openMolcas安装过程中报错

hmlyz

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
    
59. 
    
60. 
    
61. -- pymolcas: disabled
    
62. CMake Error at CMakeLists.txt:3021 (message):
    
63.   Failed to configure the pymolcas driver.
    
64. 
    
65. 
    
66. -- Configuring incomplete, errors occurred!
    
67. See also "/home/Fangma/LYZ/xiugai/OpenMolcas-v21.06/build/CMakeFiles/CMakeOutput.log".
    

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snljty

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。

hmlyz

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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snljty

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

zjxitcc

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

bluewhale

用intel PS编译出来后的运行也有问题，考虑用openmpi + gcc编译.

zjxitcc

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。