when i tired running it again, i got an error as <div><br></div><div><span class="Apple-style-span" style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//<a href="http://bbsort.cu/" target="_blank" style="color:rgb(17,85,204)">bbsort.cu</a>' in line 176 : unspecified launch failure.<br>
/bin/cat: file_loc: No such file or directory</span><br><br><div class="gmail_quote">On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar <span dir="ltr"><<a href="mailto:aiswarya.pawar@gmail.com">aiswarya.pawar@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Has the tesla card got to do anything with the error. Am using <span style="font-family:Verdana,Arial,Helvetica,sans-serif;font-size:12px">Nvidia Tesla S1070 1U server.</span><div class="HOEnZb">
<div class="h5"><div><font face="Verdana, Arial, Helvetica, sans-serif"><span style="font-size:12px"><br>
</span></font><br><div class="gmail_quote">On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll <span dir="ltr"><<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
And sorting out where the /bin/cat error comes from because that is<br>
surely not a Gromacs message!<br>
<br>
Cheers,<br>
<span><font color="#888888">--<br>
Szilárd<br>
</font></span><div><div><br>
<br>
<br>
On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>> wrote:<br>
> On 19/01/2012 8:45 PM, aiswarya pawar wrote:<br>
><br>
> Mark,<br>
><br>
> THe normal mdrun also hangs thus not generating any output.<br>
><br>
><br>
> OK. It's your problem to solve... keep simplifying stuff until you can<br>
> isolate a small number of possible causes. Top of the list is file system<br>
> availability.<br>
><br>
> Mark<br>
><br>
><br>
><br>
> On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
> wrote:<br>
>><br>
>> On 19/01/2012 2:59 AM, <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> Its going into the running mode but gets hang there for long hours which<br>
>> generating any data in the output file. And am not able to figure out the<br>
>> error file_doc. Please anyone knows what's going wrong.<br>
>><br>
>><br>
>> No, but you should start trying to simplify what you're doing to see where<br>
>> the problem lies. Does normal mdrun work?<br>
>><br>
>> Mark<br>
>><br>
>><br>
>> Thanks<br>
>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for<br>
>> it!<br>
>><br>
>> -----Original Message-----<br>
>> From: Szilárd Páll <<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a>><br>
>> Sender: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
>> Date: Wed, 18 Jan 2012 14:47:59<br>
>> To: Discussion list for GROMACS users<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
>> Reply-To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
>> Subject: Re: [gmx-users] mdrun-gpu error<br>
>><br>
>> Hi,<br>
>><br>
>> Most of those are just warnings, the only error I see there comes from<br>
>> the shell, probably an error in your script.<br>
>><br>
>> Cheers,<br>
>> --<br>
>> Szilárd<br>
>><br>
>><br>
>><br>
>> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar<br>
>> <<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>> wrote:<br>
>><br>
>> Hi users,<br>
>><br>
>> Am running mdrun on gpu . I receive an error such as=<br>
>><br>
>> WARNING: This run will generate roughly 38570 Mb of data<br>
>><br>
>><br>
>> WARNING: OpenMM does not support leap-frog, will use velocity-verlet<br>
>> integrator.<br>
>><br>
>><br>
>> WARNING: OpenMM supports only Andersen thermostat with the<br>
>> md/md-vv/md-vv-avek integrators.<br>
>><br>
>><br>
>> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.<br>
>><br>
>><br>
>> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and<br>
>> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"<br>
>> option.<br>
>><br>
>> /bin/cat: file_loc: No such file or directory<br>
>><br>
>><br>
>> and the job is running but the nothing written into .xtc, .trr, .edr files<br>
>> .<br>
>> What could have gone wrong?<br>
>><br>
>> --<br>
>> Aiswarya B Pawar<br>
>><br>
>> Bioinformatics Dept,<br>
>> Indian Institute of Science<br>
>> Bangalore<br>
>><br>
>><br>
>><br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
>> <a 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<br>
>> <a 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<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>><br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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>> Please don't post (un)subscribe requests to the list. Use the<br>
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>><br>
>><br>
>><br>
>><br>
>><br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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>> Please search the archive at<br>
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><br>
><br>
><br>
><br>
> --<br>
> Aiswarya B Pawar<br>
><br>
> Bioinformatics Dept,<br>
> Indian Institute of Science<br>
> Bangalore<br>
><br>
><br>
><br>
><br>
><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> <a 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<br>
> <a 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<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a 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 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<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Aiswarya B Pawar<br><br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br><br>
</div>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Aiswarya B Pawar<br><br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br><br>
</div>