[gmx-users] Gromacs4: minimization hangs

[David van der Spoel]

Lillian Chong wrote:
> I ran the following for the minimization using mpich2:
> mpiexec -n 8 mdrun_mpi -s min.tpr -c min.gro -o min.trr -g min.log -e min.edr
And does it work on fewer processors? In particular on one processor?
If so please submit a bugzilla.

> 
> On Fri, Oct 17, 2008 at 12:36 PM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> Lillian Chong wrote:
>>> Dear Gromacs Users,
>>>
>>> When I run a steepest descent minimization with the parallel version
>>> of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but
>>> does not exit.  See below for the tail end of the log file (notice
>>> there are not timings and the usual Gromacs quote at the end).  The
>>> serial version of the Gromacs 4 mdrun runs this minimization fine and
>>> exits as it should.  I did not have this issue with the Gromacs4rc3
>>> parallel mdrun.  Do you know what might be going wrong?
>> Which mpi version are you using?
>>> I've attached the min.mdp and min.tpr files.
>>>
>>> Best regards,
>>> Lillian
>>> ====================
>>> Tail end of log file:
>>>          Step           Time         Lambda
>>>          1000     1000.00000        0.00000
>>>
>>>  Energies (kJ/mol)
>>>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>>>   2.75995e+01    1.01358e+02    5.12660e+00    1.82811e+02    2.18810e+02
>>>    Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>>   8.24670e+02    1.97157e+04   -9.79168e+02   -1.44989e+05   -1.75892e+04
>>>     Potential Pressure (bar)
>>>  -1.42482e+05    1.42736e+04
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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>>
>> --
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Professor of Biology
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> _______________________________________________
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> 
> 
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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