给老爷机离线安装CP2K-2022.2的笔记

冰释之川 · 发表于 Post on 2022-11-11 09:35:39

本帖最后由冰释之川于 2023-3-5 18:16 编辑

由于北京科音的CP2K培训班马上就要开办了，这两天本人抽空把集群里的CP2K-9.1升级到最新版的CP2K-2022.2。

本次部署CP2K采用全离线方式安装(集群上安装居然没法自动下载工具链，太坑爹了。。我暂时没工夫调查原因，先pass了)
注意，安装CP2K-2022.2需要GCC 8以上的支持，老系统的小伙伴，需要额外安装新版gcc。

本笔记涉及到的软件包(cp2k-2022.2)下载地址：
链接：https://pan.baidu.com/s/1fj9i-Wu1PVHAy8dCmQvJqA?pwd=1rjy
提取码：1rjy

cp2k-2023.1安装包与依赖库(安装流程与cp2k-2022.2的安装流程一模一样)下载地址：
链接：https://pan.baidu.com/s/1OAF3XtCFtFNhpMe3EOpgZQ?pwd=b5c7
提取码：b5c7

夸克网盘下载地址：链接：https://pan.quark.cn/s/890fe6775a11
提取码：K76R

参考博文：
1. GCC一键安装/升级脚本参考(白嫖)学术之友公众号的Tamas分享的脚本：https://mp.weixin.qq.com/s/cugih07DXpRNo0hXkBd_LQ
2. CP2K安装过程参考(照搬)《CP2K第一性原理程序在CentOS中的简易安装方法》：http://sobereva.com/586

一、安装GCC 9.3 (不需要的同学直接忽视掉这一部分的安装)
(1)进入CP2K-2022.2/gcc_install目录，直接运行install_gcc_9.3.0.sh，这里安装gcc所需的4个工具包已经在同一目录下了，所以不需要再联网下载。

./install_gcc_9.3.0.sh

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这个脚本特别傻瓜，全程不需要人为干涉，你只需要设置一下gcc的安装位置即可，
在这里，我把gcc安装在/home/yjy/softwares/gcc9/目录下

(2)最后需要记住的是如何激活gcc，那就是

source ~/softwares/gcc9/env.sh

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这里附上install_gcc_9.3.0.sh里的代码供大家参考：

#!/bin/bash
#来自学术之友公众号的Tamas，我把7.1.0改成了9.3.0
#wget https://www.mpfr.org/mpfr-current/mpfr-4.1.0.tar.gz
#wget http://mirrors.nju.edu.cn/gnu/mpc/mpc-1.2.0.tar.gz
#wget http://mirrors.nju.edu.cn/gnu/gcc/gcc-9.3.0/gcc-9.3.0.tar.gz
#wget https://ftp.gnu.org/pub/gnu/gmp/gmp-6.2.0.tar.bz2
if [[ -f "mpfr-4.1.0.tar.gz" ]] && [[ -f "mpc-1.2.0.tar.gz" ]] && [[ -f "gcc-9.3.0.tar.gz" ]] && [[ -f "gmp-6.2.0.tar.bz2" ]] ;then
true
else
echo "One of mpfr-4.1.0.tar.gz,mpc-1.2.0.tar.gz,gmp-6.2.0.tar.bz2,gcc-9.3.0.tar.gz is missing."
exit 1
fi
#gcc1=`gcc -dumpversion | awk '{split($0,a,"."); print a[1]}'`
#if [ $gcc1 -gt 9 ];then
# echo "GCC version is higher than 9, no need to install gcc-9"
# exit 1
#fi
read -p "Input installation directory for 9.3.0--->" gcc9dir
# gcc9dir=/home/yjy/softwares/gcc9/
if [ ! -n "$gcc9dir" ]; then
echo "Wrong: not a valid directory";
exit 1
fi
mkdir -p $gcc9dir
if [ ! -d "$gcc9dir" ]; then
echo "Wrong: no permission or not a valid directory."
exit 1
fi
read -p "To use 9.3.0 after installation: source $gcc9dir/env.sh hit ENTER to continue!" ok
function install_needed(){
echo "installing gmp ..."
tar -jxvf gmp-6.2.0.tar.bz2
cd gmp-6.2.0
CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/gmp-6.2.0
make
make install
export GMP_HOME=$gcc9dir/gmp-6.2.0
export PATH=$GMP_HOME/bin:$PATH
export LD_LIBRARY_PATH=$GMP_HOME/lib:$LD_LIBRARY_PATH
export INCLUDE=$GMP_HOME/include:$INCLUDE
cd ../
rm -rf gmp-6.2.0
echo "installing mpfr ..."
tar -zxvf mpfr-4.1.0.tar.gz
cd mpfr-4.1.0
CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/mpfr-4.1.0 --with-gmp=$GMP_HOME
make
make install
export MPFR_HOME=$gcc9dir/mpfr-4.1.0
export PATH=$MPFR_HOME/bin:$PATH
export LD_LIBRARY_PATH=$MPFR_HOME/lib:$LD_LIBRARY_PATH
export INCLUDE=$MPFR_HOME/include:$INCLUDE
cd ../
rm -rf mpfr-4.1.0
echo "installing mpc ..."
tar -zxvf mpc-1.2.0.tar.gz
cd mpc-1.2.0
CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/mpc-1.2.0 --with-gmp=$GMP_HOME --with-mpfr=$MPFR_HOME
make
make install
export MPC_HOME=$gcc9dir/mpc-1.2.0
export PATH=$MPC_HOME/bin:$PATH
export LD_LIBRARY_PATH=$MPC_HOME/lib:$LD_LIBRARY_PATH
export INCLUDE=$MPC_HOME/include:$INCLUDE
cd ../
rm -rf mpc-1.2.0
}
install_needed
#to prevent LIBRARY_PATH containing the current directory
unset LIBRARY_PATH
echo "installing gcc-9 ..."
tar -zxvf gcc-9.3.0.tar.gz
cd gcc-9.3.0
CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/gcc-9.3.0 --with-gmp=$GMP_HOME --with-mpfr=$MPFR_HOME --with-mpc=$MPC_HOME --disable-multilib --enable-languages=c,c++,fortran
make
make install
export GCC_HOME=$gcc9dir/gcc-9.3.0
export PATH=$GCC_HOME/bin:$PATH
export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBRARY_PATH
export INCLUDE=$GCC_HOME/include:$INCLUDE
cd ../
rm -rf gcc-9.3.0
echo "export GMP_HOME=$gcc9dir/gmp-6.2.0" >> $gcc9dir/env.sh
echo 'export PATH=$GMP_HOME/bin:$PATH' >> $gcc9dir/env.sh
echo 'export LD_LIBRARY_PATH=$GMP_HOME/lib:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
echo 'export INCLUDE=$GMP_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
echo "export MPFR_HOME=$gcc9dir/mpfr-4.1.0" >> $gcc9dir/env.sh
echo 'export PATH=$MPFR_HOME/bin:$PATH' >> $gcc9dir/env.sh
echo 'export LD_LIBRARY_PATH=$MPFR_HOME/lib:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
echo 'export INCLUDE=$MPFR_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
echo "export MPC_HOME=$gcc9dir/mpc-1.2.0" >> $gcc9dir/env.sh
echo 'export PATH=$MPC_HOME/bin:$PATH' >> $gcc9dir/env.sh
echo 'export LD_LIBRARY_PATH=$MPC_HOME/lib:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
echo 'export INCLUDE=$MPC_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
echo "export GCC_HOME=$gcc9dir/gcc-9.3.0/" >> $gcc9dir/env.sh
echo 'export PATH=$GCC_HOME/bin:$PATH' >> $gcc9dir/env.sh
echo 'export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
echo 'export INCLUDE=$GCC_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
# gcc-9.3.0 in ~/.bashrc
#source /home/yjy/softwares/gcc9/env.sh
echo
echo "###### Installation completed ! ######"
echo

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二、编译安装CP2K-2022.2
(1)软件本体位于网盘CP2K-2022.2/cp2k-2022.2.tar.bz2，利用如下命令进行解压

tar -xvf cp2k-2022.2.tar.bz2

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(2)进入解压后的目录并且创建build文件夹：

cd /home/yjy/softwares/cp2k-2022.2/tools/toolchain/
mkdir build
cd ..

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然后将网盘下载的CP2K-2022.2/toolchains中的所有工具包复制到 build文件夹里

(3)编译部署工具链：

source ~/softwares/gcc9/env.sh
./install_cp2k_toolchain.sh --with-sirius=no --with-openmpi=install --with-plumed=install --with-gcc=system --with-intel=no

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你会看到如下编译信息：

MPI is detected and it appears to be OpenMPI
Compiling with 32 processes.
==================== Finding GCC from system paths ====================
path to gcc is /home/yjy/softwares/gcc9//gcc-9.3.0//bin/gcc
path to g++ is /home/yjy/softwares/gcc9//gcc-9.3.0//bin/g++
path to gfortran is /home/yjy/softwares/gcc9//gcc-9.3.0//bin/gfortran
Found include directory /usr/include
Found lib directory /home/yjy/softwares/gcc9/gcc-9.3.0/lib64
Step gcc took 0.00 seconds.
Step intel took 0.00 seconds.
==================== Getting proc arch info using OpenBLAS tools ====================
OpenBLAS-0.3.20.tar.gz is found
OpenBLAS detected LIBCORE = zen
OpenBLAS detected ARCH = x86_64
==================== Installing CMake ====================
cmake-3.22.1-linux-x86_64.sh is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/cmake-3.22.1
Step cmake took 1146.00 seconds.
==================== Installing OpenMPI ====================
openmpi-4.1.1.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1
Found directory /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin
Found directory /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/lib
Found directory /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/include
mpirun is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpirun
mpicc is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpicc
mpicxx is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpicxx
mpif90 is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpif90
Step openmpi took 1490.00 seconds.
==================== Installing OpenBLAS ====================
OpenBLAS-0.3.20.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openblas-0.3.20
Step openblas took 351.00 seconds.
==================== Installing FFTW ====================
fftw-3.3.10.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/fftw-3.3.10
Step fftw took 202.00 seconds.
==================== Installing LIBINT ====================
libint-v2.6.0-cp2k-lmax-5.tgz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5
Step libint took 1553.00 seconds.
==================== Installing LIBXC ====================
libxc-5.2.3.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxc-5.2.3
Step libxc took 251.00 seconds.
==================== Installing Libxsmm ====================
libxsmm-1.17.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxsmm-1.17
Step libxsmm took 81.00 seconds.
==================== Installing ScaLAPACK ====================
scalapack-2.1.0.tgz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/scalapack-2.1.0
Step scalapack took 139.00 seconds.
==================== Installing COSMA ====================
COSMA-v2.5.1.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/COSMA-2.5.1
Step cosma took 75.00 seconds.
==================== Installing ELPA ====================
elpa-2021.11.002.tar.gz is found
patching file nvcc_wrap
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/elpa-2021.11.002/cpu
Step elpa took 605.00 seconds.
Step ptscotch took 0.00 seconds.
Step superlu took 1.00 seconds.
Step pexsi took 0.00 seconds.
Step quip took 0.00 seconds.
==================== Installing gsl ====================
gsl-2.7.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/gsl-2.7
Step gsl took 144.00 seconds.
==================== Installing PLUMED ====================
plumed-src-2.8.0.tgz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/plumed-2.8.0
Step plumed took 225.00 seconds.
Step hdf5 took 0.00 seconds.
Step libvdwxc took 0.00 seconds.
==================== Installing spglib ====================
spglib-1.16.2.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/spglib-1.16.2
Step spglib took 9.00 seconds.
==================== Installing libvori ====================
libvori-220621.tar.gz is found
Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libvori-220621
Step libvori took 62.00 seconds.
Step spfft took 0.00 seconds.
Step spla took 0.00 seconds.
Step sirius took 0.00 seconds.
==================== generating arch files ====================
arch files can be found in the /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch subdirectory
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.ssmp
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_static.ssmp
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.sdbg
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_coverage.sdbg
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.psmp
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.pdbg
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_static.psmp
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_warn.psmp
Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_coverage.pdbg
========================== usage =========================
Done!
Now copy:
cp /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
To build CP2K you should change directory:
cd cp2k/
make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"
arch files for GPU enabled CUDA versions are named "local_cuda.*"
arch files for GPU enabled HIP versions are named "local_hip.*"
arch files for OpenCL (GPU) versions are named "local_opencl.*"
arch files for coverage versions are named "local_coverage.*"
Note that these pre-built arch files are for the GNU compiler, users have to adapt them for other compilers.
It is possible to use the provided CP2K arch files as guidance.

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(4)编译CP2K本体：

cp ./install/arch/* ../../arch/
source ./install/setup && cd ../..
make -j 32 ARCH=local VERSION="ssmp psmp"

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成功编译完后会有如下信息：

/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpif90 -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native -O3 -funroll-loops -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openblas-0.3.20/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/fftw-3.3.10/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxc-5.2.3/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxsmm-1.17/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/COSMA-2.5.1/include' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/elpa-2021.11.002/cpu/include/elpa_openmp-2021.11.002/modules' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/elpa-2021.11.002/cpu/include/elpa_openmp-2021.11.002/elpa' -I'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/gsl-2.7/include' -I/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/spglib-1.16.2/include -fbacktrace -ffree-form -fimplicit-none -std=f2008 -Werror=aliasing -Werror=ampersand -Werror=c-binding-type -Werror=intrinsic-shadow -Werror=intrinsics-std -Werror=line-truncation -Werror=tabs -Werror=target-lifetime -Werror=underflow -Werror=unused-but-set-variable -Werror=unused-variable -Werror=unused-dummy-argument -Werror=conversion -Werror=zerotrip -Wno-maybe-uninitialized -Wuninitialized -Wuse-without-only -D__LIBXSMM -D__parallel -D__FFTW3 -D__LIBINT -D__LIBXC -D__SCALAPACK -D__COSMA -D__ELPA -D__GSL -D__PLUMED2 -D__SPGLIB -D__LIBVORI -D__COMPILE_ARCH=""local"" -D__COMPILE_DATE=""Fri Nov 11 10:45:51 CST 2022"" -D__COMPILE_HOST=""master"" -D__COMPILE_REVISION=""git:a95ec40"" -D__DATA_DIR=""/home/yjy/softwares/cp2k-2022.2/data"" -Wl,--enable-new-dtags -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openblas-0.3.20/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openblas-0.3.20/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/fftw-3.3.10/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/fftw-3.3.10/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxc-5.2.3/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxc-5.2.3/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxsmm-1.17/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxsmm-1.17/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/scalapack-2.1.0/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/scalapack-2.1.0/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/COSMA-2.5.1/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/COSMA-2.5.1/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/elpa-2021.11.002/cpu/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/elpa-2021.11.002/cpu/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/gsl-2.7/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/gsl-2.7/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/plumed-2.8.0/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/plumed-2.8.0/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/spglib-1.16.2/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/spglib-1.16.2/lib' -L'/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libvori-220621/lib' -Wl,-rpath='/home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libvori-220621/lib' -L/home/yjy/softwares/cp2k-2022.2/lib/local/psmp -o /home/yjy/softwares/cp2k-2022.2/exe/local/cp2k.psmp cp2k.o -lcp2kstart -lcp2kmc -lcp2kswarm -lcp2kmotion -lcp2kthermostat -lcp2kemd -lcp2ktmc -lcp2kmain -lcp2kdbt -lcp2ktas -lcp2kdbm -lcp2kgrid -lcp2kgridcpu -lcp2kgridref -lcp2kgridcommon -ldbcsrarnoldi -ldbcsrx -lcp2kshg_int -lcp2keri_mme -lcp2kminimax -lcp2khfxbase -lcp2ksubsys -lcp2kxc -lcp2kao -lcp2kpw_env -lcp2kinput -lcp2kpw -lcp2kgpu -lcp2kfft -lcp2kfpga -lcp2kfm -lcp2kcommon -lcp2koffload -lcp2kmpiwrap -lcp2kbase -L/home/yjy/softwares/cp2k-2022.2/lib/local/psmp/exts/dbcsr -ldbcsr -lsymspg -lplumed -ldl -lstdc++ -lz -ldl -lgsl -lelpa_openmp -lcosma_prefixed_pxgemm -lcosma -lcosta -lscalapack -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lfftw3_mpi -lfftw3 -lfftw3_omp -lmpi -lopenblas -lvori -lstdc++ -lstdc++
cd /home/yjy/softwares/cp2k-2022.2/exe/local; ln -sf cp2k.psmp cp2k_shell.psmp
cd /home/yjy/softwares/cp2k-2022.2/exe/local; ln -sf cp2k.psmp cp2k.popt

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(5)把以下内容加入到~/.bashrc文件里：

#source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
export PATH=$PATH:/home/yjy/softwares/cp2k-2022.2/exe/local

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(6)利用网盘CP2K-2022.2/test目录下的测试文件进行测试：

source ~/softwares/gcc9/env.sh
source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
mpirun -np 32 cp2k.popt H2O-64.inp |tee H2O-64.out

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(7)网盘CP2K-2022.2/cp2kmonitor 文件是本人编写的监控CP2K几何优化输出的脚本，感兴趣的童鞋可以给它加上可执行权限后丢到/home/yjy/softwares/cp2k-2022.2/exe/local目录里使用
具体使用方法参见：《CP2K几何优化的监控/诊断小脚本-cp2kmonitor》：http://bbs.keinsci.com/thread-28109-1-1.html

附：cp2k-2023.1在ubuntu22-wsl1中的安装脚本[钟成老师(ggdh)亲情奉献]

#### cp2k-2023.1 在ubuntu22/wsl1中的安装
直接复制命令即可，手敲容易错。
1. 安装wsl ubuntu 22.04 版本
2. 从群附件中下载cp2k-2023.1.tar.bz2 (这个里面已经有预下载好的软件包，不要用官方版本），放桌面
3. 在桌面上shift+右键，打开命令行，启动wsl，把cp2k-2023.1.tar.bz2拷贝到家目录
```
wsl
cp cp2k-2023.1.tar.bz2 ~
cd ~
```
4. 安装gcc和cmake，并确认gcc版本是gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu1~22.04)
```
sudo apt-get update
sudo apt install build-essential cmake
gcc -v
```
5. 解压缩并安装ubuntu补丁
```
tar -jxvf cp2k-2023.1.tar.bz2
cd cp2k-2023.1/tools/toolchain
sudo sh install_requirements_ubuntu.sh
```
6. 安装
```
./install_cp2k_toolchain.sh --with-openmpi=install --with-cmake=system --with-gcc=system --with-sirius=no
```
7. 如果第6步出现错误，运行下面的命令，否则，略过此步，跳到第8步
```
rm -rf ./install/*
rm -rf ./build/*/
./install_cp2k_toolchain.sh --with-openmpi=install --with-cmake=system --with-gcc=system --with-sirius=no --target-cpu=generic
```
8. 编译程序本体（下面第三行命令，可能需要1小时左右）
```
cp ~/cp2k-2023.1/tools/toolchain/install/arch/* ~/cp2k-2023.1/arch/
cd ~/cp2k-2023.1
make -j ARCH=local VERSION="ssmp psmp"
```
9. 设置环境变量（下面4行命令一起复制粘贴即可）
```
echo "source ~/cp2k-2023.1/tools/toolchain/install/setup" >> ~/.bashrc
echo 'export PATH=~/cp2k-2023.1/exe/local:$PATH' >> ~/.bashrc
echo 'export CP2K_DATA_DIR=~/cp2k-2023.1/data' >> ~/.bashrc
source ~/.bashrc
```
10. 测试一下，下面的-np 4和OMP_NUM_THREADS=4可以改成电脑实际的物理核数。
```
cd ~/cp2k-2023.1/benchmarks/QS
mpirun -np 4 cp2k.popt H2O-32.inp
export OMP_NUM_THREADS=4
cp2k.ssmp H2O-32.inp
```
每次测试完成后，在最后找到类似如下的行：
```
------------------------------------------------------------------------
- -
- T I M I N G - - -
------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.016 0.016 44.940 44.940
qs_mol_dyn_low 1 2.0 0.002 0.002 44.754 44.754
qs_forces 11 3.9 0.001 0.001 44.727 44.727
qs_energies 11 4.9 0.000 0.000 40.268 40.268
```
其中CP2K哪一行的右边就是运行时间，我13900k的台式机，第一个测试时间是44秒，第二个测试是45秒
11. 打开文件夹
可能有小伙伴不知道怎么在windows中打开wsl系统下的文件夹，在命令行中输入下面的命令即可
```
explorer.exe .
```

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下载链接：https://pan.baidu.com/s/1Xdy-cJDI8gU-MhLzbTiN0Q?pwd=sb5o
提取码：sb5o

LittlePupil · 发表于 Post on 2022-11-12 11:22:42

关于没法自动下载的问题，在“./install_cp2k_toolchain.sh”后面加上“--no-check-certificate”选项或许会有帮助。

冰释之川 · 发表于 Post on 2022-11-12 18:46:15

LittlePupil 发表于 2022-11-12 11:22
关于没法自动下载的问题，在“./install_cp2k_toolchain.sh”后面加上“--no-check-certificate”选项或许 ...

或者直接注释掉脚本开头四行的下载链接，因为网盘里已经提供了四个依赖包

乐平 · 发表于 Post on 2022-11-19 17:43:18

本帖最后由乐平于 2022-11-19 17:52 编辑

怀着试一试的心情在 CentOS 7 系统（GCC 已经升级到 9.3.0）编译了 CP2K 2022.2。编译过程比以往 CP2K 8.1, 9.1 顺利。

rpath='/public1/apps/cp2k202202/tools/toolchain/install/sirius-7.3.1/lib' -L/public1/apps/cp2k202202/lib/local/psmp -o /public1/apps/cp2k202202/exe/local/cp2k.psmp cp2k.o -lcp2kstart -lcp2kmc -lcp2kswarm -lcp2kmotion -lcp2kthermostat -lcp2kemd -lcp2ktmc -lcp2kmain -lcp2kdbt -lcp2ktas -lcp2kdbm -lcp2kgrid -lcp2kgridcpu -lcp2kgridref -lcp2kgridcommon -ldbcsrarnoldi -ldbcsrx -lcp2kshg_int -lcp2keri_mme -lcp2kminimax -lcp2khfxbase -lcp2ksubsys -lcp2kxc -lcp2kao -lcp2kpw_env -lcp2kinput -lcp2kpw -lcp2kgpu -lcp2kfft -lcp2kfpga -lcp2kfm -lcp2kcommon -lcp2koffload -lcp2kmpiwrap -lcp2kbase -L/public1/apps/cp2k202202/lib/local/psmp/exts/dbcsr -ldbcsr -lsirius -lspla -lspfft -lsymspg -lhdf5 -lhdf5_hl -lz -lplumed -ldl -lstdc++ -lz -ldl -lgsl -lpexsi -lsuperlu_dist -lptscotchparmetis -lptscotch -lptscotcherr -lscotchmetis -lscotch -lscotcherr -lelpa_openmp -lcosma_prefixed_pxgemm -lcosma -lcosta -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lmpi -L/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 -Wl,-rpath=/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -Wl,--start-group -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64 -Wl,--end-group -lpthread -lm -ldl -lvori -lstdc++ -lstdc++
cd /public1/apps/cp2k202202/exe/local; ln -sf cp2k.psmp cp2k_shell.psmp
cd /public1/apps/cp2k202202/exe/local; ln -sf cp2k.psmp cp2k.popt

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(base) [root@master cp2k202202]#
(base) [root@master cp2k202202]# cd exe/local/
(base) [root@master local]# ls
cp2k.popt cp2k.sopt dbt_tas_unittest.psmp dumpdcd.psmp grid_miniapp.psmp libcp2k_unittest.psmp parallel_rng_types_unittest.psmp
cp2k.psmp cp2k.ssmp dbt_tas_unittest.ssmp dumpdcd.ssmp grid_miniapp.ssmp libcp2k_unittest.ssmp parallel_rng_types_unittest.ssmp
cp2k_shell.psmp dbm_miniapp.psmp dbt_unittest.psmp graph.psmp grid_unittest.psmp memory_utilities_unittest.psmp xyz2dcd.psmp
cp2k_shell.ssmp dbm_miniapp.ssmp dbt_unittest.ssmp graph.ssmp grid_unittest.ssmp memory_utilities_unittest.ssmp xyz2dcd.ssmp
(base) [root@master local]# la
bash: la: command not found...
(base) [root@master local]# ls -lhtr
total 2.0G
-rwxr-xr-x 1 root root 2.1M Nov 18 21:08 graph.ssmp
-rwxr-xr-x 1 root root 121K Nov 18 21:08 memory_utilities_unittest.ssmp
-rwxr-xr-x 1 root root 1.2M Nov 18 21:08 dbm_miniapp.ssmp
-rwxr-xr-x 1 root root 3.2M Nov 18 21:08 parallel_rng_types_unittest.ssmp
-rwxr-xr-x 1 root root 8.7M Nov 18 21:08 dbt_tas_unittest.ssmp
-rwxr-xr-x 1 root root 2.1M Nov 18 21:08 graph.psmp
-rwxr-xr-x 1 root root 121K Nov 18 21:08 memory_utilities_unittest.psmp
-rwxr-xr-x 1 root root 1.2M Nov 18 21:08 dbm_miniapp.psmp
-rwxr-xr-x 1 root root 3.8M Nov 18 21:08 parallel_rng_types_unittest.psmp
-rwxr-xr-x 1 root root 9.7M Nov 18 21:08 dbt_tas_unittest.psmp
-rwxr-xr-x 1 root root 11M Nov 18 21:09 dbt_unittest.ssmp
-rwxr-xr-x 1 root root 12M Nov 18 21:09 dbt_unittest.psmp
-rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_miniapp.ssmp
-rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_unittest.ssmp
-rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_unittest.psmp
-rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_miniapp.psmp
-rwxr-xr-x 1 root root 997K Nov 18 21:16 dumpdcd.ssmp
-rwxr-xr-x 1 root root 941K Nov 18 21:16 xyz2dcd.ssmp
-rwxr-xr-x 1 root root 293M Nov 18 21:16 libcp2k_unittest.ssmp
-rwxr-xr-x 1 root root 293M Nov 18 21:16 cp2k.ssmp
lrwxrwxrwx 1 root root 9 Nov 18 21:16 cp2k.sopt -> cp2k.ssmp
lrwxrwxrwx 1 root root 9 Nov 18 21:16 cp2k_shell.ssmp -> cp2k.ssmp
-rwxr-xr-x 1 root root 997K Nov 18 21:16 dumpdcd.psmp
-rwxr-xr-x 1 root root 941K Nov 18 21:16 xyz2dcd.psmp
-rwxr-xr-x 1 root root 668M Nov 18 21:16 libcp2k_unittest.psmp
-rwxr-xr-x 1 root root 668M Nov 18 21:16 cp2k.psmp
lrwxrwxrwx 1 root root 9 Nov 18 21:16 cp2k_shell.psmp -> cp2k.psmp
lrwxrwxrwx 1 root root 9 Nov 18 21:16 cp2k.popt -> cp2k.psmp
(base) [root@master local]#

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用 make -j 8 ARCH=local VERSION="ssmp psmp" test 命令测试的时候却遇到问题…… ssmp 顺利通过所有测试，如下

------------------------------- Errors ---------------------------------
------------------------------- Timings --------------------------------
Plot: name="timings", title="Timing Distribution", ylabel="time [s]"
PlotPoint: name="100th_percentile", plot="timings", label="100th %ile", y=55.89, yerr=0.0
PlotPoint: name="99th_percentile", plot="timings", label="99th %ile", y=23.38, yerr=0.0
PlotPoint: name="98th_percentile", plot="timings", label="98th %ile", y=16.99, yerr=0.0
PlotPoint: name="95th_percentile", plot="timings", label="95th %ile", y=10.95, yerr=0.0
PlotPoint: name="90th_percentile", plot="timings", label="90th %ile", y=8.01, yerr=0.0
PlotPoint: name="80th_percentile", plot="timings", label="80th %ile", y=4.84, yerr=0.0
------------------------------- Summary --------------------------------
Number of FAILED tests 0
Number of WRONG tests 0
Number of CORRECT tests 3719
Total number of tests 3719
Summary: correct: 3719 / 3719; 24min
Status: OK
*************************** Testing ended *****************************
[huan[url=home.php?mod=space&uid=37877]@Master[/url] cp2k202202]#

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但是，smp 却无法运行，不知道为何。

[huan@master cp2k202202]$ make -j 8 ARCH=local VERSION=psmp test
Discovering programs ...
make -C /public2/huan/cp2k202202/exts/dbcsr -f /public2/huan/cp2k202202/exts/build_dbcsr/Makefile \
ARCHFILE=/public2/huan/cp2k202202/arch/local.psmp \
LIBDIR=/public2/huan/cp2k202202/lib/local/psmp/exts/dbcsr \
OBJDIR=/public2/huan/cp2k202202/obj/local/psmp/exts/dbcsr \
USE_ACCEL="" \
ACC="" \
ACCFLAGS=""
Removing stale archives for psmp ...
Removing stale archives ...
Resolving dependencies ...
Resolving dependencies for psmp ...
echo git:a95ec40 > "/public2/huan/cp2k202202/obj/git-ref.tmp"
--------------------------- GIT ------------------------------------------
CommitSHA: <N/A>
--------------------------- Resource limits ------------------------------
RESOURCE DESCRIPTION SOFT HARD UNITS
AS address space limit unlimited unlimited bytes
CORE max core file size 0 unlimited blocks
CPU CPU time unlimited unlimited seconds
DATA max data size unlimited unlimited bytes
FSIZE max file size unlimited unlimited blocks
LOCKS max number of file locks held unlimited unlimited
MEMLOCK max locked-in-memory address space unlimited unlimited bytes
MSGQUEUE max bytes in POSIX mqueues 819200 819200 bytes
NICE max nice prio allowed to raise 0 0
NOFILE max number of open files 1024 4096
NPROC max number of processes 4096 257124
RSS max resident set size unlimited unlimited pages
RTPRIO max real-time priority 0 0
RTTIME timeout for real-time tasks unlimited unlimited microsecs
SIGPENDING max number of pending signals 257124 257124
STACK max stack size unlimited unlimited bytes
--------------------------- SELinux --------------------------------------
SELinux is installed and is Disabled
--------------------------- ARCH-file ------------------------------------
CC = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpicc
CXX = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpicxx
AR = ar -r
FC = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpif90
LD = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpif90
#
DFLAGS = -D__LIBXSMM -D__parallel -D__MKL -D__FFTW3 -D__SCALAPACK -D__LIBINT -D__LIBXC -D__COSMA -D__ELPA -D__LIBPEXSI -D__GSL -D__PLUMED2 -D__HDF5 -D__SPGLIB -D__LIBVORI -D__SPFFT -D__SPLA -D__SIRIUS
#
WFLAGS = -Werror=aliasing -Werror=ampersand -Werror=c-binding-type -Werror=intrinsic-shadow -Werror=intrinsics-std -Werror=line-truncation -Werror=tabs -Werror=target-lifetime -Werror=underflow -Werror=unused-but-set-variable -Werror=unused-variable -Werror=unused-dummy-argument -Werror=conversion -Werror=zerotrip -Wno-maybe-uninitialized -Wuninitialized -Wuse-without-only
#
FCDEBFLAGS = -fbacktrace -ffree-form -fimplicit-none -std=f2008
CFLAGS = -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native -O3 -funroll-loops $(PROFOPT) -I'/public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/include' -m64 -I/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/include -I/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/include/fftw -I'/public2/huan/cp2k202202/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/libxc-5.2.3/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/libxsmm-1.17/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/COSMA-2.5.1/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/elpa-2021.11.002/cpu/include/elpa_openmp-2021.11.002/modules' -I'/public2/huan/cp2k202202/tools/toolchain/install/elpa-2021.11.002/cpu/include/elpa_openmp-2021.11.002/elpa' -I'/public2/huan/cp2k202202/tools/toolchain/install/scotch-6.0.0/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/superlu_dist-6.1.0/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/pexsi-1.2.0/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/gsl-2.7/include' -I/public2/huan/cp2k202202/tools/toolchain/install/hdf5-1.12.0/include -I/public2/huan/cp2k202202/tools/toolchain/install/spglib-1.16.2/include -I'/public2/huan/cp2k202202/tools/toolchain/install/SpFFT-1.0.6/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/SpLA-1.5.4/include/spla' -I/public2/huan/cp2k202202/tools/toolchain/install/sirius-7.3.1/include -std=c11 -Wall -Wextra -Werror -Wno-vla-parameter -Wno-deprecated-declarations $(DFLAGS)
FCFLAGS = -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native -O3 -funroll-loops $(PROFOPT) -I'/public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/include' -m64 -I/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/include -I/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/include/fftw -I'/public2/huan/cp2k202202/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/libxc-5.2.3/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/libxsmm-1.17/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/COSMA-2.5.1/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/elpa-2021.11.002/cpu/include/elpa_openmp-2021.11.002/modules' -I'/public2/huan/cp2k202202/tools/toolchain/install/elpa-2021.11.002/cpu/include/elpa_openmp-2021.11.002/elpa' -I'/public2/huan/cp2k202202/tools/toolchain/install/scotch-6.0.0/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/superlu_dist-6.1.0/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/pexsi-1.2.0/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/gsl-2.7/include' -I/public2/huan/cp2k202202/tools/toolchain/install/hdf5-1.12.0/include -I/public2/huan/cp2k202202/tools/toolchain/install/spglib-1.16.2/include -I'/public2/huan/cp2k202202/tools/toolchain/install/SpFFT-1.0.6/include' -I'/public2/huan/cp2k202202/tools/toolchain/install/SpLA-1.5.4/include/spla' -I/public2/huan/cp2k202202/tools/toolchain/install/sirius-7.3.1/include $(FCDEBFLAGS) $(WFLAGS) $(DFLAGS)
CXXFLAGS = -O2 -fPIC -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native --std=c++11 $(DFLAGS) -Wno-deprecated-declarations
#
LDFLAGS = $(FCFLAGS) -Wl,--enable-new-dtags -L'/public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/libxc-5.2.3/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/libxc-5.2.3/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/libxsmm-1.17/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/libxsmm-1.17/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/COSMA-2.5.1/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/COSMA-2.5.1/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/elpa-2021.11.002/cpu/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/elpa-2021.11.002/cpu/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/scotch-6.0.0/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/scotch-6.0.0/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/superlu_dist-6.1.0/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/superlu_dist-6.1.0/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/pexsi-1.2.0/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/pexsi-1.2.0/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/gsl-2.7/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/gsl-2.7/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/plumed-2.8.0/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/plumed-2.8.0/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/hdf5-1.12.0/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/hdf5-1.12.0/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/spglib-1.16.2/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/spglib-1.16.2/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/libvori-220621/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/libvori-220621/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/SpFFT-1.0.6/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/SpFFT-1.0.6/lib' -L'/public2/huan/cp2k202202/tools/toolchain/install/sirius-7.3.1/lib' -Wl,-rpath='/public2/huan/cp2k202202/tools/toolchain/install/sirius-7.3.1/lib'
LIBS = -lsirius -lspla -lspfft -lsymspg -lhdf5 -lhdf5_hl -lz -lplumed -ldl -lstdc++ -lz -ldl -lgsl -lpexsi -lsuperlu_dist -lptscotchparmetis -lptscotch -lptscotcherr -lscotchmetis -lscotch -lscotcherr -lelpa_openmp -lcosma_prefixed_pxgemm -lcosma -lcosta -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lmpi -L/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 -Wl,-rpath=/public1/apps/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -Wl,--start-group -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64 -Wl,--end-group -lpthread -lm -ldl -lvori -lstdc++ -lstdc++
#
FYPPFLAGS = -n --line-marker-format=gfortran5
-------------------------- Build-Tools -----------------------------------
make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule.
=========== FC (psmp) ===========
/public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpif90 --version
GNU Fortran (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
=========== CC (psmp) ===========
/public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpicc --version
gcc (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
=========== AR (psmp) ===========
ar V
GNU ar version 2.32-16.el7
Copyright (C) 2019 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) any later version.
This program has absolutely no warranty.
========== Make (psmp) ==========
make --version
GNU Make 3.82
Built for x86_64-redhat-linux-gnu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
========= Python (psmp) =========
/usr/bin/env python3 --version
Python 3.8.7
----------------------- External Modules ---------------------------------
make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule.
DBCSR Version: 2.3.0 (2022-06-26)
---------------------------- Modules -------------------------------------
No Modulefiles Currently Loaded.
*************************** Testing started ****************************
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 1 with PID 0 on node master exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Could not parse feature flags.
make[3]: *** [test] Error 1
make[2]: *** [test] Error 2
make[1]: *** [psmp] Error 2
make: *** [test] Error 2
[huan@master cp2k202202]$
[huan@master cp2k202202]$

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用 H2O-32.inp 作为输入文件测试，也是如此报错

--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node node05 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

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不清楚原因是什么……

冰释之川 · 发表于 Post on 2022-11-19 20:09:02

乐平发表于 2022-11-19 17:43
怀着试一试的心情在 CentOS 7 系统（GCC 已经升级到 9.3.0）编译了 CP2K 2022.2。编译过程比以往 CP2K 8.1, ...

source ~/softwares/gcc9/env.sh
source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
mpirun -np 4 cp2k.popt test.inp |tee test.out

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你是按照上面三行命令这么运行的吗？

ghifi37 · 发表于 Post on 2022-11-19 22:52:40

用singularity是不是更方便一点？

乐平 · 发表于 Post on 2022-11-20 15:08:18

本帖最后由乐平于 2022-11-20 15:15 编辑

冰释之川发表于 2022-11-19 20:09
你是按照上面三行命令这么运行的吗？

我不是第一次编译 CP2K 了……
不这样设置的话，ssmp 测试也不可能通过呀

我重新加上 --with-gcc=install 编译

./install_cp2k_toolchain.sh --math-mode=mkl --with-gcc=install --with-openmpi=install --with-pexsi=install --with-plumed=install

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编译过程依旧很顺利，比之前 CP2K-8.1, CP2K-9.1 都顺利
编译结束后立即测试

make -j 16 ARCH=local VERSION=psmp test

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结果如下：

------------------------------- Timings --------------------------------
Plot: name="timings", title="Timing Distribution", ylabel="time [s]"
PlotPoint: name="100th_percentile", plot="timings", label="100th %ile", y=402.30, yerr=0.0
PlotPoint: name="99th_percentile", plot="timings", label="99th %ile", y=402.19, yerr=0.0
PlotPoint: name="98th_percentile", plot="timings", label="98th %ile", y=402.19, yerr=0.0
PlotPoint: name="95th_percentile", plot="timings", label="95th %ile", y=402.10, yerr=0.0
PlotPoint: name="90th_percentile", plot="timings", label="90th %ile", y=402.09, yerr=0.0
PlotPoint: name="80th_percentile", plot="timings", label="80th %ile", y=292.11, yerr=0.0
------------------------------- Summary --------------------------------
Number of FAILED tests 53
Number of WRONG tests 0
Number of CORRECT tests 345
Total number of tests 398
Summary: correct: 345 / 398; failed: 53; 288min
Status: FAILED
*************************** Testing ended ******************************
make[3]: *** [test] Error 53
make[2]: *** [test] Error 2
make[1]: *** [psmp] Error 2
make: *** [test] Error 2
[huan[url=home.php?mod=space&uid=37877]@Master[/url] cp2k202202]$

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有一部分任务测试失败。

但是提交任务的时候遇到很奇怪的现象。

pbs 脚本设置如下：

#!/bin/bash
#PBS -N cp2k_H2O-32
#PBS -l nodes=1:ppn=40
#PBS -j n
#PBS -e ${PBS_JOBNAME}.e
#PBS -o ${PBS_JOBNAME}.o
#PBS -q v5
scl enable devtoolset-9 bash
source /public1/apps/cp2k202202/tools/toolchain/install/setup
cd $PBS_O_WORKDIR
NP=`cat $PBS_NODEFILE|wc -l`
EXEC=/public1/apps/cp2k202202/exe/local/cp2k.popt
mpirun -np $NP -x OMP_NUM_THREADS=1 $EXEC -i H2O-32.inp -o H2O-32.out

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提交任务后，H2O-32.out 文件是空的，程序也会自动断掉。

但是，如果我直接登录到计算节点提交任务，则可以在 20 核的条件下运行，虽然会打印出一堆看不懂的内容…… -_____-！

[huan@n8 H2O-32]$
[huan@n8 H2O-32]$ ls
H2O-32.inp
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$ source /public1/apps/cp2k202202/tools/toolchain/install/setup
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/public1/apps/cp2k202202/tools/toolchain/install/gcc-12.1.0/libexec/gcc/x86_64-pc-linux-gnu/12.1.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /public1/apps/cp2k202202/tools/toolchain/build/gcc-12.1.0/configure --prefix=/public1/apps/cp2k202202/tools/toolchain/install/gcc-12.1.0 --libdir=/public1/apps/cp2k202202/tools/toolchain/install/gcc-12.1.0/lib --enable-languages=c,c++,fortran --disable-multilib --disable-bootstrap --enable-lto --enable-plugins
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 12.1.0 (GCC)
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$ which mpirun
/public1/apps/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpirun
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$ mpirun -np 16 /public1/apps/cp2k202202/exe/local/cp2k.popt -i H2O-32.inp -o H2O-32.out
[n8:246223] mca_base_component_repository_open: unable to open mca_plm_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
[n8:246223] mca_base_component_repository_open: unable to open mca_ras_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
--------------------------------------------------------------------------
By default, for Open MPI 4.0 and later, infiniband ports on a device
are not used by default. The intent is to use UCX for these devices.
You can override this policy by setting the btl_openib_allow_ib MCA parameter
to true.
Local host: n8
Local adapter: hfi1_0
Local port: 1
--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.
Local host: n8
Local device: hfi1_0
--------------------------------------------------------------------------
[n8:246223] [[25958,0],0] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file util/show_help.c at line 501
[n8:246223] 15 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected
[n8:246223] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[n8:246223] 14 more processes have sent help message help-mpi-btl-openib.txt / error in device init
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$ ls -lhtr
total 208K
-rw-r--r-- 1 huan huan 5.8K Nov 20 2022 H2O-32.inp
-rw-rw-r-- 1 huan huan 1.6K Nov 20 2022 H2O-32-1.ener
-rw-rw-r-- 1 huan huan 68K Nov 20 2022 H2O-32-pos-1.xyz
-rw-rw-r-- 1 huan huan 20K Nov 20 2022 H2O-32-1.restart
-rw-rw-r-- 1 huan huan 107K Nov 20 2022 H2O-32.out
[huan@n8 H2O-32]$
[huan@n8 H2O-32]$

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可以看到，上面的 .out 文件有内容，不为空

[huan@n8 H2O-32]$ tail -20 H2O-32.out
qs_scf_post_efg 11 6.9 0.000 0.000 0.000 0.000
qs_scf_post_local_stress 11 8.9 0.000 0.000 0.000 0.000
qs_scf_post_molopt 11 6.9 0.000 0.000 0.000 0.000
qs_scf_post_local_energy 11 8.9 0.000 0.000 0.000 0.000
topology_constraint_pack 1 3.0 0.000 0.000 0.000 0.000
external_c_potential 22 5.9 0.000 0.000 0.000 0.000
qs_scf_post_epr 11 6.9 0.000 0.000 0.000 0.000
write_mos_molden 11 8.9 0.000 0.000 0.000 0.000
check_diag 50 13.0 0.000 0.000 0.000 0.000
topology_generate_molecule 1 4.0 0.000 0.000 0.000 0.000
-------------------------------------------------------------------------------
The number of warnings for this run is : 52
-------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2022-11-20 14:57:26.690
***** ** *** *** ** PROGRAM RAN ON n8
** **** ****** PROGRAM RAN BY huan
***** ** ** ** ** PROGRAM PROCESS ID 436612
**** ** ******* ** PROGRAM STOPPED IN /public2/huan/testcp2k/H2O-32

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用 40 核就无法正常运行

--------------------------------------------------------------------------
MPI_INIT has failed because at least one MPI process is unreachable
from another. This *usually* means that an underlying communication
plugin -- such as a BTL or an MTL -- has either not loaded or not
allowed itself to be used. Your MPI job will now abort.
You may wish to try to narrow down the problem;
* Check the output of ompi_info to see which BTL/MTL plugins are
available.
* Run your application with MPI_THREAD_SINGLE.
* Set the MCA parameter btl_base_verbose to 100 (or mtl_base_verbose,
if using MTL-based communications) to see exactly which
communication plugins were considered and/or discarded.
--------------------------------------------------------------------------

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可能是集群上开启了超线程的原因？ （疑惑的是，CP2K-7.1 的时代是可以用 40 核并行计算的。）

乐平 · 发表于 Post on 2022-11-20 15:10:51

本帖最后由乐平于 2022-11-20 15:12 编辑

ghifi37 发表于 2022-11-19 22:52
用singularity是不是更方便一点？

emmmmmm……

如果您看过本论坛里 singularity 的超长帖子（docker-singularity方法安装可随意移植的cp2k - 第一性原理 (First Principle) - 计算化学公社 (keinsci.com)），我在里面有接近十层楼的讨论和回复，记录了我死活运行不起来的惨痛经历……

ghifi37 · 发表于 Post on 2022-11-20 18:35:41

乐平发表于 2022-11-20 15:10
emmmmmm……

如果您看过本论坛里 singularity 的超长帖子（docker-singularity方法安装可随意移植的cp ...

的确有这样的问题，我也遇到过换了很多linux发行版，不同编译器，死活在某台或某类机器上跑不起来的事。后来猜测可能是host安装singularity时的环境问题导致运行不起来……那样的话，可能就得折腾host了。

冰释之川 · 发表于 Post on 2022-11-21 08:38:15

本帖最后由冰释之川于 2022-11-21 08:41 编辑

乐平发表于 2022-11-20 15:08
我不是第一次编译 CP2K 了……
不这样设置的话，ssmp 测试也不可能通过呀

有没有可能一部分测试任务不支持popt版本？另外，如果集群开了超线程，设置MPI并行数的话，还是得看物理核数，不要看逻辑核数

乐平 · 发表于 Post on 2022-11-21 10:55:44

冰释之川发表于 2022-11-21 08:38
有没有可能一部分测试任务不支持popt版本？另外，如果集群开了超线程，设置MPI并行数的话，还是得看物理 ...

谢谢回复！

刚刚用论坛里 http://bbs.keinsci.com/forum.php ... mp;page=3#pid227334 的脚本确认了，集群没有开超线程。

不太理解您说的“不支持 popt 版本”…… 按理说测试任务，也就是编译好 CP2K 之后立即运行

make -j 16 ARCH=local VERSION=psmp test

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不至于所以的测试项都不支持吧……

冰释之川 · 发表于 Post on 2022-11-21 11:35:30

乐平发表于 2022-11-21 10:55
谢谢回复！

刚刚用论坛里 http://bbs.keinsci.com/forum.php?mod=viewthread&tid=32750&page=3#pid227 ...

Number of FAILED tests 53
Number of WRONG tests 0
Number of CORRECT tests 345
Total number of tests 398

这里不是大多数测试pass了吗

乐平 · 发表于 Post on 2022-11-21 19:29:44

冰释之川发表于 2022-11-21 11:35
Number of FAILED tests 53
Number of WRONG tests 0
Number of CORRECT tests 345

抱歉，是我表达有问题。

从最终编译的结果来看，cp2k.popt 实际上就是 cp2k.psmp 的软连接（如下所示），按理说应该是一样的。

-rwxr-xr-x 1 root root 2.1M Nov 20 10:43 graph.psmp
-rwxr-xr-x 1 root root 119K Nov 20 10:44 memory_utilities_unittest.psmp
-rwxr-xr-x 1 root root 3.5M Nov 20 10:44 parallel_rng_types_unittest.psmp
-rwxr-xr-x 1 root root 1.1M Nov 20 10:44 dbm_miniapp.psmp
-rwxr-xr-x 1 root root 8.9M Nov 20 10:44 dbt_tas_unittest.psmp
-rwxr-xr-x 1 root root 11M Nov 20 10:44 dbt_unittest.psmp
-rwxr-xr-x 1 root root 2.5M Nov 20 10:44 grid_miniapp.psmp
-rwxr-xr-x 1 root root 2.5M Nov 20 10:44 grid_unittest.psmp
-rwxr-xr-x 1 root root 981K Nov 20 10:50 dumpdcd.psmp
-rwxr-xr-x 1 root root 929K Nov 20 10:50 xyz2dcd.psmp
-rwxr-xr-x 1 root root 473M Nov 20 10:50 libcp2k_unittest.psmp
-rwxr-xr-x 1 root root 473M Nov 20 10:50 cp2k.psmp
lrwxrwxrwx 1 root root 9 Nov 20 10:50 cp2k_shell.psmp -> cp2k.psmp
lrwxrwxrwx 1 root root 9 Nov 20 10:50 cp2k.popt -> cp2k.psmp

复制代码

不懂为什么测试可以运行，但是通过 pbs 脚本提交任务，或者直接登录集群提交任务，都会遇到用 40 核运行的无法正常计算的问题（计算节点是双路 CPU，每个 CPU 的物理核心 20 核，共 40 核。没有开超线程）。

Oxygen · 发表于 Post on 2022-11-24 11:52:10

求助

在离线安装gcc的时候报错（系统CentOS6.5）

dest=../../host-x86_64-pc-linux-gnu/gcc/include/tmp$-unwind.h; \
cp unwind.h $dest; \
chmod a+r $dest; \
sh ../.././libgcc/../move-if-change $dest ../../host-x86_64-pc-linux-gnu/gcc/include/unwind.h
forrtl: No such file or directory
forrtl: severe (29): file not found, unit 1, file /backup/home/wsr/softpackge/gcc-7-source/gcc-7.1.0/x86_64-pc-linux-gnu/libgcc/sh.inp
Image PC Routine Line Source
sh 00000000009F8D1D Unknown Unknown Unknown
sh 00000000009F7825 Unknown Unknown Unknown
sh 000000000099F0C0 Unknown Unknown Unknown
sh 000000000094904F Unknown Unknown Unknown
sh 0000000000948882 Unknown Unknown Unknown
sh 000000000095969D Unknown Unknown Unknown
sh 00000000004207A0 Unknown Unknown Unknown
sh 0000000000401F5C Unknown Unknown Unknown
sh 0000000000A035F1 Unknown Unknown Unknown
sh 0000000000401E21 Unknown Unknown Unknown
make[3]: *** [install-unwind_h-forbuild] Error 29
make[3]: Leaving directory `/backup/home/wsr/softpackge/gcc-7-source/gcc-7.1.0/x86_64-pc-linux-gnu/libgcc'

复制代码

冰释之川 · 发表于 Post on 2022-11-24 13:42:29

Oxygen 发表于 2022-11-24 11:52
求助在离线安装gcc的时候报错（系统CentOS6.5）

我提供的是gcc9.3啊，你这怎么是gcc7?

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[CP2K] 给老爷机离线安装CP2K-2022.2的笔记

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