From d0ac14b4b22ef88ace3e5497262c34aa45c8f74c Mon Sep 17 00:00:00 2001 From: chenshaoheng Date: Wed, 5 Mar 2025 18:05:02 +0800 Subject: [PATCH 1/3] add templates/psi4/1.3.2/data.psi4-common.arm.cpu.config --- package/boost/1.72.0/clang/install.sh | 6 +- .../1.3.2/data.psi4-common.arm.cpu.config | 113 ++++++++++++++++++ 2 files changed, 116 insertions(+), 3 deletions(-) create mode 100644 templates/psi4/1.3.2/data.psi4-common.arm.cpu.config diff --git a/package/boost/1.72.0/clang/install.sh b/package/boost/1.72.0/clang/install.sh index 06b1f1e..187c7a4 100755 --- a/package/boost/1.72.0/clang/install.sh +++ b/package/boost/1.72.0/clang/install.sh @@ -1,10 +1,10 @@ #!/bin/bash set -x set -e -. ${DOWNLOAD_TOOL} -u https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz +. ${DOWNLOAD_TOOL} -u https://nchc.dl.sourceforge.net/project/boost/boost/1.72.0/boost_1_72_0.tar.bz2 cd ${JARVIS_TMP} -tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz +tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.bz2 cd boost_1_72_0 sed -i '60s/.*/#ifdef PTHREAD_STACK_MIN/' ./boost/thread/pthread/thread_data.hpp ./bootstrap.sh --with-toolset=clang --with-libraries=system,serialization,program_options -./b2 toolset=clang cxxflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" linkflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" install --prefix=$1 \ No newline at end of file +./b2 toolset=clang cxxflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" linkflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" install --prefix=$1 diff --git a/templates/psi4/1.3.2/data.psi4-common.arm.cpu.config b/templates/psi4/1.3.2/data.psi4-common.arm.cpu.config new file mode 100644 index 0000000..824dbdb --- /dev/null +++ b/templates/psi4/1.3.2/data.psi4-common.arm.cpu.config @@ -0,0 +1,113 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +psi4/1.3.2 https://github.com/psi4/psi4/archive/v1.3.2.tar.gz + +[DEPENDENCY] + +./jarvis -install package/hpckit/2024.12.30/ any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi + +yum install cmake -y +export CC=gcc FC=gfortran CXX=g++ + +./jarvis -install package/python3/3.7.10 gcc +module use ${JARVIS_ROOT}/software/moduledeps/gcc12.3.1/ +module add python3/3.7.10 +which python3 +#pip3 install numpy==1.19.4 Cython==0.29.21 -i https://pypi.mirrors.ustc.edu.cn/simple +pip3 install numpy==1.19.4 Cython==0.29.21 + +./jarvis -install package/openblas/0.3.14 gcc +module add openblas/0.3.14 + +sed -i "11c #" package/gau2grid/1.3.0/install.sh +sed -i "13c #" package/gau2grid/1.3.0/install.sh +sed -i "14c #" package/gau2grid/1.3.0/install.sh +sed -i "15c cmake .. -DCMAKE_INSTALL_PREFIX=\$1 -DPYTHON_EXECUTABLE=`which python3`" package/gau2grid/1.3.0/install.sh +./jarvis -install package/gau2grid/1.3.0 gcc +module add gau2grid/1.3.0 +./jarvis -install package/libint/1.2.0 gcc +module add libint/1.2.0 +./jarvis -install package/libxc/4.3.0 gcc +module add libxc/4.3.0 +sed -i "11c #" package/pybind11/2.6.2/install.sh +sed -i "12c cmake .. -DCMAKE_INSTALL_PREFIX=\$1 -DPYTHON_EXECUTABLE=`which python3`" package/pybind11/2.6.2/install.sh +./jarvis -install package/pybind11/2.6.2 gcc +module add pybind11/2.6.2 + + +[ENV] +module use ${JARVIS_ROOT}/software/moduledeps/gcc12.3.1 +module add python3/3.7.10 +module add openblas/0.3.14 +module add gau2grid/1.3.0 +module add libint/1.2.0 libxc/4.3.0 pybind11/2.6.2 +export MATH_ROOT=$OPENBLAS_PATH +export PATH=$JARVIS_ROOT/software/apps/gcc12.3.1/psi4/bin:$PATH + + +[APP] +app_name = psi4 +build_dir = $JARVIS_ROOT +binary_dir = $JARVIS_ROOT/software/apps/gcc12.3.1/psi4/bin +case_dir = $JARVIS_ROOT/software/apps/gcc12.3.1/psi4/share/psi4/samples/opt-multi-frozen-dimer-c2h + +[BUILD] +set -x +cd ${JARVIS_TMP} +pip3 install pint pydantic==1.10.7 deepdiff==6.3.0 -i https://pypi.mirrors.ustc.edu.cn/simple +rm psi4-1.3.2 -rf +tar -xvf ${JARVIS_DOWNLOAD}/v1.3.2.tar.gz +cd psi4-1.3.2 +mkdir build +cd build +export CC=gcc FC=gfortran CXX=g++ +cmake .. -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$JARVIS_ROOT/software/apps/gcc12.3.1/psi4 -Dpybind11_DIR=${PYBIND11_PATH}/share/cmake/pybind11 -Dgau2grid_DIR=${GAU2GRID_PATH}/share/cmake/gau2grid -DLibint_DIR=${LIBINT_PATH}/share/cmake/Libint -DLibxc_DIR=${LIBXC_PATH}/share/cmake/Libxc +sed -i "34a #include " ${JARVIS_TMP}/psi4-1.3.2/psi4/src/create_new_plugin.cc +make -j +make install + +[CLEAN] +cd $JARVIS_TMP/psi4-1.3.2/build +make clean + +[RUN] +run = +binary = +nodes = 1 + +[BATCH] + +LOG_FILE="psi4-proformance.log" + +>"$LOG_FILE" + +#$RUN_TOOL "psi4 input.dat" +echo $PWD +time -p psi4 input.dat + +echo "ALL commands executed. Performance log saved to $LOG_FILE" + + +[JOB] +#!/bin/sh +#DSUB -n psi4_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -oo psi4.%J.out +#DSUB -oe psi4.%J.err + +LOG_FILE="psi4-proformance.log" + +>"$LOG_FILE" + +#$RUN_TOOL "Psi4 Run" "psi4 -i input.dat" +time -p psi4 -i input.dat 2>&1 |tee $LOG_FILE + +echo "ALL commands executed. Performance log saved to $LOG_FILE" -- Gitee From 01723e2618795b155a834eb7270c9854a1b0dec6 Mon Sep 17 00:00:00 2001 From: chenshaoheng Date: Thu, 6 Mar 2025 14:47:14 +0800 Subject: [PATCH 2/3] add ./templates/qmcpack/3.17.1 --- .../3.17.1/data.qmcpack-common.arm.cpu.config | 119 ++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config diff --git a/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config b/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config new file mode 100644 index 0000000..9c53511 --- /dev/null +++ b/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config @@ -0,0 +1,119 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +qmcpack/3.17.1 ${JARVIS_PROXY}/QMCPACK/qmcpack/archive/refs/tags/v3.17.1.tar.gz + +[DEPENDENCY] +set -e +set -x +./jarvis -install package/hpckit/2024.12.30/ any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi + +export CC=clang CXX=clang++ FC=flang + +export CFLAGS="-Wno-implicit-function-declaration -Wno-enum-constexpr-conversion -Wno-int-conversion" +./jarvis -install openblas/0.3.14 clang +module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.1.0 +module add openblas/0.3.14 +sed -i "8a sed -i '130c struct hash_base : std::__unary_function {};' ./boost/container_hash/hash.hpp" package/boost/1.72.0/clang/install.sh +sed -i '11c ./b2 toolset=clang cxxflags="-stdlib=libc++ -Wno-enum-constexpr-conversion" linkflags="-stdlib=libc++" install --prefix=\$1 ' package/boost/1.72.0/clang/install.sh +./jarvis -install boost/1.72.0/clang clang +module load boost-clang/1.72.0 +./jarvis -install zlib/1.2.11 clang +module load zlib/1.2.11 +./jarvis -install libxml2/2.10.1 clang +module load libxml2/2.10.1 +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort +./jarvis -install fftw/3.3.8 clang+mpi +module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.1.0-hmpi2.4.3 +module load fftw/3.3.8 +sed -i '10c ./configure --prefix=$1 --enable-fortran --enable-static=yes --enable-parallel --enable-shared CFLAGS="-O3 -fPIC -Wno-incompatible-pointer-types-discards-qualifiers -Wno-non-literal-null-conversion -Wno-int-conversion -Wno-implicit-function-declaration" FCFLAGS="-O3 -fPIC" LDFLAGS="-Wl,--build-id"' package/hdf5/1.10.1/clang/install.sh +./jarvis -install hdf5/1.10.1/clang clang+mpi +module load hdf5-clang/1.10.1 + +[ENV] +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +module use software/moduledeps/bisheng4.1.0 +module add boost-clang/1.72.0 zlib/1.2.11 libxml2/2.10.1 +module load openblas/0.3.14 +module use software/moduledeps/bisheng4.1.0-hmpi2.4.3/ +module load hdf5-clang/1.10.1 fftw/3.3.8 +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort +export PATH=${JARVIS_ROOT}/software/apps/bisheng4.1.0/hmpi2.4.3/qmcpack/3.17.1/bin:$PATH +export PYTHONPATH=${JARVIS_ROOT}/qmcpack-3.17.1/nexus/lib:$PYTHONPATH + + +[APP] +app_name = qmcpack +build_dir = ${JARVIS_ROOT} +binary_dir = ${JARVIS_ROOT}/software/apps/bisheng4.1.0/hmpi2.4.3/qmcpack/3.17.1/bin +case_dir = ${JARVIS_ROOT}/software/apps/bisheng4.1.0/hmpi2.4.3/qmcpack/3.17.1/examples/molecules/H2O/ + +[BUILD] +cd ${JARVIS_TMP} +rm qmcpack-3.17.1 -rf +tar -xvf ${JARVIS_DOWNLOAD}/v3.17.1.tar.gz + +cd ${JARVIS_TMP}/qmcpack-3.17.1/build +export CC=mpicc FC=mpifort CXX=mpicxx +export BLAS="-L${JARVIS_ROOT}/software/libs/bisheng4.1.0/openblas/0.3.14/lib -lblas" +export CFLAGS="-Wno-implicit-function-declaration -Wno-enum-constexpr-conversion -Wno-int-conversion" +cmake \ +-DCMAKE_BUILD_TYPE=Release \ +-DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/bisheng4.1.0/hmpi2.4.3/qmcpack/3.17.1 \ +-DLIBXML2_LIBRARY=${JARVIS_LIBS}/bisheng4.1.0/libxml2/2.10.1/lib/libxml2.so \ +-DZLIB_LIBRARY=${JARVIS_LIBS}/bisheng4.1.0/zlib/1.2.11/lib/libz.so \ +-DFFTW_HOME=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8 \ +-DBOOST_ROOT=${JARVIS_LIBS}/bisheng4.1.0/boost-clang/1.72.0 \ +../ +sed -i '130c struct hash_base : std::unary_function {};' ${JARVIS_LIBS}/bisheng4.1.0/boost-clang/1.72.0/include/boost/container_hash/hash.hpp +make -j +make install +cp -r ${JARVIS_TMP}/qmcpack-3.17.1/examples/ ${JARVIS_ROOT}/software/apps/bisheng4.1.0/hmpi2.4.3/qmcpack/3.17.1 + +[RUN] +run = +binary = +nodes = 1 + + +[BATCH] + +LOG_FILE="qmcpack-proformance.log" + +>"$LOG_FILE" +sed -i '81s/.*/ 100 <\/parameter>/' simple-H2O.xml +sed -i '81s|^| |' simple-H2O.xml + +#$RUN_TOOL "" "" + +time -p mpirun --allow-run-as-root -np 120 qmcpack simple-H2O.xml 2>&1 |tee $LOG_FILE +echo "ALL commands executed. Performance log saved to $LOG_FILE" + + +[JOB] +#!/bin/sh +#DSUB -n qmcpack_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -oo qmcpack.%J.out +#DSUB -oe qmcpack.%J.err + +LOG_FILE="qmcpack-proformance.log" + +>"$LOG_FILE" + +#$RUN_TOOL "Run qmcpack" "" +sed -i '81s/.*/ 100 <\/parameter>/' simple-H2O.xml +sed -i '81s|^| |' simple-H2O.xml + +time -p mpirun --allow-run-as-root -np 120 qmcpack simple-H2O.xml 2>&1 |tee $LOG_FILE + +echo "ALL commands executed. Performance log saved to $LOG_FILE" -- Gitee From 2255ffde3876bdae8abaded80039b9bc7ddcb155 Mon Sep 17 00:00:00 2001 From: chenshaoheng Date: Thu, 6 Mar 2025 19:20:48 +0800 Subject: [PATCH 3/3] add mopac/22.0.4/data.mopac-common fix data.qmcpack-common --- .../22.0.4/data.mopac-common.arm.cpu.config | 85 +++++++++++++++++++ .../3.17.1/data.qmcpack-common.arm.cpu.config | 2 +- 2 files changed, 86 insertions(+), 1 deletion(-) create mode 100644 templates/mopac/22.0.4/data.mopac-common.arm.cpu.config diff --git a/templates/mopac/22.0.4/data.mopac-common.arm.cpu.config b/templates/mopac/22.0.4/data.mopac-common.arm.cpu.config new file mode 100644 index 0000000..0fbf77e --- /dev/null +++ b/templates/mopac/22.0.4/data.mopac-common.arm.cpu.config @@ -0,0 +1,85 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +mopac/22.0.4 https://github.com/openmopac/mopac/archive/refs/tags/v22.0.4.tar.gz + + +[DEPENDENCY] +./jarvis -install package/hpckit/2024.12.30/ any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi +module add gcc/kml2.5.0/kml +module unload gcc/kml2.5.0/kblas/pthread +module add gcc/kml2.5.0/kblas/omp + +[ENV] +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi +module add gcc/kml2.5.0/kml +module unload gcc/kml2.5.0/kblas/pthread +module add gcc/kml2.5.0/kblas/omp +export PATH=${JARVIS_ROOT}/software/apps/gcc12.3.1/hmpi2.4.3/mopac/22.0.4/bin:$PATH +export LD_LIBRARY_PATH=${JARVIS_ROOT}/software/apps/gcc12.3.1/hmpi2.4.3/mopac/22.0.4/lib64:$LD_LIBRARY_PATH + + + +[APP] +app_name = mopac +build_dir = ${JARVIS_ROOT} +binary_dir = ${JARVIS_ROOT}/software/apps/gcc12.3.1/hmpi2.4.3/mopac/22.0.4/bin +case_dir = ${JARVIS_ROOT}/software/apps/gcc12.3.1/hmpi2.4.3/mopac/22.0.4/tests + +[BUILD] +rm mopac-22.0.4 -rf +cd ${JARVIS_TMP} +rm mopac-22.0.4 -rf +tar -xf ${JARVIS_DOWNLOAD}/v22.0.4.tar.gz +yum install numactl-libs -y +cd mopac-22.0.4 +mkdir build && cd build +export KML_LIB_PATH=${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/kml/gcc/lib +cmake -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/gcc12.3.1/hmpi2.4.3/mopac/22.0.4 .. -DCMAKE_EXE_LINKER_FLAGS="-L$KML_LIB_PATH -L$KML_LIB_PATH/sve -lkml_rt -lklapack_full -lkscalapack_full" +make -j +make install + +cp ../tests -r ${JARVIS_ROOT}/software/apps/gcc12.3.1/hmpi2.4.3/mopac/22.0.4/ + +[RUN] +run = +binary = +nodes = 1 + + +[BATCH] + +LOG_FILE="mopac-proformance.log" + +>"$LOG_FILE" + +#$RUN_TOOL "" +echo $PWD +time -p mopac Crambin_1SCF.mop 2>&1 |tee $LOG_FILE +echo "ALL commands executed. Performance log saved to $LOG_FILE" + + +[JOB] +#!/bin/sh +#DSUB -n mopac_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -oo mopac.%J.out +#DSUB -oe mopac.%J.err + +LOG_FILE="mopac-proformance.log" + +>"$LOG_FILE" + +#$RUN_TOOL "" "" +time -p mopac Crambin_1SCF.mop 2>&1 |tee $LOG_FILE + +echo "ALL commands executed. Performance log saved to $LOG_FILE" diff --git a/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config b/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config index 9c53511..d83bdb0 100644 --- a/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config +++ b/templates/qmcpack/3.17.1/data.qmcpack-common.arm.cpu.config @@ -114,6 +114,6 @@ LOG_FILE="qmcpack-proformance.log" sed -i '81s/.*/ 100 <\/parameter>/' simple-H2O.xml sed -i '81s|^| |' simple-H2O.xml -time -p mpirun --allow-run-as-root -np 120 qmcpack simple-H2O.xml 2>&1 |tee $LOG_FILE +time -p mpirun --allow-run-as-root -x $PATH -x $LD_LIBRARY_PATH -np 120 qmcpack simple-H2O.xml 2>&1 |tee $LOG_FILE echo "ALL commands executed. Performance log saved to $LOG_FILE" -- Gitee