diff --git a/README.md b/README.md index 9712cde36fbe9a7084886859b18d3b798227b372..43002aa4e3dde7256aedbc04d2f6c5ce12406a7a 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ HPC被喻为是IT行业“金字塔上的明珠”，其部署、编译、运行 ## 下载贾维斯 执行如下命令安装相关依赖并下载贾维斯 ``` -yum -y install environment python3 python3-devel cmake +yum -y install git environment-modules python python3 python3-devel python3-libs python3-pip cmake make numactl-libs rpmbuild rpmdevtools wget unzip flex tar patch git clone https://gitee.com/openeuler/hpcrunner.git ``` @@ -164,12 +164,13 @@ option支持列表如下所示 # FAQ -Q1：如何在没有网络的环境下使用贾维斯部署软件？ +Q1：如何在没有网络的环境或者网速很慢的环境下，使用贾维斯完成软件安装部署？ ``` A： -步骤1：寻找一台有外网链接的服务器环境，执行jarvis -d命令，下载相关依赖 -步骤2：将事先下载好的安装包放置到downloads目录下即可进行后续安装操作。 +步骤1：寻找一台有外网链接的服务器环境B，执行jarvis -d命令，下载相关依赖 +步骤2：将事先下载好的安装包即环境B下downloads目录里所有内容，放置到原环境的downloads目录下 +步骤3：在原来环境下进行后续安装操作 ``` # 欢迎贡献 diff --git a/container/bowtie2/openeuler-bisheng2-bowtie2-2.4.5.def b/container/bowtie2/openeuler-bisheng2-bowtie2-2.4.5.def index 878517802ab3e4a4fe396e26c254aad9bf14aabb..6f46ae446e14cad52c0aa0e825b7f634798b3b2d 100644 --- a/container/bowtie2/openeuler-bisheng2-bowtie2-2.4.5.def +++ b/container/bowtie2/openeuler-bisheng2-bowtie2-2.4.5.def @@ -9,7 +9,7 @@ From: openeuler/openeuler %post # Install the necessary development environment - yum install -y environment-modules git wget unzip make flex tar + # Install base gcc yum install -y gcc gcc-c++ make cmake automake zlib-devel bzip2-devel xz-devel curl-devel openssl-devel source /etc/profile || true diff --git a/container/bowtie2/openeuler-gcc-9.3.0-bowtie2-2.4.5.def b/container/bowtie2/openeuler-gcc-9.3.0-bowtie2-2.4.5.def index 0c6b191d3be19c7a8d29f8efeb6be647e1ec1170..2ee369bc4af6da40bd82e5f09e5eade8ba2637f2 100644 --- a/container/bowtie2/openeuler-gcc-9.3.0-bowtie2-2.4.5.def +++ b/container/bowtie2/openeuler-gcc-9.3.0-bowtie2-2.4.5.def @@ -9,7 +9,6 @@ From: openeuler/openeuler %post # Install the necessary development environment - yum install -y environment-modules git flex wget vim tar unzip coreutils # Install base gcc yum install -y gcc gcc-c++ make cmake libgfortran automake zlib-devel bzip2-devel xz-devel curl-devel openssl-devel source /etc/profile || true diff --git a/container/imb/openeuler-bisheng2-hmpi1-imb-2021.3.def b/container/imb/openeuler-bisheng2-hmpi1-imb-2021.3.def index af93037ecb57ba3cb351e1c9490817e730f3a095..0b8ab62bfa459cde164c17d2dc5f863b542f9c19 100644 --- a/container/imb/openeuler-bisheng2-hmpi1-imb-2021.3.def +++ b/container/imb/openeuler-bisheng2-hmpi1-imb-2021.3.def @@ -10,7 +10,6 @@ From: openeuler/openeuler %post # Install the necessary development environment - yum install -y environment-modules git wget unzip make flex tar source /etc/profile || true git config --global http.sslVerify false git clone https://gitee.com/openeuler/hpcrunner diff --git a/container/mfem/openeuler-bisheng2-hmpi1-mfem-4.4.def b/container/mfem/openeuler-bisheng2-hmpi1-mfem-4.4.def index 2d09bab0e9cb18473b80e8ec3f1366d798a24f34..dd540c01097f6c83ef22c5d537a805c2709691fa 100644 --- a/container/mfem/openeuler-bisheng2-hmpi1-mfem-4.4.def +++ b/container/mfem/openeuler-bisheng2-hmpi1-mfem-4.4.def @@ -10,7 +10,6 @@ From: openeuler/openeuler %post # Install the necessary development environment - yum install -y environment-modules git wget unzip make flex tar source /etc/profile || true git config --global http.sslVerify false git clone https://gitee.com/openeuler/hpcrunner diff --git a/container/ncl/data.NCL.arm.cpu.config.def b/container/ncl/data.NCL.arm.cpu.config.def index 8ef74d745de4253f03ec4c171e633f4a25794044..59c7b7e064c7341df12f8a640daca5e5c85f818a 100644 --- a/container/ncl/data.NCL.arm.cpu.config.def +++ b/container/ncl/data.NCL.arm.cpu.config.def @@ -31,11 +31,9 @@ From: centos:8.2.2004 sed -i '16 s/^#//' /etc/yum.repos.d/CentOS-PowerTools.repo sed -i '18c enabled=1' /etc/yum.repos.d/CentOS-PowerTools.repo yum makecache - yum install -y rpm-build - yum install rpmdevtools -y rpmdev-setuptree cd / - yum install -y tar + # Install the necessary development environment yum install -y environment-modules git dmidecode pciutils wget vim zlib expat-devel python3 cpio # Install base gcc diff --git a/package/R/4.3.0/install.sh b/package/R/4.3.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..b583b31b8e2a59362842f73bc1be6350427203f2 --- /dev/null +++ b/package/R/4.3.0/install.sh @@ -0,0 +1,16 @@ +#!/bin/bash +set -x +set -e + +. $CHECK_ROOT +yum install libXt-devel.aarch64 readline-devel.aarch64 -y +yum install libX11-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel libcurl-devel -y + +. ${DOWNLOAD_TOOL} -u https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz + +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/R-4.3.0.tar.gz +cd R-4.3.0 +./configure -enable-R-shlib -enable-R-static-lib --with-libpng --with-jpeglib --prefix=$1 +make all -j +make install \ No newline at end of file diff --git a/package/admixtools/7.0.2/install.sh b/package/admixtools/7.0.2/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..2acdbbd57d63f52112f649851355cc00894642f3 --- /dev/null +++ b/package/admixtools/7.0.2/install.sh @@ -0,0 +1,15 @@ +#!/bin/bash +set -x +set -e + +wget https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz -O ${JARVIS_DOWNLOAD}/AdmixTools-7.0.2.tar.gz + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/AdmixTools-7.0.2.tar.gz +cd AdmixTools-7.0.2/src +sed -i '14d' Makefile +sed -i '18d' Makefile +sed -i "14s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile +sed -i "15s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install \ No newline at end of file diff --git a/package/blat/35.1/install.sh b/package/blat/35.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..fddc861aa9ffb3b03976a2b58676518f625593d0 --- /dev/null +++ b/package/blat/35.1/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash +set -x +set -e + +wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1 -O ${JARVIS_DOWNLOAD}/blat-35.1.tar.gz +yum -y install libpng-devel + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/blat-35.1.tar.gz +cd blat-35.1/ +sed -i 's/jmp_buf htmlRecover/\/\/jmp_buf htmlRecover/g' src/inc/htmshell.h +export MACHTYPE=aarch64 +make \ No newline at end of file diff --git a/package/darshan/1.1.0/install.sh b/package/darshan/1.1.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..1d062616c7fdc461d704cddb1c7b39d1b0a7d94c --- /dev/null +++ b/package/darshan/1.1.0/install.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# please build with gcc/icc+openmpi +# gcc: export CC=mpicc +# icc: export CC=mpiicc +set -x +set -e +version='1.1.0' +. $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser zlib-devel ghostscript +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz +cd darshan-${version} +./prepare.sh +# install darshan runtime to collect IO info. +cd darshan-runtime +mkdir -p $1/runtime +./configure --prefix=$1/runtime --with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_DIR_PATH --with-jobid-env=NONE +make -j +make install +# install darshan util to analysis IO info. +cd ../darshan-util +mkdir -p $1/util +./configure --prefix=$1/util +make -j +make install \ No newline at end of file diff --git a/package/darshan/2.3.0/install.sh b/package/darshan/2.3.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..1c0cc1a9bca65b4d144dac851cfec67ac928ecd9 --- /dev/null +++ b/package/darshan/2.3.0/install.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# please build with gcc/icc+openmpi +# gcc: export CC=mpicc +# icc: export CC=mpiicc +set -x +set -e +version='2.3.0' +. $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser zlib-devel ghostscript +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz +cd darshan-${version} +./prepare.sh +# install darshan runtime to collect IO info. +cd darshan-runtime +mkdir -p $1/runtime +./configure --prefix=$1/runtime --with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_DIR_PATH --with-jobid-env=NONE +make -j +make install +# install darshan util to analysis IO info. +cd ../darshan-util +mkdir -p $1/util +./configure --prefix=$1/util +make -j +make install \ No newline at end of file diff --git a/package/darshan/3.4.6/install.sh b/package/darshan/3.4.6/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..0be079b645a5a329ba81303040a04d34404ce43b --- /dev/null +++ b/package/darshan/3.4.6/install.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# please build with gcc/icc+openmpi +# gcc: export CC=mpicc +# icc: export CC=mpiicc +set -x +set -e +version='3.4.6' +. $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser zlib-devel ghostscript +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz +cd darshan-${version} +./prepare.sh +# install darshan runtime to collect IO info. +cd darshan-runtime +mkdir -p $1/runtime +./configure --prefix=$1/runtime --with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_DIR_PATH --with-jobid-env=NONE +make -j +make install +# install darshan util to analysis IO info. +cd ../darshan-util +mkdir -p $1/util +./configure --prefix=$1/util +make -j +make install \ No newline at end of file diff --git a/package/deeptool/3.5.1/install.sh b/package/deeptool/3.5.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..8099282e8f0e35210419322c9778e51e47ceeac3 --- /dev/null +++ b/package/deeptool/3.5.1/install.sh @@ -0,0 +1,14 @@ +#!/bin/bash +set -x +set -e + + +wget https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz -O ${JARVIS_DOWNLOAD}/deepTools-3.5.1.tar.gz +yum -y install doxygen cmake +yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/deepTools-3.5.1.tar.gz + +cd deepTools-3.5.1 +python3 setup.py install \ No newline at end of file diff --git a/package/eig/8.0.0/install.sh b/package/eig/8.0.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..929d52753b30166a9723f231aa27217b07540e32 --- /dev/null +++ b/package/eig/8.0.0/install.sh @@ -0,0 +1,19 @@ +#!/bin/bash +set -x +set -e + +./jarvis -install openblas/0.3.23 clang +./jarvis -install gsl/2.7.1 clang + +wget https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz -O ${JARVIS_DOWNLOAD}/EIG-8.0.0.tar.gz + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/EIG-8.0.0.tar.gz > /dev/null 2>&1 +cd cd EIG-8.0.0/src +sed -i "1s%^.*$%override CFLAGS += -I../include -I$targetdir/openblas/openblas_install/include%g" Makefile +sed -i '10d' Makefile +sed -i '12d' Makefile +sed -i "10s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile +sed -i "11s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install \ No newline at end of file diff --git a/package/gau2grid/1.3.0/install.sh b/package/gau2grid/1.3.0/install.sh index 6b83b29723936600c870ca67c7497e404308499f..2b95d9d29ac9560ecb56972e1a759c1e44276f8e 100755 --- a/package/gau2grid/1.3.0/install.sh +++ b/package/gau2grid/1.3.0/install.sh @@ -8,7 +8,7 @@ tar -xvf ${JARVIS_DOWNLOAD}/v1.3.0.tar.gz cd gau2grid-1.3.0 mkdir build cd build -yum install python python3-pip -y + #pip3 install numpy wget https://files.pythonhosted.org/packages/bd/54/15a0ba87e6335d02475201c9767a6a424ee39ed438ebdb6438f34abc2c25/numpy-2.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl pip3 install numpy-2.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl diff --git a/package/gcc/10.3.1/install.sh b/package/gcc/10.3.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..987235b09235995282dc54179a051c78306db595 --- /dev/null +++ b/package/gcc/10.3.1/install.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-10.3.1-2022.06-aarch64-linux.tar.gz +cd ${JARVIS_TMP} +rm -rf gcc-10.3.1 +tar -xzvf ${JARVIS_DOWNLOAD}/gcc-10.3.1-2022.06-aarch64-linux.tar.gz diff --git a/package/gcc/12.3.1/install.sh b/package/gcc/12.3.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..ef3aed6abc3cd388e8fba50a9f3c9bdd0f7f8ce5 --- /dev/null +++ b/package/gcc/12.3.1/install.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-12.3.1-2024.09-aarch64-linux.tar.gz +cd ${JARVIS_TMP} +rm -rf gcc-12.3.1 +tar -xzvf ${JARVIS_DOWNLOAD}/gcc-12.3.1-2024.09-aarch64-linux.tar.gz \ No newline at end of file diff --git a/package/gdal/3.7.0/install.sh b/package/gdal/3.7.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..e197565c8516dca3b8e5c5b22661f0f9df7bef1d --- /dev/null +++ b/package/gdal/3.7.0/install.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://download.osgeo.org/gdal/3.7.0/gdal-3.7.0.tar.xz +cd ${JARVIS_TMP} +rm -rf gdal-2.2.4 +tar -xvf ${JARVIS_DOWNLOAD}/gdal-3.7.0.tar.xz > /dev/null 2>&1 +cd gdal-3.7.0/ +mkdir build +cd build +cmake ../ +make install \ No newline at end of file diff --git a/package/gsl/2.7.1/install.sh b/package/gsl/2.7.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..15368bf77afad09d36d4d5d305776efbdea2d5fa --- /dev/null +++ b/package/gsl/2.7.1/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://ftpmirror.gnu.org/gsl/gsl-2.7.1.tar.gz +cd ${JARVIS_TMP} +rm -rf gsl-2.7.1 +tar -xvf ${JARVIS_DOWNLOAD}/gsl-2.7.1.tar.gz +cd gsl-2.7.1 +./configure --prefix=$1 +make -j +make install \ No newline at end of file diff --git a/package/hmpi/1.1.1/install.sh b/package/hmpi/1.1.1/install.sh index 0de33156c175feb6fb71b82bd3e95913146361c2..5e4c152862083444a28436b3e821b0172d83c0f9 100755 --- a/package/hmpi/1.1.1/install.sh +++ b/package/hmpi/1.1.1/install.sh @@ -1,26 +1,17 @@ #!/bin/bash set -x set -e + +if [[ $UseGitee -eq 1 ]]; then +. ${DOWNLOAD_TOOL} -u https://gitee.com/kp-hpc-mod/hpc-src/raw/master/hucx-1.1.1-huawei.zip -f hucx-1.1.1-huawei.zip +. ${DOWNLOAD_TOOL} -u https://gitee.com/kp-hpc-mod/hpc-src/raw/master/xucg-1.1.1-huawei.zip -f xucg-1.1.1-huawei.zip +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -f hmpi-1.1.1-huawei.zip +else . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -f hucx-1.1.1-huawei.zip . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -f xucg-1.1.1-huawei.zip . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -f hmpi-1.1.1-huawei.zip +fi + cd ${JARVIS_TMP} . $CHECK_ROOT && yum install -y perl-Data-Dumper autoconf automake libtool binutils flex -rm -rf hmpi-1.1.1-huawei hucx-1.1.1-huawei xucg-1.1.1-huawei -unzip ${JARVIS_DOWNLOAD}/hucx-1.1.1-huawei.zip -unzip ${JARVIS_DOWNLOAD}/xucg-1.1.1-huawei.zip -unzip ${JARVIS_DOWNLOAD}/hmpi-1.1.1-huawei.zip -\cp -rf xucg-1.1.1-huawei/* hucx-1.1.1-huawei/src/ucg/ -sleep 3 -cd hucx-1.1.1-huawei -./autogen.sh -./contrib/configure-opt --prefix=$1/hucx CFLAGS="-DHAVE___CLEAR_CACHE=1" --disable-numa --without-java -for file in `find . -name Makefile`;do sed -i "s/-Werror//g" $file;done -for file in `find . -name Makefile`;do sed -i "s/-implicit-function-declaration//g" $file;done -make -j64 -make install -cd ../hmpi-1.1.1-huawei -./autogen.pl -./configure --prefix=$1 --with-platform=contrib/platform/mellanox/optimized --enable-mpi1-compatibility --with-ucx=$1/hucx -make -j64 -make install +rm -rf hmpi-1.1.1-huawei hucx-1.1.1-huawei xucg-1.1.1-huawei \ No newline at end of file diff --git a/package/hpckit/latest/install.sh b/package/hpckit/latest/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..3aeed9a88ea94474b108835e270355086d75232c --- /dev/null +++ b/package/hpckit/latest/install.sh @@ -0,0 +1,4 @@ +#!/bin/bash +set -e +export hpckit_ver=`curl https://mirrors.huaweicloud.com/kunpeng/archive/HPC/HPCKit/| awk -F "HPCKit_" '{print $2}'|awk -F "_Linux-aarch64" '{print $1}'|awk '{lines[NR]=$0} END{print lines[NR-1]}'` +../meta.sh $1 \ No newline at end of file diff --git a/package/kp-hpc/2.1.0/install.sh b/package/kp-hpc/2.1.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..14067a881a7a107789e7b5e6af81d1eb13743d35 --- /dev/null +++ b/package/kp-hpc/2.1.0/install.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -x +set -e +file_name=kunpeng-hpc-2.1.0-aarch64-linux +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/Kunpeng_SDK/HPC/${file_name}.tar.gz +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/${file_name}.tar.gz +cd ${file_name}/script +./install.sh \ No newline at end of file diff --git a/package/ncbi-vdb/3.0.0/install.sh b/package/ncbi-vdb/3.0.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..b31b8956e176ba0a7fc125d9bd464579523d6f11 --- /dev/null +++ b/package/ncbi-vdb/3.0.0/install.sh @@ -0,0 +1,15 @@ +#!/bin/bash +set -x +set -e + +wget https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.0.tar.gz -O ${JARVIS_DOWNLOAD}/ncbi-vdb-3.0.0.tar.gz +yum -y install doxygen cmake +yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/ncbi-vdb-3.0.0.tar.gz + +cd ncbi-vdb-3.0.0 +cp -r interfaces/cc/gcc/arm64 interfaces/cc/gcc/aarch64 +./configure --relative-build-out-dir +make -j && make install \ No newline at end of file diff --git a/package/openblas/0.3.23/install.sh b/package/openblas/0.3.23/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..54172ab6f8eab5409fe6c1b965d75fed6ac9121a --- /dev/null +++ b/package/openblas/0.3.23/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +ver="0.3.23" +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v${ver}.tar.gz -f OpenBLAS-${ver}.tar.gz +cd ${JARVIS_TMP} +rm -rf OpenBLAS-${ver} +tar -xzvf ${JARVIS_DOWNLOAD}/OpenBLAS-${ver}.tar.gz +cd OpenBLAS-${ver} +make -j 16 +make PREFIX=$1 install \ No newline at end of file diff --git a/package/pnetcdf/1.9.0/install.sh b/package/pnetcdf/1.9.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..4a07f42d35826198adf92f2b7357219ec166b65f --- /dev/null +++ b/package/pnetcdf/1.9.0/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +set -x +set -e +pnetcdf_ver='1.9.0' +. ${DOWNLOAD_TOOL} -u https://parallel-netcdf.github.io/Release/parallel-netcdf-1.9.0.tar.gz +cd ${JARVIS_TMP} +rm -rf pnetcdf-${pnetcdf_ver} +tar zxvf ${JARVIS_DOWNLOAD}/parallel-netcdf-1.9.0.tar.gz +cd parallel-netcdf-1.9.0 +./configure --prefix=$1 --enable-shared --enable-fortran --enable-large-file-test +make -j16 +make install \ No newline at end of file diff --git a/package/relion/3.1.2/install.sh b/package/relion/3.1.2/install.sh index dddc79ec96297557c4851c66bfbdfaeec9d71322..b11d46bf80552be8aaaf5aed8c7dcaaab4aed929 100755 --- a/package/relion/3.1.2/install.sh +++ b/package/relion/3.1.2/install.sh @@ -3,7 +3,7 @@ set -x set -e -. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/3dem/relion/archive/refs/tags/3.1.2.tar.gz -f relion-3.1.2.tar.gz cd ${JARVIS_TMP} rm -rf relion-3.1.2 tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz diff --git a/package/samtools/0.1.9/install.sh b/package/samtools/0.1.9/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..432b54b84d13850aa98b66e110ef12bc877ff785 --- /dev/null +++ b/package/samtools/0.1.9/install.sh @@ -0,0 +1,8 @@ +#!/bin/bash +set -x +set -e +wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O ${JARVIS_DOWNLOAD}/samtools-0.1.9.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/samtools-0.1.9.tar.gz > /dev/null 2>&1 +cd samtools-0.1.9 +make \ No newline at end of file diff --git a/templates/amber/20/data.amber.arm.gpu.config b/templates/amber/20/data.amber.arm.gpu.config index bf505f370d4d2db7ef85475dc1b078ad17b761f9..223b8c8f3aceddd4025f08bbbe57e7335c9a94ca 100644 --- a/templates/amber/20/data.amber.arm.gpu.config +++ b/templates/amber/20/data.amber.arm.gpu.config @@ -1,6 +1,8 @@ [SERVER] 1.1.1.1 +[DOWNLOAD] + [DEPENDENCY] yum install -y flex* bison* zlib* libzip* boost* bzip2* diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index de43a144e76d4bf5bd7a26ca57c9a1675cf5cbda..4d31578c4cb44de90398eeede23b94728412d1a8 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -7,7 +7,7 @@ set -e set -x -yum install -y cmake + module purge ./jarvis -install package/anaconda3/2024.10 any module use ./software/modulefiles diff --git a/templates/dlPoly/1.1/dl_poly.arm.cpu.bisheng.hmpi.config b/templates/dlPoly/1.1/dl_poly.arm.cpu.bisheng.hmpi.config index d096daa5d46d8bde9657aaeb92e8bf44d5a53e39..804b0fe54f4762e0114b17d498af8c34ffe7a701 100644 --- a/templates/dlPoly/1.1/dl_poly.arm.cpu.bisheng.hmpi.config +++ b/templates/dlPoly/1.1/dl_poly.arm.cpu.bisheng.hmpi.config @@ -8,7 +8,7 @@ TEST41 https://gitlab.com/DL_POLY_Classic/tests/-/raw/master/TEST41.tar.gz TEST4 [DEPENDENCY] set -e set -x -yum install -y make cmake + module purge ./jarvis -install bisheng/4.1.0 com module use ./software/modulefiles diff --git a/templates/duns/2.7.1/data.container-duns.arm.cpu.config b/templates/duns/2.7.1/data.container-duns.arm.cpu.config index 3f0cf26954549a4dcc4a085b4fc485dd508b98f7..c05ef157c9d80b27059d2fa4368ea85c56946544 100644 --- a/templates/duns/2.7.1/data.container-duns.arm.cpu.config +++ b/templates/duns/2.7.1/data.container-duns.arm.cpu.config @@ -14,7 +14,6 @@ tar -xjf ${JARVIS_DOWNLOAD}/duns-2.7.1-src.tar.bz2 -C ${JARVIS_ROOT} tar -xjf ${JARVIS_DOWNLOAD}/duns-2.7.1-test.tar.bz2 -C ${JARVIS_ROOT} [ENV] -export JARVIS_ROOT=/hpcrunner export DUNSARCH=linux export DUNSPATH27=${JARVIS_ROOT}/duns-2.7.1 export PATH=$DUNSPATH27/util:${JARVIS_ROOT}/software/libs/bisheng4.0.0/duns/2.7.1/bin:$PATH diff --git a/templates/duns/2.7.1/data.container-duns_sve.arm.cpu.config b/templates/duns/2.7.1/data.container-duns_sve.arm.cpu.config index f1b43c5003a204c61a30f0aee546c5db81823133..d0587aed85f9ec4426e9f3ce4828aae27a2e8e4a 100644 --- a/templates/duns/2.7.1/data.container-duns_sve.arm.cpu.config +++ b/templates/duns/2.7.1/data.container-duns_sve.arm.cpu.config @@ -14,7 +14,6 @@ tar -xjf ${JARVIS_DOWNLOAD}/duns-2.7.1-src.tar.bz2 -C ${JARVIS_ROOT} tar -xjf ${JARVIS_DOWNLOAD}/duns-2.7.1-test.tar.bz2 -C ${JARVIS_ROOT} [ENV] -export JARVIS_ROOT=/hpcrunner export DUNSARCH=linux export DUNSPATH27=${JARVIS_ROOT}/duns-2.7.1 export PATH=$DUNSPATH27/util:${JARVIS_ROOT}/software/libs/bisheng4.0.0/duns/2.7.1/bin:$PATH diff --git a/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config b/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config index 8a13cf7ec0407929428d0c80c3b471c5cc84b386..9693b5fc5d6726f07a29f615b41a37ed589b3be7 100644 --- a/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config +++ b/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config @@ -15,7 +15,7 @@ export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` -yum install -y python3 + yum install -y qt5 qt5-devel ./jarvis -install boost-python/1.72.0 gcc diff --git a/templates/eccodes/2.18.0/data.eccodes.arm.cpu.config b/templates/eccodes/2.18.0/data.eccodes.arm.cpu.config index 40911b9959134ddc276606eccaa93c04fee7d3d7..a7c09bcebeeb3662918ecee85233bc8f2f7e2fbb 100644 --- a/templates/eccodes/2.18.0/data.eccodes.arm.cpu.config +++ b/templates/eccodes/2.18.0/data.eccodes.arm.cpu.config @@ -7,7 +7,7 @@ eccodes/2.18.0 http://confluence.ecmwf.int/download/attachments/45757960/Eccodes [DEPENDENCY] set -e set -x -yum install -y cmake + yum install -y libcurl-devel module use ./software/modulefiles module purge diff --git a/templates/eigen/3.4/data.eigen.arm-920.cpu.config b/templates/eigen/3.4/data.eigen.arm-920.cpu.config index b7b0ec563a451e694e84b478c08d8abb34071617..9309105010a2533f35655d38b7fea529f7d42d09 100644 --- a/templates/eigen/3.4/data.eigen.arm-920.cpu.config +++ b/templates/eigen/3.4/data.eigen.arm-920.cpu.config @@ -5,7 +5,6 @@ eigen/3.4 https://gitlab.com/libeigen/eigen/-/archive/3.4/eigen-3.4.tar.gz [DEPENDENCY] -yum install make cmake -y module purge ./jarvis -install bisheng/4.1.0 com diff --git a/templates/eman2/2.99.64/data.eman2.arm.cpu.config b/templates/eman2/2.99.64/data.eman2.arm.cpu.config index dfa3f0aa320b0eb6564f9b50600f02f764bd6c1b..aebc17c3854fc6dd9c9384822b8304e165c773da 100644 --- a/templates/eman2/2.99.64/data.eman2.arm.cpu.config +++ b/templates/eman2/2.99.64/data.eman2.arm.cpu.config @@ -8,7 +8,7 @@ eman2/2.99.64 https://github.com/cryoem/eman2/archive/refs/tags/v2.99.64.tar.gz set -e set -x -yum install -y make cmake -y + module purge ./jarvis -install package/anaconda3/2023.3 any source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh diff --git a/templates/fasta/36.3.8/data.fasta.arm.cpu.config b/templates/fasta/36.3.8/data.fasta.arm.cpu.config index 45651c68bfcc4570004258e912c0c9a3f11256af..532907951f0cdd1fa8d0f6fa0b3f8e68fb7e5e20 100644 --- a/templates/fasta/36.3.8/data.fasta.arm.cpu.config +++ b/templates/fasta/36.3.8/data.fasta.arm.cpu.config @@ -9,7 +9,7 @@ sse2neon/master https://github.com/DLTcollab/sse2neon/archive/refs/heads/master. [DEPENDENCY] set -e set -x -yum install -y make + module purge ./jarvis -install kgcc/10.3.1 com diff --git a/templates/gadget2/2.3.5/data.gadget2.arm.cpu.kgcc.config b/templates/gadget2/2.3.5/data.gadget2.arm.cpu.kgcc.config index 6c2ecff0bf057d366fc8c8e814015fad616c2d6a..6727f253c68b2e21ad172ed490f4a7304bde4b35 100644 --- a/templates/gadget2/2.3.5/data.gadget2.arm.cpu.kgcc.config +++ b/templates/gadget2/2.3.5/data.gadget2.arm.cpu.kgcc.config @@ -7,7 +7,7 @@ gadget2/2.3.5 https://github.com/gadget-framework/gadget2/archive/refs/tags/v2.3 [DEPENDENCY] set -e set -x -yum install -y make cmake libX11 libX11-devel +yum install -y libX11 libX11-devel ./jarvis -install hpckit/2024.12.30 any module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module purge diff --git a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config index 95b22f57872508aac2b1066763fb3e41373ebf5f..d0b7f1e7d2e6338124c42e2d39fbf67e630dd1d8 100644 --- a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config +++ b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config @@ -8,7 +8,7 @@ cuda/11.4.0 https://developer.download.nvidia.com/compute/cuda/11.4.0/local_inst [DEPENDENCY] set -e set -x -yum install -y cmake make + module use ./software/modulefiles module purge ./jarvis -install kgcc/9.3.1 com diff --git a/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config b/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config index 8024d8b9a06beb868a06952ba82c5d9fc17f2b0d..9bcdd7af11d94887a8a2408c75001fac9fb67cee 100644 --- a/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config +++ b/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config @@ -7,7 +7,7 @@ gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz [DEPENDENCY] #set -e #set -x -yum install -y cmake make + module purge module use ./software/modulefiles ./jarvis -install bisheng/2.1.0 com diff --git a/templates/gromacs/2022.5/data.gromacs.arm.gpu.config b/templates/gromacs/2022.5/data.gromacs.arm.gpu.config index 6280a155cb5b8efb09c316b737cdbed0afa1fe72..d5c140504499677afad5ade109a93bff834a9539 100644 --- a/templates/gromacs/2022.5/data.gromacs.arm.gpu.config +++ b/templates/gromacs/2022.5/data.gromacs.arm.gpu.config @@ -8,7 +8,7 @@ gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz #set -e #set -x -yum install -y cmake make + module purge module use ./software/modulefiles ./jarvis -install bisheng/2.1.0 com diff --git a/templates/gsea/4.3.2/data.gsea.arm.cpu.config b/templates/gsea/4.3.2/data.gsea.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..6eb711e993facf4d514de5912971a1c3a32f5795 --- /dev/null +++ b/templates/gsea/4.3.2/data.gsea.arm.cpu.config @@ -0,0 +1,51 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +GSEA/4.3.2 https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip GSEA_4.3.2.zip + +[DOWNLOADORI] +GSEA/4.3.2 https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip GSEA_4.3.2.zip + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install kgcc/9.3.1 com +module load kgcc/9.3.1 + + + +[ENV] +module use ./software/modulefiles +module purge +module load kgcc/9.3.1 + +[APP] +app_name = STAR +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + + + +[BUILD] +set -x +set -e +module use ./software/modulefiles +module purge +module load kgcc/9.3.1 + + +cd ${JARVIS_TMP} +rm -rf GSEA_4.3.2 +uinzip $JARVIS_DOWNLOAD/GSEA_4.3.2.zip +cd ${JARVIS_TMP}/GSEA_4.3.2 + + +[CLEAN] +./clean_build + +[RUN] +run = +binary = +nodes = 1 \ No newline at end of file diff --git a/templates/hycom/2.3.01/data.hycom.arm-920.cpu.config b/templates/hycom/2.3.01/data.hycom.arm-920.cpu.config index 022cf0e42a67867458793ee75bd79a8066d4b5c7..28490a8d8e055bc8271bde552fa6b79acbed7c88 100644 --- a/templates/hycom/2.3.01/data.hycom.arm-920.cpu.config +++ b/templates/hycom/2.3.01/data.hycom.arm-920.cpu.config @@ -8,7 +8,7 @@ hycom/2.3.01 https://github.com/HYCOM/HYCOM-src/releases/download/2.3.01/HYCOM-s set -e set -x -yum install -y make cmake gcc g++ csh +yum install -y csh ./jarvis -install bisheng/4.1.0 com module purge diff --git a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config index 4038fd5a0891586594297bfc3ebf851e13849194..03effe4fa6bf63f8adb4330c3a710ef20a09715e 100644 --- a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config +++ b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config @@ -7,7 +7,7 @@ kallisto/0.51.1 https://github.com/pachterlab/kallisto/archive/refs/tags/v0.51.1 [DEPENDENCY] set -e set -x -yum install -y make cmake + yum install -y autoconf automake libtool yum -y install xz-devel yum install libarchive -y diff --git a/templates/likwid/5.2.2/likwid.arm.cpu.bisheng.hmpi.config b/templates/likwid/5.2.2/likwid.arm.cpu.bisheng.hmpi.config index 6eb47a0cc4e4db7722239d299f87d28ba10302ad..9d277e31e5d6d9a6427801cf698a275f9208a607 100644 --- a/templates/likwid/5.2.2/likwid.arm.cpu.bisheng.hmpi.config +++ b/templates/likwid/5.2.2/likwid.arm.cpu.bisheng.hmpi.config @@ -7,7 +7,7 @@ likwid/5.2.2 https://github.com/RRZE-HPC/likwid/archive/refs/tags/v5.2.2.tar.gz [DEPENDENCY] set -e set -x -yum install -y make cmake + module purge ./jarvis -install hpckit/2024.12.30 any module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles diff --git a/templates/mopac/22.0.4/data.container-mopac-sve.arm.cpu.config b/templates/mopac/22.0.4/data.container-mopac-sve.arm.cpu.config index be1d945c5c341be99329ebabd2443533d31cc4f5..8f2c684ad3702a2b4a23a113392dccb9b74ca4e7 100644 --- a/templates/mopac/22.0.4/data.container-mopac-sve.arm.cpu.config +++ b/templates/mopac/22.0.4/data.container-mopac-sve.arm.cpu.config @@ -7,23 +7,26 @@ mopac/22.0.4 https://github.com/openmopac/mopac/archive/refs/tags/v22.0.4.tar.gz [DEPENDENCY] export CC=mpicc CXX=mpicxx FC=mpifort -yum install python -y + ./jarvis -install package/lapack/3.8.0/bisheng/ bisheng -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0 +module use software/moduledeps/bisheng4.0.0 module add lapack-bisheng/3.8.0 export LAPACK_PATH=$LAPACK_BISHENG_PATH export CFLAGS="-Wno-implicit-function-declaration" -./jarvis -install package/openblas/0.3.14/ bisheng+mpi -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0-hmpi2.4.1 +./jarvis -install package/openblas/0.3.14 bisheng+mpi +module use software/moduledeps/bisheng4.0.0-hmpi2.4.1 module add openblas/0.3.14 [ENV] -export JARVIS_ROOT=/hpcrunner -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0 +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +export CC=mpicc CXX=mpicxx FC=mpifort +module use ./software/moduledeps/bisheng4.1.0 module add lapack-bisheng/3.8.0 export LAPACK_PATH=$LAPACK_BISHENG_PATH export CFLAGS="-Wno-implicit-function-declaration" -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0-hmpi2.4.1 +module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 module add openblas/0.3.14 export PATH=$JARVIS_ROOT/software/mopac/22.0.4/bin:$PATH export LD_LIBRARY_PATH=$JARVIS_ROOT/software/mopac/22.0.4/lib64:$LD_LIBRARY_PATH diff --git a/templates/mopac/22.0.4/data.container-mopac.arm.cpu.config b/templates/mopac/22.0.4/data.container-mopac.arm.cpu.config index 60d260e657818124d63674289fd2699ae4a736ab..2aeb840af098e6f668c1243c1a78989ff459fb2a 100644 --- a/templates/mopac/22.0.4/data.container-mopac.arm.cpu.config +++ b/templates/mopac/22.0.4/data.container-mopac.arm.cpu.config @@ -6,24 +6,31 @@ mopac/22.0.4 https://github.com/openmopac/mopac/archive/refs/tags/v22.0.4.tar.gz [DEPENDENCY] +./jarvis -install 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=mpicc CXX=mpicxx FC=mpifort -yum install python -y + ./jarvis -install package/lapack/3.8.0/bisheng/ bisheng -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0 +module use ./software/moduledeps/bisheng4.1.0 module add lapack-bisheng/3.8.0 export LAPACK_PATH=$LAPACK_BISHENG_PATH export CFLAGS="-Wno-implicit-function-declaration" ./jarvis -install package/openblas/0.3.14 bisheng+mpi -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0-hmpi2.4.1 +module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 module add openblas/0.3.14 [ENV] -export JARVIS_ROOT=/hpcrunner -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0 +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +export CC=mpicc CXX=mpicxx FC=mpifort +module use ./software/moduledeps/bisheng4.1.0 module add lapack-bisheng/3.8.0 export LAPACK_PATH=$LAPACK_BISHENG_PATH export CFLAGS="-Wno-implicit-function-declaration" -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0-hmpi2.4.1 +module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 module add openblas/0.3.14 export PATH=$JARVIS_ROOT/software/mopac/22.0.4/bin:$PATH export LD_LIBRARY_PATH=$JARVIS_ROOT/software/mopac/22.0.4/lib64:$LD_LIBRARY_PATH diff --git a/templates/mpb/1.11.1/data.mpb.arm.cpu.config b/templates/mpb/1.11.1/data.mpb.arm.cpu.config index 4a2d4a7178ce819c1c0e0e43f5624a611d2797cf..5ad8f5e699df5f0569fd5aa354c89e88a0634345 100644 --- a/templates/mpb/1.11.1/data.mpb.arm.cpu.config +++ b/templates/mpb/1.11.1/data.mpb.arm.cpu.config @@ -17,11 +17,13 @@ module purge ./jarvis -install package/hpckit/2024.12.30 any module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles module add bisheng/compiler4.1.0/bishengmodule +module add bisheng/hmpi2.4.3/hmpi [ENV] module purge module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles module add bisheng/compiler4.1.0/bishengmodule +module add bisheng/hmpi2.4.3/hmpi export MPB_DEPENDENCIES_DIR=${JARVIS_ROOT}/MPB_DEPENDENCIES export MPB_DIR=${JARVIS_ROOT}/software/apps/bisheng/mpb/1.11.1 export PATH=${MPB_DEPENDENCIES_DIR}/bin:${MPB_DIR}/bin:$PATH diff --git a/templates/ncl/6.5.0/data.NCL.arm.cpu.config b/templates/ncl/6.5.0/data.NCL.arm.cpu.config index 484ce91c80acc005d89b09ea3f7ffe93387f74e3..066a5c91eb7b9339676f5950d13fd924e3f8671f 100644 --- a/templates/ncl/6.5.0/data.NCL.arm.cpu.config +++ b/templates/ncl/6.5.0/data.NCL.arm.cpu.config @@ -39,8 +39,7 @@ sed -i -e 's|$releasever|8|g' /etc/yum.repos.d/epel* yum install -y netcdf-fortran-devel hdf-static hdf-devel g2clib-static gdal-devel proj-devel imake libXaw-devel flex-static udunits2-devel byacc cairo-devel flex gsl-devel openblas-devel yum -y install xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -yum install -y rpmbuild -yum install rpmdevtools -y + rpmdev-setuptree diff --git a/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config b/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config index 60097699ccad19549b79865167e39c1af618aaf4..dc951cd477bfc2457faeeaae049b0da4864698b4 100644 --- a/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config +++ b/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config @@ -39,8 +39,7 @@ sed -i -e 's|$releasever|8|g' /etc/yum.repos.d/epel* yum install -y netcdf-fortran-devel hdf-static hdf-devel g2clib-static gdal-devel proj-devel imake libXaw-devel flex-static udunits2-devel byacc cairo-devel flex gsl-devel openblas-devel yum -y install xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -yum install -y rpmbuild -yum install rpmdevtools -y + rpmdev-setuptree diff --git a/templates/nemo/3.6/bisheng/data.nemo-container-sve.arm.cpu.config b/templates/nemo/3.6/bisheng/data.nemo-container-sve.arm.cpu.config index 0f0b61446f979402136841088ec2f79c7fdfbf55..6670b603bffd52c05d16cc531de434de480f1c2d 100644 --- a/templates/nemo/3.6/bisheng/data.nemo-container-sve.arm.cpu.config +++ b/templates/nemo/3.6/bisheng/data.nemo-container-sve.arm.cpu.config @@ -6,8 +6,8 @@ nemo/3.6 http://forge.ipsl.jussieu.fr/nemo/changeset/15814/NEMO/releases/release [DEPENDENCY] yum install -y svn python3 -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0 -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0-hmpi2.4.1 +module use software/moduledeps/bisheng4.0.0 +module use software/moduledeps/bisheng4.0.0-hmpi2.4.1 export CC=mpicc CXX=mpicxx FC=mpifort 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-int -Wno-implicit-function-declaration -Wno-incompatible-function-pointer-types" FCFLAGS="-O3 -fPIC" LDFLAGS="-Wl,--build-id"' package/hdf5/1.10.1/clang/install.sh ./jarvis -install package/hdf5/1.10.1/clang/ bisheng+mpi @@ -27,9 +27,8 @@ sed -i '5c cp -r /mnt/xios-1.0/* $1' package/xios/1.0/install.sh [ENV] -#export JARVIS_ROOT=/hpcrunner -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0 -module use $JARVIS_ROOT/software/moduledeps/bisheng4.0.0-hmpi2.4.1 +module use software/moduledeps/bisheng4.0.0 +module use software/moduledeps/bisheng4.0.0-hmpi2.4.1 module load pnetcdf/1.12.1 hdf5-clang/1.10.1 netcdf-clang/4.7.4 blitz/1.0.1 xios/1.0 export CC=mpicc CXX=mpicxx FC=mpifort export PATH=$JARVIS_ROOT/NEMO/releases/release-3.6/NEMOGCM/CONFIG/MY_AMM12/BLD/bin:$JARVIS_ROOT/NEMO/releases/release-3.6/NEMOGCM/CONFIG/MY_AMM12/EXP00:$PATH diff --git a/templates/nemo/3.6/bisheng/data.nemo-container.arm.cpu.config b/templates/nemo/3.6/bisheng/data.nemo-container.arm.cpu.config index c20b573eddb85d16b050c8472c6d28bb77b515d7..0d19620f2cd3133f89891ecbf117a3451be61651 100644 --- a/templates/nemo/3.6/bisheng/data.nemo-container.arm.cpu.config +++ b/templates/nemo/3.6/bisheng/data.nemo-container.arm.cpu.config @@ -27,7 +27,6 @@ sed -i '5c cp -r /mnt/xios-1.0/* $1' package/xios/1.0/install.sh [ENV] -#export JARVIS_ROOT=/hpcrunner module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.0.0 module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.0.0-hmpi2.4.1 module load pnetcdf/1.12.1 hdf5-clang/1.10.1 netcdf-clang/4.7.4 blitz/1.0.1 xios/1.0 diff --git a/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config b/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config index 2deb3d3722c2bb4db87d21ad2b5c55282f64343e..1ac733164b26b78d658679b4f5b657dd7402ef8e 100644 --- a/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config +++ b/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config @@ -6,7 +6,7 @@ octopus/10.3 https://octopus-code.org/download/10.3/octopus-10.3.tar.gz octopus- [DEPENDENCY] module purge -yum install -y cmake + yum install blas-devel lapack-devel -y ./jarvis -install kgcc/9.3.1 com module use ./software/modulefiles diff --git a/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config b/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config index 62b03151a7e04616ad163cfe046bd4c14e7f1d53..716bdc000315ae5696b04285ea03931e1105c0d9 100644 --- a/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config +++ b/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config @@ -45,7 +45,7 @@ case_dir = [BUILD] ./configure --prefix=${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4 CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true' FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true' --with-gsl-prefix=${JARVIS_LIBS}/bisheng3.2.0/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/bisheng3.2.0/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/bisheng3.2.0/hmpi2.3.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/liblapack.so --enable-mpi -yum install -y patch + patch -p0 < /hpcrunner/templates/octopus/11.4/cuda.F90.patch patch -p0 < /hpcrunner/templates/octopus/11.4/run.F90.patch patch -p0 < /hpcrunner/templates/octopus/11.4/accel_inc.F90.patch diff --git a/templates/octopus/11.4/data.octopus.arm.bs.cpu.config b/templates/octopus/11.4/data.octopus.arm.bs.cpu.config index 8e1c169009d565fabff2a5f3ce8f00292e8b7369..b7cca51ccc149825e8d81a436ce897dc6345e983 100644 --- a/templates/octopus/11.4/data.octopus.arm.bs.cpu.config +++ b/templates/octopus/11.4/data.octopus.arm.bs.cpu.config @@ -46,7 +46,7 @@ case_dir = [BUILD] ./configure --prefix=${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4 CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 ' FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 ' --with-gsl-prefix=${JARVIS_LIBS}/bisheng3.2.0/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/bisheng3.2.0/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/bisheng3.2.0/hmpi2.3.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/liblapack.so --enable-mpi -yum install -y patch + patch -p0 < /hpcrunner/templates/octopus/11.4/cuda.F90.patch patch -p0 < /hpcrunner/templates/octopus/11.4/run.F90.patch patch -p0 < /hpcrunner/templates/octopus/11.4/accel_inc.F90.patch diff --git a/templates/openfoam/1906/data.openfoam.new.SVE.cpu.config b/templates/openfoam/1906/data.openfoam.new.SVE.cpu.config index 603bd2de13c3b0bc76a91e271f9ad90d539ffc80..45ec0f1e8b7686fab040c400eefbb2df33d7d8cb 100644 --- a/templates/openfoam/1906/data.openfoam.new.SVE.cpu.config +++ b/templates/openfoam/1906/data.openfoam.new.SVE.cpu.config @@ -28,7 +28,7 @@ module use ./software/modulefiles module load bisheng/3.2.0-mini module use ./software/moduledeps module load bisheng3.2.0/hmpi/2.3.0 -export JARVIS_ROOT=/hpcrunner + export PATH=${JARVIS_ROOT}/OpenFOAM-v1906/platforms/linuxARM64ClangDPInt32Opt/bin:$PATH export LD_LIBRARY_PATH=${JARVIS_ROOT}/OpenFOAM-v1906/platforms/linuxARM64ClangDPInt32Opt/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=${JARVIS_ROOT}/OpenFOAM-v1906/platforms/linuxARM64ClangDPInt32Opt/lib/dummy:$LD_LIBRARY_PATH diff --git a/templates/openfoam/1906/data.openfoam.new.bisheng.cpu.config b/templates/openfoam/1906/data.openfoam.new.bisheng.cpu.config index df77caf9d7e8743562823260b470939fd1dbb77b..a316793ddbf37b1d0b94d5c757d25c006eab5c3a 100644 --- a/templates/openfoam/1906/data.openfoam.new.bisheng.cpu.config +++ b/templates/openfoam/1906/data.openfoam.new.bisheng.cpu.config @@ -28,7 +28,7 @@ module load bisheng/3.2.0-mini module use ./software/moduledeps module load bisheng3.2.0/hmpi/2.3.0 #source /hpcrunner/OpenFOAM-v1906/etc/bashrc -export JARVIS_ROOT=/hpcrunner + export PATH=${JARVIS_ROOT}/OpenFOAM-v1906/platforms/linuxARM64ClangDPInt32Opt/bin:$PATH export LD_LIBRARY_PATH=${JARVIS_ROOT}/OpenFOAM-v1906/platforms/linuxARM64ClangDPInt32Opt/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=${JARVIS_ROOT}/OpenFOAM-v1906/platforms/linuxARM64ClangDPInt32Opt/lib/dummy:$LD_LIBRARY_PATH diff --git a/templates/palabos/2.1/data.palabos-common.arm.cpu.config b/templates/palabos/2.1/data.palabos-common.arm.cpu.config index 050c955dc390ce4e49cefdf7aa0a2f97836aa193..d37e9ace820c7ebe1467881e12f9ba250697c084 100644 --- a/templates/palabos/2.1/data.palabos-common.arm.cpu.config +++ b/templates/palabos/2.1/data.palabos-common.arm.cpu.config @@ -16,7 +16,7 @@ export CC=clang CXX=clang++ FC=flang module use software/moduledeps/bisheng4.1.0 module load cmake/3.23.1 yum install ImageMagick -y -#yum install python3 python3-devel -y + ./jarvis -install package/python3/3.6.8 clang module add python3/3.6.8 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 824dbdb4c8277a8f2d6493285bcc80dce49679ee..64fc231693a723b4a8b28cf6b6485c7f659f1665 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 @@ -11,7 +11,7 @@ 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 diff --git a/templates/psi4/1.3.2/data.psi4-container-sve.arm.cpu.config b/templates/psi4/1.3.2/data.psi4-container-sve.arm.cpu.config index 23c276eb9b8714ddd5dca9d9d86e17abdbfc4da6..39021fc1e2f152b3c3c392f0702e0e0a9f536462 100644 --- a/templates/psi4/1.3.2/data.psi4-container-sve.arm.cpu.config +++ b/templates/psi4/1.3.2/data.psi4-container-sve.arm.cpu.config @@ -5,12 +5,12 @@ psi4/1.3.2 https://github.com/psi4/psi4/archive/v1.3.2.tar.gz [DEPENDENCY] -yum install cmake -y + export CC=clang FC=flang CXX=clang++ export CFLAGS="-Wno-implicit-function-declaration" sed -i '9c ./configure --prefix=\$1 --with-ensurepip=yes CFLAGS="-O3 -Wno-implicit-function-declaration"' package/python3/3.7.10/install.sh ./jarvis -install package/python3/3.7.10 bisheng -module use $JARVIS_ROOT/software/moduledeps +module use software/moduledeps module add bisheng4.0.0/python3/3.7.10 ./jarvis -install package/openblas/0.3.14/ bisheng module add bisheng4.0.0/openblas/0.3.14 @@ -31,8 +31,8 @@ module add bisheng4.0.0/pybind11/2.6.2 [ENV] -#export JARVIS_ROOT=/hpcrunner -module use $JARVIS_ROOT/software/moduledeps + +module use software/moduledeps module add bisheng4.0.0/python3/3.7.10 module add bisheng4.0.0/openblas/0.3.14 module add bisheng4.0.0/gau2grid/1.3.0 diff --git a/templates/psi4/1.3.2/data.psi4-container.arm.cpu.config b/templates/psi4/1.3.2/data.psi4-container.arm.cpu.config index 57f28b70a6b4b75dab93e880a8ec93ec1291069c..6c18e3e9262c1c598d33f1ac01db0f6916d81576 100644 --- a/templates/psi4/1.3.2/data.psi4-container.arm.cpu.config +++ b/templates/psi4/1.3.2/data.psi4-container.arm.cpu.config @@ -5,7 +5,7 @@ psi4/1.3.2 https://github.com/psi4/psi4/archive/v1.3.2.tar.gz [DEPENDENCY] -yum install cmake -y + export CC=clang FC=flang CXX=clang++ export CFLAGS="-Wno-implicit-function-declaration" sed -i '9c ./configure --prefix=\$1 --with-ensurepip=yes CFLAGS="-O3 -Wno-implicit-function-declaration"' package/python3/3.7.10/install.sh @@ -31,7 +31,7 @@ module add bisheng4.0.0/pybind11/2.6.2 [ENV] -#export JARVIS_ROOT=/hpcrunner + module use ${JARVIS_ROOT}/software/moduledeps module add bisheng4.0.0/python3/3.7.10 module add bisheng4.0.0/openblas/0.3.14 diff --git a/templates/psi4/1.3.2/data.psi4.arm.cpu.kgcc.config b/templates/psi4/1.3.2/data.psi4.arm.cpu.kgcc.config index 4e1499f08f25a9243a51df069b594d732124d3c0..8cedc2f5c8ed1fe79e0e474767d64abfe548ec75 100644 --- a/templates/psi4/1.3.2/data.psi4.arm.cpu.kgcc.config +++ b/templates/psi4/1.3.2/data.psi4.arm.cpu.kgcc.config @@ -7,11 +7,10 @@ psi4/1.3.2 https://github.com/psi4/psi4/archive/v1.3.2.tar.gz psi4-1.3.2.tar.gz [DEPENDENCY] set -e set -x -yum install -y python3 python3-devel python3-libs python3-pip + pip3 install QCElemental QCEngine deepdiff sudo yum groupinstall "Development Tools" -y && sudo yum install glibc-devel -y pip3 install numpy --upgrade --force-reinstall -sudo yum install -y make cmake ./jarvis -install kgcc/10.3.1 com module use software/modulefiles module purge @@ -32,7 +31,6 @@ module load libint/1.2.0 ./jarvis -install libxc/4.3.0 gcc module use ./software/moduledeps/kgcc10.3.1 module load libxc/4.3.0 -sudo yum install python3-devel ./jarvis -install pybind11/2.6.2 gcc module use ./software/moduledeps/kgcc10.3.1 module load pybind11/2.6.2 diff --git a/templates/qdk/2.3.12/data.qdk.arm-920.cpu.config b/templates/qdk/2.3.12/data.qdk.arm-920.cpu.config index b9551a5b804e5dc0a037b6ba075879dc71914817..fbd11e6e2f054a0eab5f4eb9da7543d28dd57620 100644 --- a/templates/qdk/2.3.12/data.qdk.arm-920.cpu.config +++ b/templates/qdk/2.3.12/data.qdk.arm-920.cpu.config @@ -8,8 +8,6 @@ qdk/2.3.12 https://github.com/qnap-dev/QDK/archive/refs/tags/v2.3.12.tar.gz qdk- set -e set -x -yum install cmake make gcc g++ -y - ./jarvis -install gcc/13.3.0 com module purge module use ./software/modulefiles diff --git a/templates/qgis/3.34.7/data.qgis.arm.cpu.config b/templates/qgis/3.34.7/data.qgis.arm.cpu.config index 2e1f7b3daa21eba028bdd6b8af25f9f028845685..29f035d36481f62707dc7616637b732513ce9c82 100644 --- a/templates/qgis/3.34.7/data.qgis.arm.cpu.config +++ b/templates/qgis/3.34.7/data.qgis.arm.cpu.config @@ -8,8 +8,6 @@ qgis/3.34.7 https://github.com/qgis/QGIS/archive/refs/tags/final-3_34_7.zip QGIS set -e set -x -yum install -y python3 python3-devel cmake - ./jarvis -install bisheng/4.1.0 com module purge module use ./software/modulefiles diff --git a/templates/qmcpack/3.14.0/data.qmcpack-sve.arm.cpu.config b/templates/qmcpack/3.14.0/data.qmcpack-sve.arm.cpu.config index 68a3bd781b0e850e3223f5d67040302981d0dd15..6182c6eee7e2e812fe3f3d2b164c00ce4c721b66 100644 --- a/templates/qmcpack/3.14.0/data.qmcpack-sve.arm.cpu.config +++ b/templates/qmcpack/3.14.0/data.qmcpack-sve.arm.cpu.config @@ -32,7 +32,7 @@ rm qmcpack-3.14.0 -rf tar -xvf ${JARVIS_DOWNLOAD}/v3.14.0.tar.gz [ENV] -export JARVIS_ROOT=/hpcrunner + module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.0.0 module add boost-clang/1.72.0 zlib/1.2.11 libxml2/2.10.1 module load openblas/0.3.14 diff --git a/templates/qmcpack/3.14.0/data.qmcpack.arm.cpu.config b/templates/qmcpack/3.14.0/data.qmcpack.arm.cpu.config index a469ae5c6af4429b69cadc2fec5a89b24cd16f12..a3b9016a1bd2b11580f1e4d3a24ba29bbd3a7829 100644 --- a/templates/qmcpack/3.14.0/data.qmcpack.arm.cpu.config +++ b/templates/qmcpack/3.14.0/data.qmcpack.arm.cpu.config @@ -32,7 +32,6 @@ rm qmcpack-3.14.0 -rf tar -xvf ${JARVIS_DOWNLOAD}/v3.14.0.tar.gz [ENV] -export JARVIS_ROOT=/hpcrunner module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.0.0 module add boost-clang/1.72.0 zlib/1.2.11 libxml2/2.10.1 module load openblas/0.3.14 diff --git a/templates/scorep/8.0/scorep.arm.cpu.kgcc.hmpi.config b/templates/scorep/8.0/scorep.arm.cpu.kgcc.hmpi.config index 09b19467465ad8a488a2cb814269213de534f50b..7847b6d3a89d902ad0acb56ad8587170d6259a1a 100644 --- a/templates/scorep/8.0/scorep.arm.cpu.kgcc.hmpi.config +++ b/templates/scorep/8.0/scorep.arm.cpu.kgcc.hmpi.config @@ -7,7 +7,6 @@ scorep/8.0 https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-8.0 [DEPENDENCY] set -e set -x -yum install cmake make -y module purge ./jarvis -install hpckit/2024.12.30 any module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles diff --git a/templates/siesta/4.0.2/data.siesta.arm.clang.cpu.config b/templates/siesta/4.0.2/data.siesta.arm.clang.cpu.config index d7106b1fd10a7c460b36a7d73235b8a8d0e19014..f078a6f1071015df81e11636da3d810e69181413 100644 --- a/templates/siesta/4.0.2/data.siesta.arm.clang.cpu.config +++ b/templates/siesta/4.0.2/data.siesta.arm.clang.cpu.config @@ -6,7 +6,6 @@ siesta/4.0.2 https://launchpadlibrarian.net/379220821/siesta-4.0.2.tar.gz [DEPENDENCY] source /root/.bashrc -yum -y install python3-devel.aarch64 ln -s /usr/bin/python3 /usr/bin/python export CC=mpicc CXX=mpicxx FC=mpifort export CFLAGS="-Wno-implicit-function-declaration -Wno-implicit-int" diff --git a/templates/siesta/4.0.2/data.siesta.arm.sve.cpu.config b/templates/siesta/4.0.2/data.siesta.arm.sve.cpu.config index 1b4eb70ccdbff8c2453c52b1a2a049bc29b3ece9..262836538595c9946ee14d8f3ea9d36bfd67abac 100644 --- a/templates/siesta/4.0.2/data.siesta.arm.sve.cpu.config +++ b/templates/siesta/4.0.2/data.siesta.arm.sve.cpu.config @@ -6,7 +6,7 @@ siesta/4.0.2 https://launchpadlibrarian.net/379220821/siesta-4.0.2.tar.gz [DEPENDENCY] source /root/.bashrc -yum -y install python3-devel.aarch64 + ln -s /usr/bin/python3 /usr/bin/python export CC=mpicc CXX=mpicxx FC=mpifort export CFLAGS="-Wno-implicit-function-declaration -Wno-implicit-int" diff --git a/templates/snappy/1.2.0/data.snappy.arm-920.cpu.config b/templates/snappy/1.2.0/data.snappy.arm-920.cpu.config index 8dc24ec6734d3314772da03d9566ccf39afaa38f..887564ca0cdf79df9052c4e7fd871fedaa141b66 100644 --- a/templates/snappy/1.2.0/data.snappy.arm-920.cpu.config +++ b/templates/snappy/1.2.0/data.snappy.arm-920.cpu.config @@ -10,8 +10,6 @@ benchmark https://github.com/google/benchmark/archive/refs/tags/v1.7.1.zip bench set -e set -x -yum install make cmake gcc g++ -y - ./jarvis -install bisheng/4.1.0 com module purge module use ./software/modulefiles 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 e4b1cd6f9a3cbd7de7239f47202fc4a3a4ae1d3f..8ff0a0bdff3a883f743369f2a0ed5d71105e07c2 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 @@ -7,7 +7,7 @@ specfem3d_globe/7.0.0 https://github.com/geodynamics/specfem3d_globe/archive/v7. [DEPENDENCY] set -e set -x -yum install -y git make cmake + module purge ./jarvis -install hpckit/2024.12.30 any module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles diff --git a/templates/sqlite/3.46.0/data.sqlite.arm-920.cpu.config b/templates/sqlite/3.46.0/data.sqlite.arm-920.cpu.config index 08ad393d249b98c7a8cbd9587274663ae5c0c66b..1fd4e84d2802f937fa5ef0741496eeb71956daba 100644 --- a/templates/sqlite/3.46.0/data.sqlite.arm-920.cpu.config +++ b/templates/sqlite/3.46.0/data.sqlite.arm-920.cpu.config @@ -8,8 +8,6 @@ sqlite/3.46.0 https://github.com/sqlite/sqlite/archive/refs/tags/version-3.16.0. set -e set -x -yum install make cmake gcc g++ -y - ./jarvis -install gcc/13.3.0 com module purge module use ./software/modulefiles diff --git a/templates/swmm/5.2.4/data.swmm.arm-920.cpu.config b/templates/swmm/5.2.4/data.swmm.arm-920.cpu.config index 91d9bc024d27c4c4cd7666b95b85125c2764ec2e..85022a35c93270b7c7cf757c6fc6583008c753b0 100644 --- a/templates/swmm/5.2.4/data.swmm.arm-920.cpu.config +++ b/templates/swmm/5.2.4/data.swmm.arm-920.cpu.config @@ -8,8 +8,6 @@ swmm/5.2.4 https://github.com/USEPA/Stormwater-Management-Model/archive/refs/hea set -e set -x -yum install make cmake gcc g++ -y - ./jarvis -install gcc/13.3.0 com module purge module use ./software/modulefiles diff --git a/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config b/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config index c650cb959e2a3e072d1d7a21983578b35c0a80c1..0b72861f31513a2e0475b6af5ea76954c16369b9 100644 --- a/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config +++ b/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config @@ -5,7 +5,6 @@ vaspkit/0.52 https://sourceforge.net/projects/vaspkit/files/Src/vaspkit.0.52.tar.gz [DEPENDENCY] -yum install make cmake gcc g++ -y module purge ./jarvis -install bisheng/4.1.0 com diff --git a/templates/want/2.6.1/data.want.arm.bisheng.hmpi.config b/templates/want/2.6.1/data.want.arm.bisheng.hmpi.config index d686fa93bf4066e2b4cecd53ebed914a55fbdb4e..8add7d7f0c7a575c4591d2040f8f125b21e0e1f3 100644 --- a/templates/want/2.6.1/data.want.arm.bisheng.hmpi.config +++ b/templates/want/2.6.1/data.want.arm.bisheng.hmpi.config @@ -8,7 +8,7 @@ want/2.6.1 https://github.com/QEF/want/archive/want-2.6.1.tar.gz want-2.6.1.tar. set -e set -x -yum install -y make cmake + ./jarvis -install bisheng/2.1.0 com module purge module use ./software/modulefiles @@ -27,7 +27,7 @@ yum install lapack* blas* -y tar -vzxf ${JARVIS_DOWNLOAD}/want-2.6.1.tar.gz [ENV] -yum install -y make cmake + module purge module use ./software/modulefiles module load bisheng/2.1.0 diff --git a/templates/wrf/4.6.1/data.wrf.arm.cpu.config b/templates/wrf/4.6.1/data.wrf.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..b986a9651e4953760263ac3a50135e79ec2c4ef0 --- /dev/null +++ b/templates/wrf/4.6.1/data.wrf.arm.cpu.config @@ -0,0 +1,120 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +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] + +module purge +module use ./software/modulefiles +./jarvis -install kgcc/9.3.1 com +module load kgcc/9.3.1 +export CC=gcc CXX=g++ FC=gfortran + +./jarvis -install hmpi/1.1.1 gcc +module load hmpi/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort +module load hdf5/1.10.1 +./jarvis -install hdf5/1.10.1 gcc +./jarvis -install package/pnetcdf/1.11.2 gcc +module load pnetcdf/1.11.2 +./jarvis -install package/netcdf/4.7.0 gcc +./jarvis -install optimized-routines/20.02 gcc +cd ${JARVIS_TMP} + +tar -zxvf $JARVIS_DOWNLOAD/wrf-4.6.1.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/9.3.1 +module load hmpi/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort +module load pnetcdf/1.11.2 +module load netcdf/4.7.0 +module load optimized-routines/20.02 + + +[APP] +app_name = WRF +build_dir = ${WRF_DIR} +binary_dir = +case_dir = ${JARVIS_ROOT}/workloads/test_wrf + +[BUILD] +cd ${JARVIS_TMP} +cd WRF-4.6.1 + +export HDF5=`which h5diff` +export HDF5=${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/9.3.1/lib64/libhpc +cat >> arch/configure.defaults <&1 | tee -a compile.log + + +[CLEAN] +./clean + +[RUN] +run = dsub -s run.sh +binary = +nodes = 1 diff --git "a/\350\264\276\347\273\264\346\226\257\345\274\200\345\217\221\350\200\205\346\263\250\346\204\217\344\272\213\351\241\271.md" "b/\350\264\276\347\273\264\346\226\257\345\274\200\345\217\221\350\200\205\346\263\250\346\204\217\344\272\213\351\241\271.md" new file mode 100644 index 0000000000000000000000000000000000000000..11cc5ca875bc01fd1e663f57400d7144d16553bf --- /dev/null +++ "b/\350\264\276\347\273\264\346\226\257\345\274\200\345\217\221\350\200\205\346\263\250\346\204\217\344\272\213\351\241\271.md" @@ -0,0 +1,17 @@ +# HPCRunner 开发者注意事项 +# 1、使用安装HPCKIT的方式替代单独安装HMPI、BISHENG以及数学库 +建议使用如下方式安装并使能hpckit +``` +./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 +``` +不建议使用如下方式 +``` +./jarvis -install hmpi/1.1.1 clang +module use software/moduledeps/bisheng2.1.0 +module load hmpi/1.1.1 +``` + +export JARVIS_ROOT=/hpcrunner