[gmx-developers] ICC 14 support

Roland Schulz roland at utk.edu
Tue Sep 30 18:34:30 CEST 2014 

Hi,

before we can automatically run those we need a benchmark suite first:
http://redmine.gromacs.org/issues/1105. Someone needs to take the lead on
it. I'm sure others will help.

Roland

On Tue, Sep 30, 2014 at 11:07 AM, Shirts, Michael R. (mrs5pt) <
mrs5pt at eservices.virginia.edu> wrote:

>
>  Is there a plan (long term) to do (essentially) automated performance
> tests so that we can perform consistent(ish) checks for new changes in
> code, then post the results in an easy(ish) way to interpret for others?
>
>  Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>   From: Mark Abraham <mark.j.abraham at gmail.com>
> Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Date: Tuesday, September 30, 2014 at 10:59 AM
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] ICC 14 support
>
>
>
> On Tue, Sep 30, 2014 at 4:48 PM, Kevin Chen <fch6699 at gmail.com> wrote:
>
>> Have you guys compared GROMACS performance between icc and gcc? Per
>> Szilárd's note, seems gcc is better, am I right?
>>
>
>  Yeah, I'd take that one to the bank. Of course, we're always interested
> to hear of observations (either way).
>
>  Mark
>
>
>> Cheers,
>>
>> Kevin
>>
>>
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of
>> Szilárd Páll
>> Sent: Monday, September 29, 2014 3:50 PM
>> To: Discussion list for GROMACS development
>> Subject: Re: [gmx-developers] ICC 14 support
>>
>>  BTW: you'll have less trouble when combining with CUDA as well as
>> better performance with gcc!
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Mon, Sep 29, 2014 at 10:14 PM, Kevin Chen <fch6699 at gmail.com> wrote:
>> > Hi Roland,
>> >
>> >
>> >
>> > Thanks for the reply! Looks like the error messages were generated by
>> > Cuda6.0 (see errors below) instead of GROMACS. Switching back to
>> > ICC13.1 and turning off static-libraries worked for us.
>> >
>> >
>> >
>> > Best,
>> >
>> >
>> >
>> > Kevin
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ======================================================================
>> > ===============================================================
>> >
>> >
>> >
>> > “In file included from /opt/apps/cuda/6.0/include/cuda_runtime.h(59),
>> >
>> > /opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error:
>> > #error
>> > directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >   #error -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >    ^
>> >
>> >
>> >
>> > /opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error:
>> > #error
>> > directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >   #error -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >    ^
>> >
>> >
>> >
>> >                  from
>> >
>> /admin/build/admin/rpms/stampede/BUILD/gromacs-5.0.1/src/gromacs/gmxlib/gpu_utils/
>> gpu_utils.cu(0):
>> >
>> > /opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error:
>> > #error
>> > directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >   #error -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >    ^
>> >
>> >
>> >
>> > In file included from /opt/apps/cuda/6.0/include/cuda_runtime.h(59),
>> >
>> >                  from
>> >
>> /admin/build/admin/rpms/stampede/BUILD/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/
>> pmalloc_cuda.cu(0):
>> >
>> > /opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error:
>> > #error
>> > directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux
>> > x86_64 is supported!
>> >
>> >
>> >
>> > “
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se
>> > [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On
>> > Behalf Of Roland Schulz
>> > Sent: Monday, September 29, 2014 11:16 AM
>> > To: gmx-developers at gromacs.org
>> > Subject: Re: [gmx-developers] ICC 14 support
>>
>> >
>> >
>> >
>> > Hi,
>> >
>> >
>> >
>> > what problem do you have with ICC14? Both ICC14 and ICC15 should work
>> fine.
>> > There was an issue with ICC14+static-libraries (9e8061e13f48, 4.6.7
>> > and
>> > 5.0.1) and ICC14+unit-tests(b0e60e91add6, 5.0.1). Both are fixed in
>> > release-5-0 and will be included 5.0.2. You can either use the
>> > release-5-0 branch, just apply the patch, wait till 5.0.2 (should be
>> > soon), or don't use static-libraries (default) and don't try to run
>> > the unit-tests (the compiler issue isn't present in the main code thus
>> > even though the unit tests fail the actual program is OK).
>> >
>> >
>> >
>> > Roland
>> >
>> >
>> >
>> > On Mon, Sep 29, 2014 at 10:35 AM, Kevin Chen <fch6699 at gmail.com> wrote:
>> >
>> > Hi Guys,
>> >
>> > Was wondering if GROMACS will support ICC 14 in the near future?
>> >
>> > Kevin Chen, Ph.D.
>> > HPC Applications, TACC
>> >
>> >
>> > -----Original Message-----
>> > From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se
>> > [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On
>> > Behalf Of Alexey Shvetsov
>> > Sent: Sunday, September 28, 2014 3:09 PM
>> > To: gmx-developers at gromacs.org
>> > Subject: Re: [gmx-developers] Possible bug in gmx
>> >
>> > Mark Abraham писал 28-09-2014 18:17:
>> >> How about a redmine issue - this thread's not about GROMACS
>> >> development, per se ;-)
>> >
>> > Sorry about that =D
>> >
>> > Redmine issue http://redmine.gromacs.org/issues/1607
>> > With relevant tpr file attached
>> >>
>> >> Mark
>> >>
>> >> On Sun, Sep 28, 2014 at 3:18 PM, Alexey Shvetsov
>> >> <alexxy at omrb.pnpi.spb.ru> wrote:
>> >>
>> >>> Hi Berk!
>> >>>
>> >>> Its not a cut and paste error, also there are no pdb dumps.
>> >>> Also I see this error before with other systems.
>> >>>
>> >>> I can provide tpr file for that system
>> >>>
>> >>> https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr [1]
>> >>>
>> >>> Berk Hess писал 28-09-2014 16:37:
>> >>>
>> >>> Hi,
>> >>>
>> >>> I assume that your old and be coordinates being identical is correct
>> >>> and not a cut-and-paste error.
>> >>> This seems a bit strange or do you freeze part of the system?
>> >>> The only things moving here are then the domain boundaries and I
>> >>> don't see an issue there, since they only moved a little.
>> >>>
>> >>> Do you have any more output besides the error message? PDB dump
>> >>> files maybe?
>> >>>
>> >>> Cheers,
>> >>>
>> >>> Berk
>> >>>
>> >>> On 09/28/2014 02:22 PM, Alexey Shvetsov wrote:
>> >>> Hi,
>> >>>
>> >>> just wanna add that this error seems to be reproducable even on
>> >>> single node. Also i get same error for gpu runs.
>> >>> However i dont see it in large systems (800k+ atoms) running on
>> >>> large number of cpus (512+)
>> >>>
>> >>> Alexey Shvetsov писал 28-09-2014 13:44:
>> >>> Hi,
>> >>>
>> >>> DD grid is
>> >>>
>> >>> Domain decomposition grid 4 x 1 x 1, separate PME ranks 0 PME domain
>> >>> decomposition: 4 x 1 x 1
>> >>>
>> >>> for 4 node setup
>> >>>
>> >>> and
>> >>>
>> >>> Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain
>> >>> decomposition: 4 x 2 x 1
>> >>>
>> >>> for 8 node setup
>> >>>
>> >>> It's reproducable with 5.0 release and latest git master. I try to
>> >>> check if its reproducable with 1 node. Also i can provide tpr file
>> >>> for this system
>> >>>
>> >>> Mark Abraham писал 28-09-2014 13:28:
>> >>> Hi,
>> >>>
>> >>> It's hard to say on that information. There were some issues fixed
>> >>> in the lead-up to GROMACS 5 with DD not always working with 2
>> >>> domains in a direction, but that's a pure guess. I'd assume you can
>> >>> reproduce this with release-5-0 branch. Do you observe it with a
>> single domain?
>> >>> If not, then it's surely a bug (and should be submitted to redmine).
>> >>>
>> >>> Mark
>> >>>
>> >>> On Sun, Sep 28, 2014 at 11:18 AM, Alexey Shvetsov
>> >>> <alexxy at omrb.pnpi.spb.ru> wrote:
>> >>>
>> >>> Hi all!
>> >>>
>> >>> I'm doing some tests with small peptide and constantly getting this
>> >>> error.
>> >>> I get it with few systems.
>> >>>
>> >>> Systems sizes are around 10k or 20k
>> >>> I run it on 4 or 8 old nodes each with two xeon 54xx series
>> >>>
>> >>> starting mdrun '2ZCH_3 in water'
>> >>> 50000000 steps, 100000.0 ps (continuing from step 1881000, 3762.0
>> >>> ps).
>> >>>
>> >>> Step 13514000:
>> >>> The charge group starting at atom 6608 moved more than the distance
>> >>> allowed by the domain decomposition (1.112924) in direction X
>> >>> distance out of cell -1.193103 Old coordinates: 5.467 0.298 3.636
>> >>> New
>> >>> coordinates: 5.467 0.298 3.636 Old cell boundaries in direction X:
>> >>> 4.037 5.382 New cell boundaries in direction X: 4.089 5.452
>> >>>
>> >>>
>> >> ---------------------------------------------------------------------
>> >> -
>> >> ----
>> >>> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with
>> >>> errorcode 1.
>> >>>
>> >>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> >>> You may or may not see output from other processes, depending on
>> >>> exactly when Open MPI kills them.
>> >>>
>> >>>
>> >> ---------------------------------------------------------------------
>> >> -
>> >> ----
>> >>>
>> >>> -------------------------------------------------------
>> >>> Program mdrun_mpi, VERSION 5.1-dev-20140922-20c00a9-dirty-unknown
>> >>> Source code file:
>> >>>
>> >>>
>> >> /var/tmp/alexxy/portage/sci-chemistry/gromacs-9999/work/gromacs-9999/
>> >> s
>> >> rc/gromacs/mdlib/domdec.cpp,
>> >>> line: 4388
>> >>>
>> >>> Fatal error:
>> >>> A charge group moved too far between two domain decomposition steps
>> >>> This usually means that your system is not well equilibrated For
>> >>> more information and tips for troubleshooting, please check the
>> >>> GROMACS website at http://www.gromacs.org/Documentation/Errors [2]
>> >>> [1]
>> >>> -------------------------------------------------------
>> >>>
>> >>> -- Best Regards,
>> >>> Alexey 'Alexxy' Shvetsov, PhD
>> >>> Department of Molecular and Radiation Biophysics FSBI Petersburg
>> >>> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad
>> >>> region, Gatchina, Russia mailto:alexxyum at gmail.com
>> >>> mailto:alexxy at omrb.pnpi.spb.ru
>> >>> -- Gromacs Developers mailing list
>> >>>
>> >>> * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>> >>> [3] [2]
>> >>> before posting!
>> >>>
>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists [4]
>> >>> [3]
>> >>>
>> >>> * For (un)subscribe requests visit
>> >>>
>> >>>
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-develope
>> >> r
>> >> s
>> >>> [5]
>> >>> [4] or send a mail to gmx-developers-request at gromacs.org.
>> >>>
>> >>> Links:
>> >>> ------
>> >>> [1] http://www.gromacs.org/Documentation/Errors [2] [2]
>> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List [3]
>> >>> [3] http://www.gromacs.org/Support/Mailing_Lists [4] [4]
>> >>>
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-develope
>> >> r
>> >> s
>> >>> [5]
>> >>
>> >>  -- Best Regards,
>> >>  Alexey 'Alexxy' Shvetsov, PhD
>> >>  Department of Molecular and Radiation Biophysics  FSBI Petersburg
>> >> Nuclear Physics Institute, NRC Kurchatov Institute,  Leningrad
>> >> region, Gatchina, Russia  mailto:alexxyum at gmail.com
>> >> mailto:alexxy at omrb.pnpi.spb.ru
>> >>
>> >>  --
>> >>  Best Regards,
>> >>  Alexey 'Alexxy' Shvetsov, PhD
>> >>  Department of Molecular and Radiation Biophysics  FSBI Petersburg
>> >> Nuclear Physics Institute, NRC Kurchatov Institute,  Leningrad
>> >> region, Gatchina, Russia  mailto:alexxyum at gmail.com
>> >> mailto:alexxy at omrb.pnpi.spb.ru
>> >>  --
>> >>  Gromacs Developers mailing list
>> >>
>> >>  * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List [3]
>> >> before posting!
>> >>
>> >>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists [4]
>> >>
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>> >>
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-develope
>>  >> r s [5] or send a mail to gmx-developers-request at gromacs.org.
>>
>>  >>
>> >>
>> >> Links:
>> >> ------
>> >> [1] https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr
>> >> [2] http://www.gromacs.org/Documentation/Errors
>> >> [3] http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>> >> [4] http://www.gromacs.org/Support/Mailing_Lists
>> >> [5]
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-develope
>> >> r
>> >> s
>> >
>> > --
>> > Best Regards,
>> > Alexey 'Alexxy' Shvetsov, PhD
>> > Department of Molecular and Radiation Biophysics FSBI Petersburg
>> > Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,
>> > Gatchina, Russia mailto:alexxyum at gmail.com
>> > mailto:alexxy at omrb.pnpi.spb.ru
>> > --
>> > Gromacs Developers mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>> > before posting!
>> >
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>> >
>> > * For (un)subscribe requests visit
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>> > s or send a mail to gmx-developers-request at gromacs.org.
>> >
>> > --
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>> >
>> >
>> >
>> >
>> >
>> > --
>> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537,
>> > ORNL PO BOX 2008 MS6309
>> >
>> >
>> > --
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>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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