<br><div class="gmail_extra"><div class="gmail_quote">On Mon, Dec 3, 2012 at 5:12 AM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="im">On Sun, Dec 2, 2012 at 12:58 PM, Shirts, Michael (mrs5pt) <span dir="ltr"><<a href="mailto:mrs5pt@eservices.virginia.edu" target="_blank">mrs5pt@eservices.virginia.edu</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div class="im">So, more progress, but no simulations running yet.<br>
<br>
mdrun -nt 8 -ntmpi 8 gives the same error as before (I actually tried that<br>
before, and forgot to include it in my error report)<br>
<br>
mdrun -ntmpi 8 -ntomp 1 gives the error<br>
Fatal error:<br>
OMP_NUM_THREADS (8) and the number of threads requested on the command line<br>
(1) have different values<br>
</div><div class="im"><div>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div></div></blockquote><div><br></div><div>We probably should print a notice that OMP_NUM_THREADS is set. Otherwise this is really confusing if OMP_NUM_THREADS isn't set by the user but by the system.</div>
</div></div></blockquote><div><br></div><div>There is a note printed whenever the number of OpenMP threads is set by OMP_NUM_THREADS instead of -ntomp.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div class="gmail_extra"><div class="gmail_quote"><div class="im">
<div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Fatal error:<br>
OMP_NUM_THREADS is invalid: '0'<br></blockquote><div><br></div></div><div>This is also for ntomp. Also there you wand to use 1 not 0 to disable OpenMP (1 because it is total number of threads and thus 1 means serial).</div>
<div class="im">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>
/var/spool/PBS/mom_priv/jobs/<a href="http://2053253.lc5.itc.virginia.edu.SC" target="_blank">2053253.lc5.itc.virginia.edu.SC</a>: line 22: 12201<br>
Illegal instruction /h3/n1/shirtsgroup/gromac<br>
s_46/install/bin/mdrun_d -ntomp 1 -ntmpi -8 -deffnm<br>
/bigtmp/mrs5pt/eth.vrescale.50<br></blockquote><div><br></div></div><div>I suppose the CPU on the compute node is different from the build host. You need to change GMX_CPU_ACCELERATION to the one correct for the compute node. It could also help to set GMX_DISTRIBUTABLE_BUILD (both are cmake options).</div>
</div></div></blockquote><div><br></div><div>GMX_DISTRIBUTABLE_BUILD only does one thing, it turns off rdtscp. Is the intention to provide more features for this option? If not, I don't see the point in not calling it GMX_DISABLE_RDTSCP.<br>
</div><div><br></div><div>Cheers,</div><div>--</div><div>Szilárd</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div class="gmail_extra"><div class="gmail_quote">
<div><br></div><div>Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>
Best,<div class="im"><br>
<div>~~~~~~~~~~~~<br>
Michael Shirts<br>
Assistant Professor<br>
Department of Chemical Engineering<br>
University of Virginia<br>
<a href="mailto:michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a><br>
<a href="tel:%28434%29-243-1821" value="+14342431821" target="_blank">(434)-243-1821</a><br>
<br>
<br>
</div></div><div class="im">> From: Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>><br>
> Date: Sun, 2 Dec 2012 09:34:11 +0100<br>
> To: "<a href="mailto:michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a>" <<a href="mailto:michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a>>, Discussion<br>
> list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
> Subject: Re: [gmx-developers] Gromacs trying to use OpenMP instead of<br>
> thread-mpi despite trying to convince it?<br>
</div><div><div>><div><div class="h5"><br>
> Hi,<br>
><br>
> You queuing system probably doesn't set OMP_NUM_THREADS then<br>
> and I assume this machine has at least 16 (HT) cores.<br>
> mdrun -ntmpi 8 -ntomp 1<br>
> will do what you want, or:<br>
> mdrun -nt 8 -ntmpi 8<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 12/02/2012 08:28 AM, Shirts, Michael (mrs5pt) wrote:<br>
>> Quick question:<br>
>><br>
>> Compiling the most recent code in release-4-6, I compile without OpenMP<br>
>> (because using group rather than verlet cutoffs), and using any of the<br>
>> below:<br>
>><br>
>> mdrun_d -ntmpi 8 -deffnm ethrun<br>
>> or<br>
>> mdrun_d -nt 8 -deffnm ethrun<br>
>> or<br>
>> mdrun_d -deffnm ethrun<br>
>> or<br>
>> mdrun_d -ntomp 0 -deffnm ethrun<br>
>> or<br>
>> mdrun_d -ntomp 0 -ntmpi8 -deffnm ethrun<br>
>><br>
>> I get:<br>
>> Fatal error:<br>
>> OpenMP threads are requested, but Gromacs was compiled without OpenMP<br>
>> support<br>
>> For more information and tips for troubleshooting, please check the GROMACS<br>
>> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
>><br>
>> Even though I'm presumably requesting thread-mpi. Worked fine with -nt<br>
>> previously (before the new -nt options introduced a few months back).<br>
>><br>
>> Any suggestions or something I'm doing wrong? Perhaps gromacs is<br>
>> interpreting the cluster environment as requesting OpenMP somehow? FWIW, the<br>
>> PBS script request line is "#PBS -l select=1:mpiprocs=8:ncpus=8".<br>
>><br>
>> Apologies if I missed this answers somewhere out there already.<br>
>><br>
>> Thanks,<br>
>> ~~~~~~~~~~~~<br>
>> Michael Shirts<br>
>> Assistant Professor<br>
>> Department of Chemical Engineering<br>
>> University of Virginia<br>
>> <a href="mailto:michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a><br>
>> <a href="tel:%28434%29-243-1821" value="+14342431821" target="_blank">(434)-243-1821</a><br>
>><br>
><br>
<br>
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<br>
</div></div></div></div></blockquote></div><span class=""><font color="#888888"><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
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