Re: [gmx-users] Checkpoint files not being written

Fri, 10 Sep 2010 11:13:20 -0700 


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: g...@hotmail.com
To: gmx-users@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: jalem...@vt.edu
 > To: gmx-users@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
 >
 > ========================================
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users

 > Please search the archive at 
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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

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