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On 19/01/2012 8:45 PM, aiswarya pawar wrote:
<blockquote
cite="mid:CAEa6cRA_KF+nuwECQKrJDcvCzkeOOL60hrM1ypL-iJY4fxmdDw@mail.gmail.com"
type="cite">Mark,<br>
<br>
THe normal mdrun also hangs thus not generating any output. <br>
</blockquote>
<br>
OK. It's your problem to solve... keep simplifying stuff until you
can isolate a small number of possible causes. Top of the list is
file system availability.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEa6cRA_KF+nuwECQKrJDcvCzkeOOL60hrM1ypL-iJY4fxmdDw@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Thu, Jan 19, 2012 at 3:09 AM, 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:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 19/01/2012 2:59 AM, <a
moz-do-not-send="true"
href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>
wrote:
<blockquote type="cite">
<pre>Hi,
Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong.</pre>
</blockquote>
<br>
</div>
No, but you should start trying to simplify what you're
doing to see where the problem lies. Does normal mdrun work?<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite">
<pre>Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: Szilárd Páll <a moz-do-not-send="true" href="mailto:szilard.pall@cbr.su.se" target="_blank"><szilard.pall@cbr.su.se></a>
Sender: <a moz-do-not-send="true" href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>
Date: Wed, 18 Jan 2012 14:47:59
To: Discussion list for GROMACS users<a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Reply-To: Discussion list for GROMACS users <a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Subject: Re: [gmx-users] mdrun-gpu error
Hi,
Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.
Cheers,
--
Szilárd
On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
<a moz-do-not-send="true" href="mailto:aiswarya.pawar@gmail.com" target="_blank"><aiswarya.pawar@gmail.com></a> wrote:
</pre>
<blockquote type="cite">
<pre>Hi users,
Am running mdrun on gpu . I receive an error such as=
WARNING: This run will generate roughly 38570 Mb of data
WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.
WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.
WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.
/bin/cat: file_loc: No such file or directory
and the job is running but the nothing written into .xtc, .trr, .edr files .
What could have gone wrong?
--
Aiswarya B Pawar
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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<br>
-- <br>
Aiswarya B Pawar<br>
<br>
Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
<br>
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