[gmx-users] gromacs parallel doesn't work
David van der Spoel
spoel at xray.bmc.uu.se
Sun Jun 4 12:15:45 CEST 2006
Beniamino Sciacca wrote:
> with "-c 2" I've two processes, each one running at nearly 50%.
> with "-c 4" I've four processes, each one running at nearly 25%
> with "-c 1" I've only one process wich runs at nearly 99%
> I tried also with mdrun_Nmpi (compiled without enabling mpi), and it
> runs at nearly 99%.
> Is it possible that the software sees only one core?
I think your OS only sees one processor.
if Linux try:
cat /proc/cpuinfo
>
> Beniamino
>
> Yang Ye ha scritto:
>
>> Use top to check, you shall have two processes running at nearly 100%
>> with "-c 2"
>>
>> Yang Ye
>>
>> Beniamino Sciacca wrote:
>>
>>> I've just tried "mpirun -c 2 mdrun..." (34 h/ns).
>>> It works, but the problem is the same... the simulation time....
>>> In fact I also tried "mpirun -c 1 mdrun" (32 h/ns) and "mpirun -c 4
>>> mdrun" (34 h/ns), but the simulation time remain the same!
>>>
>>>
>>> Yang Ye ha scritto:
>>>
>>>> Beniamino Sciacca wrote:
>>>>
>>>>> I never used mprun -np 2, and I had not problem. Before I didn't
>>>>> use "mprun -np 2", now I don't use "mprun -np 2" but simulation
>>>>> time now is twice. It has changed from a day to the other.
>>>>> However I've just tried, like you suggested, to use " -np 2" (in
>>>>> grompp and in mdrun) but I obtain an error:
>>>>> -------------------------------------------
>>>>> "Program mdrun_d, VERSION 3.3.1
>>>>> Source code file: init.c, line: 69
>>>>>
>>>>> Fatal error:
>>>>> run input file DNA8_mdEq.tpr was made for 2 nodes,
>>>>> while mdrun_d expected it to be for 1 nodes.
>>>>> "
>>>>> -------------------------------------------
>>>>> In fact I've only one node.
>>>>
>>>> Try David's mpirun -c 2 mdrun
>>>>
>>>>>
>>>>> Laptop should be running in top speed, I never modified the
>>>>> configuration of energy profile.
>>>>> Beniamino
>>>>>
>>>>>
>>>>> 2006/6/3, Yang Ye <leafyoung81-group at yahoo.com
>>>>> <mailto:leafyoung81-group at yahoo.com>>:
>>>>>
>>>>> First, make sure that you used mdrun -np 2.
>>>>> Second, check your energy profile. Is your laptop running in top
>>>>> speed?
>>>>> or does it have sleep time?
>>>>>
>>>>> Yang Ye
>>>>>
>>>>> Beniamino Sciacca wrote:
>>>>> > I don't understand what you talking about...
>>>>> > I didn't write any hostfile.... I'm not in a cluster. I only
>>>>> use my
>>>>> > notebook with the two cores.
>>>>> > In fact I type "lamboot" without -v.......
>>>>> >
>>>>> > Beniamino
>>>>> >
>>>>> > Mark Abraham ha scritto:
>>>>> >> Did your default LAM hostfile configuration (or whatever it is)
>>>>> >> change from 2 processors to one?
>>>>> >>
>>>>> >> Mark
>>>>> >> _______________________________________________
>>>>> >> gmx-users mailing list gmx-users at gromacs.org
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>>>>> >>
>>>>> > _______________________________________________
>>>>> > gmx-users mailing list gmx-users at gromacs.org
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>>>>>
>>>>> --
>>>>> /Regards,/
>>>>> Yang Ye
>>>>> /Computational Biology Lab
>>>>> School of Biological Sciences
>>>>> Nanyang Technological University
>>>>> Singapore
>>>>> Tel: 6316-2884
>>>>> /
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>>
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>>>>
>>>>
>>>>
>>>>
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>>
>>
>>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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