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

[Suman Chakrabarty]

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: suman at sscu.iisc.ernet.in
>> To: gmx-users at 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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