[gmx-users] gromacs parallel doesn't work
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Sun Jun 4 15:36:46 CEST 2006
On Sunday 04 June 2006 15:10, Beniamino Sciacca wrote:
> 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?
No.
For calculation of bogomips see http://www.clifton.nl/index.html?bogomips.html
If os "sees" more cpus it will say that there are more cpus.
processor : 3 would be 4 cpus.
Install correct kernel with smp support.
>
> 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
> > >>>>> > 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
> >
> > >>>>> --
> > >>>>> /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>
> > >>>>> 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
> >
> > ------------------------------------------------------------------------
> >
> > >>>>> _______________________________________________
> > >>>>> gmx-users mailing list 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.
> > >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >>>>
> > >>>> _______________________________________________
> > >>>> gmx-users mailing list 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.
> > >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >>>
> > >>> _______________________________________________
> > >>> gmx-users mailing list 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.
> > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >>
> > >> _______________________________________________
> > >> gmx-users mailing list 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.
> > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > > _______________________________________________
> > > gmx-users mailing list 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.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list 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.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------
More information about the gromacs.org_gmx-users
mailing list