[gmx-users] problem with particle decomposition in gromacs 4.0.4
suman at sscu.iisc.ernet.in
Wed May 6 19:27:40 CEST 2009
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
In any case, I shall file a report after I reproduce this for a few
slightly different systems.
On Wed, 6 May 2009, Berk Hess wrote:
> 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.
>> Date: Wed, 6 May 2009 20:23:56 +0530
>> From: suman at sscu.iisc.ernet.in
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] problem with particle decomposition in gromacs 4.0.4
>> 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:
>> 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 --- -------- --------
>> 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.
>> 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,
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