[gmx-users] gromacs parallel doesn't work

Miguel Ortiz-Lombardia molatwork at yahoo.es
Sun Jun 4 16:05:19 CEST 2006


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Hi Beniamino,

Perhaps you upgraded/updated your system kernel and for some reason
didn't choose the smp-enabled kernel. If the update/upgrade is done
automatically, check that its parameters are well chosen. Also, if you
don't use it, remove any kernel package not being -smp, and then the
upgrade will not try to install it.

Enjoy your simulations,



Miguel

En/na Beniamino Sciacca ha escrit:
> 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
>     >>>>>>     >> _______________________________________________
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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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- --
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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