[gmx-users] problem with particle decomposition in gromacs 4.0.4
gmx3 at hotmail.com
Wed May 6 17:03:14 CEST 2009
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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