[gmx-users] gromacs parallel doesn't work
Miguel Ortiz-Lombardia
molatwork at yahoo.es
Sun Jun 4 15:34:31 CEST 2006
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Hi Beniamino,
No, you should see a line:
processor : 1
together with its full description. Your output means your system sees a
single processor. Looks like a hardware problem, then.
HTH,
Miguel
En/na Beniamino Sciacca ha escrit:
> 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
> <mailto: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>
> >>>>> <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
> >>>>> >> _______________________________________________
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> >>>>> >> Can't post? Read
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> >>>>> >>
> >>>>> > _______________________________________________
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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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> >>
> > _______________________________________________
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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
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> ------------------------------------------------------------------------
>
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- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: molatwork at yahoo.es
- ----------------------------------------------------------------------
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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