<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div></div><div>You can use tools/amg_hypre instead of amg_matlab2. </div><div><br>On 23 Sep 2017, at 02:15, "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br><br></div><blockquote type="cite"><div>
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Hi,
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<div class="">the job run until it threw the following error message:</div>
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<div class="">EXIT: Problem size requires AMG solver 1</div>
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<div class="">I attached the log file.</div>
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<div 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.</div>
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<div class="">Thanks,</div>
<div class="">Marco</div>
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</pre></div></blockquote><blockquote type="cite"><div><Actesys.1.000></div></blockquote><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html charset=utf-8"><div class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 22, 2017, at 8:26 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a> wrote:</div><br class="Apple-interchange-newline"><div class="">
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I generated the ma2 file and submitted the job. I will let you know how it goes.
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<div class="">How different is the ma2 file from a map file?<br class="">
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<div class="">Thanks,</div>
<div class="">Marco</div>
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<div class="">
<blockquote type="cite" class="">
<div class="">On Sep 22, 2017, at 8:03 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">
nek5000-users@lists.mcs.anl.gov</a> wrote:</div>
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<div class="">This looks like a bug. </div>
<div class="">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.</div>
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<div class="">If this works I have to check why the old .map doesn’t.</div>
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<div class="">Stefan</div>
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On 22 Sep 2017, at 13:56, "<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br class="">
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<!-- Converted from text/plain format --><p class=""><font style="font-family: courier" size="2" class="">Stefan,<br class="">
<br class="">
below is the log file of the run:<br class="">
<br class="">
| _ __ ______ __ __ ______ ____ ____ ____ |<br class="">
| / | / // ____// //_/ / ____/ / __ <a href="smb:///" class="">\\/</a> __ <a href="smb:///" class="">
\\/</a> __ \\ |<br class="">
| / |/ // __/ / ,< /___ \\ / / / // / / // / / / |<br class="">
| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |<br class="">
| /_/ |_//_____//_/ |_|/_____/ <a href="smb://___/" class="">\\___/</a> <a href="smb://___/" class="">
\\___/</a> <a href="smb://___/" class="">\\___/</a> |<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: <a href="http://nek5000.mcs.anl.gov/" class="">http://nek5000.mcs.anl.gov</a> |<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, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">
nek5000-users@lists.mcs.anl.gov</a> 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:<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a>><br class="">
>> Sent: Friday 22nd September 2017 2:40<br class="">
>> To: <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a><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="">
>> <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">mailto:nek5000-users@lists.mcs.anl.gov</a>> <<a href="mailto:Nek5000-users@lists.mcs.anl.gov" class="">Nek5000-users@lists.mcs.anl.gov</a>
<<a href="mailto:Nek5000-users@lists.mcs.anl.gov" class="">mailto:Nek5000-users@lists.mcs.anl.gov</a>>> 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 <<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov" class="">nek5000-users-bounces@lists.mcs.anl.gov</a> <<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov" class="">mailto:nek5000-users-bounces@lists.mcs.anl.gov</a>>><br class="">
>> on behalf of <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">mailto:nek5000-users@lists.mcs.anl.gov</a>> <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">nek5000-users@lists.mcs.anl.gov</a>
<<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="">mailto:nek5000-users@lists.mcs.anl.gov</a>>><br class="" /><br class="">
>> Sent: Thursday, September 21, 2017 3:37:55 PM<br class="" /><br class="">
>> To: <a href="mailto:Nek5000-users@lists.mcs.anl.gov" class="">Nek5000-users@lists.mcs.anl.gov</a> <<a href="mailto:Nek5000-users@lists.mcs.anl.gov" class="">mailto:Nek5000-users@lists.mcs.anl.gov</a>><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="">
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