[Nek5000-users] Simulation hanging at 'mapping elements to processors'
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Sep 22 07:26:16 CDT 2017
I generated the ma2 file and submitted the job. I will let you know how it goes.
How different is the ma2 file from a map file?
Thanks,
Marco
On Sep 22, 2017, at 8:03 AM, nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> wrote:
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.
If this works I have to check why the old .map doesn’t.
Stefan
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:
Stefan,
below is the log file of the run:
| _ __ ______ __ __ ______ ____ ____ ____ |
| / | / // ____// //_/ / ____/ / __ \\/<smb:///> __ \\/<smb:///> __ \\ |
| / |/ // __/ / ,< /___ \\ / / / // / / // / / / |
| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |
| /_/ |_//_____//_/ |_|/_____/ \\___/<smb://___/> \\___/<smb://___/> \\___/<smb://___/> |
| |
|----------------------------------------------------------|
| |
| NEK5000: Open Source Spectral Element Solver |
| COPYRIGHT (c) 2008-2017 UCHICAGO ARGONNE, LLC |
| Version: 17.0.0-dev |
| Web: http://nek5000.mcs.anl.gov<http://nek5000.mcs.anl.gov/> |
| |
\\----------------------------------------------------------/
Number of processors: 1024
REAL wdsize : 8
INTEGER wdsize : 4
Timer accuracy : 9.54E-08
Reading /home/mxd/Nek5000/run/actasys/3d-model/actuatorA.rea
Switch on stress formulation to support PN/PN and IFUSERVP=T
Reading /home/mxd/Nek5000/run/actasys/3d-model/actuatorA.re2
mapping elements to processors
Reading /home/mxd/Nek5000/run/actasys/3d-model/actuatorA.map
I run my case with 1024 processors as suggested by Paul. The run hung for two hours before reaching the wall time.
Marco
> On Sep 22, 2017, at 3:09 AM, nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> wrote:
>
> Marco,
>
> can you please post your logfile. What version of Nek5000 do you use?
>
> Cheers,
> Stefan
>
> -----Original message-----
>> 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>>
>> Sent: Friday 22nd September 2017 2:40
>> To: nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>
>> Subject: Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors'
>>
>> Hi Paul,
>> <br class="" />
>> thanks for the help. I will give it a try tomorrow. I am indeed using the XXT coarse grid solver.
>> <br class="" />
>> Marco
>> <br class="" />
>> On Sep 21, 2017, at 6:49 PM,
>> 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>> wrote:
>> <br class="Apple-interchange-newline" />
>> <br class="Apple-interchange-newline" />
>> Hi Marco,
>> <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="" />
>> 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="" />
>> Best,
>> <br class="" />
>> Paul
>> <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>>
>> 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> <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="" />
>> Sent: Thursday, September 21, 2017 3:37:55 PM<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><br class="" />
>> Subject: [Nek5000-users] Simulation hanging at 'mapping elements to processors'
>> Hello,<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
>> re2 file. Genmap runs fine on the re2 file.<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="" />
>> Thanks,<br class="" />
>> Marco<br class="" />
>> <br class="" />
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