[gmx-developers] mdrun with pulling - "Bad file descriptor"

[Carsten Kutzner]

Thanks! Works for me now.

Carsten


On Nov 23, 2009, at 6:19 PM, Roland Schulz wrote:

> Hi,
> 
> I already fixed this bug 2 weeks ago but forgot to push it on the git server. Sorry! Ironically I noticed 5min before you wrote this email ;-).
> Please check whether it fixes it for you. I fixed it by not computing the md5 sum for xvg. I think it is sufficient to check the md5 for the standard files. In case you would like the md5sum also for xvg files, I'm happy to change it.
> 
> Roland
> 
> 
> On Mon, Nov 23, 2009 at 11:21 AM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
> Hi,
> 
> when using the master branch version with pulling, I get the
> following message on stderr as soon as a checkpoint file is written:
> 
> pullx.xvg: Bad file descriptor
> pullf.xvg: Bad file descriptor
> 
> This is due to the fact that xvg files are opened in 'w' mode in
> the xvgropen() routine, which prevents that gmx_fio_get_file_md5_lock()
> can rewind them with fseek/fseeko.
> 
> The solution is to open xvg files in 'w+' mode in xvgropen(), so that
> they are readable when the checkpoint is written. I think none of the
> analysis tools do care whether the mode is w or w+? I assume that all
> xvg files opened by mdrun would yield these problems.
> 
> Carsten
> 
> 
> 
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics Department
> Am Fassberg 11
> 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> www.mpibpc.mpg.de/home/grubmueller/
> www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/
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