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 now
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 d
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 t
the
checkpoint already exists.
On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham
wrote:
- Original Message -
From: Jack Shultz
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users, Andrey
Voronkov
We have mdrun integrated into our
, Feb 2, 2010 at 6:18 PM, Mark Abraham
>> wrote:
>>>
>>>
>>> ----- Original Message -
>>> From: Jack Shultz
>>> Date: Wednesday, February 3, 2010 2:36
>>> Subject: [gmx-users] Checkpointing
>>> To: Discussion list for GROMACS
-
From: Jack Shultz
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users, Andrey
Voronkov
We have mdrun integrated into our distributed computing project. When
your users suspend or close the manger it checkpoints, so when they
ope
ednesday, February 3, 2010 2:36
> Subject: [gmx-users] Checkpointing
> To: Discussion list for GROMACS users , Andrey
> Voronkov
>
>> We have mdrun integrated into our distributed computing project. When
>> your users suspend or close the manger it checkpoints, so when th
- Original Message -
From: Jack Shultz
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users , Andrey Voronkov
> We have mdrun integrated into our distributed computing project. When
> your users suspend or close the man
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.
m
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
.
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
...but no
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 wri
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 l
d van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
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)
> simulation
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 (t
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
processors,
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