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

Roland Schulz roland at utk.edu
Mon Nov 23 18:19:54 CET 2009


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.


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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