[gmx-users] problem with particle decomposition in gromacs 4.0.4

[Suman Chakrabarty]

Hi,

I am trying particle decomposition with gromacs 4.0.4 for a small
polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at
the very beginning without any useful error message, when I use
version 4.0.4 with option -pd. Whereas everything remaining same it's
still running fine in version 3.3.3. I have tried 4, 8, 16 nodes with
the same result. How do I troubleshoot this? I need to use the
particle decomposition method since the PLUMED plugin to perform
metadynamics supports only pd as of now.

Here are the last few lines from the log, stderr and stdout files:

log:
============================================
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
==============================================

stderr:
==============================================
Getting Loaded...
Reading file c20.G53a6.eq.gmx404.tpr, VERSION 4.0.4 (single precision)
Loaded with Money

starting mdrun 'Protein in water'
2500000 steps,   5000.0 ps.
===============================================

stdout:
===============================================
/opt/gridengine/default/spool/compute-0-4/active_jobs/5329.1/pe_hostfile
ibc4
ibc4
ibc4
ibc4
rank 2 in job 1  compute-0-4.local_46551   caused collective abort of all ranks
  exit status of rank 2: killed by signal 9
rank 1 in job 1  compute-0-4.local_46551   caused collective abort of all ranks
  exit status of rank 1: killed by signal 9
=================================================

Thanks for any suggestion.


Best regards,
Suman.