计算化学公社

标题: gmx_MMPBSA计算过程中出现了Segmentation fault (signal 11)问题 [打印本页]

作者
Author: Sunca 时间: 2024-12-12 18:01
标题: gmx_MMPBSA计算过程中出现了Segmentation fault (signal 11)问题
gmx_MMPBSA计算过程中出现了下面的问题。

mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 0 1 -ct gm_md_fit.xtc -cp com.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO ] Starting gmx_MMPBSA 1.6.4
[INFO ] Command-line
  mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 0 1 -ct gm_md_fit.xtc -cp com.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO ] Checking mmpbsa.in input file...
......
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.

[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /home/sunca/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
         100%|##########| 10001/10001 [elapsed: 15:49 remaining: 00:00]
[INFO ] calculating receptor contribution...
         100%|##########| 10001/10001 [elapsed: 06:07 remaining: 00:00]
[INFO ] calculating ligand contribution...
         100%|##########| 10001/10001 [elapsed: 06:07 remaining: 00:00]
[INFO ] Beginning GBNSR6 calculations with /home/sunca/anaconda3/envs/gmxMMPBSA/bin/gbnsr6
[INFO ] calculating complex contribution...
[INFO ]    calculating MM...
         100%|##########| 10001/10001 [elapsed: 15:48 remaining: 00:00]
[INFO ]    calculating GB...
            6%|6       | 636/10001 [elapsed: 01:19 remaining: 19:43]
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 907147 RUNNING AT WL
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

期待有经验或知道原因的大佬回复。

作者
Author: Loading0760 时间: 2024-12-12 20:32
Segmentation Fault这种错误是最难解决的了。你可以重新跑一遍然后监控一下计算的内存，我怀疑是内存超了。你这个mpirun也只给两个核。
如果不是内存的问题，那我就不知道了。看你任务像是做结合自由能分解，不行的话，可以先试试简单的模型。

作者
Author: Sunca 时间: 2024-12-12 22:21

Loading0760 发表于 2024-12-12 20:32
Segmentation Fault这种错误是最难解决的了。你可以重新跑一遍然后监控一下计算的内存，我怀疑是内存超了。 ...

内存我看了最高也才占用百分之十几。
我试了试不用mpi，直接跑着跑着电脑卡死了
我又试了试-np 12，报错：
[INFO ]    calculating MM...
         56%|#####6 | 5633/10001 [elapsed: 00:15 remaining: 00:16]
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.

Backtrace for this error:
#0  0x6bf46a4251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#1  0x6bf46e43e08 in do_sin
at ../sysdeps/ieee754/dbl-64/s_sin.c:135
#2  0x6bf46e43e08 in __sincos
at ../sysdeps/ieee754/dbl-64/s_sincos.c:56
#3  0x61c01a93ab4f in ???
#4  0x61c01a96351e in ???
#5  0x61c01a92bc3e in ???
#6  0x61c01a92b767 in ???
#7  0x61c01a916a3d in ???
#8  0x61c01a918c55 in ???
#9  0x61c01a918cd4 in ???
#10  0x6bf46a29d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#11  0x6bf46a29e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#12  0x61c01a915068 in ???
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
         ^^^^^^^^^^^
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.run_mmpbsa()
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/calculation.py", line 142, in run
calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/calculation.py", line 198, in run
raise CalcError(f'{command_args[0]} failed with prmtop {command_args[1]}!')
CalcError: /home/sunca/anaconda3/envs/gmxMMPBSA/bin/gbnsr6 failed with prmtop -i!
Error occurred on rank 11.
Exiting. All files have been retained.
Abort(1) on node 11 (rank 11 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11

欢迎光临计算化学公社 (http://bbs.keinsci.com/)