<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks! Works for me now.<div><br></div><div>Carsten</div><div><br></div><div><br><div><div>On Nov 23, 2009, at 6:19 PM, Roland Schulz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>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 ;-).<br>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.<br>
<br>Roland<br><br><br><div class="gmail_quote">On Mon, Nov 23, 2009 at 11:21 AM, Carsten Kutzner <span dir="ltr"><<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
when using the master branch version with pulling, I get the<br>
following message on stderr as soon as a checkpoint file is written:<br>
<br>
pullx.xvg: Bad file descriptor<br>
pullf.xvg: Bad file descriptor<br>
<br>
This is due to the fact that xvg files are opened in 'w' mode in<br>
the xvgropen() routine, which prevents that gmx_fio_get_file_md5_lock()<br>
can rewind them with fseek/fseeko.<br>
<br>
The solution is to open xvg files in 'w+' mode in xvgropen(), so that<br>
they are readable when the checkpoint is written. I think none of the<br>
analysis tools do care whether the mode is w or w+? I assume that all<br>
xvg files opened by mdrun would yield these problems.<br>
<br>
Carsten<br>
<br>
<br>
<br>
--<br>
Dr. Carsten Kutzner<br>
Max Planck Institute for Biophysical Chemistry<br>
Theoretical and Computational Biophysics Department<br>
Am Fassberg 11<br>
37077 Goettingen, Germany<br>
Tel. +49-551-2012313, Fax: +49-551-2012302<br>
<a href="http://www.mpibpc.mpg.de/home/grubmueller/" target="_blank">www.mpibpc.mpg.de/home/grubmueller/</a><br>
<a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/" target="_blank">www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/</a><br>
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