[gmx-users] gromacs parallel doesn't work

Beniamino Sciacca superbenji83 at gmail.com
Sun Jun 4 15:38:19 CEST 2006


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>:
>
> 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>>:
> >>>>>>
> >>>>>>     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>
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> >>>>>>     >> Can't post? Read
> >>>>>> http://www.gromacs.org/mailing_lists/users.php
> >>>>>>     <http://www.gromacs.org/mailing_lists/users.php>
> >>>>>>     >>
> >>>>>>     > _______________________________________________
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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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