js at drugdiscoveryathome.com
Wed Feb 3 05:44:03 CET 2010
I will try it without the checkpointing flags. 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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