diff --git a/LifeSciences/pymol/build.sh b/LifeSciences/pymol/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..99eff62b63a3766c3a1dcd0f3dc9b99abe30981e --- /dev/null +++ b/LifeSciences/pymol/build.sh @@ -0,0 +1,99 @@ +#!/bin/bash +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash build.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" =~ ^/.* || "$1" = "/" ]] && echo "请输入正确的构建路径" && exit 1 +[[ ! "$2" =~ ^/.* || "$2" = "/" ]] && echo "请输入正确的安装路径" && exit 1 + +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) + +yum install -y m4 environment-modules systemd-devel +source /etc/profile +module purge + +set -e +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/hmpi-1.1.1.sh $buildpath $installpath +module use $installpath/hmpi-1.1.1 +module load $installpath/hmpi-1.1.1/hmpi_modulefiles + +bash $dep_dir/zlib-1.2.11.sh $buildpath $installpath +module use $installpath/zlib-1.2.11 +module load $installpath/zlib-1.2.11/zlib_modulefiles + +bash $dep_dir/hdf5-1.12.1.sh $buildpath $installpath +module use $installpath/hdf5-1.12.1 +module load $installpath/hdf5-1.12.1/hdf5_modulefiles + +bash $dep_dir/pnetcdf-1.12.2.sh $buildpath $installpath +module use $installpath/pnetcdf-1.12.2 +module load $installpath/pnetcdf-1.12.2/pnetcdf_modulefiles + +bash $dep_dir/netcdf-c-4.8.1.sh $buildpath $installpath +module use $installpath/netcdf +module load $installpath/netcdf/netcdf_modulefiles + +bash $dep_dir/netcdf-fortran-4.5.3.sh $buildpath $installpath +module use $installpath/netcdf +module load $installpath/netcdf/netcdf_modulefiles + + +bash $dep_dir/GTest.sh $buildpath $installpath +bash $dep_dir/cJSON.sh $buildpath $installpath +bash $dep_dir/msgpack-c.sh $buildpath $installpath + +bash $dep_dir/mmtf-cpp.sh $buildpath $installpath + +bash $dep_dir/glm-0.9.9.8.sh $buildpath $installpath + +bash $dep_dir/Python-3.7.6.sh $buildpath $installpath + +#bash $dep_dir/PyQT5.sh $buildpath $installpath + +bash $dep_dir/Pmw.sh $buildpath $installpath + + +bash $dep_dir/pymol-v2.5.0.sh $buildpath $installpath + + +mkdir -p pkg/pymol-v2.5.0-hpc && cp -r $installpath/* pkg/pymol-v2.5.0-hpc/ +cat>"pkg/pymol-v2.5.0-hpc/run.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! \$d =~ "pymol" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done +cd \$current_dir +[[ ! -d "$installpath/hdf5-1.12.1/lib/" ]] && { +mkdir -p $installpath/hdf5-1.12.1/lib/; \ +ln -sf \$current_dir/hdf5-1.12.1/lib/libhdf5_hl.so $installpath/hdf5-1.12.1/lib/; \ +ln -sf \$current_dir/hdf5-1.12.1/lib/libhdf5.so $installpath/hdf5-1.12.1/lib/ +} +[[ ! -d "$installpath/hmpi-1.1.1" ]] && mkdir -p $installpath/hmpi-1.1.1 && cp -r \$current_dir/hmpi-1.1.1/* $installpath/hmpi-1.1.1/ +EOF +cd pkg/ && tar zcvf pymol-v2.5.0-hpc.tar.gz pymol-v2.5.0-hpc + +rm -rf $buildpath $installpath + diff --git a/LifeSciences/pymol/dependency/GTest.sh b/LifeSciences/pymol/dependency/GTest.sh new file mode 100644 index 0000000000000000000000000000000000000000..6f4d8019f8fc11dff6a02db594a74f6d2a8cf792 --- /dev/null +++ b/LifeSciences/pymol/dependency/GTest.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash msgpack-c.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=${installpath%/*} +[[ "$buildpath" == "$installpath" ]] && echo "构建路径与安装路径需为不同路径" && exit 1 + +set -e +yum install -y wget tar environment-modules cmake + +cd $buildpath +git clone https://github.com/google/googletest +cd googletest +export CC=clang +export CXX=clang++ +export FC=flang +cmake CMakeLists.txt +make +cp lib/libgtest*.a /usr/lib +cp -a googletest/include/gtest/ /usr/include/ + diff --git a/LifeSciences/pymol/dependency/Pmw.sh b/LifeSciences/pymol/dependency/Pmw.sh new file mode 100644 index 0000000000000000000000000000000000000000..daf6ca6372bdb803fd0d1fe969710839c5f2f096 --- /dev/null +++ b/LifeSciences/pymol/dependency/Pmw.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./Pmw.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 wget tar environment-modules libatomic + +wget -t 0 -c -P $buildpath https://udomain.dl.sourceforge.net/project/pmw/Pmw-2.1.tar.gz +tar -xvf $buildpath/Pmw-2.1.tar.gz -C $buildpath && rm -rf $buildpath/Pmw-2.1.tar.gz +cd $buildpath/Pmw-2.1 +/usr/local/bin/python3 setup.py build install + diff --git a/LifeSciences/pymol/dependency/PyQT5.sh b/LifeSciences/pymol/dependency/PyQT5.sh new file mode 100644 index 0000000000000000000000000000000000000000..4bf8318d448a03469cdba71f9ade38e234e1b8fa --- /dev/null +++ b/LifeSciences/pymol/dependency/PyQT5.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./PyQT5.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" = "$installpath" ]]; then echo "构建路径和安装路径相同,请重新输入"; exit 1; fi + +set -e +yum install -y wget tar environment-modules libatomic +yum groupinstall "Development Tools" -y +yum install -y qt5-qtbase qt5-qtbase-devel +yum install -y qt5-qtquickcontrols2-devel +yum install -y qt5-qtquickcontrols qt5-qtdeclarative-devel +yum install -y qt5* + +export PATH=/usr/lib64/qt5/bin/:$PATH + +/usr/local/bin/pip3 install PyQt5 + diff --git a/LifeSciences/pymol/dependency/Python-3.7.6.sh b/LifeSciences/pymol/dependency/Python-3.7.6.sh new file mode 100644 index 0000000000000000000000000000000000000000..88eda3e12818d26938cde8a4d15b148be49a9269 --- /dev/null +++ b/LifeSciences/pymol/dependency/Python-3.7.6.sh @@ -0,0 +1,30 @@ +#!/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 +yum install -y zlib-devel bzip2-devel ncurses-devel sqlite-devel tk-devel gdbm-devel xz-devel + +wget -t 0 -c -P $buildpath https://www.python.org/ftp/python/3.7.6/Python-3.7.6.tgz +tar -xvf $buildpath/Python-3.7.6.tgz -C $buildpath && rm -rf $buildpath/Python-3.7.6.tgz +cd $buildpath/Python-3.7.6 +./configure CC=clang CXX=clang++ FC=flang +make -j$(nproc) +make install + diff --git a/LifeSciences/pymol/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/pymol/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..a53069995751e081370ff3e2559fbc3b2dfd3f4c --- /dev/null +++ b/LifeSciences/pymol/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=${installpath%/*} +[[ "$buildpath" == "$installpath" ]] && echo "构建路径与安装路径需为不同路径" && exit 1 +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"<"$installpath/hdf5-1.12.1/hdf5_modulefiles"<"$installpath/hmpi-1.1.1/hmpi_modulefiles"<"$installpath/netcdf/netcdf_modulefiles"<"$installpath/pnetcdf-1.12.2/pnetcdf_modulefiles"<"$installpath/zlib-1.2.11/zlib_modulefiles"<"$installpath/pymol_modulefiles"<