[gmx-users] mpirun SIGSEGV error on dual xeon

Y. U. Sasidhar sasidhar at chem.iitb.ac.in
Wed Jul 9 17:22:01 CEST 2003

I see this error on our dual xeon 1.8 GHz, RH 8.0 ( OS sees 4 cpus ).
We compile tpr file for 4 nodes and use lam from gromacs web site. gmx 3.1.4.
We are using PME. gmx installed from rpms.
We are doing a MD of a 13 residue peptide in spc water.
1. WE compile for 4 nodes; mpirun stops at various stages before ~ 10,000 steps
no error messages !
2. WE compile for 2 nodes and this is what we are getting.
commands used: mpirun -np 4 mdrun_mpi... etc
 From archives I got an impression that PME may be the reason.
We have not yet tried with shift and GR.
We would like to continue with PME.

step 159090, will finish at Thu Jul 10 12:19:18 2003
step 159100, will finish at Thu Jul 10 12:19:19 2003
step 159110, will finish at Thu Jul 10 12:19:20 2003
step 159120, will finish at Thu Jul 10 12:19:21 2003
step 159130, will finish at Thu Jul 10 12:19:22 2003
MPI process rank 1 (n0, p8340) caught a SIGSEGV.

One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 8340 failed on node n0 with exit status 1.


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