Mark.Abraham at anu.edu.au
Wed Feb 3 05:56:48 CET 2010
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.
> 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.abraham at anu.edu.au> wrote:
>> ----- Original Message -----
>> From: Jack Shultz<js at drugdiscoveryathome.com>
>> Date: Wednesday, February 3, 2010 2:36
>> Subject: [gmx-users] Checkpointing
>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>, Andrey Voronkov<av at 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.
>>> 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).
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