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Hi Berk,<br>
<br>
Thanks for your reply! The result of "gmxdump -cp T298.cpt" is given
as follows (the long list of x, v, E is not shown)<br>
**************************************<br>
number of output files = 4<br>
output filename = T298.log<br>
file_offset_high = 0<br>
file_offset_low = 7228659<br>
output filename = T298.trr<br>
file_offset_high = 0<br>
file_offset_low = 0<br>
output filename = T298.xtc<br>
file_offset_high = 0<br>
file_offset_low = -2020699160<br>
output filename = T298.edr<br>
file_offset_high = 0<br>
file_offset_low = 13270732<br>
**************************************<br>
But I don't know what this number means! On the other hand, another
system, which can be continued using "mdrun -cpi T298.cpt", gives the
following result of "gmxdump -cp T298.cpt"<br>
***************************************<br>
number of output files = 4<br>
output filename = T298.log<br>
file_offset_high = 0<br>
file_offset_low = 7066641<br>
output filename = T298.trr<br>
file_offset_high = 0<br>
file_offset_low = 0<br>
output filename = T298.xtc<br>
file_offset_high = 0<br>
file_offset_low = 2144960064<br>
output filename = T298.edr<br>
file_offset_high = 0<br>
file_offset_low = 19540796<br>
***************************************<br>
It seems that the difference is: there is a negative number
(-2020699160) in the former case. <br>
<br>
So what should I do?<br>
<br>
regards,<br>
<br>
<br>
Berk Hess wrote:
<blockquote cite="mid:COL113-W25E4F4ACF1CACFBCF622F28E0B0@phx.gbl"
type="cite">
<pre wrap="">My guess would be that for some reason (which I don't know),
your xtc file has not been written to disk completely.
You can check this by using gmxdump -cp on your checkpoint file
and looking at the size of the xtc file.
Berk
</pre>
<blockquote type="cite">
<pre wrap="">Date: Fri, 7 Aug 2009 10:19:35 +0200
From: <a class="moz-txt-link-abbreviated" href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
Subject: [gmx-users] question about mdrun -append
Hi all,
I meet one problem when I am using mdrun -append. In some cases, the
following error information happens, and mdrun is halted
*************************************************
Program mdrun, VERSION 4.0.5
Source code file: checkpoint.c, line: 1248
Fatal error:
Truncation of file T298.xtc failed.
*************************************************
Line 1248 in checkpoint.c is the inner loop as follows
*********************************************************************************
if(bAppendOutputFiles) {
for(i=0;i<nfiles;i++) {
if(0 !=
truncate(outputfiles[i].filename,outputfiles[i].offset) ) {
gmx_fatal(FARGS,"Truncation of file %s
failed.",outputfiles[i].filename);
}
}
}
*********************************************************************************
But I don't know how to solve it. Please give some suggestions! Thanks a
lot!
The following script is used
grompp -f T298.mdp -c pre2.gro -p system.top -o T298
mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5
mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 -cpi T298.cpt -append
regards,
Baofu Qiao
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</blockquote>
<pre wrap=""><!---->
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Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></pre>
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