[gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

[Berk Hess]

Hi,

VAR should be an environment variable that is set by your MPI implementation.
Try:
mpirun -np 2 env

For OpenMPI I use:
OMPI_MCA_universe

Berk

Date: Fri, 6 Feb 2009 16:38:57 +0000
Subject: Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2
From: jmdamas at itqb.unl.pt
To: gmx-users at gromacs.org



On Fri, Feb 6, 2009 at 4:12 PM, Berk Hess <gmx3 at hotmail.com> wrote:






Hi,

I always compile Gromacs with --enable_mpi --enable-mpi-environment=...
such that you can run a serial mdrun without using mpirun.
Interesting. So what does that "..." (or VAR in the help of configure) means? I'm sorry, but I can't find any information about it anywhere. If it's just a variable we come up with, how or when do we set it (and what do we set it to) when running the MPI mdrun? It doesn't seem to work when I don't set it at all...


Regards,
João


Berk

Date: Fri, 6 Feb 2009 15:22:54 +0000

Subject: Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2
From: jmdamas at itqb.unl.pt
To: gmx-users at gromacs.org


On Mon, Jan 19, 2009 at 6:09 PM, Berk Hess <gmx3 at hotmail.com> wrote:






Hi,

When running in parallel on a cluster through a queuing system
one usually does not (or can not) see or check the nice level
of the mdrun processes. But the nice level can have a significant
impact on performance, especially when running in parallel,


since all processes have to wait for the slowest one.
Therefore I set the nicelevel to 0 when running in parallel.

Note that if you configure mdrun with --enable_mpi --enable-mpi-environment,
running an MPI mdrun binary without mpirun will still give nice 19.


Hi Berk,

Thanks for the answer and for the tip. It worked out
fine. But still, I was intrigued when you said "running an MPI mdrun
binary without mpirun". What do you mean with that? Do you mean that
you don't need to launch the mpirun before the MPI mdrun?


Regards,
João 



Berk

Date: Mon, 19 Jan 2009 16:29:16 +0000

From: jmdamas at itqb.unl.pt
To: gmx-users at gromacs.org
Subject: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2



Hello,

I would like to know if there is any reason for mdrun_mpi to have a nicelevel default of zero in Gromacs 4.0.2 instead of the default 19 of mdrun of every version or mdrun_mpi of the other versions. I searched the mailing list for any discussion related to this but I haven't found anything.




Thanks in advance,
João
-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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-- 
João M. Damas
PhD Student


Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

Express yourself instantly with MSN Messenger! MSN Messenger


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Please search the archive at http://www.gromacs.org/search before posting!

Please don't post (un)subscribe requests to the list. Use the

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


-- 
João M. Damas
PhD Student

Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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