On 03/02/10 16:38, Jack Shultz wrote:
So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll
try this approach again. I had a little trouble doing it this way
previously. I think I had trouble with the extension scripts doing it
this way.
I'd equilibrate, then use "mdrun -cpi state" and see from the timestamps
where the output .cpt is, and arrange future mdrun to use that. IIRC
GROMACS handles life to not lose data, but does so differently according
to the presence of -append. The more things you specify on the command
line, the lower the chance of you have of having work done for you, in
this regard.
Mark
On Tue, Feb 2, 2010 at 11:56 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 03/02/10 15:44, Jack Shultz wrote:
I will try it without the checkpointing flags.
That's not quite what I said. I suggested not using *different* filenames
for -cpo and -cpi. What you want is the output file from a former run to
transparently become the input file for the subsequent one, and I expect
GROMACS will handle this for you if you let it. Try some things and see.
Mark
If that fails, maybe
I'll introduce some python into this integration. Check if the
checkpoint already exists.
On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham<mark.abra...@anu.edu.au>
wrote:
----- Original Message -----
From: Jack Shultz<j...@drugdiscoveryathome.com>
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users<gmx-users@gromacs.org>, Andrey
Voronkov<a...@drugdiscoveryathome.com>
We have mdrun integrated into our distributed computing project. When
your users suspend or close the manger it checkpoints, so when they
open again it continues mdrun where it left off. However, when users
reboot, it starts from the beginning. We are using this command line
to execute the work.
mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt -
deffnm md)
If you're using this input line always, then you're getting what you're
asking for - an mdrun that begins from the state in md.cpt. Since you're
never updating that, it doesn't change.
Try not stipulating different -cpo and -cpi and see what the native
coping mechanism is. Otherwise, you'll have to write a bunch of scripting
logic to decide which .cpt to use each restart.
Mark
I have a seperate checkpoint for output so after this simulation we
can extend the workunit. Should we try using this append option?
Checkpoints containing the complete state of the system are
written at
regular intervals (option -cpt) to the file -cpo, unless option -cpt
is set to -1. A simulation can be continued by reading the full state
from file with option -cpi. This option is intelligent in the
way that
if no checkpoint file is found, Gromacs just assumes a normal
run and
starts from the first step of the tpr file.
With checkpointing you can also use the option -append to just
continue writing to the previous output files. This is not
enabled by
default since it is potentially dangerous if you move files, but if
you just leave all your files in place and restart mdrun with exactly
the same command (with options -cpi and -append) the result will be
the same as from a single run. The contents will be binary identical
(unless you use dynamic load balancing), but for technical reasons
there might be some extra energy frames when using checkpointing
(necessary for restarts without appending).
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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