[gmx-users] gromacs parallel doesn't work
Beniamino Sciacca
superbenji83 at gmail.com
Sun Jun 4 15:10:46 CEST 2006
superbenji at beniamino:~$ cat /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 14
model name : Genuine Intel(R) CPU T2400 @ 1.83GHz
stepping : 8
cpu MHz : 1829.111
cache size : 2048 KB
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 10
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pni monitor vmx
est tm2 xtpr
bogomips : 3662.13
that's all.
bogomips is twice cpu frquency.... it seems that OS sees two cpu.... isn't
it?
2006/6/4, David van der Spoel <spoel at xray.bmc.uu.se>:
>
> 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
> >>>>> <mailto:gmx-users at gromacs.org>
> >>>>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>>>> >> Please don't post (un)subscribe requests to the list. Use
> >>>>> the www
> >>>>> >> interface or send it to gmx-users-request at gromacs.org
> >>>>> <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>
> >>>>> >>
> >>>>> > _______________________________________________
> >>>>> > gmx-users mailing list gmx-users at gromacs.org
> >>>>> <mailto:gmx-users at gromacs.org>
> >>>>> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >>>>> >
> >>>>>
> >>>>> --
> >>>>> /Regards,/
> >>>>> Yang Ye
> >>>>> /Computational Biology Lab
> >>>>> School of Biological Sciences
> >>>>> Nanyang Technological University
> >>>>> Singapore
> >>>>> Tel: 6316-2884
> >>>>> /
> >>>>>
> >>>>> _______________________________________________
> >>>>> gmx-users mailing list gmx-users at gromacs.org
> >>>>> <mailto:gmx-users at gromacs.org>
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> >>>>>
> >>>>>
> >>>>>
> ------------------------------------------------------------------------
> >>>>>
> >>>>>
> >>>>> _______________________________________________
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> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>>
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> >>>
> >>
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
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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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