diff --git a/package/R/4.3.0/install.sh b/package/R/4.3.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..5f90662815328847cc476b4dfe29614c458e21b5 --- /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 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$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install \ No newline at end of file diff --git a/package/bisheng/4.1.0/install.sh b/package/bisheng/4.1.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..ea7f4e6aab7cea3932cebdded7f9254f34181bc0 --- /dev/null +++ b/package/bisheng/4.1.0/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -e +export bisheng_ver='BiShengCompiler-4.1.0' +arch='x86' +if [ x$(arch) = xaarch64 ];then + arch='aarch64' +fi +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/${bisheng_ver}-${arch}-linux.tar.gz +cd ${JARVIS_TMP} +. $CHECK_ROOT && yum -y install libatomic libstdc++ libstdc++-devel +tar xzvf ${JARVIS_DOWNLOAD}/${bisheng_ver}-${arch}-linux.tar.gz -C $1 --strip-components=1 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..70709ca0eb6f99323569e83db028d00607969421 --- /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 diff --git a/package/eig/8.0.0/install.sh b/package/eig/8.0.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..a16317ca5bb32f151e92ae1eb125268b33cc3e9a --- /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 diff --git a/package/gcc/10.3.1/install.sh b/package/gcc/10.3.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..a35f403663ac8a48683330cab52dc02736db76fa --- /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 \ No newline at end of file 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..d6eaabddf90118ef367bdea968cd8410e5e694dd --- /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 diff --git a/package/gsl/2.7.1/install.sh b/package/gsl/2.7.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..a651de9f4c64a572f21d35431fa0dffb0a833544 --- /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 diff --git a/package/hmpi/1.1.1/install.sh b/package/hmpi/1.1.1/install.sh index 0de33156c175feb6fb71b82bd3e95913146361c2..3d1b40a5f5f84202c32ea50d255ef9fc060a48c1 100755 --- a/package/hmpi/1.1.1/install.sh +++ b/package/hmpi/1.1.1/install.sh @@ -1,9 +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 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..614821dccee05ecaf02a44a16eae619bad7f3781 --- /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 diff --git a/package/octopus/11.4/install.sh b/package/octopus/11.4/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..a494c9dd5f77ad1efb0cef787e86604b5576bdf8 --- /dev/null +++ b/package/octopus/11.4/install.sh @@ -0,0 +1,155 @@ +#!/bin/bash + +##全局变量 +#--------------------------------# +#having test +version=$1; + +##全局变量 +#--------------------------------# +passwd=123456; +install_path=/share/home/top_software/sunqian +target_path=$install_path/bin +source_file=$install_path/source_sun.sh +cpu_num=`grep -c "processor" /proc/cpuinfo`; #CPU核数 +netcard=`cat /proc/net/dev|sort -rn -k2|awk '{print $1}'|awk NR==1|awk -F ':' '{print $1}'`;#网卡名称 +ip_addr=`ip a|grep $netcard|grep inet|awk '{print $2}'|awk -F '/' '{print $1}'` #ip地址 +osType=`cat /etc/os-release|grep ID |awk NR==1|awk -F \" '{print $2}'` +basearch=`arch` +#--------------------------------# +echo install_path=/share/home/top_software/sunqian >> $source_file +touch $source_file +#--------------------------------# +#下载全部所需的依赖 +cd $install_path +wget https://ftp.gnu.org/gnu/gsl/gsl-2.5.tar.gz +wget https://launchpad.net/libvdwxc/stable/0.4.0/+download/libvdwxc-0.4.0.tar.gz +wget https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.10.1.tar.gz +wget http://forge.abinit.org/fallbacks/libxc-4.0.1.tar.gz +wget http://www.fftw.org/fftw-3.3.8.tar.gz +wget https://octopus-code.org/download/11.4/octopus-11.4.tar.gz +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.tar.gz + + + + +#安装libxc 4.0.1 +cd $install_path +tar -xvf libxc-4.0.1.tar.gz +cd libxc-4.0.1 +CC=gcc +FC="gfortran -fallow-argument-mismatch" +./configure --prefix=$target_path/libxc --enable-shared=yes --enable-static=yes +make -j$(nproc) +make install + + +cat>"$target_path/libxc/libxc_modulefiles"<"$target_path/octopus/octopus-11.4/octopus_modulefiles"< /dev/null 2>&1 +cd samtools-0.1.9 +make diff --git a/package/samtools/1.15/install.sh b/package/samtools/1.15/install.sh index 357b1cbaa8e25426619c02107d11083f5de21eac..8479ba09a7ff44d454d27b1657acbdceacd08381 100755 --- a/package/samtools/1.15/install.sh +++ b/package/samtools/1.15/install.sh @@ -7,4 +7,4 @@ tar xvf ${JARVIS_DOWNLOAD}/samtools-1.15.tar.bz2 cd samtools-1.15 ./configure --prefix=$1 make -j -make install +make install \ No newline at end of file diff --git a/proxy.sh b/proxy.sh index b44a75e92633584ef80f08c024de02b5852ff441..80620c89457967769644798176ec04a8ba024b32 100644 --- a/proxy.sh +++ b/proxy.sh @@ -17,8 +17,8 @@ echo '3) 缇庡浗楂橀熸簮2' echo '4) 缇庡浗楂橀熸簮3' echo '5) 闊╁浗楂橀熸簮1' echo '6) 闊╁浗楂橀熸簮2' -echo '7) Gitee楂橀熸簮' -echo '8) 鎭㈠瀹樻柟婧' +echo 'a) Gitee楂橀熸簮' +echo 'b) 鎭㈠瀹樻柟婧' read -p '浣犺緭鍏ョ殑鏁板瓧涓: ' aNum @@ -28,12 +28,15 @@ if [[ $aNum =~ ^[1-6]$ ]]; then source ./init.sh elif [[ $aNum -eq 'a' ]]; then # 澶囦唤骞舵浛鎹ataService.py鏂囦欢 + echo "you are using the gitee source" rm -rf src/dataService.py cp src/dataService.py.fast src/dataService.py + export UseGitee=1 elif [[ $aNum -eq 'b' ]]; then # 鎭㈠dataService.py鏂囦欢 rm -rf src/dataService.py cp src/dataService.py.ori src/dataService.py + export UseGitee=0 else - echo '鏃犳晥杈撳叆锛岃杈撳叆 1 鍒 7 涔嬮棿鐨勬暟瀛' + echo '鏃犳晥杈撳叆锛岃杈撳叆 1~6|a,b 涔嬮棿鐨勬暟瀛' fi \ No newline at end of file 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..4034bff044570e8e756e92b9adc6805d6dcb9f72 --- /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 diff --git a/templates/openblas/0.3.23/data.openblas.arm.cpu.config b/templates/openblas/0.3.23/data.openblas.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..943d849a5f3fbf3000f9fb1643a3f516a33722c6 --- /dev/null +++ b/templates/openblas/0.3.23/data.openblas.arm.cpu.config @@ -0,0 +1,53 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +OpenBLAS/0.3.23 $JARVIS_PROXY/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz OpenBLAS-0.3.23.tar.gz + +[DOWNLOADORI] +OpenBLAS/0.3.23 $JARVIS_PROXY/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz OpenBLAS-0.3.23.tar.gz + +[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 OpenBLAS-0.3.23 +tar -xvf $JARVIS_DOWNLOAD/OpenBLAS-0.3.23.tar.gz +cd OpenBLAS-0.3.23 +make -j 16 ARCH=aarch64 all +make PREFIX=$targetdir/openblas/openblas_install install + + +[CLEAN] +./clean_build + +[RUN] +run = +binary = +nodes = 1 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 4c1721be3cef3a8dad0915e2fcbb3e8490677ec1..cf6cd86ff0a26c3b34aae64321126dcdc884092f 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 @@ -1,6 +1,10 @@ [SERVER] 11.11.11.11 +[DOWNLOAD] +vtstcode/179 http://theory.cm.utexas.edu/code/vtstcode-179.tgz + + [DEPENDENCY] # add gcc/mpi module use ${JARVIS_ROOT}/software/modulefiles diff --git a/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config b/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config index 2e834608aaab70c2f923fedf157a249cf859fd73..e3b131274a023d078be1e41470bf41ecd2d3973d 100644 --- a/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config +++ b/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config @@ -9,32 +9,32 @@ set -e set -x module purge module use ./software/modulefiles -./jarvis -install kml/1.6.0/gcc any -./jarvis -install bisheng/2.5.0 com -module load bisheng/2.5.0 +./jarvis -install bisheng/3.2.0 com +module load bisheng/3.2.0 export CC=clang CXX=clang++ FC=flang ./jarvis -install jasper/1.900.2 clang module load jasper/1.900.2 -./jarvis -install hmpi/1.2.0 clang -module load hmpi/1.2.0 +./jarvis -install hmpi/2.3.0 clang +module load hmpi/2.3.0 export CC=mpicc CXX=mpicxx FC=mpifort ./jarvis -install hdf5/1.12.0/clang clang+mpi module load hdf5-clang/1.12.0 -./jarvis -install netcdf/4.7.4/clang clang+mpi -module load netcdf-clang/4.7.4 ./jarvis -install pnetcdf/1.12.1 clang+mpi module load pnetcdf/1.12.1 -#tar -zxvf $JARVIS_DOWNLOAD/wrf-4.3.3.tar.gz +./jarvis -install netcdf/4.8.1/clang clang+mpi +module load netcdf-clang/4.8.1 +./jarvis -install kml/2.4.0/bisheng clang +tar -zxvf $JARVIS_DOWNLOAD/wrf-4.3.3.tar.gz [ENV] #!/bin/bash module purge module use ./software/modulefiles -module load bisheng/2.5.0 +module load bisheng/3.2.0 module load jasper/1.900.2 -module load hmpi/1.2.0 -module load hdf5-clang/1.12.0 netcdf-clang/4.7.4 pnetcdf/1.12.1 -module load kml-gcc/1.6.0 +module load hmpi/2.3.0 +module load hdf5-clang/1.12.0 netcdf-clang/4.8.1 pnetcdf/1.12.1 +module load kml-bisheng/2.4.0 export WRFIO_NCD_LARGE_FILE_SUPPORT=1 export NETCDF=$NETCDF_CLANG_PATH export HDF5=$HDF5_CLANG_PATH @@ -55,18 +55,67 @@ export WRFIO_NCD_LARGE_FILE_SUPPORT=1 [APP] app_name = WRF build_dir = ${WRF_DIR} -binary_dir = +binary_dir = case_dir = ${JARVIS_ROOT}/workloads/test_wrf [BUILD] +cat << \EOF > ./arch/configure.defaults +########################################################### +#ARCH Linux aarch64,clang HYPERMPI#serial smpar dmpar dm+sm +DESCRIPTION = CLANG ($SFC/$SCC) +DMPARALLEL = 1 +OMPCPP = -D_OPENMP +OMP = -fopenmp +OMPCC = -fopenmp +SFC = flang +SCC = clang +CCOMP = clang +DM_FC = mpif90 -f90=$(SFC) +DM_CC = mpicc -cc=$(SCC) -DMPI2_SUPPORT +FC = CONFIGURE_FC +CC = CONFIGURE_CC +LD = $(FC) -L$(KML_BISHENG_PATH)/lib -lkm +RWORDSIZE = CONFIGURE_RWORDSIZE +PROMOTION = #-fdefault-real-8 +ARCH_LOCAL = -DNONSTANDARD_SYSTEM_SUBR -DWRF_USE_CLM +CFLAGS_LOCAL = -mcpu=native -w -O3 -c -march=armv8.2-a +LDFLAGS_LOCAL = +CPLUSPLUSLIB = +ESMF_LDFLAG = $(CPLUSPLUSLIB) +FCOPTIM = -O3 -march=armv8.2-a +FCREDUCEDOPT = $(FCOPTIM) +FCNOOPT = -O0 +FCDEBUG = -g # -fbacktrace -ggdb-fcheck=bounds,do,mem,pointer -ffpe-trap=invalid,zero,overflow +FORMAT_FIXED = -ffixed-form +FORMAT_FREE = -ffree-form -ffree-line-length-0 +FCSUFFIX = +BYTESWAPIO = -fconvert=big-endian +FCBASEOPTS_NO_G = -w $(FORMAT_FREE) $(BYTESWAPIO) +FCBASEOPTS = -mcpu=native $(OMP) $(FCBASEOPTS_NO_G) +MODULE_SRCH_FLAG = +TRADFLAG = -traditional +CPP = /lib/cpp -P +AR = ar +ARFLAGS = ru +M4 = m4 -G +RANLIB = ranlib +RLFLAGS = +CC_TOOLS = $(SCC) + +#insert new stanza before the Fujitsu block, keep Fujitsu at the end of the list +########################################################### +#ARCH NULL +#insert new stanza before the Fujitsu block, keep Fujitsu at the end of the list +########################################################### +#ARCH NULL +EOF echo 4 | ./configure -./compile -j 16 em_real 2>&1 | tee compile.log +./compile -j 16 em_real 2>&1 | tee compile.log [CLEAN] ./clean [RUN] run = dsub -s run.sh -binary = -nodes = 1 - +binary = +nodes = 1 \ No newline at end of file diff --git a/templates/wrf/4.6.1/wrf.4.6.1.config b/templates/wrf/4.6.1/wrf.4.6.1.config new file mode 100644 index 0000000000000000000000000000000000000000..6c66af19a66f832bb9d8461f399427c8bcbb5b28 --- /dev/null +++ b/templates/wrf/4.6.1/wrf.4.6.1.config @@ -0,0 +1,121 @@ +[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 +