[gmx-users] gromacs parallel doesn't work
Arneh Babakhani
ababakha at mccammon.ucsd.edu
Wed Jun 14 08:13:27 CEST 2006
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:
[ababakha at chemcca50 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 <leafyoung81-group at yahoo.com
> <mailto:leafyoung81-group at yahoo.com>>:
>
> 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 <leafyoung81-group at yahoo.com
> <mailto:leafyoung81-group at yahoo.com>
> >>>>>> <mailto: 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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> >>>>>> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> >>>>>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
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> <mailto:gmx-users-request at gromacs.org>>.
> >>>>>> >> Can't post? Read
> >>>>>> http://www.gromacs.org/mailing_lists/users.php
> >>>>>> < http://www.gromacs.org/mailing_lists/users.php>
> >>>>>> >>
> >>>>>> > _______________________________________________
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> >>>>>> <mailto: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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