diff --git a/package/amara/1.2.0.2/install.sh b/package/amara/1.2.0.2/install.sh index e0333dec48939d3043ad8108e91b48974d61d209..4a67c8ae56ea877eabb1b2a93a965f98adffdb43 100755 --- a/package/amara/1.2.0.2/install.sh +++ b/package/amara/1.2.0.2/install.sh @@ -2,15 +2,9 @@ set -x set -e . ${DOWNLOAD_TOOL} -u https://repo.huaweicloud.com/repository/pypi/packages/af/0e/e81dfe4b4fb24023207d86e4d4ff418b0e83927f2155ed3552b0e3196846/Amara-1.2.0.2.tar.gz#sha256=0814dae65bfeb3b309d65d7efb01e2e7a8c30611e7232f839c390816edac27cb -f Amara-1.2.0.2.tar.gz -. ${DOWNLOAD_TOOL} -u https://pypi.tuna.tsinghua.edu.cn/packages/0e/ae/3c5b4fffb12be7c3a80c99475853349e1cf8477f99051921ea06fbf5e3b9/4Suite-XML-1.0.2.tar.gz#sha256=f0c24132eb2567e64b33568abff29a780a2f0236154074d0b8f5262ce89d8c03 -f 4Suite-XML-1.0.2.tar.gz cd ${JARVIS_TMP} -rm -rf Amara-1.2.0.2 4Suite-XML-1.0.2 +rm -rf Amara-1.2.0.2 tar -xvzf ${JARVIS_DOWNLOAD}/Amara-1.2.0.2.tar.gz -tar -xvzf ${JARVIS_DOWNLOAD}/4Suite-XML-1.0.2.tar.gz - -cd 4Suite-XML-1.0.2 -python setup.py install -cd .. cd Amara-1.2.0.2 python setup.py install diff --git a/package/must/1.11.0/install.sh b/package/must/1.11.0/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..7a0abdbf282c020f4e9409ca90ab6653333f489e --- /dev/null +++ b/package/must/1.11.0/install.sh @@ -0,0 +1,14 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://hpc.rwth-aachen.de/must/files/MUST-v1.11.0.tar.gz +cd ${JARVIS_TMP} +rm -rf MUST-v1.11.0 +tar -xvf ${JARVIS_DOWNLOAD}/MUST-v1.11.0.tar.gz + +#yum install elfutils-devel binutils-devel libdwarf-devel -y +cd MUST-v1.11.0 +sed -i "1046s/va_alist/\&va_alist/g" ./externals/GTI/externals/PnMPI/src/pnmpi/wrapper.c +mkdir build && cd build +cmake .. -DCMAKE_INSTALL_PREFIX=$1 -DCMAKE_BUILD_TYPE=Release +make install -j diff --git a/package/petsc/3.6.2/install.sh b/package/petsc/3.6.2/install.sh index 43a556683d4d17691ee2908205bf588577a7523c..71461df4a99b82caddc9abc062341d5aa628349f 100755 --- a/package/petsc/3.6.2/install.sh +++ b/package/petsc/3.6.2/install.sh @@ -2,16 +2,25 @@ 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://ftp.mcs.anl.gov/pub/petsc/externalpackages/parmetis-4.0.3-p2.tar.gz +. ${DOWNLOAD_TOOL} -u http://ftp.mcs.anl.gov/pub/petsc/externalpackages/metis-5.1.0-p1.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 + +yum install -y lapack lapack-devel + 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 +export PETSC_DIR=${JARVIS_TMP}/petsc-3.6.2 PETSC_ARCH=arch-linux-c-debug ./configure CFLAGS="-fPIC -Wno-implicit-int -Wno-int-conversion" FFLAGS="-fPIC" F90=$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 + --with-make-np=64 \ + --download-parmetis=${JARVIS_DOWNLOAD}/parmetis-4.0.3-p2.tar.gz \ + --download-metis=${JARVIS_DOWNLOAD}/metis-5.1.0-p1.tar.gz \ + --download-hdf5=${JARVIS_DOWNLOAD}/hdf5-1.10.11.tar.bz2 \ + --force + make MAKE_NP=64 make check make test diff --git a/templates/chaste/2019.1/data.chaste.arm.cpu.config b/templates/chaste/2019.1/data.chaste.arm.cpu.config index 73108d38b63c0dd73253c31bf2965386165dd774..1ab014b74d403839717907877f2554d9aed8d461 100644 --- a/templates/chaste/2019.1/data.chaste.arm.cpu.config +++ b/templates/chaste/2019.1/data.chaste.arm.cpu.config @@ -1,105 +1,105 @@ -[SERVER] -11.11.11.11 - -[DOWNLOAD] -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 -module use ./software/modulefiles -./jarvis -install bisheng/4.1.0 com -./jarvis -install python2/2.7.16 com - -module load bisheng/4.1.0 -export CC=clang CXX=clang++ FC=flang - -./jarvis -install kml/2.4.0/bisheng clang -./jarvis -install hmpi/2.4.2 clang -./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/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/3.6.2 clang+mpi - -module load python2/2.7.16 -./jarvis -install amara/1.2.0.2/ clang -yum install libxml2-devel libxslt-devel -y -pip install rdflib lxml - -[ENV] -module purge -module use ./software/modulefiles -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/3.6.2 -module load sundials/5.8.0 -module load xerces/3.3.0 -module load xsd/4.0.0 -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/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 '6s|\-Werror||g' ./cmake/Modules/ChasteCompilerFlags.cmake -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=${BOOST_CLANG_PATH}/include \ - -DPETSC_DIR=${JARVIS_TMP}/petsc-3.6.2 \ - -DPETSC_ARCH=linux_gnu \ - -DPETSC_INCLUDES=${PETSC_PATH}/include \ - -DPETSC_LIBRARIES=${PETSC_PATH}/lib \ - -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-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 clean - -[RUN] -run = mpirun --allow-run-as-root -np 32 -x OMP_NUM_THREADS=1 -binary = Chaste ChasteParameters.xml -nodes = 1 +[SERVER] +11.11.11.11 + +[DOWNLOAD] +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 +yum install libxml2-devel libxslt-devel libXt-devel libX11-devel libXext-devel -y + +set -x +set -e +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +./jarvis -install python2/2.7.16 com + +module load bisheng/4.1.0 +export CC=clang CXX=clang++ FC=flang + +./jarvis -install kml/2.4.0/bisheng clang +./jarvis -install hmpi/2.4.2 clang +./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/6.2.0 clang + +module load xerces/3.3.0 +./jarvis -install xsd/4.0.0 clang + +module load hmpi/2.4.2 +module load python2/2.7.16 +./jarvis -install amara/1.2.0.2/ clang +pip install rdflib lxml + +export CC=mpicc CXX=mpicxx FC=mpifort +./jarvis -install petsc/3.6.2 clang+mpi + +[ENV] +module purge +module use ./software/modulefiles +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/3.6.2 +module load sundials/5.8.0 +module load xerces/3.3.0 +module load xsd/4.0.0 +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/examples/Propagation3d + +[BUILD] +cd /pacific_ext/l00855193/work/chaste +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 '6s|\-Werror||g' ./cmake/Modules/ChasteCompilerFlags.cmake +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=${BOOST_CLANG_PATH}/include \ + -DPETSC_DIR=${JARVIS_TMP}/petsc-3.6.2 \ + -DPETSC_ARCH=arch-linux-c-debug \ + -DPETSC_INCLUDES=${PETSC_PATH}/include \ + -DPETSC_LIBRARIES=${PETSC_PATH}/lib \ + -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=${XERCES_PATH}/lib/libxerces-c.so \ + -DCMAKE_C_FLAGS="-O3 -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ + -DCMAKE_CXX_FLAGS="-O3 -std=c++14 -stdlib=libc++ -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${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 -j + +cd ../examples +tar -xvzf ${JARVIS_DOWNLOAD}/Propagation3d.tgz + +[CLEAN] +make clean + +[RUN] +run = time -p mpirun -np 32 --allow-run-as-root --map-by ppr:8:numa:pe=1 -x UCX_TLS=self,sm -mca pml ucx -mca btl ^vader,tcp,openib,uct -x OMP_NUM_THREADS=1 +binary = Chaste ChasteParameters.xml +nodes = 1