CP2K第一性原理程序在Linux中的安装方法

Gzh_NJ

卢老师好，请教下我原来是在centos下装的cp2k，然后现在要换系统换成ubuntu，这样会影响cp2k的使用吗？

sobereva

Gzh_NJ 发表于 2024-6-13 15:03
卢老师好，请教下我原来是在centos下装的cp2k，然后现在要换系统换成ubuntu，这样会影响cp2k的使用吗？

肯定得重新编译

jinboscience

今天安装cp2k，斑竹讲的error的地方都出现了，然后照着改，直接成功。
程序相关的就是这样：懂的话几分钟解决，不懂的话几个小时几天都没有进展。
非常感谢科音论坛提供的教程。

Gzh_NJ

sobereva 发表于 2024-6-14 02:08
肯定得重新编译

谢谢卢老师

小强

牧生 发表于 2023-11-7 07:43
之前安装的CP2K2023.1，正常使用。近日安装CP2K2023.2，始终在这里就进行不下去了

[jing@Jing cp2k-2023 ...

你好，我也遇到这个问题。具体怎么操作的啊

小强

请教大家，我在运行make -j 4 ARCH=local VERSION="ssmp psmp" 时，提示No DBCSR submodule available, please run 'git submodule update  --init  --recursive'. 然后，我运行了git submodule update  --init  --recursive，又提示not a git repository (or any of the parent directories)。请问怎么解决改问题？
系统是Centos 9 stream, 安装的CP2K-2024.1版本。

牧生

小强 发表于 2024-6-15 12:16
你好，我也遇到这个问题。具体怎么操作的啊

看155楼最后一句话

小强

牧生 发表于 2024-6-15 13:42
看155楼最后一句话

感谢回复。下载完之后，对安装路径有要求吗？

caiyan

想问一下，我在vasp中Linux系统下能直接将cp2k压缩包加压，然后修改环境变量进行安装吗？试了一下，老是没安装上，不知道是不是环境变量修改错误还是根本不能这样安装呀？下图是环境变量的修改，和报错内容

sobereva

caiyan 发表于 2024-6-18 20:54
想问一下，我在vasp中Linux系统下能直接将cp2k压缩包加压，然后修改环境变量进行安装吗？试了一下，老是没 ...

跟VASP有什么关系？

检查路径、PATH环境变量是否生效、指定的路径里是否有CP2K可执行文件。结合Linux基本常识不可能搞不明白怎么回事

943436427

谢谢

Uus/pMeC6H4-/キ

某Slurm集群内Red Hat Enterprise Linux 8.9系统上已安装gcc 8.5.0、cmake 3.26.5，module list显示已启用模块有intel/2023.2(default)和intelmpi/2023.2(default)。用module load openmpi可加载非默认的openmpi/4.1.5_intel-2022.3，之后mpicxx --version返回icpc (ICC) 2021.10.0 20230609，which mpicxx返回/opt/system/app/openmpi/4.1.5/intel-2022.3/bin/mpicxx。

今欲按本帖首页社长的教程，在此环境下安装CP2K 2024.1，发现安装至COSMA-v2.6.6（应与toolchain/scripts/stage4/install_cosma.sh相关）时报错无法找到MPI_CXX：

1. ==================== Installing COSMA ====================
   
2. COSMA-v2.6.6.tar.gz is found
   
3. Installing from scratch into /home/xxxxxx/cp2k-2024.1/tools/toolchain/install/COSMA-2.6.6
   
4. -- The CXX compiler identification is GNU 8.5.0
   
5. -- Detecting CXX compiler ABI info
   
6. -- Detecting CXX compiler ABI info - done
   
7. -- Check for working CXX compiler: /usr/bin/g++ - skipped
   
8. -- Detecting CXX compile features
   
9. -- Detecting CXX compile features - done
   
10. -- Selected ScaLAPACK backend (or implementation) for COSTA: MKL
    
11. -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
    
12. CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
    
13.   Could NOT find MPI (missing: MPI_CXX_FOUND CXX)
    
14. Call Stack (most recent call first):
    
15.   /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
    
16.   /usr/share/cmake/Modules/FindMPI.cmake:1837 (find_package_handle_standard_args)
    
17.   CMakeLists.txt:55 (find_package)
    
18. 
    
19. 
    
20. -- Configuring incomplete, errors occurred!
    
21. make: *** No targets specified and no makefile found.  Stop.
    
22. make: *** No rule to make target 'install'.  Stop.
    
23. -- The CXX compiler identification is GNU 8.5.0
    
24. -- The C compiler identification is GNU 8.5.0
    
25. -- Detecting CXX compiler ABI info
    
26. -- Detecting CXX compiler ABI info - done
    
27. -- Check for working CXX compiler: /usr/bin/g++ - skipped
    
28. -- Detecting CXX compile features
    
29. -- Detecting CXX compile features - done
    
30. -- Detecting C compiler ABI info
    
31. -- Detecting C compiler ABI info - done
    
32. -- Check for working C compiler: /usr/bin/gcc - skipped
    
33. -- Detecting C compile features
    
34. -- Detecting C compile features - done
    
35. -- Selected SCALAPACK backend for COSMA: MKL
    
36. -- The Fortran compiler identification is GNU 8.5.0
    
37. -- Detecting Fortran compiler ABI info
    
38. -- Detecting Fortran compiler ABI info - done
    
39. -- Check for working Fortran compiler: /usr/bin/gfortran - skipped
    
40. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
    
41. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
    
42. -- Found Threads: TRUE
    
43. -- Found MPI_C: /opt/system/app/intel/2023.2/mpi/2021.12/lib/libmpi.so (found version "3.1")
    
44. -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
    
45. -- Found MPI_Fortran: /opt/system/app/intel/2023.2/mpi/2021.12/lib/libmpifort.so (found version "3.1")
    
46. -- Could NOT find MPI (missing: MPI_CXX_FOUND CXX) (found version "3.1")
    
47. -- Found OpenMP_CXX: -fopenmp (found version "4.5")
    
48. -- Found OpenMP_C: -fopenmp (found version "4.5")
    
49. -- Found OpenMP_Fortran: -fopenmp (found version "4.5")
    
50. -- Found OpenMP: TRUE (found version "4.5") found components: CXX C Fortran
    
51. -- Found MKL: /opt/system/app/intel/2023.2/mkl/2023.2.0/include
    
52. -- Found Blas: ;/opt/system/app/intel/2023.2/mkl/2023.2.0/lib/intel64/libmkl_gf_lp64.so;/opt/system/app/intel/2023.2/mkl/2023.2.0/lib/intel64/libmkl_gnu_thread.so;/opt/system/app/intel/2023.2/mkl/2023.2.0/lib/intel64/libmkl_core.so;;;Threads::Threads
    
53. -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
    
54. CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
    
55.   Could NOT find MPI (missing: MPI_CXX_FOUND CXX) (found version "3.1")
    
56. Call Stack (most recent call first):
    
57.   /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
    
58.   /usr/share/cmake/Modules/FindMPI.cmake:1837 (find_package_handle_standard_args)
    
59.   CMakeLists.txt:107 (find_package)
    
60. 
    
61. 
    
62. -- Configuring incomplete, errors occurred!
    
63. make: *** No targets specified and no makefile found.  Stop.
    
64. make: *** No rule to make target 'install'.  Stop.
    
65. /home/xxxxxx/cp2k-2024.1/tools/toolchain/scripts/tool_kit.sh: line 663: /home/xxxxxx/cp2k-2024.1/tools/toolchain/install/COSMA-2.6.6/install_successful: No such file or directory

复制代码

除此之外，其余库已通过执行./install_cp2k_toolchain.sh --with-sirius=no --with-openmpi=system --with-cmake=system --with-cosma=no正常安装完毕。上述安装过程未在toolchain/build/COSMA-2.6.6内产生.log文件。

第二天编辑：用module load cmake/3.24.3_gnu-8.5.0可加载非默认的cmake 3.24.3，但此时亦无法解决上述问题。

编辑2：试图跳过COSMA包编译CP2K 2024.1，产生形如此帖的报错“This module file was not generated by any release of this compiler.   [LIBXSMM]”

编辑3：读了这个帖子的内容才明白，估计自带的OpenMPI是Intel编译的，与GNU编译的gcc，cmake，gfortran之类不兼容。现在放弃module load openmpi调用，而用./install_cp2k_toolchain.sh --with-sirius=no --with-cmake=system --with-openmpi=install --with-intelmpi=no --with-mpich=no --with-intel=no --with-gcc=system自己另外装openmpi，这样COSMA可以顺利完成，CP2K 2024.1编译也正常完成了。

zhangtp

老师，我在在运行cp2k.ssmp test.inp |tee test.out进行测试时，计算出现报错，安装的是Ubuntu。错误内容如下：
An error occurred opening the file 'test-RESTART.wfn' (UNIT = 1, IOSTAT = 13). Cannot open file 'test-RESTART.wfn': Permission denied. Current working directory:/inputmodel。
这个要怎么解决呢

sobereva

zhangtp 发表于 2024-9-27 03:16
老师，我在在运行cp2k.ssmp test.inp |tee test.out进行测试时，计算出现报错，安装的是Ubuntu。错误内容如 ...

弄清楚当前目录下有没有test-RESTART.wfn，没有就没法读

zhangtp

sob老师，请问我计算亚铁磁尖晶石切面结构吸附N2O小分子（切面结构扩胞后大约100多个原子），以及计算结构表面催化分解小分子的过渡态和反应动力学参数，适合使用CP2K吗？我正在按照您提供的例子简单跑一跑CP2K。