<div dir="ltr">Hi,<div><br></div><div>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).</div><div><br></div><div>Roland</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 29, 2014 at 10:35 AM, Kevin Chen <span dir="ltr"><<a href="mailto:fch6699@gmail.com" target="_blank">fch6699@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Guys,<br>
<br>
Was wondering if GROMACS will support ICC 14 in the near future?<br>
<br>
Kevin Chen, Ph.D.<br>
HPC Applications, TACC<br>
<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [mailto:<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] On Behalf Of Alexey Shvetsov<br>
Sent: Sunday, September 28, 2014 3:09 PM<br>
To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
Subject: Re: [gmx-developers] Possible bug in gmx<br>
<br>
Mark Abraham писал 28-09-2014 18:17:<br>
> How about a redmine issue - this thread's not about GROMACS<br>
> development, per se ;-)<br>
<br>
Sorry about that =D<br>
<br>
Redmine issue <a href="http://redmine.gromacs.org/issues/1607" target="_blank">http://redmine.gromacs.org/issues/1607</a><br>
With relevant tpr file attached<br>
><br>
> Mark<br>
><br>
> On Sun, Sep 28, 2014 at 3:18 PM, Alexey Shvetsov<br>
> <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
><br>
>> Hi Berk!<br>
>><br>
>> Its not a cut and paste error, also there are no pdb dumps.<br>
>> Also I see this error before with other systems.<br>
>><br>
>> I can provide tpr file for that system<br>
>><br>
>> <a href="https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr" target="_blank">https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr</a> [1]<br>
>><br>
>> Berk Hess писал 28-09-2014 16:37:<br>
>><br>
>> Hi,<br>
>><br>
>> I assume that your old and be coordinates being identical is correct<br>
>> and not a cut-and-paste error.<br>
>> This seems a bit strange or do you freeze part of the system?<br>
>> The only things moving here are then the domain boundaries and I<br>
>> don't see an issue there, since they only moved a little.<br>
>><br>
>> Do you have any more output besides the error message? PDB dump files<br>
>> maybe?<br>
>><br>
>> Cheers,<br>
>><br>
>> Berk<br>
>><br>
>> On 09/28/2014 02:22 PM, Alexey Shvetsov wrote:<br>
>> Hi,<br>
>><br>
>> just wanna add that this error seems to be reproducable even on<br>
>> single node. Also i get same error for gpu runs.<br>
>> However i dont see it in large systems (800k+ atoms) running on large<br>
>> number of cpus (512+)<br>
>><br>
>> Alexey Shvetsov писал 28-09-2014 13:44:<br>
>> Hi,<br>
>><br>
>> DD grid is<br>
>><br>
>> Domain decomposition grid 4 x 1 x 1, separate PME ranks 0 PME domain<br>
>> decomposition: 4 x 1 x 1<br>
>><br>
>> for 4 node setup<br>
>><br>
>> and<br>
>><br>
>> Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain<br>
>> decomposition: 4 x 2 x 1<br>
>><br>
>> for 8 node setup<br>
>><br>
>> It's reproducable with 5.0 release and latest git master. I try to<br>
>> check if its reproducable with 1 node. Also i can provide tpr file<br>
>> for this system<br>
>><br>
>> Mark Abraham писал 28-09-2014 13:28:<br>
>> Hi,<br>
>><br>
>> It's hard to say on that information. There were some issues fixed in<br>
>> the lead-up to GROMACS 5 with DD not always working with 2 domains in<br>
>> a direction, but that's a pure guess. I'd assume you can reproduce<br>
>> this with release-5-0 branch. Do you observe it with a single domain?<br>
>> If not, then it's surely a bug (and should be submitted to redmine).<br>
>><br>
>> Mark<br>
>><br>
>> On Sun, Sep 28, 2014 at 11:18 AM, Alexey Shvetsov<br>
>> <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
>><br>
>> Hi all!<br>
>><br>
>> I'm doing some tests with small peptide and constantly getting this<br>
>> error.<br>
>> I get it with few systems.<br>
>><br>
>> Systems sizes are around 10k or 20k<br>
>> I run it on 4 or 8 old nodes each with two xeon 54xx series<br>
>><br>
>> starting mdrun '2ZCH_3 in water'<br>
>> 50000000 steps, 100000.0 ps (continuing from step 1881000, 3762.0<br>
>> ps).<br>
>><br>
>> Step 13514000:<br>
>> The charge group starting at atom 6608 moved more than the distance<br>
>> allowed by the domain decomposition (1.112924) in direction X<br>
>> distance out of cell -1.193103 Old coordinates: 5.467 0.298 3.636 New<br>
>> coordinates: 5.467 0.298 3.636 Old cell boundaries in direction X:<br>
>> 4.037 5.382 New cell boundaries in direction X: 4.089 5.452<br>
>><br>
>><br>
> ----------------------------------------------------------------------<br>
> ----<br>
>> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with<br>
>> errorcode 1.<br>
>><br>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
>> You may or may not see output from other processes, depending on<br>
>> exactly when Open MPI kills them.<br>
>><br>
>><br>
> ----------------------------------------------------------------------<br>
> ----<br>
>><br>
>> -------------------------------------------------------<br>
>> Program mdrun_mpi, VERSION 5.1-dev-20140922-20c00a9-dirty-unknown<br>
>> Source code file:<br>
>><br>
>><br>
> /var/tmp/alexxy/portage/sci-chemistry/gromacs-9999/work/gromacs-9999/s<br>
> rc/gromacs/mdlib/domdec.cpp,<br>
>> line: 4388<br>
>><br>
>> Fatal error:<br>
>> A charge group moved too far between two domain decomposition steps<br>
>> This usually means that your system is not well equilibrated For more<br>
>> 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> [2] [1]<br>
>> -------------------------------------------------------<br>
>><br>
>> -- Best Regards,<br>
>> Alexey 'Alexxy' Shvetsov, PhD<br>
>> Department of Molecular and Radiation Biophysics FSBI Petersburg<br>
>> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,<br>
>> Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
>> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
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> -- Best Regards,<br>
> Alexey 'Alexxy' Shvetsov, PhD<br>
> Department of Molecular and Radiation Biophysics FSBI Petersburg<br>
> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,<br>
> Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
><br>
> --<br>
> Best Regards,<br>
> Alexey 'Alexxy' Shvetsov, PhD<br>
> Department of Molecular and Radiation Biophysics FSBI Petersburg<br>
> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,<br>
> Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
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> Links:<br>
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> [1] <a href="https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr" target="_blank">https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr</a><br>
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> s<br>
<br>
--<br>
Best Regards,<br>
Alexey 'Alexxy' Shvetsov, PhD<br>
Department of Molecular and Radiation Biophysics FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region, Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
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