August 2016 - Nek5000-users - mailman3.cels.anl.gov

Visualization of simulation
by nek5000-users＠lists.mcs.anl.gov 08 Aug '16

08 Aug '16

Hello Users I am facing some difficulties in visualising the result of simulation. On running " postx" a blank screen appears without any side menu, as mentioned in manual. Is this is a result of any error during building postnek ? Because i didn't encountered any ! Thanks Shivang

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Patel, Mansi A wants to share the file Screenshot-5.png with you
by nek5000-users＠lists.mcs.anl.gov 05 Aug '16

05 Aug '16

To view Screenshot-5.png, sign in<https://uflorida-my.sharepoint.com/personal/mansipatel_ufl_edu/_layouts/15/…> or create an account.

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Re: [Nek5000-users] Nek5000-users Digest, Vol 89, Issue 10
by nek5000-users＠lists.mcs.anl.gov 05 Aug '16

05 Aug '16

Patel,Mansi A has shared a OneDrive for Business file with you. To view it, click the link below. <https://uflorida-my.sharepoint.com/personal/mansipatel_ufl_edu/Documents/Em…> [https://r1.res.office365.com/owa/prem/images/dc-png_20.png]<https://uflorida-my.sharepoint.com/personal/mansipatel_ufl_edu/Documents/Em…> Screenshot-5.png<https://uflorida-my.sharepoint.com/personal/mansipatel_ufl_edu/Documents/Em…> Hello users, Thanks Ron Rahaman that was much helpful. I am having redhat linux workstation and I have downloaded openmpi in it to run it parallel I typed ./nekbmpi eddy_uv 4 I getting different error it says p= 4 has passed but not compiled with DMPI. I have no clue what does that mean. I have attached screen shot of the error(screen shot 5) Thanks, Mansi Patel ________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: Thursday, July 14, 2016 1:00:10 PM To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 89, Issue 10 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. problems in compiling the code for parallel run (nek5000-users(a)lists.mcs.anl.gov) 2. Re: problems in compiling the code for parallel run (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 13 Jul 2016 20:27:38 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov>, "tanvikaushik13(a)gmail.com" <tanvikaushik13(a)gmail.com> Subject: [Nek5000-users] problems in compiling the code for parallel run Message-ID: <mailman.25937.1468441664.24727.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Hello Users, I have Redhat linux workstation, I have already compiled code with nekb by making changes in makenek file, but now I want to run it parallel. At first when I compiled it by making F77 = mpif77 and cc= mpicc and commenting IFMPI ="false" I got errors that mpi not found than I installed openmpi Now when I compile using makenek it gets compiled successfully but when I try to run it using nekbmpi i get errors like mv: cannot stat `eddy_uv.sch': No such file or directory and sometimes if i do ./nekbmpi eddy_uv 4 it and put enter i get no errors on first time but if i enter again for second time I get same error that is mv: cannot stat `eddy_uv.sch': No such file or directory I want to understand what mistake I am doing and what should I do to get rid of errors and also which file can help me to see whats going on in simulation Thanks, Mansi Patel -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160713/39dfe…> ------------------------------ Message: 2 Date: Thu, 14 Jul 2016 07:20:10 -0500 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] problems in compiling the code for parallel run Message-ID: <mailman.25984.1468498816.24727.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="utf-8" Hi Mansi, I suspect that you can safely ignore the error. The error probably comes from line 7 of the "nekbmpi" script: mv $1.sch $1.sch1 This command is intended to move the .sch file from a previous run, in case there's one in your directory. If this is your first run, there will be no .sch file in your directory, and the "mv" command will give the error you saw. So it probably doesn't indicate a problem. Best, Ron Rahaman Argonne National Laboratory, Math and Computer Science Division University of Chicago, Department of Computer Science On Wed, Jul 13, 2016 at 3:27 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > Hello Users, > > I have Redhat linux workstation, I have already compiled code with nekb by > making changes in makenek file, but now I want to run it parallel. At first > when I compiled it by making F77 = mpif77 and cc= mpicc and commenting > IFMPI ="false" I got errors that mpi not found than I installed openmpi > > Now when I compile using makenek it gets compiled successfully but when I > try to run it using nekbmpi i get errors like > mv: cannot stat `eddy_uv.sch': No such file or directory > and sometimes if i do ./nekbmpi eddy_uv 4 it and put enter i get no errors > on first time but if i enter again for second time I get same error that is mv: > cannot stat `eddy_uv.sch': No such file or directory > I want to understand what mistake I am doing and what should I do to get > rid of errors and also which file can help me to see whats going on in > simulation > > > Thanks, > Mansi Patel > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160714/d1c4a…> ------------------------------ _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users End of Nek5000-users Digest, Vol 89, Issue 10 *********************************************

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Running NekExamples
by nek5000-users＠lists.mcs.anl.gov 02 Aug '16

02 Aug '16

Hello, I am trying to run a standalone Nek5000 Example. I have Nek5000 installed and I am following the Examples instructions from https://github.com/Nek5000/NekExamples When I try to run any particular example, using: python -m 'unittest' NekTests.ConjHt I face two issues: 1) It looks like some Nek5000 files keep getting rebuilt each time I execute the above command, even if they have been built before. 2) I always get an error: Successfully compiled nek5000! Running nek5000... Using command "~/github/NekExamples/conj_ht/nek5000" Using working directory "~/github/NekExamples/conj_ht" Using .rea file "conj_ht" Could not remove ~/github/NekExamples/conj_ht/conj_ht.sch: [Errno 2] No such file or directory: '~/github/NekExamples/conj_ht/conj_ht.sch' Could not successfully run nek5000! Caught error: [Errno 2] No such file or directory I tried looking through the Makefiles and the Python script but cannot see where the sch file is specified. Also, I tried creating a dummy sch file so that the build can find and remove it, but that didn't work either. Please advise on how I can resolve the errors. Thanks, K.N.Ramachandran Ph: 814-441-4279

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Spectral method with Nek
by nek5000-users＠lists.mcs.anl.gov 02 Aug '16

02 Aug '16

All, I was wondering if the following statement is true or false: "If a single element is used for the whole domain then one can claim the Nek simulation is spectral instead of spectral element". Based on this, I carried out DNS on cavity for relatively large Reynolds numbers and I was not able to capture the instability mechanisms with one element (even when I increased the power of polynomial to 12 or 18). While I'm not surprised, I just wanted to see if anyone else has a similar experience. As a side question, why Nek utilizes Legendre polynomials instead of Chebyshev for each element? Is this because we're also interested in modeling non-uniformly spaced nodes? Best, Saleh

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maketools prenek
by nek5000-users＠lists.mcs.anl.gov 01 Aug '16

01 Aug '16

Hello Paul, I had already tried switching BIGMEM to false but the same error appears. I am using Cygwin platform on windows to provide the linux environment and compiling on gcc 5.4.0 and gfortran compilers. Shivang

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