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

Carsten Kutzner ckutzne at gwdg.de
Mon Nov 23 17:21:27 CET 2009


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.


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

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