<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 10/04/2012 5:07 AM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQFjzp8-EhFPYqYF20Uh+sctcgCvGWqaBm=MuerEpcy+-g@mail.gmail.com"
type="cite">Well, I did not change anything. I use Gromacs 4.5.4.
Other windows work fine, just 2 out of 30 failed like this. Shall
I rerun it from the begining then?<br>
</blockquote>
<br>
OK, I'll spell it out then... if your file system might have been
transiently failing to serve a file, try the command again. Make a
backup. Try the backup you may have created previously.<br>
<br>
Do some detective work... what was the file size? when was it last
modified? what size is it now? is 641K the whole file or just part
of it? What can you deduce from all of this?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKZJqQFjzp8-EhFPYqYF20Uh+sctcgCvGWqaBm=MuerEpcy+-g@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Mon, Apr 9, 2012 at 8:04 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5">On 10/04/2012 4:50 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
<br>
I am running umbrella sampling on the cluster. The wall
time is 72 hours so I have to rerun my simulation every
time. After first 72 hours I rerun my simulation:<br>
<br>
pbsexec mpiexec mdrun -s umbrella0.tpr -cpi
umbrella0.cpt -append -deffnm umbrella0 -pf
pullf-umbrella0.xvg -px pullx-umbrella0.xvg<br>
<br>
where tpr file is the one used in the initial MD run.
Then I got:<br>
<br>
Fatal error:<br>
Can't read 640794 bytes of 'pullx-umbrella0.xvg' to
compute checksum. The file has been replaced or its
contents has been modified.<br>
<br>
<br>
Do you have any clue?<br>
</blockquote>
<br>
</div>
</div>
It means what it says. The files cannot change between runs if
you wish to use -append. It is possible your filesystem was
transiently failing to serve the correct file.<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>