Hi Mark,
thanks a lot for your reply. I checked the 4.0.7 version installed
on blugene and it also doesnt write checkpoints during simulations.
How it was compiled by support team i dont know, but in my
compilation i mostly used options from gromacs wiki page.
I think i'll not trace this issue
Hello everybody,
does anyone have a similar problem writing checkpoints
from Gromacs 4.0.7?
I have two Gromacs versions, 4.0.5 and 4.0.7, compiled for
bluegene. The 4.0.5 writes state.cpt during mdrun and at
the end of simulation too. The 4.0.7 does it at the end of the
run only, but not during
On 25/03/2010 10:01 PM, Dr. Leonid Yelash wrote:
Hello everybody,
does anyone have a similar problem writing checkpoints
from Gromacs 4.0.7?
I have two Gromacs versions, 4.0.5 and 4.0.7, compiled for
bluegene. The 4.0.5 writes state.cpt during mdrun and at
the end of simulation too. The 4.0.7
We have mdrun integrated into our distributed computing project. When
your users suspend or close the manger it checkpoints, so when they
open again it continues mdrun where it left off. However, when users
reboot, it starts from the beginning. We are using this command line
to execute the work.
- Original Message -
From: Jack Shultz j...@drugdiscoveryathome.com
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users gmx-users@gromacs.org, Andrey Voronkov
a...@drugdiscoveryathome.com
We have mdrun integrated into our
...@drugdiscoveryathome.com
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users gmx-users@gromacs.org, Andrey
Voronkov a...@drugdiscoveryathome.com
We have mdrun integrated into our distributed computing project. When
your users suspend
:
- Original Message -
From: Jack Shultzj...@drugdiscoveryathome.com
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS usersgmx-users@gromacs.org, Andrey
Voronkova...@drugdiscoveryathome.com
We have mdrun integrated into our distributed computing
:
- Original Message -
From: Jack Shultzj...@drugdiscoveryathome.com
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS usersgmx-users@gromacs.org, Andrey
Voronkova...@drugdiscoveryathome.com
We have mdrun integrated into our distributed
if the
checkpoint already exists.
On Tue, Feb 2, 2010 at 6:18 PM, Mark Abrahammark.abra...@anu.edu.au
wrote:
- Original Message -
From: Jack Shultzj...@drugdiscoveryathome.com
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS usersgmx-users
Hello all,
I tried to use checkpointing with the following command:
mdrun -v -cpi status.cpt -o status.cpt -cpt 1
...but no checkpoints are written after 1 minute in current (this morning) cvs
version. Am I using it wrong? Do .mdp options such as output frequencies
influence the checkpoint
.
Berk
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Date: Tue, 7 Oct 2008 15:11:04 +0200
Subject: [gmx-users] Checkpointing: Status in current CVS version?
Hello all,
I tried to use checkpointing with the following command:
mdrun -v -cpi status.cpt -o status.cpt -cpt 1
Am Tuesday, 7. October 2008 schrieb Berk Hess:
Hey Berk,
Today I realized that I introduced a bug in the checkpoint writing just
before the RC1 release. Checkpointing are only written when the step is
coincidentally an energy output step (or correctly when the -nosum option
is used).
I have
Hello,
I have been using GROMACS for some very long (in wall clock terms)
simulations, and am curious as to how other users on this list solve the
problem of checkpointing long MD runs. It's a problem because of the
tendency of computational nodes in large HPC facilities (the more
Steven Kirk wrote:
/ Hello,
//
// I have been using GROMACS for some very long (in wall clock terms)
// simulations, and am curious as to how other users on this list solve the
// problem of checkpointing long MD runs. It's a problem because of the
// tendency of computational nodes in large
[EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, January 28, 2008 7:09:29 PM
Subject: Re: [gmx-users] Checkpointing GROMACS jobs
Steven Kirk wrote:
Hello,
I have been using GROMACS for some very long (in wall clock terms)
simulations, and am curious
Steven Kirk wrote:
Hello,
I have been using GROMACS for some very long (in wall clock terms)
simulations, and am curious as to how other users on this list solve the
problem of checkpointing long MD runs. It's a problem because of the
tendency of computational nodes in large HPC facilities
16 matches
Mail list logo
