[gmx-users] Parallel Problem

[Ashish Misra]

Hi all,

I am having a problem getting Gromacs to run in parallel. When running
as a serial job, the system runs fine.
While running in parallel, I get the following error lines when running
grompp It seems to me that there is a problem when atoms are being
distributed across the nodes.

"
Moltype       PEG       SOL    #atoms
CPU   0         2      2591      8013
CPU   1         2      2591      8013
CPU   2         2      2590      8010
CPU   3         2      2590      8010
Made a shuffling table with 10370 entries [molecules]
processing coordinates...
Shuffling coordinates...
Entering shuffle_xv
Sorting coordinates for     8 copies of molecule PEG
Sorting coordinates for 10362 copies of molecule SOL
Warning: atom names in topol.top and conf.gro don't match (OW - CBY)
Warning: atom names in topol.top and conf.gro don't match (HW1 - CBV)
Warning: atom names in topol.top and conf.gro don't match (HW2 - CBS)
Warning: atom names in topol.top and conf.gro don't match (OW - CBP)
Warning: atom names in topol.top and conf.gro don't match (HW1 - CBM)
Warning: atom names in topol.top and conf.gro don't match (HW2 - CBJ)
Warning: atom names in topol.top and conf.gro don't match (OW - CBE)
Warning: atom names in topol.top and conf.gro don't match (HW1 - OBF)
Warning: atom names in topol.top and conf.gro don't match (HW2 - OBB)
Warning: atom names in topol.top and conf.gro don't match (OW - CAV)
Warning: atom names in topol.top and conf.gro don't match (HW1 - CAU)
Warning: atom names in topol.top and conf.gro don't match (HW2 - OAQ)
Warning: atom names in topol.top and conf.gro don't match (OW - OAT)
Warning: atom names in topol.top and conf.gro don't match (HW1 - CAW)
Warning: atom names in topol.top and conf.gro don't match (HW2 - OAR)
Warning: atom names in topol.top and conf.gro don't match (OW - CAM)
Warning: atom names in topol.top and conf.gro don't match (HW1 - OAN)
Warning: atom names in topol.top and conf.gro don't match (HW2 - CAK)
Warning: atom names in topol.top and conf.gro don't match (OW - CAI)
Warning: atom names in topol.top and conf.gro don't match (HW1 - CAG)
(more than 20 non-matching atom names)
WARNING 1 [file "topol.top", line 12]:
  1440 non-matching atom names
  atom names from topol.top will be used
  atom names from conf.gro will be ingnored
"

When running mdrun, the system crashes with the following message.

"
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
[2] MPI Abort by user Aborting program !
[2] Aborting program!
    p4_error: latest msg from perror: Resource temporarily unavailable
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
"

can someone tell me how to resolve this problem.


Thanks

Ashish