[gmx-developers] ICC 14 support

Mon Sep 29 18:16:13 CEST 2014

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-developer
> > 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-developer
> > 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]
> >
> >  * For (un)subscribe requests visit
> >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer
> > 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-developer
> > 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
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> posting!
>
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>
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>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
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> posting!
>
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>
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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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