[gmx-users] Re: writing checkpoint

[xianghong qi]

Hi, Berk:

the nodes I've been using each have two
quad-core Xeon CPUs - Gromacs4 was compiled for use over an Infiniband
network.  Do you need more information?

Yes, I think this situation is so strange.  Thanks.
-Xianghong Qi

On Wed, Nov 5, 2008 at 7:36 AM, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
>
> That is very strange.
> If you did not set the -cpt option, mdrun should only write a checkpoint
> file
> every 15 minutes, not every 5 seconds.
>
> What kind of machine are you running on?
>
> Berk
>
>
> ------------------------------
> Date: Wed, 5 Nov 2008 06:58:33 -0500
> From: xianghong001 at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: writing checkpoint
>
>
> Thanks, Berk:
>
> My log file actually stop somewhere since its size didn't change for a long
> time.
> Yes, looks like it keeps writing checkpoint info.
> I should continue the simulation since the other file looks reasonable.
>
> I didn't use option -cpt.
> Thanks.
> -Xianghong Qi
> On Wed, Nov 5, 2008 at 6:39 AM, Berk Hess <gmx3 at hotmail.com> wrote:
>
> Hi,
>
> Why do the log file seem to stop?
> It keeps writing checkpoint info, right?
> So I assume it is still running fine.
>
> But it seems you have selected checkpointing at (nearly) every step.
> Did you use -cpt 0?
> If you don't want checkpoints, you have to set -cpt -1.
>
> Berk
>
> ------------------------------
> Date: Wed, 5 Nov 2008 06:10:03 -0500
> From: xianghong001 at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: writing checkpoint
>
>
> Hello, all:
>
> I got a message when I run my simulation:
>
> Writing checkpoint, step 100200 at Wed Nov  5 05:22:42 2008
> Writing checkpoint, step 100210 at Wed Nov  5 05:22:46 2008
> Writing checkpoint, step 100220 at Wed Nov  5 05:22:51 2008
> Writing checkpoint, step 100230 at Wed Nov  5 05:22:55 2008
> Writing checkpoint, step 100240 at Wed Nov  5 05:23:00 2008
> .log file seems stop, but simulation is still running, and I can see
> .xtc , .edr file are growing.  Does anyone has some idea about this
> situation?  Thanks in advance.
>
> -Xianghong Qi
>
>
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