diff --git a/templates/namd/2.13/data.namd.arm.cpu.config b/templates/namd/2.13/data.namd.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..226f25b9388e66a7368006e8e8ea92763e3820b1 --- /dev/null +++ b/templates/namd/2.13/data.namd.arm.cpu.config @@ -0,0 +1,158 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +namd/2.13 https://www.ks.uiuc.edu/Research/namd/2.13/download/412487/NAMD_2.13_Source.tar.gz +tcl/8.5 http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-arm64-threaded.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 load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi + +export CC=mpicc FC=mpifort CXX=mpicxx + +./jarvis -install package/fftw/3.3.8 bisheng+mpi +module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.1.0-hmpi2.4.3/ +module load fftw/3.3.8 + +[ENV] +module use ${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.1.0-hmpi2.4.3/ +module load fftw/3.3.8 +export PATH=$JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/namd/Linux-ARM64-clang:$PATH + +[APP] +app_name = namd +build_dir = $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/namd +binary_dir = $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/namd/Linux-ARM64-${CXX} +case_dir = ${JARVIS_TMP}/stmv + +[BUILD] +set -x +export CC=mpicc FC=mpifort CXX=mpicxx +mkdir -p ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/namd +cd ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/namd +rm -rf ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/namd/* +tar -xf ${JARVIS_DOWNLOAD}/NAMD_2.13_Source.tar.gz +export installdir=${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/namd +export sourcedir=${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/namd/NAMD_2.13_Source +cd ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/namd/NAMD_2.13_Source + +#安装charm-6.10.2.tar +tar -xvf charm-6.8.2.tar +cd charm-6.8.2 + +sed -i '8a CMK_CC_FLAGS="-Wno-unused-command-line-argument"' src/arch/common/cc-clang.sh +sed -i '9a CMK_CXX_FLAGS="-Wno-unused-command-line-argument"' src/arch/common/cc-clang.sh +cp src/arch/mpi-linux-x86_64 src/arch/mpi-linux-arm8 -rf +grep -rl 'm64' src/arch/mpi-linux-arm8 | xargs sed -i 's/\-m64//g' +./build charm++ mpi-linux-arm8 smp --with-production + +#安装tcl +mkdir -p ${installdir}/tcl_install +cd ${installdir}/tcl_install +tar -xf ${JARVIS_DOWNLOAD}/tcl8.5.9-linux-arm64-threaded.tar.gz +echo "Install is success install_dir: $installdir/tcl_install" + +export PATH=$PATH:$installdir/tcl_install/tcl8.5.9-linux-arm64-threaded/bin +export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$installdir/tcl8.5.9-linux-arm64-threaded/lib +export INCLUDE=$INCLUDE:$installdir/tcl8.5.9-linux-arm64-threaded/include +export TCL_DIR=$installdir/tcl_install/tcl8.5.9-linux-arm64-threaded + + +#安装NAMD +cd $sourcedir + +#修改配置文件 +rm -rf ./arch/Linux-ARM64.tcl ./arch/Linux-ARM64.fftw3 + +#func_fftw3_info +cat > ./arch/Linux-ARM64.fftw3 < ./arch/Linux-ARM64.tcl < ./arch/Linux-ARM64-${CXX}.arch <"$LOG_FILE" +$RUN_TOOL "namd " "time -p mpirun --allow-run-as-root -np 1 namd2 +ppn 127 ${test_name}.namd +setcpuaffinity" $LOG_FILE +#time -p mpirun --allow-run-as-root -np 1 namd2 +ppn 127 ${test_name}.namd +setcpuaffinity) + +echo "All commands executed. Performance log saved to $LOG_FILE" + +[JOB] +#!/bin/sh +#DSUB -n namd_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -oo roms.%J.out +#DSUB -oe roms.%J.err + +LOG_FILE="namd-run.log" + +>"$LOG_FILE" +$RUN_TOOL "namd" "time -p mpirun --allow-run-as-root -np 1 namd2 +ppn 127 ${test_name}.namd +setcpuaffinity" $LOG_FILE + +echo "ALL commands executed. Performance log saved to $LOG_FILE" +