[gmx-developers] ICC 14 support

Mon Sep 29 22:50:21 CEST 2014

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
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>>>
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>>> [3] [2]
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>>>
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer
>> s
>>> [5]
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>>> Links:
>>> ------
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>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List [3]
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>>>
>> 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
>>
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>> before posting!
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>>
>>
>> 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
> --
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