Hello, I'm having a similar problem, although my OS sees all 4 of my
processors just fine.
When I run mpirun -c 4 mdrun . . .
all 4 of my processors are running, but only at 50% each. Furthermore,
in present working directory, I see several backed up files:
[EMAIL PROTECTED] TEMP]$ ls
AfterResMD1.gro #mdout.mdp.1# ResMD1.job ResMD1.trr
#AfterResMD1.gro.1# NoBadWater.top ResMD1.log #ResMD1.trr.1#
#AfterResMD1.gro.2# posre.itp #ResMD1.log.1# #ResMD1.trr.2#
dmpc.itp ResMD1.edr #ResMD1.log.2# #ResMD1.trr.3#
lipid.itp #ResMD1.edr.1# #ResMD1.log.3#
lipid_posre.itp #ResMD1.edr.2# ResMD1.mdp
mdout.mdp #ResMD1.edr.3# ResMD1.tpr
It's almost as if I'm running 4 identical jobs (one on each processor) ,
instead of one job in parallel using 4 processors.
Any thoughts?
Thanks,
Arneh
Beniamino Sciacca wrote:
OK!!!
now it works.
I installed a kernel-image smp (for my kernel 2.6)
and now with "-c 2" it works!!!
I've two processes running at nearly 100%, and the simulation time is
reduced at 50%!
But now i don't understand why before (one week ago without smp it
worked....) mah....
I thank all you very much
regards
Beniamino
2006/6/4, Yang Ye <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>:
So, the kernel you used from Debian could be a non-SMP one. Change
another in the boot screen if there is.
\
Yang Ye
David van der Spoel wrote:
> 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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
>>>>>> <mailto: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>:
>>>>>>
>>>>>> 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@gromacs.org
<mailto:gmx-users@gromacs.org>
>>>>>> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
>>>>>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>>> >> Please don't post (un)subscribe requests to the
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>>>>>> >> interface or send it to
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>>>>>> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>.
>>>>>> >> Can't post? Read
>>>>>> http://www.gromacs.org/mailing_lists/users.php
>>>>>> < http://www.gromacs.org/mailing_lists/users.php>
>>>>>> >>
>>>>>> > _______________________________________________
>>>>>> > gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
>>>>>> <mailto:gmx-users@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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