[gmx-users] help needed

[Chetan Mahajan]

Dear All,

I am testing my gromacs code using user-specified potential functions (LJ
as well as Buckingham as non-bonded potentials). *Minimization run with
these potentials runs fine*. However, equilibration run gives following
error at which I am clueless. Could anyone help? Is it because total charge
is -0.018 and not zero?

...........

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
starting mdrun 'tio2_formate'
1000000 steps,   1000.0 ps.
[c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught
error: Segmentation fault (signal 11)
[c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected
End-Of-File on file descriptor 7. MPI process died?
[c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error
while reading PMI socket. MPI process died?
[c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process
(rank: 5, pid: 122921) terminated with signal 11 -> abort job
[c418-701.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection]
mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4)
[c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while
reading PMI socket. MPI process died?
[c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while
reading PMI socket. MPI process died?
TACC: MPI job exited with code: 1

TACC: Shutdown complete. Exiting.


NOTE 1 [file lnanopf3.top, line 4422]:
  System has non-zero total charge: -0.018000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.




-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file:
/work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line:
593

File input/output error:
/work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro

...........

Thanks a lot!

regards
Chetan