[Nek5000-users] Simulation hanging at 'mapping elements to processors'
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Mon Sep 25 07:39:13 CDT 2017
Can you please re-run your case with your old .map file.
I was not able to reproduce your problem and I trying to understand if there a bug in the .map reader.
-----Original message-----
> From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> Sent: Monday 25th September 2017 14:25
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors'
>
> Thanks, it did work.
> <br class="" />
> Marco<br class="" />
> On Sep 23, 2017, at 1:21 AM,
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
> <br class="Apple-interchange-newline" />
> You can use tools/amg_hypre instead of amg_matlab2.
> <br class="" />
> On 23 Sep 2017, at 02:15, "nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:<br class="" />
> <br class="" />
> Hi,
> <br class="" />
> the job run until it threw the following error message:
> <br class="" />
> EXIT: Problem size requires AMG solver 1
> <br class="" />
> I attached the log file.
> <br class="" />
> My mesh has 478946 elements. Do I have to use the AMG solver, or is there a workaround? If I remember correctly the AMG solver requires Matlab which I do not have access to.
> <br class="" />
> Thanks,
> Marco
> <br class="" />
> _______________________________________________<br class="" />
> Nek5000-users mailing list<br class="" />
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> <Actesys.1.000><br class="" />
> On Sep 22, 2017, at 8:26 AM,
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
> <br class="Apple-interchange-newline" />
> I generated the ma2 file and submitted the job. I will let you know how it goes.
> <br class="" />
> How different is the ma2 file from a map file?<br class="" />
> <br class="" />
> Thanks,
> Marco
> <br class="" />
> On Sep 22, 2017, at 8:03 AM,
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
> <br class="Apple-interchange-newline" />
> This looks like a bug.
> Can you try with the latest version and run genmap again (this will produce a .ma2 file). Make sure you have just a .ma2 and no .map in your case directory.
> <br class="" />
> If this works I have to check why the old .map doesn’t.
> <br class="" />
> Stefan
> <br class="" />
> On 22 Sep 2017, at 13:56, "nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:<br class="" />
> <br class="" />
> Stefan,<br class="" />
> <br class="" />
> below is the log file of the run:<br class="" />
> <br class="" />
> | _ __ ______ __ __ ______ ____ ____ ____ |<br class="" />
> | / | / // ____// //_/ / ____/ / __ \\/ <smb:///> __
> \\/ <smb:///> __ \\ |<br class="" />
> | / |/ // __/ / ,< /___ \\ / / / // / / // / / / |<br class="" />
> | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |<br class="" />
> | /_/ |_//_____//_/ |_|/_____/ \\___/ <smb://___/>
> \\___/ <smb://___/> \\___/ <smb://___/> |<br class="" />
> | |<br class="" />
> |----------------------------------------------------------|<br class="" />
> | |<br class="" />
> | NEK5000: Open Source Spectral Element Solver |<br class="" />
> | COPYRIGHT (c) 2008-2017 UCHICAGO ARGONNE, LLC |<br class="" />
> | Version: 17.0.0-dev |<br class="" />
> | Web: http://nek5000.mcs.anl.gov <http://nek5000.mcs.anl.gov/> |<br class="" />
> | |<br class="" />
> \\----------------------------------------------------------/<br class="" />
> <br class="" />
> <br class="" />
> Number of processors: 1024<br class="" />
> REAL wdsize : 8<br class="" />
> INTEGER wdsize : 4<br class="" />
> Timer accuracy : 9.54E-08<br class="" />
> <br class="" />
> Reading /home/mxd/Nek5000/run/actasys/3d-model/actuatorA.rea<br class="" />
> Switch on stress formulation to support PN/PN and IFUSERVP=T<br class="" />
> Reading /home/mxd/Nek5000/run/actasys/3d-model/actuatorA.re2<br class="" />
> mapping elements to processors<br class="" />
> Reading /home/mxd/Nek5000/run/actasys/3d-model/actuatorA.map<br class="" />
> <br class="" />
> I run my case with 1024 processors as suggested by Paul. The run hung for two hours before reaching the wall time.<br class="" />
> <br class="" />
> Marco<br class="" />
> > On Sep 22, 2017, at 3:09 AM,
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> wrote:<br class="" />
> > <br class="" />
> > Marco,<br class="" />
> > <br class="" />
> > can you please post your logfile. What version of Nek5000 do you use?<br class="" />
> > <br class="" />
> > Cheers,<br class="" />
> > Stefan<br class="" />
> > <br class="" />
> > -----Original message-----<br class="" />
> >> From:nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>><br class="" />
> >> Sent: Friday 22nd September 2017 2:40<br class="" />
> >> To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />
> >> Subject: Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors'<br class="" />
> >> <br class="" />
> >> Hi Paul,<br class="" />
> >> <br class="" /><br class="" />
> >> thanks for the help. I will give it a try tomorrow. I am indeed using the XXT coarse grid solver.<br class="" />
> >> <br class="" /><br class="" />
> >> Marco<br class="" />
> >> <br class="" /><br class="" />
> >> On Sep 21, 2017, at 6:49 PM, <br class="" />
> >> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> <mailto:nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>> <Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov>
> <mailto:Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov>>> wrote:<br class="" />
> >> <br class="Apple-interchange-newline" /><br class="" />
> >> <br class="Apple-interchange-newline" /><br class="" />
> >> Hi Marco,<br class="" />
> >> <br class="" /><br class="" />
> >> I'm not 100 % about the hanging point, but I suggest - especially for larger problems like this - running on a power of 2 processors (i.e., 1024 in your case).<br class="" />
> >> <br class="" /><br class="" />
> >> This is particularly critical for performance when the XXT (default) coarse grid solver is used. Less so, perhaps, for the AMG coarse solver...I'm assuming you're using the XXT one - but not certain.<br class="" />
> >> <br class="" /><br class="" />
> >> Best,<br class="" />
> >> <br class="" /><br class="" />
> >> Paul<br class="" />
> >> <br class="" /><br class="" />
> >> -----------<br class="" />
> >> From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov <mailto:nek5000-users-bounces at lists.mcs.anl.gov> <mailto:nek5000-users-bounces at lists.mcs.anl.gov <mailto:nek5000-users-bounces at lists.mcs.anl.gov>>><br class="" />
> >> on behalf of nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> <mailto:nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>> <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>
> <mailto:nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>>><br class="" /><br class="" />
> >> Sent: Thursday, September 21, 2017 3:37:55 PM<br class="" /><br class="" />
> >> To: Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov> <mailto:Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov>><br class="" /><br class="" />
> >> Subject: [Nek5000-users] Simulation hanging at 'mapping elements to processors'<br class="" />
> >> Hello,<br class="" /><br class="" />
> >> <br class="" /><br class="" />
> >> I am trying to run a simulation that has ~500,000 elements on 1280 processors with lx1=4 for debugging purposes. My simulation hangs after outputting 'mapping elements to processors’. I generated the mesh with Cubit and then used the exo2nek script to
> get the<br class="" />
> >> re2 file. Genmap runs fine on the re2 file.<br class="" /><br class="" />
> >> <br class="" /><br class="" />
> >> I was wondering if this problem has been encountered in the past, and what I could do to fix it.<br class="" /><br class="" />
> >> <br class="" /><br class="" />
> >> Thanks,<br class="" /><br class="" />
> >> Marco<br class="" /><br class="" />
> >> <br class="" /><br class="" />
> >> _______________________________________________<br class="" /><br class="" />
> >> Nek5000-users mailing list<br class="" /><br class="" />
> >> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov> <mailto:Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov>><br class="" /><br class="" />
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>><br
> class="" /><br class="" />
> >> _______________________________________________<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform:
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> >> Nek5000-users<br class="" />
> >> mailing list<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows:
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> class="" /><br class="" />
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