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标题: openMolcas安装过程中报错 [打印本页]
作者
Author: hmlyz    时间: 2021-10-14 17:15
标题: openMolcas安装过程中报错
按照这个博文《量子化学程序OpenMolcas的简易安装》安装openMolcas时提示报错请问是什么原因？（cmake是按照卢老师的文章：GROMACS的安装方法 安装的）
  1. [haorui@mafang build]$ CC=icc CXX=icpc FC=ifort cmake3 -DLINALG=MKL -DOPENMP=ON \-DCMAKE_INST          ALL_PREFIX=/home/haorui/soft/OpenMolcas-v21.06 ../
  2. -- The Fortran compiler identification is Intel 15.0.0.20140723
  3. -- The C compiler identification is Intel 15.0.0.20140723
  4. -- Check for working Fortran compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort
  5. -- Check for working Fortran compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort -           works
  6. -- Detecting Fortran compiler ABI info
  7. -- Detecting Fortran compiler ABI info - done
  8. -- Checking whether /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort supports Fortran 90
  9. -- Checking whether /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort supports Fortran 90 -           yes
  10. -- Check for working C compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/icc
  11. -- Check for working C compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/icc - works
  12. -- Detecting C compiler ABI info
  13. -- Detecting C compiler ABI info - done
  14. -- Detecting C compile features
  15. -- Detecting C compile features - done
  16. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.6.8", minimum required is           "3.0")
  17. Configuring compilers:
  18. Detecting Molcas version info:
  19. -- OPENMOLCAS_VERSION: v21.06 ?
  20. Detecting system info:
  21. -- OS: Linux-x86_64
  22. -- ADDRMODE: 64
  23. -- PLATFORM: LINUX64
  24. Configuring HDF5 support:
  25. -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
  26. -- HDF5 not found, it will be deactivated
  27. Configuring linear algebra libraries:
  28. -- Using Intel Math Kernel Library (MKL)
  29. -- MKLROOT = /opt/intel/composer_xe_2015.0.090/mkl
  30. -- MKL_INCLUDE_PATH = /opt/intel/composer_xe_2015.0.090/mkl/include
  31. -- MKL_LIBRARY_PATH = /opt/intel/composer_xe_2015.0.090/mkl/lib/intel64
  32. -- LINALG_LIBRARIES: /opt/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_ilp64.so;          /opt/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.so;/opt/intel/composer_xe_2015.          0.090/mkl/lib/intel64/libmkl_intel_thread.so
  33. Gromacs interface DISABLED
  34. BLOCK interface DISABLED
  35. CHEMPS2 interface DISABLED
  36. MSYM support DISABLED
  37. QCMaquis DMRG support DISABLED
  38. NECI interface DISABLED
  39. EFP interface DISABLED
  40. GEN1INT support DISABLED
  41. libwfa support DISABLED
  42. NEVPT2 support DISABLED
  43. MolGUI DISABLED
  44. Configuring runtime environment settings:
  45. -- DEFMOLCASMEM:  2048
  46. -- DEFMOLCASDISK: 20000
  47. -- RUNSCRIPT:    $program $input
  48. -- RUNBINARY:    $program
  49. -- RUNBINARYSER: $program
  50. Build type: Release
  51. -- C compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/icc
  52. -- C compiler flags:  -std=gnu99 -qopenmp -O2
  53. -- Fortran compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort
  54. -- Fortran compiler flags:   -fpp -i8 -r8 -heap-arrays -qopenmp -O2 -fno-alias -traceback
  55. -- Definitions: _MOLCAS_;_I8_;_LINUX_
  56. -- Debug definitions:
  57. CMake Warning at Tools/pymolcas/CMakeLists.txt:37 (message):
  58.   Some python modules are not available: pyparsing


  61. -- pymolcas: disabled
  62. CMake Error at CMakeLists.txt:3021 (message):
  63.   Failed to configure the pymolcas driver.


  66. -- Configuring incomplete, errors occurred!
  67. See also "/home/Fangma/LYZ/xiugai/OpenMolcas-v21.06/build/CMakeFiles/CMakeOutput.log".
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作者
Author: snljty    时间: 2021-10-15 09:30
你要么没装anaconda3要么没启动anaconda3环境。再看一遍那篇推送，或者你自己pip补一个pyparsing包试试。
作者
Author: hmlyz    时间: 2021-10-16 14:58
snljty 发表于 2021-10-15 09:30
你要么没装anaconda3要么没启动anaconda3环境。再看一遍那篇推送，或者你自己pip补一个pyparsing包试试。

感谢老师的解答 这个问题解决了 我再进行下一步make -j16时又报错了请问是什么原因？
  1. Scanning dependencies of target espf.exe
  2. [ 96%] Linking Fortran executable ../../bin/rasscf.exe
  3. Scanning dependencies of target expbas.exe
  4. Scanning dependencies of target extf.exe
  5. Scanning dependencies of target false.exe
  6. [ 96%] Building Fortran object CMakeFiles/espf/CMakeFiles/espf.exe.dir/main.F90.o
  7. [ 96%] Building Fortran object CMakeFiles/dynamix/CMakeFiles/dynamix.exe.dir/main.F90.o
  8. [ 96%] Building Fortran object CMakeFiles/expbas/CMakeFiles/expbas.exe.dir/main.F90.o
  9. [ 96%] Building Fortran object CMakeFiles/extf/CMakeFiles/extf.exe.dir/main.F90.o
  10. /tmp/ifortb0YunI.i90: catastrophic error: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report.  Note: File and line given may not be explicit cause of this error.
  11. [ 96%] Building Fortran object CMakeFiles/false/CMakeFiles/false.exe.dir/main.F90.o
  12. compilation aborted for /home/Fangma/LYZ/xiugai/OpenMolcas-v21.06/unit_tests/linalg_mod/test_linalg.F90 (code 1)
  13. make[2]: *** [unit_tests/linalg_mod/CMakeFiles/test_linalg.dir/test_linalg.F90.o] Error 1
  14. make[1]: *** [unit_tests/linalg_mod/CMakeFiles/test_linalg.dir/all] Error 2
  15. make[1]: *** Waiting for unfinished jobs....
  16. [ 96%] Linking Fortran executable ../../bin/casvb.exe
  17. [ 96%] Linking Fortran executable ../../bin/alaska.exe
  18. [ 96%] Linking Fortran executable ../../bin/averd.exe
  19. [ 96%] Linking Fortran executable ../../bin/cht3.exe
  20. [ 96%] Linking Fortran executable ../../bin/chcc.exe
  21. [ 96%] Linking Fortran executable ../../bin/caspt2.exe
  22. [ 96%] Linking Fortran executable ../../bin/cpf.exe
  23. [ 96%] Linking Fortran executable ../../bin/ccsdt.exe
  24. [ 96%] Linking Fortran executable ../../bin/espf.exe
  25. [ 96%] Linking Fortran executable ../../bin/dynamix.exe
  26. [ 96%] Linking Fortran executable ../../bin/extf.exe
  27. [ 96%] Linking Fortran executable ../../bin/expbas.exe
  28. [ 97%] Linking Fortran executable ../bin/test_sorting
  29. [ 97%] Linking Fortran executable ../../bin/false.exe
  30. [ 97%] Built target averd.exe
  31. [ 97%] Built target test_sorting
  32. [ 97%] Built target extf.exe
  33. [ 97%] Built target false.exe
  34. [ 97%] Built target ccsdt.exe
  35. [ 97%] Built target dynamix.exe
  36. [ 97%] Built target cht3.exe
  37. [ 97%] Built target expbas.exe
  38. [ 97%] Built target cpf.exe
  39. [ 97%] Built target chcc.exe
  40. [ 97%] Built target espf.exe
  41. [ 97%] Built target caspt2.exe
  42. [ 97%] Built target alaska.exe
  43. [ 97%] Built target casvb.exe
  44. [ 97%] Built target rasscf.exe
  45. make: *** [all] Error 2
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作者
Author: snljty    时间: 2021-10-16 16:13
hmlyz 发表于 2021-10-16 14:58
感谢老师的解答 这个问题解决了 我再进行下一步make -j16时又报错了请问是什么原因？

不好说，改成make -j 1继续编译试试
作者
Author: zjxitcc    时间: 2021-10-17 10:15
hmlyz 发表于 2021-10-16 14:58
感谢老师的解答 这个问题解决了 我再进行下一步make -j16时又报错了请问是什么原因？

先去掉-j16试试，你机子有16核么？没有的话不要-j16. 另外，机子有多少内存？别是1GB都不到
作者
Author: bluewhale    时间: 2021-10-17 11:35
用intel PS编译出来后的运行也有问题，考虑用openmpi + gcc编译.
作者
Author: zjxitcc    时间: 2021-10-17 11:44
本帖最后由 zjxitcc 于 2021-10-17 11:46 编辑
bluewhale 发表于 2021-10-17 11:35
用intel PS编译出来后的运行也有问题，考虑用openmpi + gcc编译.

我用intel parallel studio 2019, oneAPI等编译过，使用了很久，没有问题。gcc/gfortran编译出的会比icc/ifort慢（对于openmolcas而言）。如果你要编译MPI版本的话，假设openmolcas用icc/ifort，那么openmpi最好也用intel编译器编译。



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