cp2k-9.1-GPU版本吐血整理安装全过程

xyyang0516

已于 2024-10-13 17:17:49 修改

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分类专栏： cp2k linux 文章标签：软件需求

于 2024-10-12 23:22:47 首次发布

本文链接：https://blog.csdn.net/xyyang0516/article/details/142891080

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参考各位大佬整理的安装过程，随后整理了一份完整的cp2k-9.1安装过程，如下所示：

先开始配置各种环境，编译环境：mkl2020+gcc11.3+openmpi

数学库采用intel mkl

source /xxx/intel2020/mkl/bin/mklvars.sh intel64

source /xxx/intel2020/parallel_studio_xe_2020/psxevars.sh

export PATH=/xxx/intel2020/compilers_and_libraries_2020.4.304/linux/mkl:$PATH

查看gcc g++ gfortran 这三个的版本

gcc -v

g++ -v

gfortran -v

确认cuda正常，nvcc -V

nvcc: NVIDIA (R) Cuda compiler driver

Built on Tue_May__3_18:49:52_PDT_2022

Cuda compilation tools, release 11.7, V11.7.64

Build cuda_11.7.r11.7/compiler.31294372_0

做完上述检查，先解压cp2k-9.1.tar.bz2

tar jxf cp2k-9.1.tar.bz2

cd /xxx /cp2k-9.1/tools/toolchain

编译所需插件，cp2k相关依赖包放在cp2k-9.1/tools/toolchain/build/中，有些包比较大，可以提前下载好(https://www.cp2k.org/static/downloads/)，放在该文件夹中

./install_cp2k_toolchain.sh --with-mkl=system --with-openmpi=install --with-cmake=system --with-libsmm=install --with-ptscotch=install --with-superlu=install --with-pexsi=install --with-plumed=install --enable-cuda=yes --gpu-ver=V100 -j 40

ps：openmpi我本身系统也装的有，还是选择install，不影响；其中gpu-ver根据./install_cp2k_toolchain.sh --help只有K20X, K40, K80, P100, V100可选，查询https://en.wikipedia.org/wiki/CUDA，选择一个和你显卡算力最接近的选项，我这里选V100，-j X，X指并行编译用的核数

MPI is detected and it appears to be OpenMPI

==================== Finding GCC from system paths ====================

path to gcc is /usr/bin/gcc

path to g++ is /usr/bin/g++

path to gfortran is /usr/bin/gfortran

Found include directory /usr/include

Step gcc took 0.00 seconds.

====================Getting proc arch info using OpenBLAS tools ====================

OpenBLAS-0.3.19.tar.gz is found

OpenBLAS detected LIBCORE = haswell

OpenBLAS detected ARCH = x86_64

==================== Installing CMake from system paths====================

cmake is found to be /xxx/cmake-3.24.1

Step cmake took 0.00 seconds.

==================== Installing OpenMPI ====================

openmpi-4.1.1.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/openmpi-4.1.1

Step openmpi took 440.00 seconds.

==================== Finding MKL from system paths ====================

MKLROOT is found to be /xxx/intel2020/compilers_and_libraries_2020.4.304/linux/mkl

libm is found in ld search path

libdl is found in ld search path

Step mkl took 0.00 seconds.

Step fftw took 0.00 seconds.

==================== Installing LIBINT ====================

libint-v2.6.0-cp2k-lmax-5.tgz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5

Step libint took 277.00 seconds.

==================== Installing LIBXC ====================

libxc-5.1.7.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/libxc-5.1.7

Step libxc took 53.00 seconds.

Step libsmm took 0.00 seconds.

==================== Installing Libxsmm ====================

libxsmm-1.17.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/libxsmm-1.17

Step libxsmm took 28.00 seconds.

Step scalapack took 0.00 seconds.

==================== Installing COSMA ====================

COSMA-v2.5.1.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/COSMA-2.5.1

Step cosma took 23.00 seconds.

==================== Installing ELPA ====================

elpa-2021.11.001.tar.gz is found

patching file nvcc_wrap

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu

Step elpa took 241.00 seconds.

==================== Installing PT-Scotch ====================

scotch_6.0.0.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/scotch-6.0.0

Step ptscotch took 4.00 seconds.

==================== Installing SuperLU_DIST ====================

superlu_dist_6.1.0.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/superlu_dist-6.1.0

Step superlu took 9.00 seconds.

==================== Installing PEXSI ====================

pexsi_v1.2.0.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/pexsi-1.2.0

Step pexsi took 80.00 seconds.

==================== Installing QUIP ====================

QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/quip-b4336484fb65b0e73211a8f920ae4361c7c353fd

Step quip took 241.00 seconds.

==================== Installing gsl ====================

gsl-2.7.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/gsl-2.7

Step gsl took 62.00 seconds.

==================== Installing PLUMED ====================

plumed-2.7.3.tgz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/plumed-2.7.3

Step plumed took 50.00 seconds.

==================== Installing hdf5 ====================

hdf5-1.12.0.tar.bz2 is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/hdf5-1.12.0

Step hdf5 took 114.00 seconds.

Step libvdwxc took 0.00 seconds.

==================== Installing spglib ====================

spglib-1.16.2.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/spglib-1.16.2

Step spglib took 6.00 seconds.

==================== Installing libvori ====================

libvori-210412.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/libvori-210412

Step libvori took 19.00 seconds.

==================== Installing spfft ====================

SpFFT-1.0.5.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/SpFFT-1.0.5

Step spfft took 5.00 seconds.

==================== Installing spla ====================

SpLA-1.5.2.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/SpLA-1.5.2

Step spla took 8.00 seconds.

==================== Installing SIRIUS ====================

sirius_7.3.0.tar.gz is found

Installing from scratch into /xxx/cp2k-9.1/tools/toolchain/install/sirius-7.3.0

patching file cmake/cudalibs_target.cmake

Step sirius took 67.00 seconds.

==================== generating arch files ====================

arch files can be found in the /xxx/cp2k-9.1/tools/toolchain/install/arch subdirectory

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local.ssmp

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local_static.ssmp

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local.sdbg

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local.psmp

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local.pdbg

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local_static.psmp

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local_warn.psmp

Wrote /xxx/cp2k-9.1/tools/toolchain/install/arch/local_coverage.pdbg

========================== usage =========================

Done!

Now copy:

cp /xxx/cp2k-9.1/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 /xxx/cp2k-9.1/tools/toolchain/install/setup

To build CP2K you should change directory:

cd cp2k/

make -j 96 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 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.

[xxx@elogin toolchain]$

接着把 /xxx/cp2k-9.1/tools/toolchain/install/arch/下所有文件拷到 /xxx/cp2k-9.1/arch目录下

cp /xxx/cp2k-9.1/tools/toolchain/install/arch/* /xxx/cp2k-9.1/arch/

然后运行

source /xxx/cp2k-9.1/tools/toolchain/install/setup

cd /xxx/cp2k-9.1

make -j X ARCH=local VERSION="ssmp sdbg psmp pdbg" X指并行编译用的核数，我设的30，大概20分钟左右，编译完最后会输出

cd /xxx/cp2k-9.1/exe/local; ln -sf cp2k.psmp cp2k_shell.psmp

cd /xxx/cp2k-9.1/exe/local; ln -sf cp2k.psmp cp2k.popt

测试 make -j 40 ARCH=local VERSION="ssmp sdbg psmp pdbg" test

--------------------------------- Summary --------------------------------

Number of FAILED tests 0

Number of WRONG tests 0

Number of CORRECT tests 3392

Total number of tests 3392

GREPME 0 0 3392 0 3392 X

Summary: correct: 3392 / 3392; 9min

Status: OK

--------------------------------------------------------------------------

Regtest took 526.00 seconds.

--------------------------------------------------------------------------

*************************** testing ended ********************************

配置环境

source /xxx/cp2k-8.1/tools/toolchain/install/setup

export PATH=/xxx/cp2k-8.1/exe/local: $PATH

执行安装依赖包过程中可能遇到的错误

（1）binutls 版本过旧，会导致 libxsmm 编译出现类似如下报错：

2528 /tmp/ccE3IUdy.s:131305: Error: no such instruction: `vcvtne2ps2bf16 %zmm9,%zmm11,%zmm5'

2529 /tmp/ccE3IUdy.s:131310: Error: no such instruction: `vcvtne2ps2bf16 %zmm15,%zmm0,%zmm13'

2530 /tmp/ccE3IUdy.s:131316: Error: no such instruction: `vcvtne2ps2bf16 %zmm4,%zmm3,%zmm6'

2531 /tmp/ccE3IUdy.s:131322: Error: no such instruction: `vcvtne2ps2bf16 %zmm8,%zmm7,%zmm2'

2532 /tmp/ccE3IUdy.s:131328: Error: no such instruction: `vcvtne2ps2bf16 %zmm1,%zmm12,%zmm10'

2533 /tmp/ccE3IUdy.s:131334: Error: no such instruction: `vcvtne2ps2bf16 %zmm11,%zmm14,%zmm9'

2534 /tmp/ccE3IUdy.s:131340: Error: no such instruction: `vcvtne2ps2bf16 %zmm0,%zmm5,%zmm15'

2535 /tmp/ccE3IUdy.s:131351: Error: no such instruction: `vcvtne2ps2bf16 %zmm3,%zmm13,%zmm4'

2536 /tmp/ccE3IUdy.s:131355: Error: no such instruction: `vcvtne2ps2bf16 %zmm7,%zmm6,%zmm8'

2537 /tmp/ccE3IUdy.s:131360: Error: no such instruction: `vcvtne2ps2bf16 %zmm12,%zmm2,%zmm1'

2538 /tmp/ccE3IUdy.s:131365: Error: no such instruction: `vcvtne2ps2bf16 %zmm14,%zmm10,%zmm11'

2539 /tmp/ccE3IUdy.s:131370: Error: no such instruction: `vcvtne2ps2bf16 %zmm5,%zmm9,%zmm0'

2540 /tmp/ccE3IUdy.s:131376: Error: no such instruction: `vcvtne2ps2bf16 %zmm13,%zmm15,%zmm3'

2541 /tmp/ccE3IUdy.s:131380: Error: no such instruction: `vcvtne2ps2bf16 %zmm6,%zmm4,%zmm7'

2542 /tmp/ccE3IUdy.s:131384: Error: no such instruction: `vcvtne2ps2bf16 %zmm2,%zmm8,%zmm12'

2543 make: [obj/intel64/libxsmm_dnn_rnncell_forward.o] Error 1 (ignored)

2544 make: *** [obj/intel64/libxsmm_dnn_rnncell_forward.o] Error 1

在这里，根据(cp2k9.1编译_mpi is detected and it appears to be intel mpi-CSDN博客)推文，通过给 make 加参数 INTRINSICS=1，即在/xxx/cp2k-9.1/tools/toolchain/scripts/stage4/install_libxsmm.sh 第 70 行以及第 76 添加 INTRINSICS=1 ，亲测可以解决该错误。

make INTRINSICS=1 -j $(get_nprocs) \

（2）ld cannot find -lcuda

我在===== generating arch files ===== 这一步

arch files can be found in the /xxx/cp2k-9.1/tools/toolchain/install/arch subdirectory时，提示我ERROR: (./scripts/generate_arch_files.sh) ld cannot find -lcuda, please check if cuda is installed or in system search path，原因是由于找不到libcuda.so这个库，然后我在我安装的/xxx/cuda11.7.0/targets/x86_64-linux/lib/stubs目录下找到了libcuda.so，因此在 .bashrc文件中加入

export LD_LIBRARY_PATH=/xxx/cuda11.7.0/targets/x86_64-linux/lib/stubs:$LD_LIBRARY_PATH

本身系统写了export LD_LIBRARY_PATH=/xxx/cuda11.7.0/lib64:$LD_LIBRARY_PATH，定义了cuda库的位置，不知道为啥没找到。