[gmx-users] Checkpoint files not being written

[Justin A. Lemkul]

Berk Hess wrote:
> Hi,
> 
> I guess you have nstlist=0.
> Try the fix below.
> 

Yes, that is the case.  I was using settings to employ the accelerated 
all-vs-all kernel.  The fix below works and I have produced a .cpt file at the 
appropriate time.

Thanks for the quick fix.

-Justin

> Berk
> 
> 
> diff --git a/src/kernel/md.c b/src/kernel/md.c
> index dd92d51..225a4bb 100644
> --- a/src/kernel/md.c
> +++ b/src/kernel/md.c
> @@ -1859,7 +1859,7 @@ double do_md(FILE *fplog,t_commrec *cr,int 
> nfile,const t_filenm fnm[],
>           * or at the last step (but not when we do not want confout),
>           * but never at the first step or with rerun.
>           */
> -        bCPT = (((gs.set[eglsCHKPT] && bNS) ||
> +        bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
>                   (bLastStep && (Flags & MD_CONFOUT))) &&
>                  step > ir->init_step && !bRerunMD);
>          if (bCPT)
> 
> ------------------------------------------------------------------------
> From: gmx3 at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Checkpoint files not being written
> Date: Fri, 10 Sep 2010 17:58:33 +0200
> 
> Hi,
> 
> Do you have no cut-off's and nstlist set to 0?
> That's the only case where I could see that checkpoints are missing.
> If that's the case, please file a bugzilla so we don't forget to fix 
> this for 4.5.2.
> 
> PS -cpnum has nothing to do with this.
> I guess it's the bCPT = assignment in md.c that only gets set at NS 
> steps or the last step.
> 
> Berk
> 
>  > Date: Fri, 10 Sep 2010 11:08:26 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: [gmx-users] Checkpoint files not being written
>  >
>  >
>  > Hi All,
>  >
>  > I don't know if this is a new (intended) feature or a bug, so I 
> figured I'd ask
>  > :) I'm running version 4.5.1 to do some implicit solvent simulations. 
> What
>  > I've noticed is that, no matter how long the simulation runs, I only 
> ever get a
>  > checkpoint file at the end of the simulation, and thus the checkpoint 
> interval
>  > (which I have left at the default value of 15) is ignored. All the 
> simulations
>  > I've done are sufficiently long (at least one hour) such that they 
> should have
>  > produced checkpoint files according to this interval.
>  >
>  > Could this issue be related to the introduction of the -cpnum flag, 
> which is set
>  > to "no" by default? I've poked around a bit in the mdrun code, but I 
> easily
>  > lose my place trying to trace what's going on. I've tried 
> specifically adding
>  > -cpnum to my mdrun command line, but still I am not receiving any 
> intermediate
>  > checkpoint files at the requested -cpt interval.
>  >
>  > -Justin
>  >
>  > --
>  > ========================================
>  >
>  > 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
>  >
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-- 
========================================

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

========================================