[gmx-users] checkpointing in 4.0.7

Dr. Leonid Yelash yelash at uni-mainz.de
Mon Mar 29 12:22:10 CEST 2010

Hi Mark,

thanks a lot for your reply. I checked the 4.0.7 version installed
on blugene and it also doesnt write checkpoints during simulations.
How it was compiled by support team i dont know, but in my
compilation i mostly used options from gromacs wiki page.
I think i'll not trace this issue now (due to time lack), but use
tpbconv for continuation runs. I though that someone perhaps
knows already solution.

Best regards,

Mark Abraham wrote:
> On 25/03/2010 10:01 PM, Dr. Leonid Yelash wrote:
>> Hello everybody,
>> does anyone have a similar problem writing checkpoints
>> from Gromacs 4.0.7?
>> I have two Gromacs versions, 4.0.5 and 4.0.7, compiled for
>> bluegene. The 4.0.5 writes state.cpt during mdrun and at
>> the end of simulation too. The 4.0.7 does it at the end of the
>> run only, but not during the simulation. All input files
>> (grompp.mdp, topol.top, conf) used to start mdrun are same.
>> To set/change the -cpt option of mdrun didnt help.
>> Will appreciate for any hint !
> I'm not aware of any BlueGene-related issue here. It's possible 
> something is causing the I/O buffering to work differently. You could 
> test this by starting a sufficiently long 4.0.7 simulation and seeing 
> what happens when you kill its job in LoadLeveler. Were the two 
> compilations done the same way linking to the same libraries?
> Also, do see if anything here 
> http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 
> pertains to your situation.
> Mark

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