August 2017 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Reflections on outlet
by nek5000-users＠lists.mcs.anl.gov 29 Aug '17

29 Aug '17

It worked for me, thanks to the files Philipp sent me. You can write me if you want. juan.robinson(a)alumnos.usm.cl Regards, Juan Pablo

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Low mach simulation
by nek5000-users＠lists.mcs.anl.gov 29 Aug '17

29 Aug '17

Hi all, Is it possible to switch off the time derivative term (d rho / d t) in the mass conservation equation for the low Mach number model. Alternatively, is it possible to impose a background variable density for a simulation that does not change with time? Thank you Swarandeep

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Set forcing in .rea and in .usr
by nek5000-users＠lists.mcs.anl.gov 29 Aug '17

29 Aug '17

Hi, Neks! Could you please shortly explain me, what is the difference between set forcing in .rea (p54&p55) and in .usr (set_forcing) files. In fact, via testing these two options I found that in case of .rea file u_bar is kept more precisely. Best regards, Mark

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Re: [Nek5000-users] Reflections on outlet
by nek5000-users＠lists.mcs.anl.gov 29 Aug '17

29 Aug '17

Thanks Philipp, I sent you an e-mail! Juan Pablo.

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Re: [Nek5000-users] Restart Hang
by nek5000-users＠lists.mcs.anl.gov 28 Aug '17

28 Aug '17

Any updates or suggestions on this please? I have tried to use older versions of Nek (prior to .par implementation) and the restart works fine on this supercomputer, as has always worked all these years of using Nek. I also tried to restart using the updated version on a workstation and it works (code does not hang) but still gives the NSPCAL warning) Regards, JP

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Non-conformal meshes
by nek5000-users＠lists.mcs.anl.gov 28 Aug '17

28 Aug '17

Hi, Neks! I saw a paper where non-conformal meshes were used in nek, does this option work with the current version? Best regards, Mark

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Error doing ./maketools for postnek
by nek5000-users＠lists.mcs.anl.gov 28 Aug '17

28 Aug '17

Hey Neks, I have recently installed Nek5000 in a different machine. Now to read my domain (which is big, 3072 elements), I have changed the NELM in basics.inc to 100 000 and MAXPTS in basicsp.inc to 20 000 000. Also my mxpro = 40000 (maximum no of profile points). These parameters were used by me previously to read same domains successfully, that is why I am using these. Now the problem is an issue while compiling maketools. It says - ./maketools postnek/ ---------------------- Make postnek... ---------------------- make[1]: Entering directory `/home/msaikat6/Nek5000/tools/postnek' gfortran -o /home/msaikat6/Nek5000/bin/postx postnek.o postnek2.o postnek3.o postnek5.o postnek6.o tsort.o postnek8.o postnek9.o plot.o getfld.o legend.o userf.o revert.o trap.o animate.o genxyz.o screen.o g3d.o subs.o xinterface.o locglob.o postnek5a.o blas.o xdriver.o scrdmp.o coef.o postnek7.o speclib.o mxm.o byte.o ssyev.o iolib.o -L/usr/lib/X11 -lX11 -lm postnek.o: In function `fprep_': postnek.f:(.text+0xf6): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x133): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x183): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x1c0): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x210): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x24d): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x29d): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x2da): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x32a): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x367): relocation truncated to fit: R_X86_64_32S against symbol `chaar_' defined in COMMON section in postnek.o postnek.f:(.text+0x3b7): additional relocation overflows omitted from the output collect2: ld returned 1 exit status make[1]: *** [postx] Error 1 make[1]: Leaving directory `/home/msaikat6/Nek5000/tools/postnek' make: *** [all] Error 1 I don't understand the problem because I have used the same parameters previously, successfully. Let me know if you know what the problem is. Thanks so much. Saikat -- Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech.

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Element mesh mismatch with mesh in re2 file
by nek5000-users＠lists.mcs.anl.gov 25 Aug '17

25 Aug '17

Hello Neks, I am trying to confirm a methodology of using icem to create an extruded hex20 mesh, converting it to hex27 in cubit, and then using exo2nek to create an re2 file. I am recreating the 3d annulus example problem for this test. I copied the rea, SIZE, and usr files from the example directory. I have also updated the usr file to convert the generic boundary conditions from the exo2nek conversion to the correct boundary conditions using the side set info. The files compile, but when I try and run the simulation I get an element mesh mismatch error. I have attached the log file of the run for reference. Any suggestions on how to fix this would be great. Thanks, Tommy

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Element mesh mismatch with mesh in re2 file
by nek5000-users＠lists.mcs.anl.gov 24 Aug '17

24 Aug '17

Hello Neks, I am trying to confirm a methodology of using icem to create an extruded hex20 mesh, converting it to hex27 in cubit, and then using exo2nek to create an re2 file. I am recreating the 3d annulus example problem for this test. I copied the rea, SIZE, and usr files from the example directory. I have also updated the usr file to convert the generic boundary conditions from the exo2nek conversion to the correct boundary conditions using the side set info. The files compile, but when I try and run the simulation I get an element mesh mismatch error. I have attached the log file of the run for reference. Any suggestions on how to fix this would be great. Thanks, Tommy?

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Reflections on outlet
by nek5000-users＠lists.mcs.anl.gov 23 Aug '17

23 Aug '17

Dear Neks, I'm simulating a vertical heated plate in an open domain. When the flux is leaving the domain through the top face I get a reflection. I've tried to simulate adding more distance from the tip of the plate to the top face, but a vortex appears and when it tries to leave sometimes the code explodes and sometimes, I get a reflection again. Turb_outflow subroutine is not working for me. I think it is because I have multiple outlets. The "ON" bc is not helping either. Has anyone implemented a convective bc like Dong's (2014) or the "stabilized O bc" mentioned in this thread: https://lists.mcs.anl.gov/pipermail/nek5000-users/2016-March/003684.html ? Any suggestion is welcomed. Thanks in advance. Juan Pablo.

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