[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 07:45:00 CDT 2017 

Yes but let's use the current Nek5000 version. You can use your existing .map or create a new one with a previous genmap version. 

-----Original message-----
> From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> Sent: Monday 25th September 2017 14:43
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors'
> 
> You want me to rerun the case with the old map file and use the AMG solver, right?
> 
> Our cluster is in maintenance today but I will do it tomorrow.
> 
> Marco
> 
> > On Sep 25, 2017, at 8:39 AM, nek5000-users at lists.mcs.anl.gov wrote:
> > 
> > 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="" />
> >> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" />
> >> <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:
> >> none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="" /><br class="" />
> >>>> 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:
> >> auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" 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 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: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" 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 class="" />
> >>>> Nek5000-users mailing list<br class="" />
> >>>> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" />
> >>> _______________________________________________<br class="" />
> >>> Nek5000-users mailing list<br class="" />
> >>> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" />
> >> <br class="" />
> >> _______________________________________________<br class="" />
> >> Nek5000-users mailing list<br class="" />
> >> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" />
> >> _______________________________________________<br class="" />
> >> Nek5000-users mailing list<br class="" />
> >> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" />
> >> <br class="" />
> >> _______________________________________________<br class="" />
> >> Nek5000-users mailing list<br class="" />
> >> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" />
> >> <br class="" />
> >> _______________________________________________<br class="" />
> >> Nek5000-users mailing list<br class="" />
> >> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<br class="" />
> >> <br class="" />
> >> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
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> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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