[Nek5000-users] Simulation hanging at 'mapping elements to processors'

Mon Sep 25 07:42:25 CDT 2017

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 doesnâ€™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 processorsâ€™. 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 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:
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>> class="" /><br class="" />
>>>> _______________________________________________<br class="" />
>>>> Nek5000-users mailing list<br class="" />
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>> <br class="" />
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