From 6c7458c6bbb1af3175aa4ea5419b96f67642b5bc Mon Sep 17 00:00:00 2001 From: root <2393110978@qq.com> Date: Thu, 23 Oct 2025 17:11:52 +0800 Subject: [PATCH] update --- package/darshan/2.3.0/install.sh | 2 +- package/darshan/3.4.6/install.sh | 2 +- package/fftw/meta.sh | 3 +- package/gmp/6.2.0/install.sh | 2 +- package/grads/2.0.a4/install.sh | 5 +- package/mfem/4.4/install.sh | 4 +- package/openblas/meta.sh | 3 +- package/tau/2.30.0/install.sh | 35 +++------- .../CP2K/8.2/data.CP2K.arm-new.cpu.config | 31 ++++----- .../common/data.exagear-centos7.cpu.config | 4 +- .../0.99.1/data.Oceananigans.arm.cpu.config | 69 +++++++++++++++++++ .../berkeleygw.arm.bisheng.hpckit.config | 4 +- .../grads/2.0.a4/data.grads.arm.cpu.config | 1 - .../ioapi/3.2/data.ioapi_clang.arm.cpu.config | 18 +---- .../2021.2.10/data.lammps.arm.cpu.config | 55 +++++++++++++++ .../data.lammps.arm.cpu.sve.hpckit.config | 22 +++--- ...ta.meso_grapes.arm.cpu.bisheng.hmpi.config | 34 +++++---- .../1.3.2/data.psi4-common.arm.cpu.config | 3 +- .../2.1.0/data.scalapack.arm.cpu.config | 4 -- ...pecfem3d_globe.arm.cpu.bisheng.hmpi.config | 2 +- .../szip/2.1.1/data.szip.arm.bisheng.config | 3 - templates/wrf/4.6.1/data.wrf.arm.cpu.config | 55 +++++++-------- 22 files changed, 219 insertions(+), 142 deletions(-) create mode 100644 templates/Oceananigans/0.99.1/data.Oceananigans.arm.cpu.config create mode 100644 templates/lammps/2021.2.10/data.lammps.arm.cpu.config diff --git a/package/darshan/2.3.0/install.sh b/package/darshan/2.3.0/install.sh index fc1a3cef..2f9f2e57 100644 --- a/package/darshan/2.3.0/install.sh +++ b/package/darshan/2.3.0/install.sh @@ -10,7 +10,7 @@ version='2.3.0' cd ${JARVIS_TMP} tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz cd darshan-${version} -#./prepare.sh +./prepare.sh # install darshan runtime to collect IO info. cd darshan-runtime mkdir -p $1/runtime diff --git a/package/darshan/3.4.6/install.sh b/package/darshan/3.4.6/install.sh index 2b6d01e8..07da2adb 100644 --- a/package/darshan/3.4.6/install.sh +++ b/package/darshan/3.4.6/install.sh @@ -6,7 +6,7 @@ set -x set -e version='3.4.6' . $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser ghostscript -. ${DOWNLOAD_TOOL} -u https://web.cels.anl.gov/projects/darshan/releases/darshan-${version}.tar.gz +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz cd ${JARVIS_TMP} tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz cd darshan-${version} diff --git a/package/fftw/meta.sh b/package/fftw/meta.sh index c717953c..1efa02ef 100644 --- a/package/fftw/meta.sh +++ b/package/fftw/meta.sh @@ -2,11 +2,10 @@ set -x set -e -export UseGitee=0 + if [[ $UseGitee -eq 1 ]]; then #. ${DOWNLOAD_TOOL} -u https://gitee.com/kp-hpc-mod/fftw3/archive/refs/tags/fftw-${fftw_ver}.tar.gz -f fftw-${fftw_ver}.tar.gz cd ${JARVIS_TMP} -rm -rf fftw fftw-${fftw_ver} git clone https://gitee.com/kp-hpc-mod/fftw3.git mv fftw3 fftw-${fftw_ver} cd fftw-${fftw_ver} diff --git a/package/gmp/6.2.0/install.sh b/package/gmp/6.2.0/install.sh index eea1c32f..d62412a3 100755 --- a/package/gmp/6.2.0/install.sh +++ b/package/gmp/6.2.0/install.sh @@ -1,7 +1,7 @@ #!/bin/bash set -x set -e -. ${DOWNLOAD_TOOL} -u https://ftp.gnu.org/gnu/gmp/gmp-6.2.0.tar.xz +. ${DOWNLOAD_TOOL} -u https://gmplib.org/download/gmp/gmp-6.2.0.tar.xz cd ${JARVIS_TMP} rm -rf gmp-6.2.0 tar -xvf ${JARVIS_DOWNLOAD}/gmp-6.2.0.tar.xz diff --git a/package/grads/2.0.a4/install.sh b/package/grads/2.0.a4/install.sh index f40014dd..284a7dfa 100755 --- a/package/grads/2.0.a4/install.sh +++ b/package/grads/2.0.a4/install.sh @@ -9,6 +9,7 @@ cd ${JARVIS_TMP} rm -rf grads-2.0.a4.oga.1 tar -xvf ${JARVIS_DOWNLOAD}/grads-2.0.a4.oga.1-src.tar.gz cd grads-2.0.a4.oga.1 -./configure --prefix=$1 --build=aarch64-unknown-linux-gnu --with-x --x-includes=/usr/include/X11 -make -j$(nproc) +#export CC=clang CXX=clang++ FC=flang +./configure --prefix=$1 --build=aarch64-unknown-linux-gnu +make -j make install diff --git a/package/mfem/4.4/install.sh b/package/mfem/4.4/install.sh index dbb6452c..28cc2beb 100755 --- a/package/mfem/4.4/install.sh +++ b/package/mfem/4.4/install.sh @@ -7,7 +7,5 @@ rm -rf mfem-4.4 tar -xvf ${JARVIS_DOWNLOAD}/v4.4.tar.gz sed -i 's/>= MINSIGSTKSZ.*/;/' mfem-4.4/tests/unit/catch.hpp cd mfem-4.4 -#make parallel -make config -make all -j +make parallel make install PREFIX=$1 \ No newline at end of file diff --git a/package/openblas/meta.sh b/package/openblas/meta.sh index 0ca62310..d0fbdfca 100644 --- a/package/openblas/meta.sh +++ b/package/openblas/meta.sh @@ -5,7 +5,6 @@ set -e if [[ $UseGitee -eq 1 ]]; then #. ${DOWNLOAD_TOOL} -u https://gitee.com/kp-hpc-mod/OpenBLAS/archive/refs/tags/v${openblas_ver}.tar.gz -f OpenBLAS-${openblas_ver}.tar.gz cd ${JARVIS_TMP} -rm -rf OpenBLAS OpenBLAS-${openblas_ver} git clone https://gitee.com/kp-hpc-mod/OpenBLAS.git mv OpenBLAS OpenBLAS-${openblas_ver} cd OpenBLAS-${openblas_ver} @@ -19,5 +18,5 @@ cd OpenBLAS-${openblas_ver} fi -make -j CFLAGS="-Wno-implicit-function-declaration" +make -j make PREFIX=$1 install \ No newline at end of file diff --git a/package/tau/2.30.0/install.sh b/package/tau/2.30.0/install.sh index 54708f1b..e7803c97 100755 --- a/package/tau/2.30.0/install.sh +++ b/package/tau/2.30.0/install.sh @@ -3,32 +3,15 @@ set -x set -e cd ${JARVIS_TMP} # install PDT -#tar -zxvf ${JARVIS_DOWNLOAD}/pdt.tgz -#cd pdtoolkit-3.25.1/ -#./configure -GNU -prefix=$1/PDT -#make -j install +tar -zxvf ${JARVIS_DOWNLOAD}/pdt.tgz +cd pdtoolkit-3.25.1/ +./configure -GNU -prefix=$1/PDT +make -j install # install TAU, using tau with external package -#tar -zxvf ${JARVIS_DOWNLOAD}/tau-2.30.0.tar.gz -#cd tau-2.30.0/ -#./configure -openmp -bfd=download -unwind=download -mpi -pdt=$1/PDT/ -pdt_c++=g++ -mpi -#export PATH=$1/tau-2.30.0/arm64_linux/bin:$PATH +tar -zxvf ${JARVIS_DOWNLOAD}/tau-2.30.0.tar.gz +cd tau-2.30.0/ +./configure -openmp -bfd=download -unwind=download -mpi -pdt=$1/PDT/ -pdt_c++=g++ -mpi +export PATH=$1/tau-2.30.0/arm64_linux/bin:$PATH + #usage: mpirun --allow-run-as-root -np 128 -x OMP_NUM_THREADS=1 --mca btl ^openib tau_exec vasp_std #pprof - -. ${DOWNLOAD_TOOL} -u https://www.cs.uoregon.edu/research/tau/tau_releases/tau-2.30.tar.gz -rm -rf tau-2.30 -tar -zxvf ${JARVIS_DOWNLOAD}/tau-2.30.tar.gz -cd tau-2.30 -sed -i '3710c # Are we on a Fujitsu FX aarch64 system with Fujitsu compilers in the path?' configure -sed -i '3711c #found_compiler=`which mpiFCC 2>/dev/null`' configure -sed -i '3712c #if [ "x$found_compiler" != "x" -a -x $found_compiler ]; then' configure -sed -i '3713c # echo "TAU: Using mpiFCC, mpifcc, and mpifrt as C++, C, and Fortran compilers respectively."' configure -sed -i '3714c cxx_compiler=mpicxx' configure -sed -i '3715c c_compiler=mpicc' configure -sed -i '3716c fortran_compiler=mpif90' configure -sed -i '3717c #fi' configure - -./configure -mpi -prefix=$1 -make clean -make -j -make install diff --git a/templates/CP2K/8.2/data.CP2K.arm-new.cpu.config b/templates/CP2K/8.2/data.CP2K.arm-new.cpu.config index ef1e03d2..5177457c 100644 --- a/templates/CP2K/8.2/data.CP2K.arm-new.cpu.config +++ b/templates/CP2K/8.2/data.CP2K.arm-new.cpu.config @@ -7,15 +7,14 @@ cp2k/8.2 https://github.com/cp2k/cp2k/releases/download/v8.2.0/cp2k-8.2.tar.bz2 [DEPENDENCY] module purge module use ./software/modulefiles -module use ./software/moduledeps/bisheng4.2.0 -module use ./software/moduledeps/bisheng4.2.0-hmpi25.0.0 -./jarvis -install package/hpckit/25.0.0 any -module use ${JARVIS_ROOT}/software/utils/hpckit/25.0.0/HPCKit/latest/modulefiles -module load bisheng/compiler4.2.0/bishengmodule +./jarvis -install bisheng/3.2.0 com +module load bisheng/3.2.0 export CC=clang CXX=clang++ FC=flang ./jarvis -install cmake/3.23.1 any module load cmake/3.23.1 +./jarvis -install hmpi/2.3.0 clang ./jarvis -install gmp/6.2.0 clang +#./jarvis -install boost/1.72.0 clang ./jarvis -install boost/1.72.0/clang clang module load boost-clang/1.72.0 ./jarvis -install openblas/0.3.18 clang @@ -23,11 +22,13 @@ module load boost-clang/1.72.0 ./jarvis -install libxc/5.1.4 clang ./jarvis -install gsl/2.6 clang ./jarvis -install libvori/21.04.12 clang -./jarvis -install lapack/3.8.0/bisheng clang -module load gmp/6.2.0 gsl/2.6 libvori/21.04.12 +module use ./software/moduledeps/bisheng3.2.0 +module load gmp/6.2.0 gsl/2.6 hmpi/2.3.0 libvori/21.04.12 module load libxc/5.1.4 openblas/0.3.18 spglib/1.16.0 +./jarvis -install lapack/3.8.0/bisheng clang module load lapack-bisheng/3.8.0 -module load bisheng/hmpi25.0.0/hmpi + +module use ./software/moduledeps/bisheng3.2.0-hmpi2.3.0 export CC=mpicc CXX=mpicxx FC=mpifort export boost_path=$BOOST_CLANG_PATH ./jarvis -install libint/2.6.0 clang+mpi @@ -38,28 +39,26 @@ module load fftw/3.3.8 libint/2.6.0 plumed/2.6.2 scalapack-clang/2.1.0 ./jarvis -install elpa/2020.11.001 clang+mpi module load elpa/2020.11.001 +rm -rf cp2k-8.2 +tar -jxvf $JARVIS_DOWNLOAD/cp2k-8.2.tar.bz2 [ENV] module purge module use ./software/modulefiles -module use ./software/moduledeps/bisheng4.2.0 -module use ./software/moduledeps/bisheng4.2.0-hmpi25.0.0 -module use ${JARVIS_ROOT}/software/utils/hpckit/25.0.0/HPCKit/latest/modulefiles -module load bisheng/compiler4.2.0/bishengmodule +module load bisheng/3.2.0 export CC=clang CXX=clang++ FC=flang module load cmake/3.23.1 module load boost-clang/1.72.0 -module load gmp/6.2.0 gsl/2.6 libvori/21.04.12 +module load gmp/6.2.0 gsl/2.6 hmpi/2.3.0 libvori/21.04.12 module load libxc/5.1.4 openblas/0.3.18 spglib/1.16.0 module load lapack-bisheng/3.8.0 -module load bisheng/hmpi25.0.0/hmpi +module use ./software/moduledeps/bisheng3.2.0-hmpi2.3.0 export CC=mpicc CXX=mpicxx FC=mpifort export boost_path=$BOOST_CLANG_PATH module load fftw/3.3.8 libint/2.6.0 plumed/2.6.2 scalapack-clang/2.1.0 module load elpa/2020.11.001 export PATH=${JARVIS_ROOT}/cp2k-8.2/exe/Linux-arm-clang-sve:$PATH - [APP] app_name = CP2K build_dir = ${JARVIS_ROOT} @@ -67,8 +66,6 @@ binary_dir = ${JARVIS_ROOT}/cp2k-8.2/exe/Linux-arm-clang-sve/ case_dir = ${JARVIS_ROOT}/cp2k-8.2/benchmarks/QS/ [BUILD] -cd ${JARVIS_ROOT} -rm -rf cp2k-8.2 cd ${JARVIS_ROOT}/cp2k-8.2/arch cp ${JARVIS_ROOT}/templates/CP2K/8.2/Linux-arm-clang-sve.psmp ./ sed -i "9s%path1%${JARVIS_ROOT}/software/libs/bisheng3.2.0/hmpi2.3.0%g" Linux-arm-clang-sve.psmp diff --git a/templates/Manufacturing/common/data.exagear-centos7.cpu.config b/templates/Manufacturing/common/data.exagear-centos7.cpu.config index 85a8275d..3dc39258 100644 --- a/templates/Manufacturing/common/data.exagear-centos7.cpu.config +++ b/templates/Manufacturing/common/data.exagear-centos7.cpu.config @@ -251,11 +251,11 @@ install_guest_driver() cd MLNX_OFED_LINUX-*rhel7.9-x86_64/ chmod +x mlnxofedinstall exagear -- yum install pciutils-libs numactl-libs gcc-gfortran tcsh libusbx libnl3 tcl fuse-libs tk -y - exagear -- echo "y" |./install --user-space-only + exagear -- echo "y" |./mlnxofedinstall --user-space-only # install ibdev2netdev cd RPMS/ - exagear -- rpm -ivh mlnx-ofa_kernel-[0-9].[0-9]-OFED.*.x86_64.rpm -y + exagear -- yum install mlnx-ofa_kernel-[0-9].[0-9]-OFED.*.x86_64.rpm -y } # 配置免密 config_trust() diff --git a/templates/Oceananigans/0.99.1/data.Oceananigans.arm.cpu.config b/templates/Oceananigans/0.99.1/data.Oceananigans.arm.cpu.config new file mode 100644 index 00000000..918d5b01 --- /dev/null +++ b/templates/Oceananigans/0.99.1/data.Oceananigans.arm.cpu.config @@ -0,0 +1,69 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +julia/1.12.1 https://julialang-s3.julialang.org/bin/linux/aarch64/1.12/julia-1.12.1-linux-aarch64.tar.gz julia-1.12.1-linux-aarch64.tar.gz + +[DEPENDENCY] +cd ${JARVIS_ROOT} +tar -zxvf $JARVIS_DOWNLOAD/julia-1.12.1-linux-aarch64.tar.gz +export PATH=${JARVIS_ROOT}/julia-1.12.1/bin:$PATH + + +[ENV] +export PATH=${JARVIS_ROOT}/julia-1.12.1/bin:$PATH + +[APP] +app_name = fftw +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +# 定义要安装的 Oceananigans 版本（可根据需求修改） +TARGET_VERSION="0.99.1" + +# 检查 Julia 是否安装 +if ! command -v julia &> /dev/null; then + echo "错误：未找到 Julia 命令。请先安装 Julia 并确保其在系统 PATH 中。" + echo "Julia 下载地址：https://julialang.org/downloads/" + exit 1 +fi + +# 打印安装信息 +echo "开始安装 Oceananigans v${TARGET_VERSION}..." +echo "使用的 Julia 版本：$(julia --version | awk '{print $3}')" + +# 通过 Julia 执行安装命令（临时代码） +julia -e ' +using Pkg + +# 定义包名和版本（与 Shell 变量同步） +package_name = "Oceananigans" +target_version = "'"${TARGET_VERSION}"'" + +try + # 安装指定版本 + Pkg.add(PackageSpec(name=package_name, version=target_version)) + + # 验证安装结果 + println("\n安装完成，当前版本信息：") + Pkg.status(package_name) + + # 预编译包（加速首次使用） + println("\n开始预编译...") + Pkg.precompile(package_name) + println("\n✅ Oceananigans v$(target_version) 安装并预编译成功！") + +catch e + # 捕获错误并提示 + println("\n❌ 安装失败：") + println(e) + exit(1) +end +' + +[RUN] +run = +binary = +nodes = 1 diff --git a/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config b/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config index a3cbf4bb..aad1f231 100644 --- a/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config +++ b/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config @@ -62,8 +62,8 @@ C_LINK = mpicxx C_OPTS = -O3 C_DEBUGFLAG = REMOVE = /bin/rm -f -FFTWLIB = \${JARVIS_LIBS}/bisheng4.1.0/fftw/3.3.8/lib/libfftw3.a -FFTWINCLUDE = \${JARVIS_LIBS}/bisheng4.1.0/fftw/3.3.8/include +FFTWLIB = \${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib/libfftw3.a +FFTWINCLUDE = \${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/include LAPACKLIB = -L\${JARVIS_UTILS}/hpckit/24.0.0/HPCKit/24.12.30/kml/bisheng/lib/${kp} -lklapack_full -L\${JARVIS_UTILS}/hpckit/24.0.0/HPCKit/24.12.30/kml/bisheng/lib/${kp}/kblas/pthread -lkblas SCALAPACKLIB = -L\${JARVIS_UTILS}/hpckit/24.0.0/HPCKit/24.12.30/kml/bisheng/lib/${kp} -lkscalapack_full \$(LAPACKLIB) TESTSCRIPT = make check-parallel diff --git a/templates/grads/2.0.a4/data.grads.arm.cpu.config b/templates/grads/2.0.a4/data.grads.arm.cpu.config index 9925903f..14599bf5 100644 --- a/templates/grads/2.0.a4/data.grads.arm.cpu.config +++ b/templates/grads/2.0.a4/data.grads.arm.cpu.config @@ -6,7 +6,6 @@ grads/2.0.a4 https://sourceforge.net/projects/opengrads/files/grads2/2.0.a4-1/gr [DEPENDENCY] -yum install libXmu-devel -y module use ./software/modulefiles module purge ./jarvis -install bisheng/2.1.0 com diff --git a/templates/ioapi/3.2/data.ioapi_clang.arm.cpu.config b/templates/ioapi/3.2/data.ioapi_clang.arm.cpu.config index f2bdb77d..3ee68710 100644 --- a/templates/ioapi/3.2/data.ioapi_clang.arm.cpu.config +++ b/templates/ioapi/3.2/data.ioapi_clang.arm.cpu.config @@ -1,9 +1,6 @@ [SERVER] 11.11.11.11 -[DOWNLOAD] -ioapi/3.2 - [DEPENDENCY] module use ${JARVIS_ROOT}/software/modulefiles module purge @@ -13,25 +10,14 @@ module load bisheng/2.1.0 ./jarvis -install hmpi/1.1.1 clang module load hmpi/1.1.1 export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort -./jarvis -install hdf5/1.12.0/clang clang+mpi -module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 -module load hdf5-clang/1.12.0 -./jarvis -install pnetcdf/1.14.0 clang+mpi -module load pnetcdf/1.14.0 -./jarvis -install netcdf/4.8.1/clang clang+mpi -module load netcdf-clang/4.8.1 + [ENV] module use ${JARVIS_ROOT}/software/modulefiles module purge -export CC=clang CXX=clang++ FC=flang module load bisheng/2.1.0 module load hmpi/1.1.1 -export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort -module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 -module load hdf5-clang/1.12.0 -module load pnetcdf/1.14.0 -module load netcdf-clang/4.8.1 + [APP] app_name = ioapi diff --git a/templates/lammps/2021.2.10/data.lammps.arm.cpu.config b/templates/lammps/2021.2.10/data.lammps.arm.cpu.config new file mode 100644 index 00000000..dc297b64 --- /dev/null +++ b/templates/lammps/2021.2.10/data.lammps.arm.cpu.config @@ -0,0 +1,55 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +lammps/2021.1.10 https://download.lammps.org/tars/lammps-10Feb2021.tar.gz + +[DEPENDENCY] +module purge +./jarvis -install bisheng/2.1.0 com +module use ./software/modulefiles +module load bisheng/2.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install hmpi/1.1.1 clang +module load hmpi/1.1.1 +./jarvis -install fftw/3.3.8 clang+mpi + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng/2.1.0 +module load hmpi/1.1.1 +export CC=clang CXX=clang++ FC=flang +module load fftw/3.3.8 +export PATH=${JARVIS_ROOT}/software/apps/bisheng/lammps/2021.2.10:$PATH + +[APP] +app_name = lammps +build_dir = ${JARVIS_ROOT} +binary_dir = ./software/apps/bisheng/lammps/2021.2.10 +case_dir = + +[BUILD] +cd ${JARVIS_ROOT} +tar -xvf ${JARVIS_DOWNLOAD}/lammps-10Feb2021.tar.gz +cd lammps-10Feb21/src +sed -i '10c\CCFLAGS = -g -O3 -I${JARVIS_ROOT}/software/compiler/bisheng/2.1.0/include/c++/v1 -L${JARVIS_ROOT}/software/compiler/bisheng/2.1.0/lib -std=c++11 -stdlib=libc++ -lc++ -lc++abi' MAKE/Makefile.mpi +sed -i '15c\LINKFLAGS = -g -O -L${JARVIS_ROOT}/software/compiler/bisheng/2.1.0/lib -std=c++11 -stdlib=libc++ -lc++ -lc++abi' MAKE/Makefile.mpi +sed -i '53c\FFT_INC = -DFFT_FFTW -I${JARVIS_ROOT}/software/libs/bisheng2.1.0/fftw/3.3.8/include ' MAKE/Makefile.mpi +sed -i '54c\FFT_PATH = -L${JARVIS_ROOT}/software/libs/bisheng2.1.0/fftw/3.3.8/lib' MAKE/Makefile.mpi +sed -i '55c\FFT_LIB = -lfftw3' MAKE/Makefile.mpi +make yes-KSPACE +make yes-MPIIO +make yes-MOLECULE +make yes-MANYBODY +make yes-USER-REAXC +make mpi -j +cp ${JARVIS_ROOT}/lammps-10Feb21/src/lmp_mpi ${JARVIS_ROOT}/software/apps/bisheng/lammps/2021.2.10/lmp_mpi +ls ${JARVIS_ROOT}/software/apps/bisheng/lammps/2021.2.10/lmp_mpi + + +[RUN] +run =lmp_mpi -h +binary = +nodes = 1 + diff --git a/templates/lammps/2023.8.2/data.lammps.arm.cpu.sve.hpckit.config b/templates/lammps/2023.8.2/data.lammps.arm.cpu.sve.hpckit.config index 544296ce..9d3e2055 100644 --- a/templates/lammps/2023.8.2/data.lammps.arm.cpu.sve.hpckit.config +++ b/templates/lammps/2023.8.2/data.lammps.arm.cpu.sve.hpckit.config @@ -6,7 +6,7 @@ lammps/2023.8.2 https://download.lammps.org/tars/lammps-2Aug2023.tar.gz [DEPENDENCY] module purge -./jarvis -install package/hpckit/25.0.0/ any +./jarvis -install package/hpckit/2025.3.30/ any module use ${JARVIS_ROOT}/software/utils/hpckit/2025.3.30/HPCKit/latest/modulefiles module load bisheng/compiler4.2.0/bishengmodule bisheng/hmpi25.0.0/hmpi bisheng/kml25.0.0/kml @@ -15,30 +15,28 @@ export CC=mpicc FC=mpifort CXX=mpicxx [ENV] module purge -module use ${JARVIS_ROOT}/software/utils/hpckit/25.0.0/HPCKit/latest/modulefiles +module use ${JARVIS_ROOT}/software/utils/hpckit/2025.3.30/HPCKit/latest/modulefiles module load bisheng/compiler4.2.0/bishengmodule bisheng/hmpi25.0.0/hmpi bisheng/kml25.0.0/kml -export KML_FFT_THREAD_TYPE=OMP [APP] app_name = lmp_mpi build_dir = ${JARVIS_ROOT} -binary_dir = ${JARVIS_ROOT}/software/apps/bisheng4.2.0-hmpi25.0.0/lammps-2Aug2023/src +binary_dir = ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/lammps-2Aug2023/src case_dir = [BUILD] cd ${JARVIS_ROOT} -mkdir -p ${JARVIS_ROOT}/software/apps/bisheng4.2.0-hmpi25.0.0/ -cd ${JARVIS_ROOT}/software/apps/bisheng4.2.0-hmpi25.0.0/ -rm -rf lammps-2Aug2023 +mkdir -p ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/ +cd ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/ tar -xvf ${JARVIS_DOWNLOAD}/lammps-2Aug2023.tar.gz cd lammps-2Aug2023/src -HPCKIT=${JARVIS_ROOT}/software/utils/hpckit/25.0.0/HPCKit -sed -i "10c\CCFLAGS = -g -O3 -fopenmp -mcpu=hip09 -mllvm -force-customized-pipeline=true -I${HPCKIT}/latest/compiler/bisheng/include/c++/v1 -L${JARVIS_ROOT}/software/utils/hpckit/25.0.0/HPCKit/latest/compiler/bisheng/lib -std=c++11 -stdlib=libc++ -lc++ -lc++abi" MAKE/Makefile.mpi +HPCKIT=${JARVIS_ROOT}/software/utils/hpckit/2025.3.30/HPCKit +sed -i "10c\CCFLAGS = -g -O3 -fopenmp -mcpu=hip09 -mllvm -force-customized-pipeline=true -I${HPCKIT}/latest/compiler/bisheng/include/c++/v1 -L${JARVIS_ROOT}/software/utils/hpckit/24.0.0/HPCKit/latest/compiler/bisheng/lib -std=c++11 -stdlib=libc++ -lc++ -lc++abi" MAKE/Makefile.mpi sed -i "15c\LINKFLAGS = -g -O3 -fopenmp -mcpu=hip09 -mllvm -force-customized-pipeline=true -L${HPCKIT}/latest/compiler/bisheng/lib -std=c++11 -stdlib=libc++ -lc++ -lc++abi" MAKE/Makefile.mpi sed -i "53c\FFT_INC = -I${HPCKIT}/latest/kml/bisheng/include" MAKE/Makefile.mpi sed -i "54c\FFT_PATH = -L${HPCKIT}/latest/kml/bisheng/lib/${kp}" MAKE/Makefile.mpi -sed -i '55c\FFT_LIB = -lkfft' MAKE/Makefile.mpi -export KML_FFT_THREAD_TYPE=OMP +sed -i '55c\FFT_LIB = -lkfft_omp -lkfft' MAKE/Makefile.mpi + make yes-KSPACE make yes-MPIIO make yes-MOLECULE @@ -49,7 +47,7 @@ make mpi -j [CLEAN] -rm -rf $JARVIS_ROOT/software/apps/bisheng4.2.0-hmpi25.0.0/lammps-2Aug2023 +rm -rf $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/lammps-2Aug2023 [RUN] run = diff --git a/templates/meso_grapes/6.0/data.meso_grapes.arm.cpu.bisheng.hmpi.config b/templates/meso_grapes/6.0/data.meso_grapes.arm.cpu.bisheng.hmpi.config index e4961c89..2239512b 100644 --- a/templates/meso_grapes/6.0/data.meso_grapes.arm.cpu.bisheng.hmpi.config +++ b/templates/meso_grapes/6.0/data.meso_grapes.arm.cpu.bisheng.hmpi.config @@ -6,7 +6,7 @@ [DEPENDENCY] set -e set -x -yum install -y time zlib zlib-devel libtirpc libtirpc-devel numactl libatomic +./CHECK_ROOT module purge ./jarvis -install hpckit/24.0.0 com module use ./software/compiler/hpckit/24.0.0/HPCKit/24.12.30/modulefiles @@ -69,21 +69,17 @@ ln -sf ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/DATABAK/cold/2024111800/grapes_i ln -sf ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/DATABAK/cold/2024111800/grapesbdy_si.2024111800 ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/fcst/grapes_model/run/grapesbdy ln -sf ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/DATABAK/cold/2024111800/qcqr_gcas_202411180000 ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/fcst/grapes_model/run/qcqr_gcas_202411180000 mkdir -p ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/fcst/grapes_model/run/log +cat << \EOF > ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/fcst/grapes_model/run/test_grapes.sh +#!/bin/bash +cd ../../../../ +. ./init.sh +cd - +source ${JARVIS_ROOT}/env.sh -[CLEAN] -cd ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/fcst/grapes_model -./clean - -[RUN] -run = -binary = -nodes = 2 - -[BATCH] HOSTLIST='node-164,node-171' nodes=2 -npx=15 -npy=16 +npx=6 +npy=40 ppn=$((npx*npy/nodes)) steps=240 numa_num=`numactl -H |grep available |awk '{print $2}'` @@ -94,4 +90,14 @@ sed -i 's/nproc_x = .*,/nproc_x = '${npx}',/' ./namelist.input sed -i 's/nproc_y = .*/nproc_y = '${npy}'/' ./namelist.input time=`date +"%y-%m-%d-%H-%M-%S"` -(time -p mpirun --allow-run-as-root --oversubscribe -np $((ppn*nodes)) -N ${ppn} -host ${HOSTLIST} --map-by socket --rank-by core --map-by ppr:$((ppn/numa_num)):numa:pe=1 --bind-to core --mca btl ^vader,tcp,openib,uct --mca io romio321 --mca pml ucx -x UCX_TLS=self,sm,ud -x UCG_PLANC_UCX_ALLREDUCE_ATTR=I:8S:200R:0 -x UCG_PLANC_UCX_BARRIER_ATTR=I:7S:200R:0 -x UCG_PLANC_UCX_BCAST_ATTR=I:4S:200R:0 -x UCG_PLANC_UCX_ALLREDUCE_FANOUT_INTRA_DEGREE=3 -x UCG_PLANC_UCX_ALLREDUCE_FANIN_INTRA_DEGREE=8 -x UCG_PLANC_UCX_ALLREDUCE_FANOUT_INTER_DEGREE=7 -x UCG_PLANC_UCX_ALLREDUCE_FANIN_INTER_DEGREE=7 -x UCG_PLANC_UCX_BARRIER_FANOUT_INTRA_DEGREE=3 -x UCG_PLANC_UCX_BARRIER_FANIN_INTRA_DEGREE=8 -x UCG_PLANC_UCX_BARRIER_FANOUT_INTER_DEGREE=7 -x UCG_PLANC_UCX_BARRIER_FANIN_INTER_DEGREE=7 -x UCG_PLANC_UCX_BCAST_NA_KNTREE_INTER_DEGREE=7 -x UCG_PLANC_UCX_BCAST_NA_KNTREE_INTRA_DEGREE=3 -x KML_VERBOSE=2 -x PATH -x LD_LIBRARY_PATH ./grapes.exe) 2>&1 |tee -a log/grapes_${time}_${npx}x${npy}.log \ No newline at end of file +(time -p mpirun --allow-run-as-root --oversubscribe -np $((ppn*nodes)) -N ${ppn} -host ${HOSTLIST} --map-by socket --rank-by core --map-by ppr:$((ppn/numa_num)):numa:pe=1 --bind-to core --mca btl ^vader,tcp,openib,uct --mca io romio321 --mca pml ucx -x UCX_TLS=self,sm,ud -x UCG_PLANC_UCX_ALLREDUCE_ATTR=I:8S:200R:0 -x UCG_PLANC_UCX_BARRIER_ATTR=I:7S:200R:0 -x UCG_PLANC_UCX_BCAST_ATTR=I:4S:200R:0 -x UCG_PLANC_UCX_ALLREDUCE_FANOUT_INTRA_DEGREE=3 -x UCG_PLANC_UCX_ALLREDUCE_FANIN_INTRA_DEGREE=8 -x UCG_PLANC_UCX_ALLREDUCE_FANOUT_INTER_DEGREE=7 -x UCG_PLANC_UCX_ALLREDUCE_FANIN_INTER_DEGREE=7 -x UCG_PLANC_UCX_BARRIER_FANOUT_INTRA_DEGREE=3 -x UCG_PLANC_UCX_BARRIER_FANIN_INTRA_DEGREE=8 -x UCG_PLANC_UCX_BARRIER_FANOUT_INTER_DEGREE=7 -x UCG_PLANC_UCX_BARRIER_FANIN_INTER_DEGREE=7 -x UCG_PLANC_UCX_BCAST_NA_KNTREE_INTER_DEGREE=7 -x UCG_PLANC_UCX_BCAST_NA_KNTREE_INTRA_DEGREE=3 -x KML_VERBOSE=2 -x PATH -x LD_LIBRARY_PATH ./grapes.exe) 2>&1 |tee -a log/grapes_${time}_${npx}x${npy}.log +EOF + +[CLEAN] +cd ${JARVIS_ROOT}/GRAPES_MESO_262794_6.0_gz/fcst/grapes_model +./clean + +[RUN] +run = +binary = +nodes = 2 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 index 23c4eec9..c5fefddd 100644 --- a/templates/psi4/1.3.2/data.psi4-common.arm.cpu.config +++ b/templates/psi4/1.3.2/data.psi4-common.arm.cpu.config @@ -59,8 +59,7 @@ case_dir = $JARVIS_ROOT/software/apps/gcc12.3.1/psi4/share/psi4/samples/opt-mult [BUILD] set -x cd ${JARVIS_TMP} -pip3 install pint pydantic==1.10.7 -i https://pypi.mirrors.ustc.edu.cn/simple -pip3 install deepdiff==6.3.0 qcelemental==0.29.0 -i https://mirrors.huaweicloud.com/repository/pypi/simple +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 diff --git a/templates/scalapack/2.1.0/data.scalapack.arm.cpu.config b/templates/scalapack/2.1.0/data.scalapack.arm.cpu.config index a35f8b11..52e6c07a 100644 --- a/templates/scalapack/2.1.0/data.scalapack.arm.cpu.config +++ b/templates/scalapack/2.1.0/data.scalapack.arm.cpu.config @@ -1,8 +1,6 @@ [SERVER] 11.11.11.11 -[DOWNLOAD] -scalapack/2.1.0 [DEPENDENCY] module use ./software/modulefiles @@ -18,9 +16,7 @@ module load hmpi/1.1.1 module use ./software/modulefiles module purge module load bisheng/2.1.0 -module use ./software/modulefiles/bisheng2.1.0 module load hmpi/1.1.1 -module load lapack-bisheng/3.8.0 export CC=mpicc CXX=mpicxx FC=mpifort [APP] diff --git a/templates/specfem3d_globe/7.0.0/data.specfem3d_globe.arm.cpu.bisheng.hmpi.config b/templates/specfem3d_globe/7.0.0/data.specfem3d_globe.arm.cpu.bisheng.hmpi.config index 8779821b..9d284c1d 100644 --- a/templates/specfem3d_globe/7.0.0/data.specfem3d_globe.arm.cpu.bisheng.hmpi.config +++ b/templates/specfem3d_globe/7.0.0/data.specfem3d_globe.arm.cpu.bisheng.hmpi.config @@ -42,7 +42,7 @@ make make clean [RUN] -run = mpirun --allow-run-as-root -np 4 --mca btl ^openib ${JARVIS_ROOT}/specfem3d_globe-7.0.0/bin/xmeshfem3D && mpirun --allow-run-as-root -np 4 --mca btl ^openib ${JARVIS_ROOT}/specfem3d_globe-7.0.0/bin/xspecfem3D && cat OUTPUT_FILES/output_solver.txt +run = mpirun --allow-run-as-root -np 4 --mca btl ^openib ${JARVIS_ROOT}/specfem3d_globe-7.0.0/bin/xmeshfem3D &&　mpirun --allow-run-as-root -np 4 --mca btl ^openib ${JARVIS_ROOT}/specfem3d_globe-7.0.0/bin/xspecfem3D && cat OUTPUT_FILES/output_solver.txt binary = nodes = 1 diff --git a/templates/szip/2.1.1/data.szip.arm.bisheng.config b/templates/szip/2.1.1/data.szip.arm.bisheng.config index 22be6aa3..6a41155e 100644 --- a/templates/szip/2.1.1/data.szip.arm.bisheng.config +++ b/templates/szip/2.1.1/data.szip.arm.bisheng.config @@ -1,9 +1,6 @@ [SERVER] 11.11.11.11 -[DOWNLOAD] -szip/2.1.1 - [DEPENDENCY] ./jarvis -install bisheng/2.1.0 com diff --git a/templates/wrf/4.6.1/data.wrf.arm.cpu.config b/templates/wrf/4.6.1/data.wrf.arm.cpu.config index d86d0c91..a122559b 100644 --- a/templates/wrf/4.6.1/data.wrf.arm.cpu.config +++ b/templates/wrf/4.6.1/data.wrf.arm.cpu.config @@ -2,62 +2,63 @@ 11.11.11.11 [DOWNLOAD] -conus12km https://www2.mmm.ucar.edu/wrf/src/conus12km.tar.gz +wrf/4.6.1 https://codeload.github.com/wrf-model/WRF/tar.gz/refs/tags/v4.6.1 wrf-4.6.1.tar.gz + [DEPENDENCY] -yum install tcsh time -y module purge module use ./software/modulefiles ./jarvis -install kgcc/10.3.1 com -module load kgcc/10.3.1 +module load ./software/modulefiles/kgcc/10.3.1 export CC=gcc CXX=g++ FC=gfortran + ./jarvis -install hmpi/1.1.1 gcc -module load hmpi/1.1.1 +module load ./software/moduledeps/kgcc10.3.1/hmpi/1.1.1 + export CC=mpicc CXX=mpicxx FC=mpifort ./jarvis -install hdf5/1.10.1 gcc+mpi ./jarvis -install package/pnetcdf/1.9.0 gcc+mpi -module load hdf5/1.10.1 -module load pnetcdf/1.9.0 -./jarvis -install package/netcdf/4.7.4 gcc+mpi -module load netcdf/4.7.4 +module load ./software/moduledeps/gcc10.3.1-hmpi1.1.1/pnetcdf/1.9.0 +./jarvis -install package/netcdf/4.7.0 gcc+mpi + ./jarvis -install optimized-routines/20.02 gcc -module load optimized-routines/20.02 cd ${JARVIS_TMP} -rm -rf WRF -git clone https://github.com/wrf-model/WRF.git -cd WRF -git checkout tags/v4.6.1 -b wrf-4.6.1 -git submodule update --init --recursive + +tar -zxvf $JARVIS_DOWNLOAD/wrf-4.6.1.tar.gz [ENV] module purge module use ./software/modulefiles module load kgcc/10.3.1 module load hmpi/1.1.1 -module load hdf5/1.10.1 +export CC=mpicc CXX=mpicxx FC=mpifort module load pnetcdf/1.9.0 -module load netcdf/4.7.4 +module load netcdf/4.7.0 module load optimized-routines/20.02 -export CC=mpicc CXX=mpicxx FC=mpifort + [APP] app_name = WRF build_dir = ${WRF_DIR} -binary_dir = -case_dir = ${JARVIS_ROOT}/conus12km +binary_dir = +case_dir = ${JARVIS_ROOT}/workloads/test_wrf [BUILD] cd ${JARVIS_TMP} -cd WRF +cd WRF-4.6.1 + export HDF5=`which h5diff` export HDF5=${HDF5%/*/*} export NETCDF=`nc-config --prefix` export PNETCDF=`pnetcdf-config --prefix` + export CPPFLAGS="-I$HDF5/include -I$PNETCDF/include -I$NETCDF/include" export LDFLAGS="-L$HDF5/lib -L$PNETCDF/lib -L$NETCDF/lib -lnetcdf -lnetcdff -lpnetcdf -lhdf5_hl -lhdf5 -lz" export WRFIO_NCD_LARGE_FILE_SUPPORT=1 + sed -i $((`sed -n '$=' arch/configure.defaults`-2)),$((`sed -n '$=' arch/configure.defaults`))d arch/configure.defaults -mathlib_path=$JARVIS_ROOT/software/compiler/kgcc/10.3.1/lib64/libhpc + +mathlib_path=$JARVIS_ROOT/software/compiler/kgcc/9.3.1/lib64/libhpc cat >> arch/configure.defaults <&1 | tee -a compile.log +./compile em_real 2>&1 | tee -a compile.log -cd ${JARVIS_ROOT} -rm -rf conus12km -tar -vxf ${JARVIS_DOWNLOAD}/conus12km.tar.gz -yes no | cp -ri ${JARVIS_TMP}/WRF/run/* conus12km -cd conus12km -ln -sf ${JARVIS_TMP}/WRF/main/*.exe ./ [CLEAN] ./clean [RUN] -run = time mpirun --allow-run-as-root -np 8 ./wrf.exe && less rsl.out.0000 -binary = +run = dsub -s run.sh +binary = nodes = 1 -- Gitee