diff --git a/LifeSciences/nanopack/build.sh b/LifeSciences/nanopack/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..cf5f0eaecff1e5a47c0eb5741ed9488673c2d1a4 --- /dev/null +++ b/LifeSciences/nanopack/build.sh @@ -0,0 +1,55 @@ +#!/bin/bash +set -e +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./nanopack_dep_install.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + +if [[ ! "$1" =~ ^/.* || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi + +create_dir() +{ + local path=$1 + [[ "$path" =~ .*/$ ]] && path=${path%/*} + if [[ ! -d "$path" && ! -f "$path" ]]; then mkdir -p $path; else path=$path`date "+%y%m%d%H%M%S"` && mkdir -p $path; fi + echo $path +} + +buildpath=$(create_dir $1) +installpath=$(create_dir $2) + +set -e +yum install -y m4 environment-modules systemd-devel +source /etc/profile +module purge + +dep_dir="dependency" +bash $dep_dir/bisheng-compiler-2.1.0.sh $buildpath $installpath +module use $installpath/bisheng-compiler-2.1.0 +module load $installpath/bisheng-compiler-2.1.0/bisheng_modulefiles + +bash $dep_dir/Python3.sh $buildpath $installpath + +bash nanopack.sh + +source /etc/profile +mkdir -p pkg/nanopack-hpc && cp -r $installpath/* pkg/nanopack-hpc/ +cat>"pkg/nanopack-hpc/run.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! \$d =~ "nanopack" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done +EOF +cd pkg/ && tar zcvf nanopack-hpc.tar.gz nanopack-hpc + +rm -rf $buildpath $installpath + diff --git a/LifeSciences/nanopack/dependency/Python3.sh b/LifeSciences/nanopack/dependency/Python3.sh new file mode 100644 index 0000000000000000000000000000000000000000..f516f4b74ba15dee3257b852801773a5742de9e5 --- /dev/null +++ b/LifeSciences/nanopack/dependency/Python3.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./Python3.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi + +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi +if [[ "$buildpath" = "$installpath" ]]; then echo "构建路径和安装路径相同,请重新输入"; exit 1; fi + +set -e +yum install -y gcc make wget openssl openssl-devel readline readline-devel zlib* libffi-devel tar + +wget -t 0 -c -P $buildpath https://www.python.org/ftp/python/3.8.2/Python-3.8.2.tgz +tar -xvf $buildpath/Python-3.8.2.tgz -C $buildpath && rm -rf $buildpath/Python-3.8.2.tgz +cd $buildpath/Python-3.8.2 + +./configure CC=clang CXX=clang++ FC=flang +make -j$(nproc) +make -j$(nproc) install + + +rm -rf $buildpath/Python-3.8.2 + diff --git a/LifeSciences/nanopack/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/nanopack/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..46756219d004f9fca427e4b233d8e8a40ab99f3b --- /dev/null +++ b/LifeSciences/nanopack/dependency/bisheng-compiler-2.1.0.sh @@ -0,0 +1,43 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash bisheng-compiler-2.1.0.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + +[[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]] && echo "请输入正确的构建路径" && exit 1 +[[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]] && echo "请输入正确的安装路径" && exit 1 + +buildpath=$1 +installpath=$2 +[[ "$buildpath" =~ .*/$ ]] && buildpath=${buildpath%/*} +[[ "$installpath" =~ .*/$ ]] && installpath=${installpath%/*} +if [[ "$buildpath" = "$installpath" ]]; then echo "构建路径和安装路径相同,请重新输入"; exit 1; fi +set -e +yum install -y wget tar environment-modules libatomic + +wget -t 0 -c -P $buildpath https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +tar xf $buildpath/bisheng-compiler-2.1.0-aarch64-linux.tar.gz -C $buildpath && rm -rf $buildpath/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +mkdir -p $installpath/bisheng-compiler-2.1.0 && cp -r $buildpath/bisheng-compiler-2.1.0-aarch64-linux/* $installpath/bisheng-compiler-2.1.0/ + +cat>"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles"<