Justin,<br><br>Sorry for not giving the correct information. <br><br>Gromacs version 4.5.5<br>Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor)<br>Cuda version 3.1<br>CMake 2.8<br><br>I installed the OpenMM from the source using commands=<br>
<br>ccmake -i .<br>make<br>make test<br>make install<br><br>everything went fine and set the paths<pre>export OPENMM_ROOT_DIR=path_to_custom_openmm_installation<br>cmake -DGMX_OPENMM=ON </pre>then <br>make<br>make install<br>
<br>The submission script used is=<br><br>#!/bin/csh<br>#PBS -l gpu=1 <br>#PBS -l ncpus=1 <br>#PBS -o /global/utemp/cuda-out2.out<br>#PBS -e /global/utemp/cuda-err2.out<br>
/home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device "OpenMM:platform=Cuda,<span class="st">DeviceID=0,Memtest=15,<em></em></span>,force-device=yes" -v -deffnm /global/utemp/md <br><br>for this i receive an error such as<br>
Cuda error in file '/home/staff/software/openmm_tesla/platforms/cuda/./src/kernels//<a href="http://bbsort.cu">bbsort.cu</a>' in line 176 : unspecified launch failure.<br>/bin/cat: file_loc: No such file or directory<br>
<br><br><br><br><div class="gmail_quote">On Thu, Jan 19, 2012 at 11:41 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:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="im"><br>
<br>
aiswarya pawar wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Szilárd,<br>
<br>
I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right.<br>
<br>
</blockquote>
<br></div>
You're trying to solve multiple problems at once. You told Mark that the normal mdrun executable (which works independently of any GPU components) also hangs, so either your filesystem is faulty or your installation procedure produced nonfunctional executables.<br>
<br>
You're posting bits and pieces of information, which makes it incredibly hard for anyone to help you. Let's recap and try again. Please provide:<br>
<br>
1. The Gromacs version you're using<br>
2. Description of the hardware (GPU and non-GPU components)<br>
3. Installation procedure for Gromacs and any of the prerequisite software and libraries that were required, including versions<br>
4. The exact command(s) you're issuing, including the full script that is causing a problem<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Thanks<div class="im"><br>
<br>
On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll <<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a> <mailto:<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a><u></u>>> wrote:<br>
<br>
That's a generic GPU kernel launch failure which can mean anything,<br>
from faulty hardware to bad driver to messed up installation.<br>
<br>
Does the memory test run? Try to compile/install again and see if it<br>
works.<br>
<br>
--<br>
Szilárd<br>
<br>
<br>
<br>
On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar<br></div><div class="im">
<<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> <mailto:<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.<u></u>com</a>>> wrote:<br>
> when i tired running it again, i got an error as<br>
><br>
> Cuda error in file<br>
><br>
'/home/staff/sec/secdpal/<u></u>software/openmm_tesla/<u></u>platforms/cuda/./src/kernels//<a href="http://bbsort.cu" target="_blank"><u></u>bbsort.cu</a><br></div>
<<a href="http://bbsort.cu" target="_blank">http://bbsort.cu</a>>'<div class="im"><br>
> in line 176 : unspecified launch failure.<br>
><br>
> /bin/cat: file_loc: No such file or directory<br>
><br>
><br>
> On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar<br></div>
<<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> <mailto:<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.<u></u>com</a>>><div class="im">
<br>
> wrote:<br>
>><br>
>> Has the tesla card got to do anything with the error. Am<br>
using Nvidia<br>
>> Tesla S1070 1U server.<br>
>><br>
>><br>
>> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll<br></div>
<<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a> <mailto:<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a><u></u>>><div class="im"><br>
>> wrote:<br>
>>><br>
>>> And sorting out where the /bin/cat error comes from because that is<br>
>>> surely not a Gromacs message!<br>
>>><br>
>>> Cheers,<br>
>>> --<br>
>>> Szilárd<br>
>>><br>
>>><br>
>>><br>
>>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham<br></div>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>><div class="im"><br>
>>> 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<br>
until you can<br>
>>> > isolate a small number of possible causes. Top of the list is<br>
file<br>
>>> > system<br>
>>> > availability.<br>
>>> ><br>
>>> > Mark<br>
>>> ><br>
>>> ><br>
>>> ><br>
>>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham<br></div>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>><div class="im"><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><br></div><div class="im">
<mailto:<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.<u></u>com</a>> wrote:<br>
>>> >><br>
>>> >> Hi,<br>
>>> >><br>
>>> >> Its going into the running mode but gets hang there for long<br>
hours<br>
>>> >> which<br>
>>> >> generating any data in the output file. And am not able to<br>
figure out<br>
>>> >> 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<br>
doing to see<br>
>>> >> where<br>
>>> >> the problem lies. Does normal mdrun work?<br>
>>> >><br>
>>> >> Mark<br>
>>> >><br>
>>> >><br>
>>> >> Thanks<br></div>
>>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1<div class="im"><br>
Network. Go<br>
>>> >> 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></div><div class="im">
<mailto:<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a><u></u>>><br>
>>> >> Sender: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@<u></u>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></div><div class="im">
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><u></u>><br>
>>> >> Reply-To: Discussion list for GROMACS users<br></div><div class="im">
<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><u></u>><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<br>
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></div>
>>> >> <<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> <mailto:<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.<u></u>com</a>>><div>
<div class="h5"><br>
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<br>
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<br>
>>> >> coupling.<br>
>>> >><br>
>>> >><br>
>>> >> WARNING: OpenMM provides contraints as a combination of<br>
SHAKE, SETTLE<br>
>>> >> and<br>
>>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the<br>
"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,<br>
.trr, .edr<br>
>>> >> 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></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
>>> >> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>Support/Mailing_Lists/Search</a> before<br>
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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
>>> >> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
>>> >> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>Support/Mailing_Lists/Search</a> before<br>
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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
>>> >> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
>>> >> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>Support/Mailing_Lists/Search</a> before<br>
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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
>>> >> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
>>> ><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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
>>> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>Support/Mailing_Lists/Search</a> before<br>
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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
>>> > Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
>>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
>><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>
> 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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>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></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
-- <br>
Aiswarya B Pawar<br>
<br>
Bioinformatics Dept,<br>
Indian Institute of Science<br>
Bangalore<br>
<br>
<br>
</div></blockquote>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<div class="HOEnZb"><div class="h5"><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/<u></u>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/<u></u>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 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/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Aiswarya B Pawar<br><br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br><br>