 +1,17 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.2.tar.gz +. ${DOWNLOAD_TOOL} -u https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.11/src/hdf5-1.10.11.tar.bz2 +cd ${JARVIS_TMP} +rm -rf petsc-3.6.2 +tar -xvf ${JARVIS_DOWNLOAD}/petsc-3.6.2.tar.gz +cd petsc-3.6.2 +export PETSC_DIR=${JARVIS_TMP}/petsc-3.6.2 PETSC_ARCH=linux_gnu +./configure CFLAGS="-fPIC -Wno-implicit-int -Wno-int-conversion" FFLAGS="-fPIC" F90=$F90 --prefix=$1 --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpifort \ + --with-shared-libraries=0 \ + --download-parmetis=1 --download-metis=1 \ + --download-hdf5=${JARVIS_DOWNLOAD}/hdf5-1.10.11.tar.bz2 --force +make MAKE_NP=64 +make check +make test diff --git a/package/vtk/6.2.0/install.sh b/package/vtk/6.2.0/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..d61267c58c48752b0e9654dea301ceebad28abea --- /dev/null +++ b/package/vtk/6.2.0/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://vtk.org/files/release/6.2/VTK-6.2.0.tar.gz +cd ${JARVIS_TMP} +rm -rf VTK-6.2.0 +tar -xvf ${JARVIS_DOWNLOAD}/VTK-6.2.0.tar.gz +cd VTK-6.2.0 +mkdir build && cd build +cmake -DCMAKE_INSTALL_PREFIX=$1 .. \ + -DCMAKE_C_FLAGS="-Wno-implicit-function-declaration" \ + -DCMAKE_CXX_FLAGS="-std=c++14 -Wno-implicit-function-declaration" +make -j && make install diff --git a/templates/chaste/2019.1/data.chaste.arm.cpu.config b/templates/chaste/2019.1/data.chaste.arm.cpu.config index a98c6744c0004a67b1d8427881a9d8901fe81c39..73108d38b63c0dd73253c31bf2965386165dd774 100644 --- a/templates/chaste/2019.1/data.chaste.arm.cpu.config +++ b/templates/chaste/2019.1/data.chaste.arm.cpu.config @@ -5,6 +5,8 @@ chaste/2019.1 $JARVIS_PROXY/Chaste/Chaste/archive/refs/tags/release_2019.1.tar.gz Chaste-release_2019.1.tar.gz [DEPENDENCY] +. ${DOWNLOAD_TOOL} -u https://chaste.github.io/old_releases/release_3.3/UserTutorials/CardiacExecutable/Propagation3d/Propagation3d.tgz + set -x set -e module purge @@ -20,14 +22,14 @@ export CC=clang CXX=clang++ FC=flang ./jarvis -install boost/1.70.0/clang clang ./jarvis -install sundials/5.8.0 clang ./jarvis -install xerces/3.3.0 clang -./jarvis -install vtk/9.4.1 clang +./jarvis -install vtk/6.2.0 clang module load xerces/3.3.0 ./jarvis -install xsd/4.0.0 clang module load hmpi/2.4.2 export CC=mpicc CXX=mpicxx FC=mpifort -./jarvis -install petsc/3.19.6 clang+mpi +./jarvis -install petsc/3.6.2 clang+mpi module load python2/2.7.16 ./jarvis -install amara/1.2.0.2/ clang @@ -41,54 +43,63 @@ module load bisheng/4.1.0 module load kml-bisheng/2.4.0 module load hmpi/2.4.2 module load boost-clang/1.70.0 -module load petsc/3.19.6 +module load petsc/3.6.2 module load sundials/5.8.0 module load xerces/3.3.0 module load xsd/4.0.0 -module load vtk/9.4.1 +module load vtk/6.2.0 module load python2/2.7.16 [APP] app_name = chaste build_dir = ${JARVIS_ROOT} binary_dir = ${JARVIS_ROOT}/Chaste-release_2019.1/chaste_build/apps -case_dir = ${JARVIS_ROOT}/Chaste-release_2019.1 +case_dir = ${JARVIS_ROOT}/Chaste-release_2019.1/examples/Propagation3d [BUILD] rm -rf Chaste-release_2019.1 tar -zxvf $JARVIS_DOWNLOAD/Chaste-release_2019.1.tar.gz cd Chaste-release_2019.1 sed -i '452s|^|#|' CMakeLists.txt -sed -i -e 's/VecLockPush/VecLockReadPush/g' \ - -e 's/VecLockPop/VecLockReadPop/g' \ - ./global/test/TestDistributedVector.hpp ./linalg/test/TestPetscVecTools.hpp +#sed -i -e 's/VecLockPush/VecLockReadPush/g' \ +# -e 's/VecLockPop/VecLockReadPop/g' \ +# ./global/test/TestDistributedVector.hpp ./linalg/test/TestPetscVecTools.hpp sed -i '6s|\-Werror||g' ./cmake/Modules/ChasteCompilerFlags.cmake -mkdir chaste_build chaste_install +sed -i '1830s|#||1' python/pycml/translators.py +sed -i '1831s|^\([[:space:]]*\)\([a-zA-Z]\)|\1#\2|' python/pycml/translators.py +sed -i '1838s|#||1' python/pycml/translators.py +sed -i '1839s|^\([[:space:]]*\)\([a-zA-Z]\)|\1#\2|' python/pycml/translators.py +mkdir chaste_build chaste_install examples cd chaste_build cmake .. -DCMAKE_INSTALL_PREFIX=$(realpath ../chaste_install) \ -DPYTHON_EXECUTABLE=${PYTHON2_PATH}/bin/python2 \ -DBoost_INCLUDE_DIR=${BOOST_CLANG_PATH}/include \ - -DPETSC_DIR=${PETSC_PATH} \ + -DPETSC_DIR=${JARVIS_TMP}/petsc-3.6.2 \ + -DPETSC_ARCH=linux_gnu \ -DPETSC_INCLUDES=${PETSC_PATH}/include \ -DPETSC_LIBRARIES=${PETSC_PATH}/lib \ - -DPARMETIS_LIBRARY=${PETSC_PATH}/lib/libparmetis.so \ + -DMETIS_LIBRARY=${PETSC_PATH}/lib/libmetis.a \ + -DPARMETIS_LIBRARY=${PETSC_PATH}/lib/libparmetis.a \ -DSUNDIALS_INCLUDE_DIRS=${SUNDIALS_PATH}/include \ -DSUNDIALS_LIBRARIES=${SUNDIALS_PATH}/lib64 \ -DSUNDIALS_sundials_cvode_LIBRARY=${SUNDIALS_PATH}/lib64/libsundials_cvode.so \ -DSUNDIALS_sundials_nvecserial_LIBRARY=${SUNDIALS_PATH}/lib64/libsundials_nvecserial.so \ -DChaste_SUNDIALS_VERSION=50800 -DSUNDIALS_VERSION_MAJOR=5 -DSUNDIALS_VERSION_MINOR=8 \ -DXERCESC_LIBRARY=${XERCES_PATH}/lib/libxerces-c.so \ - -DCMAKE_C_FLAGS="-Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-9.4 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ - -DCMAKE_CXX_FLAGS="-std=c++14 -stdlib=libc++ -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-9.4 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" + -DCMAKE_C_FLAGS="-Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ + -DCMAKE_CXX_FLAGS="-std=c++14 -stdlib=libc++ -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ -DX11_X11_INCLUDE_PATH=/usr/include/X11/ -DX11_X11_LIB=/usr/lib64 make VERBOSE=1 -j Continuous make install +cd ../examples +tar -xvzf ${JARVIS_DOWNLOAD}/Propagation3d.tgz + [CLEAN] -make -j 128 ARCH=Linux-arm-clang VERSION=psmp clean +make clean [RUN] -run = numactl -C 0 mpirun --allow-run-as-root -np 1 -x OMP_NUM_THREADS=1 +run = mpirun --allow-run-as-root -np 32 -x OMP_NUM_THREADS=1 binary = Chaste ChasteParameters.xml nodes = 1