August 2013 - Nek5000-users - mailman3.cels.anl.gov

compiler optimizations
by nek5000-users＠lists.mcs.anl.gov 17 Aug '13

17 Aug '13

Hello, I have been playing with compiler flags and directives to see if I can improve the time-to-solution of the turbChannel example. I have had some success and would like to give back to the community. What is the best procedure for doing this? I'm using the Intel-13.1.3.192 compiler on a Sandybridge Xeon. baseline timing for 1000 iterations on 8 cpu is total time 443.08s With a few compiler directives and optimization flags I got it down to total time 304.52s Dan

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Maketools compile issue of prenek
by nek5000-users＠lists.mcs.anl.gov 16 Aug '13

16 Aug '13

Dear Neks I updated my tools today to the latest version and then after "./maketools clean" and "./maketools all" I encountered a problem in compiling prenek. Even after "rm -rf tools" and "svn update tools", I still see the same problem regardless. Also note that I have set BIGMEM="true" in my maketools. Since I did not have this problem the first time I built the tools, I am not sure how this could be related to my compiler or machine memory (which are all the same). So I would appreciate it if anyone can help me figure this out. Regards, Hesam ---------------------- Make prenek... ---------------------- make[1]: Entering directory `/home/p/peltier/hsalehip/src/nek5_svn/trunk/tools/prenek' gfortran -o /home/p/peltier/hsalehip/bin/prex prenek.o curve.o edit.o build.o build1.o build2.o bound.o plot.o xinterface.o glomod.o legend.o vprops.o iolib.o subs.o zipper2.o postnek6.o screen.o revert.o crs.o mxm.o xdriver.o -L/usr/lib/X11 -lX11 -lm curve.o: In function `hex_transition_3d_e_': curve.f:(.text+0x6309): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o curve.f:(.text+0x637e): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o curve.f:(.text+0x63ab): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o curve.f:(.text+0x63d8): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o curve.o: In function `hexagon_refine_e_': curve.f:(.text+0x75a5): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o curve.f:(.text+0x763d): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o curve.f:(.text+0x768d): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o build.o: In function `list_delete_': build.f:(.text+0x2d37): relocation truncated to fit: R_X86_64_32S against symbol `idelt_' defined in COMMON section in build.o build.f:(.text+0x2dd1): relocation truncated to fit: R_X86_64_32S against symbol `idelt_' defined in COMMON section in build.o build.o: In function `imp_mesh_vtx_': build.f:(.text+0x30f3): relocation truncated to fit: R_X86_64_32S against symbol `c_xyz_' defined in COMMON section in build.o build.f:(.text+0x3124): additional relocation overflows omitted from the output collect2: error: ld returned 1 exit status make[1]: *** [prex] Error 1 make[1]: Leaving directory `/home/p/peltier/hsalehip/src/nek5_svn/trunk/tools/prenek' make: *** [all] Error 1

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Re: [Nek5000-users] Nek5000-users Digest, Vol 54, Issue 1
by nek5000-users＠lists.mcs.anl.gov 06 Aug '13

06 Aug '13

Hi Paul, Thanks so much for the help and quick response. The code is running fine. I do realize that this is not a Womersley inlet. In fact I have access to patient specific Doppler measured velocity profiles (V of T in this case) that I am implementing with the assumption of a fully developed flow. This is justified to some extent since the vein in reality, before the spot that we consider the inlet for our study, is long enough to develop a parabolic profile in the tube. Am still waiting for any ideas if the Sponge outlet condition can be used with stress formulation for non-Newtonian flows. Cheers, Javid On Tue, Aug 6, 2013 at 12:00 PM, <nek5000-users-request(a)lists.mcs.anl.gov>wrote: > 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. Pulsatile Flow in NEK5000 (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Pulsatile Flow in NEK5000 (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 5 Aug 2013 16:19:37 -0500 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov, Cassel Kevin <cassel(a)iit.edu> > Subject: [Nek5000-users] Pulsatile Flow in NEK5000 > Message-ID: > <mailman.12039.1375737604.15097.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi There NEKs, > > I am currently trying to run a case with pulsatile inlet condition. The > context is pulsatile stenotic flows. I have two Question regrading the set > up: > > 1st Question) How do I access the "Time" variable in NEK5000? I need to > define a time dependent inlet velocity condition in the user file. V as a > function of Y and T. I already have the function which is a patient > specific velocity inlet profile. Please note that this should be a > pulsatile flow. This, I assume, is different than a periodic flow. I'll be > investigation the effect of pulsatility on some 2D geometries. > It would be wonderful to know how to implement time dependent inlet > velocity condition in user file. Previously I have only used steady > and parabolic inlet velocity. > > 2nd Question) I will be using a simple Dirichlet BC on pressure for the > outlet. I have also used the Nozzle outlet condition but, as it turns out, > I cannot use the Nozzle condition with stress formulation. I wanted to know > if the Sponge condition for outlet is proper and if it can be coupled with > stress formulation? I am considering a non-Newtonian fluid with variable > viscosity for my simulation. > > Any assistance is greatly appreciated. > > Best of luck to everyone, > Javid >

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Pulsatile Flow in NEK5000
by nek5000-users＠lists.mcs.anl.gov 05 Aug '13

05 Aug '13

Hi There NEKs, I am currently trying to run a case with pulsatile inlet condition. The context is pulsatile stenotic flows. I have two Question regrading the set up: 1st Question) How do I access the "Time" variable in NEK5000? I need to define a time dependent inlet velocity condition in the user file. V as a function of Y and T. I already have the function which is a patient specific velocity inlet profile. Please note that this should be a pulsatile flow. This, I assume, is different than a periodic flow. I'll be investigation the effect of pulsatility on some 2D geometries. It would be wonderful to know how to implement time dependent inlet velocity condition in user file. Previously I have only used steady and parabolic inlet velocity. 2nd Question) I will be using a simple Dirichlet BC on pressure for the outlet. I have also used the Nozzle outlet condition but, as it turns out, I cannot use the Nozzle condition with stress formulation. I wanted to know if the Sponge condition for outlet is proper and if it can be coupled with stress formulation? I am considering a non-Newtonian fluid with variable viscosity for my simulation. Any assistance is greatly appreciated. Best of luck to everyone, Javid

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