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October 2017

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Strong divergence and Laplacian operator
by nek5000-users＠lists.mcs.anl.gov 04 Oct '17

04 Oct '17

Hi all, I need to compute some operators in the strong form directly for a project, i.e. without the mass matrix included in the operator. For the convection and gradient operators, I am using the functions convop and gradm1 respectively. However, I would also need to compute strong divergence and Laplacian and I did not find the corresponding functions (opdiv and axhelm are computing the weak form if I understand correctly). Do such functions exist? Or what modifications should I bring to the existing routines to change them to strong form? Best regards, Nicolas

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Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors'
by nek5000-users＠lists.mcs.anl.gov 03 Oct '17

03 Oct '17

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:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Monday 25th September 2017 14:25 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors' > > Thanks, it did work. > > Marco > On Sep 23, 2017, at 1:21 AM, > nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> wrote: > > You can use tools/amg_hypre instead of amg_matlab2. > > On 23 Sep 2017, at 02:15, "nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>" <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > > Hi, > > the job run until it threw the following error message: > > EXIT: Problem size requires AMG solver 1 > > I attached the log file. > > 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. > > Thanks, > Marco > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > <Actesys.1.000> > On Sep 22, 2017, at 8:26 AM, > nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> wrote: > > 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(a)lists.mcs.anl.gov <mailto:[email protected]> 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 doesnâ€™t. > > Stefan > > On 22 Sep 2017, at 13:56, "nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>" <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> 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(a)lists.mcs.anl.gov <mailto:[email protected]> wrote: > > > > Marco, > > > > can you please post your logfile. What version of Nek5000 do you use? > > > > Cheers, > > Stefan > > > > -----Original message----- > >> From:[email protected] <mailto:[email protected]> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> > >> Sent: Friday 22nd September 2017 2:40 > >> To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > >> Subject: Re: [Nek5000-users] Simulation hanging at 'mapping elements to processors' > >> > >> Hi Paul, > >> > >> thanks for the help. I will give it a try tomorrow. I am indeed using the XXT coarse grid solver. > >> > >> Marco > >> > >> On Sep 21, 2017, at 6:49 PM, > >> nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> wrote: > >> > >> > >> Hi Marco, > >> > >> 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). > >> > >> 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. > >> > >> Best, > >> > >> Paul > >> > >> ----------- > >> From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > >> on behalf of nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> > >> Sent: Thursday, September 21, 2017 3:37:55 PM > >> To: Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > >> Subject: [Nek5000-users] Simulation hanging at 'mapping elements to processors' > >> Hello, > >> > >> 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 > >> re2 file. Genmap runs fine on the re2 file. > >> > >> I was wondering if this problem has been encountered in the past, and what I could do to fix it. > >> > >> Thanks, > >> Marco > >> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > >> 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>> 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="" /> > >> Nek5000-users > >> 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="" /> > >> Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> 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="" /> > >> 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>> class="" /> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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