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[CP2K] 给老爷机离线安装CP2K-2022.2的笔记

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发表于 Post on 2022-11-11 09:35:39 | 显示全部楼层 Show all |阅读模式 Reading model
本帖最后由 冰释之川 于 2023-1-26 19:50 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下载地址:
链接:https://pan.baidu.com/s/1fj9i-Wu1PVHAy8dCmQvJqA?pwd=1rjy
提取码:1rjy

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_online_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。
  1. ./install_online_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
  1. source ~/softwares/gcc9/env.sh
复制代码

这里附上install_online_gcc_9.3.0.sh里的代码供大家参考:
  1. #!/bin/bash
  2. #来自学术之友公众号的Tamas,我把7.1.0改成了9.3.0
  3. wget https://www.mpfr.org/mpfr-current/mpfr-4.1.0.tar.gz         
  4. wget http://mirrors.nju.edu.cn/gnu/mpc/mpc-1.2.0.tar.gz            
  5. wget http://mirrors.nju.edu.cn/gnu/gcc/gcc-9.3.0/gcc-9.3.0.tar.gz  
  6. wget https://ftp.gnu.org/pub/gnu/gmp/gmp-6.2.0.tar.bz2  
  7.            
  8. 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
  9.     true
  10. else
  11.   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."
  12.   exit 1
  13. fi

  14. gcc1=`gcc -dumpversion | awk '{split($0,a,"."); print a[1]}'`

  15. if [ $gcc1 -gt 9 ];then
  16.     echo "GCC version is higher than 9, no need to install gcc-9"
  17.     exit 1
  18. fi
  19.    
  20. read -p "Input installation directory for 9.3.0--->" gcc9dir
  21. # gcc9dir=/home/yjy/softwares/gcc9/

  22. if [ ! -n "$gcc9dir" ]; then
  23.   echo "Wrong: not a valid directory";
  24.   exit 1
  25. fi
  26. mkdir -p $gcc9dir
  27. if [ ! -d "$gcc9dir" ]; then
  28.   echo "Wrong: no permission or not a valid directory."
  29.   exit 1
  30. fi

  31. read -p "To use 9.3.0 after installation: source $gcc9dir/env.sh   hit ENTER to continue!" ok

  32. function install_needed(){
  33.     echo "installing gmp ..."
  34.     tar -jxvf  gmp-6.2.0.tar.bz2
  35.     cd gmp-6.2.0

  36.     CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/gmp-6.2.0
  37.     make
  38.     make install
  39.     export GMP_HOME=$gcc9dir/gmp-6.2.0
  40.     export PATH=$GMP_HOME/bin:$PATH
  41.     export LD_LIBRARY_PATH=$GMP_HOME/lib:$LD_LIBRARY_PATH
  42.     export INCLUDE=$GMP_HOME/include:$INCLUDE

  43.     cd ../
  44.     rm -rf gmp-6.2.0

  45.     echo "installing mpfr ..."
  46.     tar -zxvf mpfr-4.1.0.tar.gz
  47.     cd mpfr-4.1.0
  48.     CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/mpfr-4.1.0 --with-gmp=$GMP_HOME
  49.     make
  50.     make install

  51.     export MPFR_HOME=$gcc9dir/mpfr-4.1.0
  52.     export PATH=$MPFR_HOME/bin:$PATH
  53.     export LD_LIBRARY_PATH=$MPFR_HOME/lib:$LD_LIBRARY_PATH
  54.     export INCLUDE=$MPFR_HOME/include:$INCLUDE

  55.     cd ../
  56.     rm -rf mpfr-4.1.0

  57.     echo "installing mpc ..."
  58.     tar -zxvf mpc-1.2.0.tar.gz
  59.     cd mpc-1.2.0
  60.     CC=gcc CXX=g++ ./configure --prefix=$gcc9dir/mpc-1.2.0 --with-gmp=$GMP_HOME --with-mpfr=$MPFR_HOME
  61.     make
  62.     make install

  63.     export MPC_HOME=$gcc9dir/mpc-1.2.0
  64.     export PATH=$MPC_HOME/bin:$PATH
  65.     export LD_LIBRARY_PATH=$MPC_HOME/lib:$LD_LIBRARY_PATH
  66.     export INCLUDE=$MPC_HOME/include:$INCLUDE

  67.     cd ../
  68.     rm -rf mpc-1.2.0
  69. }

  70. install_needed

  71. #to prevent LIBRARY_PATH containing the current directory
  72. unset LIBRARY_PATH
  73. echo "installing gcc-9 ..."
  74. tar -zxvf gcc-9.3.0.tar.gz
  75. cd gcc-9.3.0
  76. 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

  77. make
  78. make install
  79. export GCC_HOME=$gcc9dir/gcc-9.3.0
  80. export PATH=$GCC_HOME/bin:$PATH
  81. export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBRARY_PATH
  82. export INCLUDE=$GCC_HOME/include:$INCLUDE
  83. cd ../
  84. rm -rf gcc-9.3.0

  85. echo "export GMP_HOME=$gcc9dir/gmp-6.2.0" >> $gcc9dir/env.sh
  86. echo 'export PATH=$GMP_HOME/bin:$PATH' >> $gcc9dir/env.sh
  87. echo 'export LD_LIBRARY_PATH=$GMP_HOME/lib:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
  88. echo 'export INCLUDE=$GMP_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
  89. echo "export MPFR_HOME=$gcc9dir/mpfr-4.1.0" >> $gcc9dir/env.sh
  90. echo 'export PATH=$MPFR_HOME/bin:$PATH' >> $gcc9dir/env.sh
  91. echo 'export LD_LIBRARY_PATH=$MPFR_HOME/lib:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
  92. echo 'export INCLUDE=$MPFR_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
  93. echo "export MPC_HOME=$gcc9dir/mpc-1.2.0" >> $gcc9dir/env.sh
  94. echo 'export PATH=$MPC_HOME/bin:$PATH' >> $gcc9dir/env.sh
  95. echo 'export LD_LIBRARY_PATH=$MPC_HOME/lib:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
  96. echo 'export INCLUDE=$MPC_HOME/include:$INCLUDE' >> $gcc9dir/env.sh
  97. echo "export GCC_HOME=$gcc9dir/gcc-9.3.0/" >> $gcc9dir/env.sh
  98. echo 'export PATH=$GCC_HOME/bin:$PATH' >> $gcc9dir/env.sh
  99. echo 'export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBRARY_PATH' >> $gcc9dir/env.sh
  100. echo 'export INCLUDE=$GCC_HOME/include:$INCLUDE' >> $gcc9dir/env.sh

  101. # gcc-9.3.0 in ~/.bashrc
  102. #source /home/yjy/softwares/gcc9/env.sh

  103. echo
  104. echo "######  Installation completed !  ######"
  105. 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

  1. tar -xvf cp2k-2022.2.tar.bz2
复制代码

(2)进入解压后的目录并且创建build文件夹:
  1. cd /home/yjy/softwares/cp2k-2022.2/tools/toolchain/
  2. mkdir build
复制代码
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:
  1. ./install_cp2k_toolchain.sh --with-sirius=no --with-openmpi=install --with-plumed=install
复制代码
你会看到如下编译信息:
  1. MPI is detected and it appears to be OpenMPI
  2. Compiling with 32 processes.
  3. ==================== Finding GCC from system paths ====================
  4. path to gcc is /home/yjy/softwares/gcc9//gcc-9.3.0//bin/gcc
  5. path to g++ is /home/yjy/softwares/gcc9//gcc-9.3.0//bin/g++
  6. path to gfortran is /home/yjy/softwares/gcc9//gcc-9.3.0//bin/gfortran
  7. Found include directory /usr/include
  8. Found lib directory /home/yjy/softwares/gcc9/gcc-9.3.0/lib64
  9. Step gcc took 0.00 seconds.
  10. Step intel took 0.00 seconds.
  11. ==================== Getting proc arch info using OpenBLAS tools ====================
  12. OpenBLAS-0.3.20.tar.gz is found
  13. OpenBLAS detected LIBCORE = zen
  14. OpenBLAS detected ARCH    = x86_64
  15. ==================== Installing CMake ====================
  16. cmake-3.22.1-linux-x86_64.sh is found
  17. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/cmake-3.22.1
  18. Step cmake took 1146.00 seconds.
  19. ==================== Installing OpenMPI ====================
  20. openmpi-4.1.1.tar.gz is found
  21. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1
  22. Found directory /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin
  23. Found directory /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/lib
  24. Found directory /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/include
  25. mpirun is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpirun
  26. mpicc is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpicc
  27. mpicxx is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpicxx
  28. mpif90 is installed as /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openmpi-4.1.1/bin/mpif90
  29. Step openmpi took 1490.00 seconds.
  30. ==================== Installing OpenBLAS ====================
  31. OpenBLAS-0.3.20.tar.gz is found
  32. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/openblas-0.3.20
  33. Step openblas took 351.00 seconds.
  34. ==================== Installing FFTW ====================
  35. fftw-3.3.10.tar.gz is found
  36. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/fftw-3.3.10
  37. Step fftw took 202.00 seconds.
  38. ==================== Installing LIBINT ====================
  39. libint-v2.6.0-cp2k-lmax-5.tgz is found
  40. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5
  41. Step libint took 1553.00 seconds.
  42. ==================== Installing LIBXC ====================
  43. libxc-5.2.3.tar.gz is found
  44. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxc-5.2.3
  45. Step libxc took 251.00 seconds.
  46. ==================== Installing Libxsmm ====================
  47. libxsmm-1.17.tar.gz is found
  48. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libxsmm-1.17
  49. Step libxsmm took 81.00 seconds.
  50. ==================== Installing ScaLAPACK ====================
  51. scalapack-2.1.0.tgz is found
  52. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/scalapack-2.1.0
  53. Step scalapack took 139.00 seconds.
  54. ==================== Installing COSMA ====================
  55. COSMA-v2.5.1.tar.gz is found
  56. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/COSMA-2.5.1
  57. Step cosma took 75.00 seconds.
  58. ==================== Installing ELPA ====================
  59. elpa-2021.11.002.tar.gz is found
  60. patching file nvcc_wrap
  61. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/elpa-2021.11.002/cpu
  62. Step elpa took 605.00 seconds.
  63. Step ptscotch took 0.00 seconds.
  64. Step superlu took 1.00 seconds.
  65. Step pexsi took 0.00 seconds.
  66. Step quip took 0.00 seconds.
  67. ==================== Installing gsl ====================
  68. gsl-2.7.tar.gz is found
  69. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/gsl-2.7
  70. Step gsl took 144.00 seconds.
  71. ==================== Installing PLUMED ====================
  72. plumed-src-2.8.0.tgz is found
  73. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/plumed-2.8.0
  74. Step plumed took 225.00 seconds.
  75. Step hdf5 took 0.00 seconds.
  76. Step libvdwxc took 0.00 seconds.
  77. ==================== Installing spglib ====================
  78. spglib-1.16.2.tar.gz is found
  79. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/spglib-1.16.2
  80. Step spglib took 9.00 seconds.
  81. ==================== Installing libvori ====================
  82. libvori-220621.tar.gz is found
  83. Installing from scratch into /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/libvori-220621
  84. Step libvori took 62.00 seconds.
  85. Step spfft took 0.00 seconds.
  86. Step spla took 0.00 seconds.
  87. Step sirius took 0.00 seconds.
  88. ==================== generating arch files ====================
  89. arch files can be found in the /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch subdirectory
  90. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.ssmp
  91. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_static.ssmp
  92. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.sdbg
  93. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_coverage.sdbg
  94. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.psmp
  95. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local.pdbg
  96. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_static.psmp
  97. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_warn.psmp
  98. Wrote /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/local_coverage.pdbg
  99. ========================== usage =========================
  100. Done!
  101. Now copy:
  102.   cp /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/arch/* to the cp2k/arch/ directory
  103. To use the installed tools and libraries and cp2k version
  104. compiled with it you will first need to execute at the prompt:
  105.   source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
  106. To build CP2K you should change directory:
  107.   cd cp2k/
  108.   make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"

  109. arch files for GPU enabled CUDA versions are named "local_cuda.*"
  110. arch files for GPU enabled HIP versions are named "local_hip.*"
  111. arch files for OpenCL (GPU) versions are named "local_opencl.*"
  112. arch files for coverage versions are named "local_coverage.*"

  113. Note that these pre-built arch files are for the GNU compiler, users have to adapt them for other compilers.
  114. It is possible to use the provided CP2K arch files as guidance.
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(4)编译CP2K本体:
  1. cp ./install/arch/* ../../arch/
  2. source ./install/setup && cd ../..
  3. make -j 32 ARCH=local VERSION="ssmp psmp"
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成功编译完后会有如下信息:
  1. /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++
  2. cd /home/yjy/softwares/cp2k-2022.2/exe/local; ln -sf cp2k.psmp cp2k_shell.psmp
  3. 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:
  1. #source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
  2. 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:
  1. source ~/softwares/gcc9/env.sh
  2. source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
  3. mpirun -np 4 cp2k.popt test.inp |tee test.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安装包与依赖库(安装流程见上文):
链接:https://pan.baidu.com/s/1OAF3XtCFtFNhpMe3EOpgZQ?pwd=b5c7
提取码:b5c7








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Stand on the shoulders of giants

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发表于 Post on 2022-11-12 11:22:42 | 显示全部楼层 Show all
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。

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計算化学の社畜

 楼主 Author| 发表于 Post on 2022-11-12 18:46:15 | 显示全部楼层 Show all
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
Stand on the shoulders of giants

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发表于 Post on 2022-11-19 17:43:18 | 显示全部楼层 Show all
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。
  1. 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++
  2. cd /public1/apps/cp2k202202/exe/local; ln -sf cp2k.psmp cp2k_shell.psmp
  3. cd /public1/apps/cp2k202202/exe/local; ln -sf cp2k.psmp cp2k.popt
复制代码
  1. (base) [root@master cp2k202202]#
  2. (base) [root@master cp2k202202]# cd exe/local/
  3. (base) [root@master local]# ls
  4. cp2k.popt        cp2k.sopt         dbt_tas_unittest.psmp  dumpdcd.psmp  grid_miniapp.psmp   libcp2k_unittest.psmp           parallel_rng_types_unittest.psmp
  5. cp2k.psmp        cp2k.ssmp         dbt_tas_unittest.ssmp  dumpdcd.ssmp  grid_miniapp.ssmp   libcp2k_unittest.ssmp           parallel_rng_types_unittest.ssmp
  6. cp2k_shell.psmp  dbm_miniapp.psmp  dbt_unittest.psmp      graph.psmp    grid_unittest.psmp  memory_utilities_unittest.psmp  xyz2dcd.psmp
  7. cp2k_shell.ssmp  dbm_miniapp.ssmp  dbt_unittest.ssmp      graph.ssmp    grid_unittest.ssmp  memory_utilities_unittest.ssmp  xyz2dcd.ssmp
  8. (base) [root@master local]# la
  9. bash: la: command not found...
  10. (base) [root@master local]# ls -lhtr
  11. total 2.0G
  12. -rwxr-xr-x 1 root root 2.1M Nov 18 21:08 graph.ssmp
  13. -rwxr-xr-x 1 root root 121K Nov 18 21:08 memory_utilities_unittest.ssmp
  14. -rwxr-xr-x 1 root root 1.2M Nov 18 21:08 dbm_miniapp.ssmp
  15. -rwxr-xr-x 1 root root 3.2M Nov 18 21:08 parallel_rng_types_unittest.ssmp
  16. -rwxr-xr-x 1 root root 8.7M Nov 18 21:08 dbt_tas_unittest.ssmp
  17. -rwxr-xr-x 1 root root 2.1M Nov 18 21:08 graph.psmp
  18. -rwxr-xr-x 1 root root 121K Nov 18 21:08 memory_utilities_unittest.psmp
  19. -rwxr-xr-x 1 root root 1.2M Nov 18 21:08 dbm_miniapp.psmp
  20. -rwxr-xr-x 1 root root 3.8M Nov 18 21:08 parallel_rng_types_unittest.psmp
  21. -rwxr-xr-x 1 root root 9.7M Nov 18 21:08 dbt_tas_unittest.psmp
  22. -rwxr-xr-x 1 root root  11M Nov 18 21:09 dbt_unittest.ssmp
  23. -rwxr-xr-x 1 root root  12M Nov 18 21:09 dbt_unittest.psmp
  24. -rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_miniapp.ssmp
  25. -rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_unittest.ssmp
  26. -rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_unittest.psmp
  27. -rwxr-xr-x 1 root root 3.5M Nov 18 21:09 grid_miniapp.psmp
  28. -rwxr-xr-x 1 root root 997K Nov 18 21:16 dumpdcd.ssmp
  29. -rwxr-xr-x 1 root root 941K Nov 18 21:16 xyz2dcd.ssmp
  30. -rwxr-xr-x 1 root root 293M Nov 18 21:16 libcp2k_unittest.ssmp
  31. -rwxr-xr-x 1 root root 293M Nov 18 21:16 cp2k.ssmp
  32. lrwxrwxrwx 1 root root    9 Nov 18 21:16 cp2k.sopt -> cp2k.ssmp
  33. lrwxrwxrwx 1 root root    9 Nov 18 21:16 cp2k_shell.ssmp -> cp2k.ssmp
  34. -rwxr-xr-x 1 root root 997K Nov 18 21:16 dumpdcd.psmp
  35. -rwxr-xr-x 1 root root 941K Nov 18 21:16 xyz2dcd.psmp
  36. -rwxr-xr-x 1 root root 668M Nov 18 21:16 libcp2k_unittest.psmp
  37. -rwxr-xr-x 1 root root 668M Nov 18 21:16 cp2k.psmp
  38. lrwxrwxrwx 1 root root    9 Nov 18 21:16 cp2k_shell.psmp -> cp2k.psmp
  39. lrwxrwxrwx 1 root root    9 Nov 18 21:16 cp2k.popt -> cp2k.psmp
  40. (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

  1. ------------------------------- Errors ---------------------------------


  2. ------------------------------- Timings --------------------------------
  3. Plot: name="timings", title="Timing Distribution", ylabel="time [s]"
  4. PlotPoint: name="100th_percentile", plot="timings", label="100th %ile", y=55.89, yerr=0.0
  5. PlotPoint: name="99th_percentile", plot="timings", label="99th %ile", y=23.38, yerr=0.0
  6. PlotPoint: name="98th_percentile", plot="timings", label="98th %ile", y=16.99, yerr=0.0
  7. PlotPoint: name="95th_percentile", plot="timings", label="95th %ile", y=10.95, yerr=0.0
  8. PlotPoint: name="90th_percentile", plot="timings", label="90th %ile", y=8.01, yerr=0.0
  9. PlotPoint: name="80th_percentile", plot="timings", label="80th %ile", y=4.84, yerr=0.0

  10. ------------------------------- Summary --------------------------------
  11. Number of FAILED  tests 0
  12. Number of WRONG   tests 0
  13. Number of CORRECT tests 3719
  14. Total number of   tests 3719

  15. Summary: correct: 3719 / 3719; 24min
  16. Status: OK

  17. *************************** Testing ended *****************************
  18. [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。
  1. [huan@master cp2k202202]$ make -j 8 ARCH=local VERSION=psmp test
  2. Discovering programs ...
  3. make -C /public2/huan/cp2k202202/exts/dbcsr -f /public2/huan/cp2k202202/exts/build_dbcsr/Makefile \
  4.    ARCHFILE=/public2/huan/cp2k202202/arch/local.psmp \
  5.    LIBDIR=/public2/huan/cp2k202202/lib/local/psmp/exts/dbcsr \
  6.    OBJDIR=/public2/huan/cp2k202202/obj/local/psmp/exts/dbcsr \
  7.    USE_ACCEL="" \
  8.    ACC="" \
  9.    ACCFLAGS=""
  10. Removing stale archives for psmp ...
  11. Removing stale archives ...
  12. Resolving dependencies ...
  13. Resolving dependencies for psmp ...
  14. echo git:a95ec40 > "/public2/huan/cp2k202202/obj/git-ref.tmp"
  15. --------------------------- GIT ------------------------------------------
  16. CommitSHA: <N/A>
  17. --------------------------- Resource limits ------------------------------
  18. RESOURCE   DESCRIPTION                             SOFT      HARD UNITS
  19. AS         address space limit                unlimited unlimited bytes
  20. CORE       max core file size                         0 unlimited blocks
  21. CPU        CPU time                           unlimited unlimited seconds
  22. DATA       max data size                      unlimited unlimited bytes
  23. FSIZE      max file size                      unlimited unlimited blocks
  24. LOCKS      max number of file locks held      unlimited unlimited
  25. MEMLOCK    max locked-in-memory address space unlimited unlimited bytes
  26. MSGQUEUE   max bytes in POSIX mqueues            819200    819200 bytes
  27. NICE       max nice prio allowed to raise             0         0
  28. NOFILE     max number of open files                1024      4096
  29. NPROC      max number of processes                 4096    257124
  30. RSS        max resident set size              unlimited unlimited pages
  31. RTPRIO     max real-time priority                     0         0
  32. RTTIME     timeout for real-time tasks        unlimited unlimited microsecs
  33. SIGPENDING max number of pending signals         257124    257124
  34. STACK      max stack size                     unlimited unlimited bytes
  35. --------------------------- SELinux --------------------------------------
  36. SELinux is installed and is Disabled
  37. --------------------------- ARCH-file ------------------------------------
  38. CC          = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpicc
  39. CXX         = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpicxx
  40. AR          = ar -r
  41. FC          = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpif90
  42. LD          = /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpif90
  43. #
  44. 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  
  45. #
  46. 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
  47. #
  48. FCDEBFLAGS  = -fbacktrace -ffree-form -fimplicit-none -std=f2008
  49. 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)
  50. 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)
  51. CXXFLAGS    = -O2 -fPIC -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native --std=c++11 $(DFLAGS) -Wno-deprecated-declarations
  52. #
  53. 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'
  54. 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++
  55. #
  56. FYPPFLAGS   = -n --line-marker-format=gfortran5
  57. -------------------------- Build-Tools -----------------------------------
  58. make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
  59. =========== FC (psmp) ===========
  60. /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpif90 --version
  61. GNU Fortran (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
  62. Copyright (C) 2019 Free Software Foundation, Inc.
  63. This is free software; see the source for copying conditions.  There is NO
  64. warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

  65. =========== CC (psmp) ===========
  66. /public2/huan/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpicc --version
  67. gcc (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
  68. Copyright (C) 2019 Free Software Foundation, Inc.
  69. This is free software; see the source for copying conditions.  There is NO
  70. warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

  71. =========== AR (psmp) ===========
  72. ar V
  73. GNU ar version 2.32-16.el7
  74. Copyright (C) 2019 Free Software Foundation, Inc.
  75. This program is free software; you may redistribute it under the terms of
  76. the GNU General Public License version 3 or (at your option) any later version.
  77. This program has absolutely no warranty.

  78. ========== Make (psmp) ==========
  79. make --version
  80. GNU Make 3.82
  81. Built for x86_64-redhat-linux-gnu
  82. Copyright (C) 2010  Free Software Foundation, Inc.
  83. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
  84. This is free software: you are free to change and redistribute it.
  85. There is NO WARRANTY, to the extent permitted by law.

  86. ========= Python (psmp) =========
  87. /usr/bin/env python3 --version
  88. Python 3.8.7
  89. ----------------------- External Modules ---------------------------------
  90. make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
  91. DBCSR Version: 2.3.0 (2022-06-26)
  92. ---------------------------- Modules -------------------------------------
  93. No Modulefiles Currently Loaded.
  94. *************************** Testing started ****************************
  95. --------------------------------------------------------------------------
  96. Primary job  terminated normally, but 1 process returned
  97. a non-zero exit code. Per user-direction, the job has been aborted.
  98. --------------------------------------------------------------------------
  99. --------------------------------------------------------------------------
  100. mpiexec noticed that process rank 1 with PID 0 on node master exited on signal 11 (Segmentation fault).
  101. --------------------------------------------------------------------------

  102. Could not parse feature flags.
  103. make[3]: *** [test] Error 1
  104. make[2]: *** [test] Error 2
  105. make[1]: *** [psmp] Error 2
  106. make: *** [test] Error 2
  107. [huan@master cp2k202202]$
  108. [huan@master cp2k202202]$
复制代码




用 H2O-32.inp 作为输入文件测试,也是如此报错

  1. --------------------------------------------------------------------------
  2. Primary job  terminated normally, but 1 process returned
  3. a non-zero exit code. Per user-direction, the job has been aborted.
  4. --------------------------------------------------------------------------
  5. --------------------------------------------------------------------------
  6. mpirun noticed that process rank 1 with PID 0 on node node05 exited on signal 11 (Segmentation fault).
  7. --------------------------------------------------------------------------
复制代码



不清楚原因是什么……


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計算化学の社畜

 楼主 Author| 发表于 Post on 2022-11-19 20:09:02 | 显示全部楼层 Show all
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, ...
  1. source ~/softwares/gcc9/env.sh
  2. source /home/yjy/softwares/cp2k-2022.2/tools/toolchain/install/setup
  3. mpirun -np 4 cp2k.popt test.inp |tee test.out
复制代码


你是按照上面三行命令这么运行的吗?
Stand on the shoulders of giants

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发表于 Post on 2022-11-19 22:52:40 | 显示全部楼层 Show all
用singularity是不是更方便一点?

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发表于 Post on 2022-11-20 15:08:18 | 显示全部楼层 Show all
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

  1. ./install_cp2k_toolchain.sh --math-mode=mkl --with-gcc=install --with-openmpi=install --with-pexsi=install --with-plumed=install
复制代码



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

  1. make -j 16 ARCH=local VERSION=psmp test
复制代码


结果如下:


  1. ------------------------------- Timings --------------------------------
  2. Plot: name="timings", title="Timing Distribution", ylabel="time [s]"
  3. PlotPoint: name="100th_percentile", plot="timings", label="100th %ile", y=402.30, yerr=0.0
  4. PlotPoint: name="99th_percentile", plot="timings", label="99th %ile", y=402.19, yerr=0.0
  5. PlotPoint: name="98th_percentile", plot="timings", label="98th %ile", y=402.19, yerr=0.0
  6. PlotPoint: name="95th_percentile", plot="timings", label="95th %ile", y=402.10, yerr=0.0
  7. PlotPoint: name="90th_percentile", plot="timings", label="90th %ile", y=402.09, yerr=0.0
  8. PlotPoint: name="80th_percentile", plot="timings", label="80th %ile", y=292.11, yerr=0.0

  9. ------------------------------- Summary --------------------------------
  10. Number of FAILED  tests 53
  11. Number of WRONG   tests 0
  12. Number of CORRECT tests 345
  13. Total number of   tests 398

  14. Summary: correct: 345 / 398; failed: 53; 288min
  15. Status: FAILED

  16. *************************** Testing ended ******************************
  17. make[3]: *** [test] Error 53
  18. make[2]: *** [test] Error 2
  19. make[1]: *** [psmp] Error 2
  20. make: *** [test] Error 2
  21. [huan[url=home.php?mod=space&uid=37877]@Master[/url] cp2k202202]$
复制代码


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:

  1. #!/bin/bash
  2. #PBS -N cp2k_H2O-32
  3. #PBS -l nodes=1:ppn=40
  4. #PBS -j n
  5. #PBS -e ${PBS_JOBNAME}.e
  6. #PBS -o ${PBS_JOBNAME}.o
  7. #PBS -q v5

  8. scl enable devtoolset-9 bash
  9. source /public1/apps/cp2k202202/tools/toolchain/install/setup

  10. cd $PBS_O_WORKDIR
  11. NP=`cat $PBS_NODEFILE|wc -l`

  12. EXEC=/public1/apps/cp2k202202/exe/local/cp2k.popt

  13. mpirun -np $NP -x OMP_NUM_THREADS=1 $EXEC -i H2O-32.inp -o H2O-32.out
复制代码


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……   -_____-!

  1. [huan@n8 H2O-32]$
  2. [huan@n8 H2O-32]$ ls
  3. H2O-32.inp
  4. [huan@n8 H2O-32]$
  5. [huan@n8 H2O-32]$
  6. [huan@n8 H2O-32]$ source /public1/apps/cp2k202202/tools/toolchain/install/setup
  7. [huan@n8 H2O-32]$
  8. [huan@n8 H2O-32]$ gcc -v
  9. Using built-in specs.
  10. COLLECT_GCC=gcc
  11. 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
  12. Target: x86_64-pc-linux-gnu
  13. 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
  14. Thread model: posix
  15. Supported LTO compression algorithms: zlib
  16. gcc version 12.1.0 (GCC)
  17. [huan@n8 H2O-32]$
  18. [huan@n8 H2O-32]$ which mpirun
  19. /public1/apps/cp2k202202/tools/toolchain/install/openmpi-4.1.1/bin/mpirun
  20. [huan@n8 H2O-32]$
  21. [huan@n8 H2O-32]$ mpirun -np 16 /public1/apps/cp2k202202/exe/local/cp2k.popt -i H2O-32.inp -o H2O-32.out
  22. [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)
  23. [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)
  24. --------------------------------------------------------------------------
  25. By default, for Open MPI 4.0 and later, infiniband ports on a device
  26. are not used by default.  The intent is to use UCX for these devices.
  27. You can override this policy by setting the btl_openib_allow_ib MCA parameter
  28. to true.

  29.   Local host:              n8
  30.   Local adapter:           hfi1_0
  31.   Local port:              1

  32. --------------------------------------------------------------------------
  33. --------------------------------------------------------------------------
  34. WARNING: There was an error initializing an OpenFabrics device.

  35.   Local host:   n8
  36.   Local device: hfi1_0
  37. --------------------------------------------------------------------------
  38. [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
  39. [n8:246223] 15 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected
  40. [n8:246223] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
  41. [n8:246223] 14 more processes have sent help message help-mpi-btl-openib.txt / error in device init
  42. [huan@n8 H2O-32]$
  43. [huan@n8 H2O-32]$
  44. [huan@n8 H2O-32]$ ls -lhtr
  45. total 208K
  46. -rw-r--r-- 1 huan huan 5.8K Nov 20  2022 H2O-32.inp
  47. -rw-rw-r-- 1 huan huan 1.6K Nov 20  2022 H2O-32-1.ener
  48. -rw-rw-r-- 1 huan huan  68K Nov 20  2022 H2O-32-pos-1.xyz
  49. -rw-rw-r-- 1 huan huan  20K Nov 20  2022 H2O-32-1.restart
  50. -rw-rw-r-- 1 huan huan 107K Nov 20  2022 H2O-32.out
  51. [huan@n8 H2O-32]$
  52. [huan@n8 H2O-32]$
复制代码


可以看到,上面的 .out 文件有内容,不为空

  1. [huan@n8 H2O-32]$ tail -20 H2O-32.out
  2. qs_scf_post_efg                     11  6.9    0.000    0.000    0.000    0.000
  3. qs_scf_post_local_stress            11  8.9    0.000    0.000    0.000    0.000
  4. qs_scf_post_molopt                  11  6.9    0.000    0.000    0.000    0.000
  5. qs_scf_post_local_energy            11  8.9    0.000    0.000    0.000    0.000
  6. topology_constraint_pack             1  3.0    0.000    0.000    0.000    0.000
  7. external_c_potential                22  5.9    0.000    0.000    0.000    0.000
  8. qs_scf_post_epr                     11  6.9    0.000    0.000    0.000    0.000
  9. write_mos_molden                    11  8.9    0.000    0.000    0.000    0.000
  10. check_diag                          50 13.0    0.000    0.000    0.000    0.000
  11. topology_generate_molecule           1  4.0    0.000    0.000    0.000    0.000
  12. -------------------------------------------------------------------------------

  13. The number of warnings for this run is : 52

  14. -------------------------------------------------------------------------------
  15.   **** **** ******  **  PROGRAM ENDED AT                 2022-11-20 14:57:26.690
  16. ***** ** ***  *** **   PROGRAM RAN ON                                        n8
  17. **    ****   ******    PROGRAM RAN BY                                      huan
  18. ***** **    ** ** **   PROGRAM PROCESS ID                                436612
  19.   **** **  *******  **  PROGRAM STOPPED IN     /public2/huan/testcp2k/H2O-32
复制代码


用 40 核就无法正常运行

  1. --------------------------------------------------------------------------
  2. MPI_INIT has failed because at least one MPI process is unreachable
  3. from another.  This *usually* means that an underlying communication
  4. plugin -- such as a BTL or an MTL -- has either not loaded or not
  5. allowed itself to be used.  Your MPI job will now abort.

  6. You may wish to try to narrow down the problem;

  7. * Check the output of ompi_info to see which BTL/MTL plugins are
  8.    available.
  9. * Run your application with MPI_THREAD_SINGLE.
  10. * Set the MCA parameter btl_base_verbose to 100 (or mtl_base_verbose,
  11.    if using MTL-based communications) to see exactly which
  12.    communication plugins were considered and/or discarded.
  13. --------------------------------------------------------------------------
复制代码


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。)

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发表于 Post on 2022-11-20 15:10:51 | 显示全部楼层 Show all
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……

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发表于 Post on 2022-11-20 18:35:41 | 显示全部楼层 Show all
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。

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 楼主 Author| 发表于 Post on 2022-11-21 08:38:15 | 显示全部楼层 Show all
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
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发表于 Post on 2022-11-21 10:55:44 | 显示全部楼层 Show all
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

  1. make -j 16 ARCH=local VERSION=psmp test
复制代码


不至于所以的测试项都不支持吧……

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 楼主 Author| 发表于 Post on 2022-11-21 11:35:30 | 显示全部楼层 Show all
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
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发表于 Post on 2022-11-21 19:29:44 | 显示全部楼层 Show all
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。

  1. -rwxr-xr-x 1 root root 2.1M Nov 20 10:43 graph.psmp
  2. -rwxr-xr-x 1 root root 119K Nov 20 10:44 memory_utilities_unittest.psmp
  3. -rwxr-xr-x 1 root root 3.5M Nov 20 10:44 parallel_rng_types_unittest.psmp
  4. -rwxr-xr-x 1 root root 1.1M Nov 20 10:44 dbm_miniapp.psmp
  5. -rwxr-xr-x 1 root root 8.9M Nov 20 10:44 dbt_tas_unittest.psmp
  6. -rwxr-xr-x 1 root root  11M Nov 20 10:44 dbt_unittest.psmp
  7. -rwxr-xr-x 1 root root 2.5M Nov 20 10:44 grid_miniapp.psmp
  8. -rwxr-xr-x 1 root root 2.5M Nov 20 10:44 grid_unittest.psmp
  9. -rwxr-xr-x 1 root root 981K Nov 20 10:50 dumpdcd.psmp
  10. -rwxr-xr-x 1 root root 929K Nov 20 10:50 xyz2dcd.psmp
  11. -rwxr-xr-x 1 root root 473M Nov 20 10:50 libcp2k_unittest.psmp
  12. -rwxr-xr-x 1 root root 473M Nov 20 10:50 cp2k.psmp
  13. lrwxrwxrwx 1 root root    9 Nov 20 10:50 cp2k_shell.psmp -> cp2k.psmp
  14. 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)。

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发表于 Post on 2022-11-24 11:52:10 | 显示全部楼层 Show all
求助在离线安装gcc的时候报错(系统CentOS6.5)
  1. dest=../../host-x86_64-pc-linux-gnu/gcc/include/tmp$-unwind.h; \
  2.         cp unwind.h $dest; \
  3.         chmod a+r $dest; \
  4.         sh ../.././libgcc/../move-if-change $dest ../../host-x86_64-pc-linux-gnu/gcc/include/unwind.h
  5. forrtl: No such file or directory
  6. 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
  7. Image              PC                Routine            Line        Source            
  8. sh                 00000000009F8D1D  Unknown               Unknown  Unknown
  9. sh                 00000000009F7825  Unknown               Unknown  Unknown
  10. sh                 000000000099F0C0  Unknown               Unknown  Unknown
  11. sh                 000000000094904F  Unknown               Unknown  Unknown
  12. sh                 0000000000948882  Unknown               Unknown  Unknown
  13. sh                 000000000095969D  Unknown               Unknown  Unknown
  14. sh                 00000000004207A0  Unknown               Unknown  Unknown
  15. sh                 0000000000401F5C  Unknown               Unknown  Unknown
  16. sh                 0000000000A035F1  Unknown               Unknown  Unknown
  17. sh                 0000000000401E21  Unknown               Unknown  Unknown
  18. make[3]: *** [install-unwind_h-forbuild] Error 29
  19. 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



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 楼主 Author| 发表于 Post on 2022-11-24 13:42:29 | 显示全部楼层 Show all
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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