[gmx-users] mdrun cpt

Mark Abraham mark.j.abraham at gmail.com
Tue Oct 29 08:10:49 CET 2013 

On Oct 29, 2013 1:26 AM, "Pavan Ghatty" <pavan.gromacs at gmail.com> wrote:
>
> Now /afterok/ might not work since technically the job is killed due to
> walltime limits - making it not ok.

Hence use -maxh!

Mark

> So I suppose /afterany/ is a better
> option. But I do appreciate your warning about spamming the queue and yes
I
> will re-read PBS docs.
>
>
> On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham <mark.j.abraham at gmail.com
>wrote:
>
> > 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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