[gmx-developers] cpt overwritten by empty file

[Sander Pronk]

As mentioned by Chris, this should've been fixed earlier, but looking at the code now there was a possibility of this happening (but only on macs & BSD machines, with file systems that don't obey rename atomicity). I've fixed that.

Sander

On Aug 14, 2010, at 16:12 , David van der Spoel wrote:

> Hi,
> 
> I found a problem with checkpoint files:
> -rw-r--r-- 1 x_davva x_davva 635264 Aug 14 04:49 mutant20.cpt
> -rw-r--r-- 1 x_davva x_davva 635264 Aug 14 04:49 mutant20_prev.cpt
> -rw-r--r-- 1 x_davva x_davva      0 Aug 14 04:49 mutant21.cpt
> -rw-r--r-- 1 x_davva x_davva      0 Aug 14 04:49 mutant21_prev.cpt
> -rw-r--r-- 1 x_davva x_davva      0 Aug 14 04:49 mutant22.cpt
> -rw-r--r-- 1 x_davva x_davva      0 Aug 14 04:49 mutant22_prev.cpt
> -rw-r--r-- 1 x_davva x_davva      0 Aug 14 04:49 mutant27.cpt
> -rw-r--r-- 1 x_davva x_davva 635264 Aug 14 04:49 mutant27_prev.cpt
> 
> As you see in some cases the _prev.cpt files have been overwritten by a newer, empty file. This means that I have no way of continuing my (REMD) run from the checkpoint file (but I have trr files). Maybe we need a check before overwriting the _prev.cpt file?
> 
> This was done with a quite recent head branch
> [neolith1:mutant/REMD] % ls -l `which mdrun`
> -rwxr-xr-x 1 x_davva x_davva 3700870 Jul  7 08:08 /home/x_davva/software-4.5b/bin/mdrun
> 
> Cheers,
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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