From 39fc70b840bd99c9b2b79f377ba2ea64a5323dff Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Mon, 11 Aug 2025 10:07:00 +0800 Subject: [PATCH 1/5] update use hmpi choose --- src/installService.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/installService.py b/src/installService.py index 59b65873..720fff96 100644 --- a/src/installService.py +++ b/src/installService.py @@ -123,7 +123,7 @@ class InstallService: version = None for version in os.listdir(libr_path): print(version) - if version != latest + if version != "latest": return self.get_version_info(version) return self.get_version_info(version) -- Gitee From 66beb71c6baf9e7808c10eef07932ed31a56de5b Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Mon, 11 Aug 2025 10:24:30 +0800 Subject: [PATCH 2/5] update use hmpi choose --- README.md | 2 +- package/fftw/yum/install.sh | 8 ++++++++ package/hdf4/4.2.15/bisheng/install.sh | 2 +- package/lmbench/3.0/install.sh | 2 +- src/installService.py | 1 - templates/ARPS/5.3.4/data.arps.arm.cpu.config | 2 +- templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config | 2 +- .../0.51.1/kallisto.arm.bisheng.hmpi.config | 1 - .../6.0/data.meso_grapes.arm.cpu.bisheng.hmpi.config | 2 +- .../6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config | 2 +- .../ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config | 2 +- templates/ncl/6.3.0/data.NCL.arm-container.cpu.config | 2 +- .../ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config | 2 +- .../4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config | 2 +- templates/wrf/4.2.1/bisheng/data.wrf.arm.cpu.config | 2 +- templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config | 2 +- templates/wrf/4.6.0/data.wrf.arm.cpu.config | 1 - templates/wrf/4.6.0/data.wrf.arm.cpu.sve.config | 1 - templates/wrf/4.6.0/data.wrf.cpu.sve.config | 3 +-- templates/wrfda/3.9.1/data.wrfda-sve.arm.cpu.config | 1 - 20 files changed, 22 insertions(+), 20 deletions(-) create mode 100644 package/fftw/yum/install.sh diff --git a/README.md b/README.md index 5fe960c3..c734eec1 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ 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 git time zlib zlib-devel gcc gcc-c++ environment-modules python python3 python3-devel python3-libs python3-pip cmake make numactl-libs rpmbuild rpmdevtools wget unzip flex tar patch +yum -y install git time zlib zlib-devel gcc gcc-c++ environment-modules python python3 python3-devel python3-libs python3-pip cmake make numactl numactl-devel numactl-libs rpmdevtools wget libtirpc libtirpc-devel unzip flex tar patch git clone https://gitee.com/openeuler/hpcrunner.git ``` diff --git a/package/fftw/yum/install.sh b/package/fftw/yum/install.sh new file mode 100644 index 00000000..fed635b3 --- /dev/null +++ b/package/fftw/yum/install.sh @@ -0,0 +1,8 @@ +#!/bin/bash +set -x +set -e + +yum install --downloadonly --downloaddir=./downloads/fftw3-devel fftw3-devel -y +yum localinstall ./downloads/fftw3-devel/*.rpm -y + + diff --git a/package/hdf4/4.2.15/bisheng/install.sh b/package/hdf4/4.2.15/bisheng/install.sh index 4e6751f8..3bb7d686 100755 --- a/package/hdf4/4.2.15/bisheng/install.sh +++ b/package/hdf4/4.2.15/bisheng/install.sh @@ -5,7 +5,7 @@ cd ${JARVIS_TMP} rm -rf hdf-4.2.15 tar -xvf ${JARVIS_DOWNLOAD}/hdf-4.2.15.tar.gz cd hdf-4.2.15/ -yum install -y libtirpc-devel + sed -i '974c #if defined(__linux__) && defined __x86_64__ && !( defined SUN) || defined(__aarch64__)' hdf/src/hdfi.h sed -i '23660a LIBS="$LIBS -ltirpc"' configure sed -i '23662c CPPFLAGS="$SYSCPPFLAGS -I/usr/include/tirpc"' configure diff --git a/package/lmbench/3.0/install.sh b/package/lmbench/3.0/install.sh index e86b61d9..6637c098 100644 --- a/package/lmbench/3.0/install.sh +++ b/package/lmbench/3.0/install.sh @@ -2,7 +2,7 @@ set -x set -e -. $CHECK_ROOT && yum install libtirpc-devel +. $CHECK_ROOT cd ${JARVIS_TMP} if [ ! -d lmbench ]; then git clone --depth=1 $JARVIS_PROXY/intel/lmbench.git diff --git a/src/installService.py b/src/installService.py index 720fff96..790e3558 100644 --- a/src/installService.py +++ b/src/installService.py @@ -48,7 +48,6 @@ class InstallService: def get_version_info(self, info, reg = r'\d+(?:\.\d+)*'): - matched_group = re.search(reg ,info) group_len = 0 if not matched_group: diff --git a/templates/ARPS/5.3.4/data.arps.arm.cpu.config b/templates/ARPS/5.3.4/data.arps.arm.cpu.config index 973a815b..3ed89dfa 100644 --- a/templates/ARPS/5.3.4/data.arps.arm.cpu.config +++ b/templates/ARPS/5.3.4/data.arps.arm.cpu.config @@ -6,7 +6,7 @@ ARPS/5.3.4 https://arps.caps.ou.edu/ARPS/download/code/arps5.3.4.tar.gz [DEPENDENCY] set -e -yum install -y tcsh libtirpc-devel libjpeg-turbo-devel +yum install -y tcsh libjpeg-turbo-devel export LIBJPEG_PATH=/usr module purge module use ./software/modulefiles diff --git a/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config b/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config index 822c79d5..4464dc5f 100644 --- a/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config +++ b/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config @@ -6,7 +6,7 @@ ARPS/5.3.4 https://arps.caps.ou.edu/ARPS/download/code/arps5.3.4.tar.gz [DEPENDENCY] set -e -yum install -y tcsh libtirpc-devel libjpeg-turbo-devel +yum install -y tcsh libjpeg-turbo-devel export LIBJPEG_PATH=/usr module purge module use ./software/modulefiles diff --git a/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config b/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config index a68a3faa..61edfa00 100755 --- a/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config +++ b/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config @@ -6,7 +6,6 @@ kallisto/0.51.1 ${JARVIS_PROXY}/pachterlab/kallisto/archive/refs/tags/v0.51.1.ta [DEPENDENCY] set -e -yum install -y zlib-devel module purge module use ./software/modulefiles ./jarvis -install bisheng/4.1.0 com 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 668e6ac4..5dbed223 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 -./CHECK_ROOT && yum install -y libtirpc.aarch64 libtirpc-devel.aarch64 numactl.aarch64 +./CHECK_ROOT module purge ./jarvis -install hpckit/24.0.0 com module use ./software/compiler/hpckit/24.0.0/HPCKit/24.12.30/modulefiles diff --git a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config index 0cd90298..4b689059 100644 --- a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config +++ b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config @@ -5,7 +5,7 @@ NCL/6.3.0 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.3.0/ncl-6.3.0.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libtirpc-devel libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y ./jarvis -install bisheng/3.2.0-mini com module use ./software/modulefiles diff --git a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config index 7db554a4..329c5d24 100644 --- a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config +++ b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config @@ -5,7 +5,7 @@ NCL/6.3.0 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.3.0/ncl-6.3.0.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libtirpc-devel libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y ./jarvis -install bisheng/3.2.0-mini com module use ./software/modulefiles diff --git a/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config b/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config index e8b85f60..0ea493ec 100644 --- a/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config +++ b/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config @@ -5,7 +5,7 @@ NCL/6.3.0 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.3.0/ncl-6.3.0.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libtirpc-devel libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel zlib-devel cairo cairo-devel pixman pixman-devel patch -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel patch -y ./jarvis -install package/kgcc/10.3.1 com module use ./software/modulefiles/ diff --git a/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config b/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config index c167a124..c079826a 100644 --- a/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config +++ b/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config @@ -5,7 +5,7 @@ NCL/6.6.2 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.6.2/ncl-6.6.2.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libtirpc-devel libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y ./jarvis -install bisheng/3.2.0-mini com module use ./software/modulefiles diff --git a/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config b/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config index 1970020f..c55311b2 100644 --- a/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config +++ b/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config @@ -15,7 +15,7 @@ if [ ! -d "${JARVIS_ROOT}/WRF-4.2" ]; then #判断wrf是否安装 ./jarvis -e ./jarvis -b" fi -yum install -y libtirpc.aarch64 libtirpc-devel.aarch64 csh +yum install -y csh module purge ./jarvis -install hpckit/25.0.0 com module use ./software/compiler/hpckit/25.0.0/HPCKit/latest/modulefiles diff --git a/templates/wrf/4.2.1/bisheng/data.wrf.arm.cpu.config b/templates/wrf/4.2.1/bisheng/data.wrf.arm.cpu.config index e80e2718..468a9387 100644 --- a/templates/wrf/4.2.1/bisheng/data.wrf.arm.cpu.config +++ b/templates/wrf/4.2.1/bisheng/data.wrf.arm.cpu.config @@ -9,7 +9,7 @@ case/conus12km https://www2.mmm.ucar.edu/wrf/src/conus12km.tar.gz set -e set -x # basic system components -./CHECK_ROOT && yum install -y libtirpc.aarch64 libtirpc-devel.aarch64 +./CHECK_ROOT module purge module use ./software/modulefiles ./jarvis -install bisheng/3.2.0-mini com diff --git a/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config b/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config index dbe60687..add81698 100644 --- a/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config +++ b/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config @@ -8,7 +8,7 @@ wrf/4.2 $JARVIS_PROXY/wrf-model/WRF/archive/refs/tags/v4.2.tar.gz wrf-4.2.tar.gz set -e set -x # basic system components -yum install -y libtirpc.aarch64 libtirpc-devel.aarch64 csh +yum install -y csh module purge ./jarvis -install hpckit/25.0.0 com module use ./software/compiler/hpckit/25.0.0/HPCKit/latest/modulefiles diff --git a/templates/wrf/4.6.0/data.wrf.arm.cpu.config b/templates/wrf/4.6.0/data.wrf.arm.cpu.config index c4b220ed..06c04d13 100644 --- a/templates/wrf/4.6.0/data.wrf.arm.cpu.config +++ b/templates/wrf/4.6.0/data.wrf.arm.cpu.config @@ -14,7 +14,6 @@ export CXX=`which mpicxx` export FC=`which mpifort` # basic system components -yum install -y time libtirpc libtirpc-devel wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.5.4.tar.gz -O /hpcrunner/downloads/netcdf-fortran-4.5.4.tar.gz --no-check-certificate wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz/ -O /hpcrunner/downloads/netcdf-c-4.8.1.tar.gz --no-check-certificate diff --git a/templates/wrf/4.6.0/data.wrf.arm.cpu.sve.config b/templates/wrf/4.6.0/data.wrf.arm.cpu.sve.config index 30e3c684..ab8b12bc 100644 --- a/templates/wrf/4.6.0/data.wrf.arm.cpu.sve.config +++ b/templates/wrf/4.6.0/data.wrf.arm.cpu.sve.config @@ -14,7 +14,6 @@ export CXX=`which mpicxx` export FC=`which mpifort` # basic system components -yum install -y libtirpc libtirpc-devel wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.5.4.tar.gz -O /hpcrunner/downloads/netcdf-fortran-4.5.4.tar.gz --no-check-certificate wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz/ -O /hpcrunner/downloads/netcdf-c-4.8.1.tar.gz --no-check-certificate diff --git a/templates/wrf/4.6.0/data.wrf.cpu.sve.config b/templates/wrf/4.6.0/data.wrf.cpu.sve.config index d6c9d31a..b92617fa 100644 --- a/templates/wrf/4.6.0/data.wrf.cpu.sve.config +++ b/templates/wrf/4.6.0/data.wrf.cpu.sve.config @@ -7,7 +7,7 @@ wrf/4.6.0 https://github.com/wrf-model/WRF/releases/download/v4.6.0/v4.6.0.tar.g [DEPENDENCY] set -e set -x -sudo yum -y install rpcbind libtirpc* +sudo yum -y install rpcbind ./jarvis -install package/hpckit/24.0.0/ any module use software/utils/hpckit/24.0.0/HPCKit/24.12.30/modulefiles module purge @@ -30,7 +30,6 @@ module load bisheng/kml2.5.0/kml bisheng/kml2.5.0/kblas/pthread ./jarvis -install jasper/1.900.2 bisheng # basic system components -yum install -y libtirpc libtirpc-devel [ENV] #!/bin/bash diff --git a/templates/wrfda/3.9.1/data.wrfda-sve.arm.cpu.config b/templates/wrfda/3.9.1/data.wrfda-sve.arm.cpu.config index b0cd6072..3f4b0b3c 100644 --- a/templates/wrfda/3.9.1/data.wrfda-sve.arm.cpu.config +++ b/templates/wrfda/3.9.1/data.wrfda-sve.arm.cpu.config @@ -8,7 +8,6 @@ wrf/3.9.1 https://github.com/wrf-model/WRF/archive/refs/tags/V3.9.1.tar.gz wrf-3 [DEPENDENCY] set -x set -e -yum install libtirpc libtirpc-devel patch time -y module purge module use ${JARVIS_ROOT}/HPCKit/latest/modulefiles module use ${JARVIS_ROOT}/software/module* -- Gitee From 1522b6a441a117116eda541323becd2dc7a2c163 Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Mon, 11 Aug 2025 10:35:45 +0800 Subject: [PATCH 3/5] update use hmpi choose --- package/fftw/yum/install.sh | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/package/fftw/yum/install.sh b/package/fftw/yum/install.sh index fed635b3..eac20d07 100644 --- a/package/fftw/yum/install.sh +++ b/package/fftw/yum/install.sh @@ -2,7 +2,23 @@ set -x set -e -yum install --downloadonly --downloaddir=./downloads/fftw3-devel fftw3-devel -y -yum localinstall ./downloads/fftw3-devel/*.rpm -y +# 检查fftw是否已安装 +if yum list installed | grep -q "fftw3-devel"; then + echo "fftw3-devel 已经安装。" +else + echo "fftw3-devel 未安装，正在进行安装..." + # 安装fftw3-devel + yum install --downloadonly --downloaddir=./downloads/fftw3-devel fftw3-devel -y + yum localinstall ./downloads/fftw3-devel/*.rpm -y + if [ $? -eq 0 ]; then + echo "fftw3-devel 安装成功。" + else + echo "fftw3-devel 安装失败。" + exit 1 + fi +fi + + + -- Gitee From 6e9f138d0a3f903b8fca6f43645eca28e189e28c Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Mon, 11 Aug 2025 10:41:13 +0800 Subject: [PATCH 4/5] update use hmpi choose --- package/fftw/yum/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/fftw/yum/install.sh b/package/fftw/yum/install.sh index eac20d07..5fd32337 100644 --- a/package/fftw/yum/install.sh +++ b/package/fftw/yum/install.sh @@ -3,7 +3,7 @@ set -x set -e # 检查fftw是否已安装 -if yum list installed | grep -q "fftw3-devel"; then +if rpm -q fftw-devel ; then echo "fftw3-devel 已经安装。" else echo "fftw3-devel 未安装，正在进行安装..." -- Gitee From 3f7d1d478f35c6ff18b6c9d29b2d9bf6f96d3be2 Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Mon, 11 Aug 2025 11:05:07 +0800 Subject: [PATCH 5/5] update use hmpi choose --- README.md | 2 +- package/R/4.3.0/install.sh | 2 +- package/relion/3.1.2/install.sh | 2 +- templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config | 2 +- templates/augustus/3.3.3/data.augustus.arm.cpu.config | 2 +- templates/bcftools/1.10.2/data.bcftools.arm.cpu.config | 2 +- templates/bcftools/1.10.2/data.bcftools.arm.cpu.hpckit.config | 2 +- templates/eccodes/2.18.0/data.eccodes.arm.cpu.config | 1 - .../4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config | 2 +- .../ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config | 2 +- templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config | 2 +- templates/ncl/6.3.0/data.NCL.arm-container.cpu.config | 2 +- templates/ncl/6.5.0/data.NCL.arm.cpu.config | 2 +- templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config | 2 +- templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config | 2 +- templates/ncview/2.1.5/data.ncview.arm.cpu.config | 2 +- .../nemo/3.6/bisheng/data.nemo-container-sve.arm.cpu.config | 2 +- templates/nemo/3.6/bisheng/data.nemo-container.arm.cpu.config | 2 +- templates/plink/1.9/data.plink.arm-920.cpu.config | 1 - templates/protobuf/27.2/data.protobuf.arm-920.cpu.config | 2 +- templates/psi4/1.3.2/data.psi4.arm.cpu.kgcc.config | 2 +- templates/qgis/3.34.7/data.qgis.arm.cpu.hpckit.config | 2 -- templates/relion/3.1.2/data.relion.arm.cpu.config | 1 - templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config | 1 - templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config | 1 - templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config | 1 - templates/relion/3.1.2/data.relion.mini.arm.cpu.config | 2 +- templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config | 1 - templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config | 1 - templates/roms/4.0/roms.arm.cpu.config | 2 +- templates/roms/4.0/roms.singularity.arm.bisheng-sve.cpu.config | 2 +- templates/roms/4.0/roms.singularity.arm.bisheng.cpu.config | 2 +- .../swan/41.31/swan.singularity.arm.bisheng.SVE.cpu.config | 2 +- templates/swan/41.31/swan.singularity.arm.bisheng.cpu.config | 2 +- templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config | 3 +-- templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config | 2 +- templates/vasp/6.3.2/data.vasp.arm_clang.cpu.config | 2 +- .../wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config | 2 +- templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config | 1 - templates/wrf/4.6.0/data.wrf.cpu.sve.config | 2 +- 40 files changed, 30 insertions(+), 42 deletions(-) diff --git a/README.md b/README.md index c734eec1..9a6442c8 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ 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 git time zlib zlib-devel gcc gcc-c++ environment-modules python python3 python3-devel python3-libs python3-pip cmake make numactl numactl-devel numactl-libs rpmdevtools wget libtirpc libtirpc-devel unzip flex tar patch +yum -y install git time zlib zlib-devel gcc gcc-c++ environment-modules python python3 python3-devel python3-libs python3-pip cmake make numactl numactl-devel numactl-libs rpmdevtools wget libtirpc libtirpc-devel unzip flex tar patch glibc-devel rpcbind csh perl-XML-LibXML xorg-x11-xauth curl curl-devel libcurl-devel git clone https://gitee.com/openeuler/hpcrunner.git ``` diff --git a/package/R/4.3.0/install.sh b/package/R/4.3.0/install.sh index b583b31b..fe562d54 100644 --- a/package/R/4.3.0/install.sh +++ b/package/R/4.3.0/install.sh @@ -4,7 +4,7 @@ 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 +yum install libX11-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel -y . ${DOWNLOAD_TOOL} -u https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz diff --git a/package/relion/3.1.2/install.sh b/package/relion/3.1.2/install.sh index b11d46bf..3d97895e 100755 --- a/package/relion/3.1.2/install.sh +++ b/package/relion/3.1.2/install.sh @@ -10,7 +10,7 @@ tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz cd relion-3.1.2 mkdir build && cd build #. $CHECK_ROOT && yum install -y libtiff-* fltk* fltk-devel* -#yum -y install xorg-x11-xauth + #export CC=clang CXX=clang++ FC=flang cmake -DCUDA=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=$1 .. make -j diff --git a/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config index b86031c3..3b8250d7 100755 --- a/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config +++ b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config @@ -6,7 +6,7 @@ CNVnator/0.4.1 ${JARVIS_PROXY}/abyzovlab/CNVnator/releases/download/v0.4.1/CNVna [DEPENDENCY] set -e -yum install -y readline-devel libcurl-devel bzip2-devel +yum install -y readline-devel bzip2-devel module purge module use ./software/modulefiles ./jarvis -install kgcc/10.3.1 com diff --git a/templates/augustus/3.3.3/data.augustus.arm.cpu.config b/templates/augustus/3.3.3/data.augustus.arm.cpu.config index 9d0063a3..11253660 100644 --- a/templates/augustus/3.3.3/data.augustus.arm.cpu.config +++ b/templates/augustus/3.3.3/data.augustus.arm.cpu.config @@ -7,7 +7,7 @@ augustus/3.3.3 $JARVIS_PROXY/Gaius-Augustus/Augustus/archive/refs/tags/v3.3.3.ta [DEPENDENCY] set -x set -e -yum install gsl* mysql-devel sqlite* suitesparse* libcurl-devel bzip2-devel -y +yum install gsl* mysql-devel sqlite* suitesparse* bzip2-devel -y pip3 install parallel_augustus -i https://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com . ${DOWNLOAD_TOOL} -u https://rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-5.5.2.5-5.mga9.aarch64.rpm . ${DOWNLOAD_TOOL} -u https://www.rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm diff --git a/templates/bcftools/1.10.2/data.bcftools.arm.cpu.config b/templates/bcftools/1.10.2/data.bcftools.arm.cpu.config index c50ea98f..29fbb133 100644 --- a/templates/bcftools/1.10.2/data.bcftools.arm.cpu.config +++ b/templates/bcftools/1.10.2/data.bcftools.arm.cpu.config @@ -11,7 +11,7 @@ set -e set -x module purge -yum install bzip2 bzip2-devel xz-devel libcurl-devel -y +yum install bzip2 bzip2-devel xz-devel -y ./jarvis -install bisheng/4.1.0 com module use ./software/modulefiles diff --git a/templates/bcftools/1.10.2/data.bcftools.arm.cpu.hpckit.config b/templates/bcftools/1.10.2/data.bcftools.arm.cpu.hpckit.config index 9ff6baf8..9e85a19d 100644 --- a/templates/bcftools/1.10.2/data.bcftools.arm.cpu.hpckit.config +++ b/templates/bcftools/1.10.2/data.bcftools.arm.cpu.hpckit.config @@ -11,7 +11,7 @@ set -e set -x module purge -yum install bzip2 bzip2-devel xz-devel libcurl-devel -y +yum install bzip2 bzip2-devel xz-devel -y ./jarvis -install hpckit/24.0.0 any source software/utils/hpckit/24.0.0/HPCKit/latest/setvars.sh --use-bisheng --force 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 a7c09bce..7ca4755b 100644 --- a/templates/eccodes/2.18.0/data.eccodes.arm.cpu.config +++ b/templates/eccodes/2.18.0/data.eccodes.arm.cpu.config @@ -8,7 +8,6 @@ eccodes/2.18.0 http://confluence.ecmwf.int/download/attachments/45757960/Eccodes set -e set -x -yum install -y libcurl-devel module use ./software/modulefiles module purge ./jarvis -install bisheng/2.1.0 com diff --git a/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config b/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config index a9578bb1..75c857ce 100644 --- a/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config +++ b/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config @@ -10,7 +10,7 @@ set -e set -x yum install glibc-headers -y -yum install fftw-devel fftw3-devel -y +./jarvis -install fftw/yum com yum install libxml2-devel libxslt-devel cmake -y pip3 install numpy --upgrade --force-reinstall pip3 install cython diff --git a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config index 4b689059..58d4a035 100644 --- a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config +++ b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng-sve.cpu.config @@ -5,7 +5,7 @@ NCL/6.3.0 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.3.0/ncl-6.3.0.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf cairo cairo-devel pixman pixman-devel -y ./jarvis -install bisheng/3.2.0-mini com module use ./software/modulefiles diff --git a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config index 329c5d24..38cf97a3 100644 --- a/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config +++ b/templates/ncl/6.3.0/data.NCL.arm-container-bisheng.cpu.config @@ -5,7 +5,7 @@ NCL/6.3.0 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.3.0/ncl-6.3.0.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf cairo cairo-devel pixman pixman-devel -y ./jarvis -install bisheng/3.2.0-mini com module use ./software/modulefiles diff --git a/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config b/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config index 0ea493ec..e1ab4700 100644 --- a/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config +++ b/templates/ncl/6.3.0/data.NCL.arm-container.cpu.config @@ -5,7 +5,7 @@ NCL/6.3.0 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.3.0/ncl-6.3.0.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel patch -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf cairo cairo-devel pixman pixman-devel patch -y ./jarvis -install package/kgcc/10.3.1 com module use ./software/modulefiles/ diff --git a/templates/ncl/6.5.0/data.NCL.arm.cpu.config b/templates/ncl/6.5.0/data.NCL.arm.cpu.config index 066a5c91..b12138b6 100644 --- a/templates/ncl/6.5.0/data.NCL.arm.cpu.config +++ b/templates/ncl/6.5.0/data.NCL.arm.cpu.config @@ -38,7 +38,7 @@ yum install -y epel-release sed -i -e 's|$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 -y install xorg-x11-server-utils xorg-x11-server-Xnest libXtst rpmdev-setuptree diff --git a/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config b/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config index c079826a..3aebe60d 100644 --- a/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config +++ b/templates/ncl/6.6.2/data.NCL.arm-container-bisheng.cpu.config @@ -5,7 +5,7 @@ NCL/6.6.2 $JARVIS_PROXY/chen-shaoheng/NCL-SOURCE/releases/download/ncl-6.6.2/ncl-6.6.2.tar.gz [DEPENDENCY] -yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf curl libcurl-devel cairo cairo-devel pixman pixman-devel -y +yum install tar byacc bison expat-devel expat libX11 libX11-devel libXmu* libXaw libXaw-devel flex flex-devel freetype-devel libpng-devel libXi libSM-devel libXi-devel libXext-devel pkgconf cairo cairo-devel pixman pixman-devel -y ./jarvis -install bisheng/3.2.0-mini com module use ./software/modulefiles diff --git a/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config b/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config index dc951cd4..ea2d5fd4 100644 --- a/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config +++ b/templates/ncl/6.6.2/data.NCL.arm_centos8.cpu.config @@ -38,7 +38,7 @@ yum install -y epel-release sed -i -e 's|$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 -y install xorg-x11-server-utils xorg-x11-server-Xnest libXtst rpmdev-setuptree diff --git a/templates/ncview/2.1.5/data.ncview.arm.cpu.config b/templates/ncview/2.1.5/data.ncview.arm.cpu.config index 9c751ee6..f41f7b45 100644 --- a/templates/ncview/2.1.5/data.ncview.arm.cpu.config +++ b/templates/ncview/2.1.5/data.ncview.arm.cpu.config @@ -42,7 +42,7 @@ binary_dir = case_dir = ${JARVIS_ROOT}/case [BUILD] -. $CHECK_ROOT && yum install libX11 libX11-devel libXaw libXaw-devel libpng-devel libpng curl curl-devel libXt-devel xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -y +. $CHECK_ROOT && yum install libX11 libX11-devel libXaw libXaw-devel libpng-devel libpnglibXt-devel xorg-x11-server-utils xorg-x11-server-Xnest libXtst -y set -x set -e cd ${JARVIS_TMP} 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 6670b603..66e611ec 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 @@ -5,7 +5,7 @@ nemo/3.6 http://forge.ipsl.jussieu.fr/nemo/changeset/15814/NEMO/releases/release-3.6?old_path=%2F\&format=zip NEMO_releases_release-3.6-15813.zip [DEPENDENCY] -yum install -y svn python3 +yum install -y svn module use software/moduledeps/bisheng4.0.0 module use software/moduledeps/bisheng4.0.0-hmpi2.4.1 export CC=mpicc CXX=mpicxx FC=mpifort 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 0d19620f..94aa9675 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 @@ -5,7 +5,7 @@ nemo/3.6 http://forge.ipsl.jussieu.fr/nemo/changeset/15814/NEMO/releases/release-3.6?old_path=%2F\&format=zip NEMO_releases_release-3.6-15813.zip [DEPENDENCY] -yum install -y svn python3 +yum install -y svn module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.0.0 module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.0.0-hmpi2.4.1 export CC=mpicc CXX=mpicxx FC=mpifort diff --git a/templates/plink/1.9/data.plink.arm-920.cpu.config b/templates/plink/1.9/data.plink.arm-920.cpu.config index fd7f5365..0840d9e8 100644 --- a/templates/plink/1.9/data.plink.arm-920.cpu.config +++ b/templates/plink/1.9/data.plink.arm-920.cpu.config @@ -5,7 +5,6 @@ plink/1.9 https://github.com/chrchang/plink-ng/archive/refs/heads/master.zip plink-master.zip [DEPENDENCY] -yum install make cmake gcc g++ -y dnf install openblas-devel zstd-devel -y module purge diff --git a/templates/protobuf/27.2/data.protobuf.arm-920.cpu.config b/templates/protobuf/27.2/data.protobuf.arm-920.cpu.config index 8bcaf7f8..033c1d2d 100644 --- a/templates/protobuf/27.2/data.protobuf.arm-920.cpu.config +++ b/templates/protobuf/27.2/data.protobuf.arm-920.cpu.config @@ -11,7 +11,7 @@ googletest https://github.com/google/googletest/archive/refs/heads/main.zip goog set -e set -x -yum install make cmake gcc g++ binutils -y +yum install binutils -y ./jarvis -install bisheng/4.1.0 com module purge 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 8cedc2f5..f4eae511 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 @@ -9,7 +9,7 @@ set -e set -x pip3 install QCElemental QCEngine deepdiff -sudo yum groupinstall "Development Tools" -y && sudo yum install glibc-devel -y +sudo yum groupinstall "Development Tools" -y pip3 install numpy --upgrade --force-reinstall ./jarvis -install kgcc/10.3.1 com module use software/modulefiles diff --git a/templates/qgis/3.34.7/data.qgis.arm.cpu.hpckit.config b/templates/qgis/3.34.7/data.qgis.arm.cpu.hpckit.config index 4f82a040..cb0c881e 100644 --- a/templates/qgis/3.34.7/data.qgis.arm.cpu.hpckit.config +++ b/templates/qgis/3.34.7/data.qgis.arm.cpu.hpckit.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 - module purge ./jarvis -install hpckit/24.0.0 com module use ./software/compiler/hpckit/24.0.0/HPCKit/24.12.30/modulefiles diff --git a/templates/relion/3.1.2/data.relion.arm.cpu.config b/templates/relion/3.1.2/data.relion.arm.cpu.config index 0bb01b01..c4114a2e 100644 --- a/templates/relion/3.1.2/data.relion.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.arm.cpu.config @@ -38,7 +38,6 @@ tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz cd relion-3.1.2 mkdir build && cd build #yum install -y libtiff-* fltk* fltk-devel* -#yum -y install xorg-x11-xauth cmake -DCUDA=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config index 56a410b9..89f3b750 100644 --- a/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config @@ -48,7 +48,6 @@ sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt mkdir build && cd build yum install -y libtiff-* fltk* fltk-devel* tbb-devel -yum -y install xorg-x11-xauth cmake -DCUDA=OFF -DGUI=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config index 3f15f012..ed55a679 100644 --- a/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config @@ -44,7 +44,6 @@ sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt mkdir build && cd build yum install -y libtiff-* fltk* fltk-devel* tbb-devel -yum -y install xorg-x11-xauth cmake -DCUDA=OFF -DGUI=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config index 1edd31df..99d40da8 100644 --- a/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config @@ -48,7 +48,6 @@ cd relion-3.1.2 #sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt mkdir build && cd build yum install -y libtiff-* fltk* fltk-devel* tbb-devel -yum -y install xorg-x11-xauth cmake -DCUDA=OFF -DGUI=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config index 3db752e9..f9b2bfcd 100644 --- a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config @@ -43,7 +43,7 @@ cd relion-3.1.2 #sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt mkdir build && cd build yum install -y libtiff-* fltk* fltk-devel* -yum -y install xorg-x11-xauth + cmake -DCUDA=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config index c1f39835..ad8a650f 100644 --- a/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config @@ -49,7 +49,6 @@ cd relion-3.1.2 #sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt mkdir build && cd build yum install -y libtiff-* fltk* fltk-devel* tbb-devel -yum -y install xorg-x11-xauth cmake -DCUDA=OFF -DGUI=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config index 4072547d..689593aa 100644 --- a/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config +++ b/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config @@ -43,7 +43,6 @@ sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt mkdir build && cd build yum install -y libtiff-* fltk* fltk-devel* -yum -y install xorg-x11-xauth cmake -DCUDA=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2 .. make -j make install diff --git a/templates/roms/4.0/roms.arm.cpu.config b/templates/roms/4.0/roms.arm.cpu.config index b03ab101..37362474 100644 --- a/templates/roms/4.0/roms.arm.cpu.config +++ b/templates/roms/4.0/roms.arm.cpu.config @@ -7,7 +7,7 @@ ROMS/4.0 $JARVIS_PROXY/kshedstrom/roms/archive/refs/tags/v3.9_cobalt.tar.gz [DEPENDENCY] set -x set -e -#yum install perl-XML-LibXML + ./jarvis -install bisheng/2.5.0 com module purge module use ./software/modulefiles diff --git a/templates/roms/4.0/roms.singularity.arm.bisheng-sve.cpu.config b/templates/roms/4.0/roms.singularity.arm.bisheng-sve.cpu.config index 33243941..f99535a8 100644 --- a/templates/roms/4.0/roms.singularity.arm.bisheng-sve.cpu.config +++ b/templates/roms/4.0/roms.singularity.arm.bisheng-sve.cpu.config @@ -7,7 +7,7 @@ ROMS/4.0 $JARVIS_PROXY/myroms/roms/archive/refs/tags/roms-4.0.tar.gz [DEPENDENCY] set -x set -e -#yum install perl-XML-LibXML + ./jarvis -install package/bisheng/3.2.0-mini com module purge module use ./software/modulefiles diff --git a/templates/roms/4.0/roms.singularity.arm.bisheng.cpu.config b/templates/roms/4.0/roms.singularity.arm.bisheng.cpu.config index ea36bf5f..5f5a0fed 100644 --- a/templates/roms/4.0/roms.singularity.arm.bisheng.cpu.config +++ b/templates/roms/4.0/roms.singularity.arm.bisheng.cpu.config @@ -7,7 +7,7 @@ ROMS/4.0 $JARVIS_PROXY/myroms/roms/archive/refs/tags/roms-4.0.tar.gz [DEPENDENCY] set -x set -e -#yum install perl-XML-LibXML + ./jarvis -install package/bisheng/3.2.0-mini com module purge module use ./software/modulefiles diff --git a/templates/swan/41.31/swan.singularity.arm.bisheng.SVE.cpu.config b/templates/swan/41.31/swan.singularity.arm.bisheng.SVE.cpu.config index db4f0112..281b5dbb 100644 --- a/templates/swan/41.31/swan.singularity.arm.bisheng.SVE.cpu.config +++ b/templates/swan/41.31/swan.singularity.arm.bisheng.SVE.cpu.config @@ -7,7 +7,7 @@ [DEPENDENCY] set -x set -e -#yum install perl-XML-LibXML + #./jarvis -install package/bisheng/4.0 com #module purge #module use ./software/modulefiles diff --git a/templates/swan/41.31/swan.singularity.arm.bisheng.cpu.config b/templates/swan/41.31/swan.singularity.arm.bisheng.cpu.config index 5ab9f9e9..accee9a7 100644 --- a/templates/swan/41.31/swan.singularity.arm.bisheng.cpu.config +++ b/templates/swan/41.31/swan.singularity.arm.bisheng.cpu.config @@ -7,7 +7,7 @@ [DEPENDENCY] set -x set -e -#yum install perl-XML-LibXML + #./jarvis -install package/bisheng/4.0 com #module purge #module use ./software/modulefiles diff --git a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config index 6278fb0c..bdb6b9e2 100644 --- a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config +++ b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config @@ -8,7 +8,6 @@ tensorflow/2.4.1 https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.4 set -e set -x -yum install -y vim tar git wget module purge ./jarvis -install package/anaconda3/2023.3 any source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh @@ -18,7 +17,7 @@ module load kgcc/10.3.1 export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` -sudo yum install -y glibc-devel + pip install cython tar -xzvf ${JARVIS_DOWNLOAD}/tensorflow-2.4.1.tar.gz mkdir -p tensorflow diff --git a/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config b/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config index 49f43b94..ae181c76 100644 --- a/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config +++ b/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config @@ -9,7 +9,7 @@ set -x module purge ./jarvis -install hpckit/25.0.0 com -yum install -y fftw3-devel +./jarvis -install fftw/yum com cd ${JARVIS_DOWNLOAD} rm -rf vasp.5.4.4 diff --git a/templates/vasp/6.3.2/data.vasp.arm_clang.cpu.config b/templates/vasp/6.3.2/data.vasp.arm_clang.cpu.config index 25453bf9..0fca9fb0 100644 --- a/templates/vasp/6.3.2/data.vasp.arm_clang.cpu.config +++ b/templates/vasp/6.3.2/data.vasp.arm_clang.cpu.config @@ -9,7 +9,7 @@ set -x module purge ./jarvis -install hpckit/2025.3.30 com -yum install -y fftw3-devel +./jarvis -install fftw/yum com cd ${JARVIS_TMP} rm -rf vasp.6.3.2 diff --git a/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config b/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config index c55311b2..dbe05be1 100644 --- a/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config +++ b/templates/wps/4.6.0/bisheng/data.wps.arm.cpu.bisheng.hmpi.config @@ -15,7 +15,7 @@ if [ ! -d "${JARVIS_ROOT}/WRF-4.2" ]; then #判断wrf是否安装 ./jarvis -e ./jarvis -b" fi -yum install -y csh + module purge ./jarvis -install hpckit/25.0.0 com module use ./software/compiler/hpckit/25.0.0/HPCKit/latest/modulefiles diff --git a/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config b/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config index add81698..74cefbe4 100644 --- a/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config +++ b/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config @@ -8,7 +8,6 @@ wrf/4.2 $JARVIS_PROXY/wrf-model/WRF/archive/refs/tags/v4.2.tar.gz wrf-4.2.tar.gz set -e set -x # basic system components -yum install -y csh module purge ./jarvis -install hpckit/25.0.0 com module use ./software/compiler/hpckit/25.0.0/HPCKit/latest/modulefiles diff --git a/templates/wrf/4.6.0/data.wrf.cpu.sve.config b/templates/wrf/4.6.0/data.wrf.cpu.sve.config index b92617fa..3b66d523 100644 --- a/templates/wrf/4.6.0/data.wrf.cpu.sve.config +++ b/templates/wrf/4.6.0/data.wrf.cpu.sve.config @@ -7,7 +7,7 @@ wrf/4.6.0 https://github.com/wrf-model/WRF/releases/download/v4.6.0/v4.6.0.tar.g [DEPENDENCY] set -e set -x -sudo yum -y install rpcbind + ./jarvis -install package/hpckit/24.0.0/ any module use software/utils/hpckit/24.0.0/HPCKit/24.12.30/modulefiles module purge -- Gitee