hi,<div><br></div><div>could you specify the system size? </div><div><br></div><div>How many steps did it run before you got the segmentation fault? Try to find if everything went ok until the segmentation fault by saving log and trajectories.</div>
<div><br></div><div>amit</div><div><br></div><div><br><br><div class="gmail_quote">On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
<a href="mailto:rainy908@yahoo.com" target="_blank">rainy908@yahoo.com</a> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
The relevant lines of my script are the following:<br>
<br>
line 27: # Run MD and write output to /nas2 disk<br>
line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr<br>
line 29:<br>
line 30: # MDRUN completes: now make the next run file for a further 200 ps, to be run by next job<br>
line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o npg3_4_2.tpr -extend 200000<br>
<br>
<br>
Since line 31 would be carried out after line 28, I'm not sure why the comment "-s: command not found" is relevant?<br>
<br>
</blockquote>
<br></div>
Because mdrun is exiting, so the script is moving on. Perhaps the system isn't recognizing the $TPBCONV environment variable, and thus is interpreting "-s" as a separately command rather than an option passed to tpbconv.<br>
<font color="#888888">
<br>
-Justin</font><div class="im"><br>
<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div class="h5">
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