[gmx-users] mdrun cpt

[Mark Abraham]

On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty <pavan.gromacs at gmail.com>wrote:

> Mark,
>
> The problem with one .tpr file set for 100ns is that when job number (say)
> 4 hits the wall limit, it crashes and never gets a chance to submit the
> next job. So it's not really automated.
>

That's why I suggested -maxh, so you can have an orderly shutdown. (Though
if a job can get suspended, that won't always help, because mdrun can't
find out about the suspension...)

Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
> till job 4 ends.


Sure - read your PBS docs and find the environment variable to read so that
job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on
it. But don't tell your sysadmins where I live. ;-) Seriously, if you live
on this edge, you could spam infinite jobs, which tends to get your account
cut off. That's why you want the afterok hold - you only want the next job
to start if the exit code from the first script correctly indicates that
mdrun exited correctly. Test carefully!

Mark

But the PBS queuing system is sometime weird and takes a
> bit of time to recognize a job and give back its jobID. So I could submit
> job 5 but be unable to change its status to /hold/ because PBS does not
> return its ID. Another problem is that if resources are available, job 5
> could start before I ever get a chance to /hold/ it.
>
>
>
>
> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty <pavan.gromacs at gmail.com
> > >wrote:
> >
> > > I have need to collect 100ns but I can collect only ~1ns (1000steps)
> per
> > > run. Since I dont have .trr files, I rely on .cpt files for restarts.
> For
> > > example,
> > >
> > > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
> > >
> > > This runs into a problem when the run gets killed due to walltime
> > limits. I
> > > now have a .xtc file which has run (say) 700 steps and a .cpt file
> which
> > > was last written at 600th step.
> > >
> >
> > You seem to have no need to use grompp, because you don't need to use a
> > workflow that generates multiple .tpr files. Do the equivalent of what
> the
> > restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
> .tpr
> > for the whole 100ns run, and then keep doing
> >
> > mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
> >
> > with or without -append, perhaps with -maxh, keeping whatever manual
> > backups you feel necessary. Then perhaps concatenate your final
> trajectory
> > files, according to your earlier choices.
> >
> > - To set up the next run I use the .cpt file from 600th step.
> > > - Now during analysis if I want to center the protein and such,
> /trjconv/
> > > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
> > know
> > > to stop at 600th step?
> >
> >
> > trjconv just operates on the contents of the trajectory file, as modified
> > by things like -b -e and -dt. The .tpr just gives it context, such as
> atom
> > names. You could give it a .tpr from any point during the run.
> >
> > Mark
> >
> > If this has to be put in manually, it becomes
> > > cumbersome.
> > >
> > > Thoughts?
> > >
> > >
> > >
> > >
> > >
> > > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >
> > > >
> > > >
> > > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
> > > >
> > > >> Hello All,
> > > >>
> > > >> Is there a way to make mdrun put out .cpt file with the same
> frequency
> > > as
> > > >> a
> > > >> .xtc or .trr file. From here
> > > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that
> > we
> > > >> can choose how often (time in mins) the .cpt file is written. But
> > > clearly
> > > >> if the frequency of output of .cpt (frequency in mins) and .xtc
> > > (frequency
> > > >> in simulation steps) do not match, it can create problems during
> > > analysis;
> > > >> especially in the event of frequent crashes. Also, I am not storing
> > .trr
> > > >> file since I dont need that precision.
> > > >> I am using Gromacs 4.6.1.
> > > >>
> > > >>
> > > > What problems are you experiencing?  There is no need for .cpt
> > frequency
> > > > to be the same as .xtc frequency, because any duplicate frames should
> > be
> > > > handled elegantly when appending.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==============================**====================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Postdoctoral Fellow
> > > >
> > > > Department of Pharmaceutical Sciences
> > > > School of Pharmacy
> > > > Health Sciences Facility II, Room 601
> > > > University of Maryland, Baltimore
> > > > 20 Penn St.
> > > > Baltimore, MD 21201
> > > >
> > > > jalemkul at outerbanks.umaryland.**edu <
> jalemkul at outerbanks.umaryland.edu
> > >
> > > | (410)
> > > > 706-7441
> > > >
> > > > ==============================**====================
> > > > --
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