Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 134
Amin,
maybe your MPI-enabled executable is called mdrun_mpi. Check
the directory where mdrun is and make shure (with ldd for example)
the mdrun* you are using is linked to the MPI library you are using.
Carsten
On Jun 24, 2010, at 6:51 AM, Amin Arabbagheri wrote:
Carsten,
Thanks for your help, I used something like mpirun -np 3 mdrun -s topol.tpr,
it works but its something like repeating a single job 3 times,
simultaneously.
here is the output on the screen :
{
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.2#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.3#
Back Off! I just backed up ener.edr to ./#ener.edr.3#
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
step 736900, will finish Fri Jun 25 07:45:04 2010
}
the estimated time is as long as one single job!
--- On Mon, 21/6/10, gmx-users-requ...@gromacs.org
gmx-users-requ...@gromacs.org wrote:
From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org
Subject: gmx-users Digest, Vol 74, Issue 134
To: gmx-users@gromacs.org
Date: Monday, 21 June, 2010, 9:03
Send gmx-users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. (no subject) (Amin Arabbagheri)
2. Re: (no subject) (Justin A. Lemkul)
3. Re: (no subject) (Linus ?stberg)
4. Re: (no subject) (Carsten Kutzner)
5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo)
6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul)
--
Message: 1
Date: Mon, 21 Jun 2010 05:00:04 -0700 (PDT)
From: Amin Arabbagheri amin_a...@yahoo.com
Subject: [gmx-users] (no subject)
To: gmx-users@gromacs.org
Message-ID: 180446.74209...@web50607.mail.re2.yahoo.com
Content-Type: text/plain; charset=utf-8
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package
manager.
I want to run a simulation in parallel on a multi processor, single PC, but
to compile via grompp, it doesn't accept -np flag, and also , using -np in
mdrun, it still runs as a single job.
Thanks a lot for any instruction.
Bests,
Amin
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Message: 2
Date: Mon, 21 Jun 2010 08:05:15 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4c1f557b.4090...@vt.edu
Content-Type: text/plain; charset=UTF-8; format=flowed
Amin Arabbagheri wrote:
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
package manager.
I want to run a simulation in parallel on a multi processor, single PC,
but to compile via grompp, it doesn't accept -np flag, and also , using
-np in mdrun, it still runs as a single job.
Thanks a lot for any instruction.
Regarding grompp:
http://www.gromacs.org/Documentation/FAQs
As for mdrun, please provide your actual command line. The mdrun -np flag is
nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np
from
which mdrun is launched.
-Justin
Bests,
Amin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
Message: 3
Date: Mon, 21 Jun 2010 14:07:54 +0200
From: Linus ?stberg bio...@talavis.eu
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
aanlktilfhuno5zfxqismsuvestyfq-igiorzujmcr...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx
On Mon, Jun 21, 2010 at 2:00 PM, Amin
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134
Carsten,
Thanks for your help, I used something like mpirun -np 3 mdrun -s topol.tpr,
it works but its something like repeating a single job 3 times, simultaneously.
here is the output on the screen :
{
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.2#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.3#
Back Off! I just backed up ener.edr to ./#ener.edr.3#
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
step 736900, will finish Fri Jun 25 07:45:04 2010
}
the estimated time is as long as one single job!
--- On Mon, 21/6/10, gmx-users-requ...@gromacs.org
gmx-users-requ...@gromacs.org wrote:
From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org
Subject: gmx-users Digest, Vol 74, Issue 134
To: gmx-users@gromacs.org
Date: Monday, 21 June, 2010, 9:03
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-requ...@gromacs.org
You can reach the person managing the list at
gmx-users-ow...@gromacs.org
When replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. (no subject) (Amin Arabbagheri)
2. Re: (no subject) (Justin A. Lemkul)
3. Re: (no subject) (Linus ?stberg)
4. Re: (no subject) (Carsten Kutzner)
5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo)
6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul)
--
Message: 1
Date: Mon, 21 Jun 2010 05:00:04 -0700 (PDT)
From: Amin Arabbagheri amin_a...@yahoo.com
Subject: [gmx-users] (no subject)
To: gmx-users@gromacs.org
Message-ID: 180446.74209...@web50607.mail.re2.yahoo.com
Content-Type: text/plain; charset=utf-8
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package
manager.
I want to run a simulation in parallel on a multi processor, single PC, but to
compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun,
it still runs as a single job.
Thanks a lot for any instruction.
Bests,
Amin
-- next part --
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Message: 2
Date: Mon, 21 Jun 2010 08:05:15 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4c1f557b.4090...@vt.edu
Content-Type: text/plain; charset=UTF-8; format=flowed
Amin Arabbagheri wrote:
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
package manager.
I want to run a simulation in parallel on a multi processor, single PC,
but to compile via grompp, it doesn't accept -np flag, and also , using
-np in mdrun, it still runs as a single job.
Thanks a lot for any instruction.
Regarding grompp:
http://www.gromacs.org/Documentation/FAQs
As for mdrun, please provide your actual command line. The mdrun -np flag is
nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np from
which mdrun is launched.
-Justin
Bests,
Amin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
Message: 3
Date: Mon, 21 Jun 2010 14:07:54 +0200
From: Linus ?stberg bio...@talavis.eu
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
aanlktilfhuno5zfxqismsuvestyfq-igiorzujmcr...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx
On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri amin_a...@yahoo.comwrote:
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
package manager.
I want to run a simulation in parallel on a multi processor, single PC, but
to compile via grompp, it doesn't accept -np flag, and also , using -np in
mdrun, it still runs as a single job.
Thanks a lot for any instruction.
Bests,
Amin
--
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