Yes, I have encountered this crash with plain Gromacs 4.0.4 as well. I
have not tried single processor, but with domain decomposition it runs
fine. I am not sure whether it has got to do anything with our parallel
architecture though.
In any case, I shall file a report after I reproduce this for a few
slightly different systems.
Regards,
Suman.
On Wed, 6 May 2009, Berk Hess wrote:
Hi,
Are the crashes with plain 4.0.4, or 4.0.4 with PLUMED?
I have not heard of crashes in 4.0.4 with particle decomposition,
so it might have to do with the link with PLUMED.
Have you tried running 4.0.4 in single processor?
If plain Gromacs 4.0.4 crahes on your system with PD,
please file a report on bugzilla.gromacs.org and attach the tpr file.
Berk
Date: Wed, 6 May 2009 20:23:56 +0530
From: su...@sscu.iisc.ernet.in
To: gmx-users@gromacs.org
Subject: [gmx-users] problem with particle decomposition in gromacs 4.0.4
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.
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