[gmx-developers] Gromacs trying to use OpenMP instead of thread-mpi despite trying to convince it?

[Szilárd Páll]

On Mon, Dec 3, 2012 at 5:12 AM, Roland Schulz <roland at utk.edu> wrote:

>
>
>
> On Sun, Dec 2, 2012 at 12:58 PM, Shirts, Michael (mrs5pt) <
> mrs5pt at eservices.virginia.edu> wrote:
>
>> So, more progress, but no simulations running yet.
>>
>> mdrun -nt 8 -ntmpi 8 gives the same error as before (I actually tried that
>> before, and forgot to include it in my error report)
>>
>> mdrun -ntmpi 8 -ntomp 1 gives the error
>> Fatal error:
>> OMP_NUM_THREADS (8) and the number of threads requested on the command
>> line
>> (1) have different values
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>
> 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.
>

There is a note printed whenever the number of OpenMP threads is set by
OMP_NUM_THREADS instead of -ntomp.


>
>
>> Fatal error:
>> OMP_NUM_THREADS is invalid: '0'
>>
>
> 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).
>
>>
>> /var/spool/PBS/mom_priv/jobs/2053253.lc5.itc.virginia.edu.SC: line 22:
>> 12201
>> Illegal instruction     /h3/n1/shirtsgroup/gromac
>> s_46/install/bin/mdrun_d -ntomp 1 -ntmpi -8 -deffnm
>> /bigtmp/mrs5pt/eth.vrescale.50
>>
>
> 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).
>

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.

Cheers,
--
Szilárd


>
> Roland
>
>
>>
>> Best,
>>
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821
>>
>>
>> > From: Berk Hess <hess at kth.se>
>> > Date: Sun, 2 Dec 2012 09:34:11 +0100
>> > To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>,
>> Discussion
>> > list for GROMACS development <gmx-developers at gromacs.org>
>> > Subject: Re: [gmx-developers] Gromacs trying to use OpenMP instead of
>> > thread-mpi despite trying to convince it?
>> >
>>
>> > Hi,
>> >
>> > You queuing system probably doesn't set OMP_NUM_THREADS then
>> > and I assume this machine has at least 16 (HT) cores.
>> > mdrun -ntmpi 8 -ntomp 1
>> > will do what you want, or:
>> > mdrun -nt 8 -ntmpi 8
>> >
>> > Cheers,
>> >
>> > Berk
>> >
>> > On 12/02/2012 08:28 AM, Shirts, Michael (mrs5pt) wrote:
>> >> Quick question:
>> >>
>> >> Compiling the most recent code in release-4-6, I compile without OpenMP
>> >> (because using group rather than verlet cutoffs), and using any of the
>> >> below:
>> >>
>> >> mdrun_d -ntmpi 8 -deffnm ethrun
>> >> or
>> >> mdrun_d -nt 8 -deffnm ethrun
>> >> or
>> >> mdrun_d -deffnm ethrun
>> >> or
>> >> mdrun_d -ntomp 0 -deffnm ethrun
>> >> or
>> >> mdrun_d -ntomp 0 -ntmpi8 -deffnm ethrun
>> >>
>> >> I get:
>> >> Fatal error:
>> >> OpenMP threads are requested, but Gromacs was compiled without OpenMP
>> >> support
>> >> For more information and tips for troubleshooting, please check the
>> GROMACS
>> >> website at http://www.gromacs.org/Documentation/Errors
>> >>
>> >> Even though I'm presumably requesting thread-mpi.  Worked fine with -nt
>> >> previously (before the new -nt options introduced a few months back).
>> >>
>> >> Any suggestions or something I'm doing wrong?  Perhaps gromacs is
>> >> interpreting the cluster environment as requesting OpenMP somehow?
>> FWIW, the
>> >> PBS script request line is "#PBS -l select=1:mpiprocs=8:ncpus=8".
>> >>
>> >> Apologies if I missed this answers somewhere out there already.
>> >>
>> >> Thanks,
>> >> ~~~~~~~~~~~~
>> >> Michael Shirts
>> >> Assistant Professor
>> >> Department of Chemical Engineering
>> >> University of Virginia
>> >> michael.shirts at virginia.edu
>> >> (434)-243-1821
>> >>
>> >
>>
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>>
>>
>>
>>
>>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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>
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