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标题: 求助利用ORCA+Multiwfn生成小分子的RESP2电荷，使用脚本时报错 [打印本页]

作者
Author: 雨中宇 时间: 2024-4-4 11:12
标题: 求助利用ORCA+Multiwfn生成小分子的RESP2电荷，使用脚本时报错
运行脚本时在一个新建的文件夹中，输入./RESP2_ORCA.sh mol.mol2
Running optimization task under solvent via ORCA...
[zzm:61038] *** Process received signal ***
[zzm:61038] Signal: Segmentation fault (11)
[zzm:61038] Signal code: Address not mapped (1)
[zzm:61038] Failing at address: (nil)
[zzm:61038] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7fe2676c4090]
[zzm:61038] [ 1] /home/zzm/ORCA/orca503/liborca_tools_5_0_3_mpi.so.5(_ZN8TSMDData24calculateAtomSurfaceAreaEv+0x194)[0x7fe26f88a8a4]
[zzm:61038] [ 2] /home/zzm/ORCA/orca503/liborca_tools_5_0_3_mpi.so.5(_ZN8TSMDData10calcSMDCDSEv+0x35c)[0x7fe26f88a6ec]
[zzm:61038] [ 3] /home/zzm/ORCA/orca503/orca_scf_mpi[0x54ef43]
[zzm:61038] [ 4] /home/zzm/ORCA/orca503/orca_scf_mpi[0x42bd56]
[zzm:61038] [ 5] /home/zzm/ORCA/orca503/orca_scf_mpi[0x432a3a]
[zzm:61038] [ 6] /home/zzm/ORCA/orca503/orca_scf_mpi[0x433134]
[zzm:61038] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fe2676a5083]
[zzm:61038] [ 8] /home/zzm/ORCA/orca503/orca_scf_mpi[0x425252]
[zzm:61038] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node zzm exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[file orca_tools/qcmsg.cpp, line 465]:
.... aborting the run

The optimization task has failed! Please check content of opt.out to find reason
The script is terminated
我自己检查了下环境变量export PATH=$PATH:/home/zzm/ORCA/openmpi-4.1.1/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/zzm/ORCA/openmpi-4.1.1/lib
export PATH=$PATH:/home/zzm/ORCA/orca503
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/zzm/ORCA/orca503
alias ORCA="/home/zzm/ORCA/orca503/orca"
在脚本中也按照要求做了修改，不知道为什么出现这个错误。请求各位大佬指教

作者
Author: sobereva 时间: 2024-4-4 16:22
你先确保你的机子里可以正常用ORCA并行计算一个普通任务，确保安装无误

其次，就是自行看opt.out末尾判断原因，提示里写明了

Please check content of opt.out to find reason

作者
Author: 雨中宇 时间: 2024-4-4 18:35
好的，老师

作者
Author: 雨中宇 时间: 2024-4-5 16:33
老师我按照教程测试ORCA是否安装成功，输入命令orca test.inp > test.out,生成相应的文件且运行成功检测Openmpi也安装成功了且能使用，我按网上帖子的建议加了两条环境变量
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
重新进行了运行./RESP2_ORCA.sh mol.mol2
与上次运行报错仍一致，检查了opt.out文件
                           *** Initiating the SOSCF procedure ***
                        *** Shutting down DIIS ***
                  *** Re-Reading the Fockian ***
                  *** Removing any level shift ***
ITER    Energy    Delta-E       Grad    Rot    Max-DP RMS-DP
  7  -2813.88757673  -0.5643098347  0.003009  0.003009  0.054565  0.000140
            *** Restarting incremental Fock matrix formation ***
  8  -2813.88796915  -0.0003924195  0.003098  0.061952  0.090032  0.000411
  9  -2813.88847229  -0.0005031446  0.004892  0.121398  0.328635  0.000819
10  -2813.88943033  -0.0009580362  0.001830  0.052605  0.051445  0.000309
11  -2813.89023839  -0.0008080609  0.001433  0.036704  0.108009  0.000422
12  -2813.89027314  -0.0000347508  0.001206  0.013877  0.075997  0.000218
13  -2813.89056650  -0.0002933590  0.001293  0.034831  0.025521  0.000167
14  -2813.89056052 0.0000059792  0.001404  0.022685  0.021749  0.000101
15  -2813.89067642  -0.0001158986  0.000337  0.003643  0.015621  0.000053
16  -2813.89067153 0.0000048871  0.000343  0.002142  0.004846  0.000031
17  -2813.89069020  -0.0000186695  0.000117  0.001270  0.007743  0.000019
18  -2813.89068955 0.0000006557  0.000124  0.000488  0.003075  0.000009
19  -2813.89069146  -0.0000019136  0.000049  0.000666  0.001786  0.000009
20  -2813.89069140 0.0000000646  0.000075  0.000485  0.001448  0.000005
21  -2813.89069176  -0.0000003608  0.000023  0.000733  0.001972  0.000008
22  -2813.89069174 0.0000000212  0.000043  0.000410  0.000895  0.000003
23  -2813.89069187  -0.0000001369  0.000014  0.000583  0.003122  0.000011
24  -2813.89069189  -0.0000000202  0.000015  0.000586  0.001700  0.000007
25  -2813.89069193  -0.0000000409  0.000008  0.000782  0.002693  0.000006
26  -2813.89069197  -0.0000000365  0.000009  0.000523  0.003440  0.000008
27  -2813.89069198  -0.0000000130  0.000006  0.000238  0.002840  0.000015
            *** Restarting incremental Fock matrix formation ***
28  -2813.89069210  -0.0000001151  0.000005  0.000104  0.002843  0.000006
               ***Gradient check signals convergence***
            ***Rediagonalizing the Fockian in SOSCF/NRSCF***

            *****************************************************
            *                   SUCCESS                      *
            *          SCF CONVERGED AFTER  29 CYCLES       *
            *****************************************************

ORCA finished by error termination in SCF
Calling Command: mpirun -np 6  /home/zzm/ORCA/orca503/orca_scf_mpi opt.gbw b opt
[file orca_tools/qcmsg.cpp, line 465]:
  .... aborting the run
具体不知道该如何更改，网上看了好多帖子也没找到最后的解决办法

作者
Author: yanyifei 时间: 2024-4-5 17:22

雨中宇发表于 2024-4-5 16:33
老师我按照教程测试ORCA是否安装成功，输入命令orca test.inp > test.out,生成相应的文件且运行成功检测Ope ...

建议用TM5之类的软件做个内存稳定性测试
我之前是16G*4的内存，EXPO 6000能正常开机，但跑ORCA经常报错
后来TM5测试发现跑不过去。把内存频率降下来就没事了

作者
Author: 雨中宇 时间: 2024-4-6 10:39

yanyifei 发表于 2024-4-5 17:22
建议用TM5之类的软件做个内存稳定性测试
我之前是16G*4的内存，EXPO 6000能正常开机，但跑ORCA经常报错
...

好的谢谢你我改一下试试

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