June 2014 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] XL compiler w/ moab
by nek5000-users＠lists.mcs.anl.gov 17 Jun '14

17 Jun '14

Hello again, Following my previous post, I tried the following libraries (as recommended by our cluster admin): libibmc++.a libibmc++.so libxl.a libxlopt.a libmc++ But apparently the link is not yet provided by these libraries as the following error message appears: "make: [obj/moab.o] Error 40" "make: waiting for unfinished jobs..." Note that I have no problem compiling Nek w/o Moab on BGQ. So I wondered if anyone has similar issue in compiling, probably related to linking. I attached the compiler output and makenek file. Thanks, Mohsen On 16-Jun-14, at 8:49 PM, Mohsen Behzad wrote: > Hello all, > I just wondered if anyone has experience in linking moab to nek on > BGQ platforms. I am looking for appropriate libraries for > USR_LFLAGS in makenek for IBM XL compilers, using to link moab to nek. > > Thanks, > Mohsen >

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XL compiler w/ moab
by nek5000-users＠lists.mcs.anl.gov 16 Jun '14

16 Jun '14

Hello all, I just wondered if anyone has experience in linking moab to nek on BGQ platforms. I am looking for appropriate libraries for USR_LFLAGS in makenek for IBM XL compilers, using to link moab to nek. Thanks, Mohsen

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quasi 3D and boundary condition
by nek5000-users＠lists.mcs.anl.gov 16 Jun '14

16 Jun '14

Hi Everyone. I am trying to run the flow past a cylinder case. I am going to move to the 3D simulation for my study. I have two questions: 1) how to run quasi 3D simulation in nek5000 ? if there is not existing code, andy suggestion to how to implement so? 2) how to specify the normal and tangential boundary condition for a curvature boundary? cheers ---------------------------------------------- Zhang Wei waynezw0618(a)gmail.com

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Monitor points, location probe
by nek5000-users＠lists.mcs.anl.gov 16 Jun '14

16 Jun '14

I need to monitor scalar gradient (scalar is modelled with temperature as in examples.pdf). So I have inserted in USERCHK parameter (lt=lx1*ly1*lz1*lelt) common /ilgrad/ dtdx(lt),dtdy(lt),dtdz(lt) if ((mod(istep,iostep).eq.0).and.(istep.ge.iostep)) then call gradm1(dtdx,dtdy,dtdz,t) endif call hpts() Next there are two options to monitor a quantity 1. in .rea file like ***** HISTORY AND INTEGRAL DATA ***** 001 POINTS. Hcode, I,J,H,IEL UV PT H 3 3 1 1 But I dont know how to tell it that I want instead of UV, and also I don't know how to calculate number of element IEL from physical location. 2. hpts.in file you can input physical coordinates of a location, but in hpts.out only the following variables # time vx vy [vz] pr T PS1 PS2 ... are being stored. So I tried to modify nek5000/branches/mvmesh/postpro.f in the following way: first I put parameter (lt=lx1*ly1*lz1*lelt) common /ilgrad/ dtdx(lt),dtdy(lt),dtdz(lt) in the beginning of subroutine hpts and later in this routine changed the code: ! pack working array nflds = 0 if(ifvo) then call copy(wrk(1,1),vx,ntot) call copy(wrk(1,2),vy,ntot) if(if3d) call copy(wrk(1,3),vz,ntot) nflds = ndim endif if(ifpo) then nflds = nflds + 1 call copy(wrk(1,nflds),pm1,ntot) endif if(ifto) then nflds = nflds + 1 call copy(wrk(1,nflds),t,ntot) endif nflds = nflds + 1 !!!!!!!!!inserted call copy(wrk(1,nflds),dtdx,ntot) !!!!!!!!!inserted nflds = nflds + 1 !!!!!!!!!inserted call copy(wrk(1,nflds),dtdy,ntot) !!!!!!!!!inserted do i = 1,ldimt if(ifpsco(i)) then nflds = nflds + 1 call copy(wrk(1,nflds),T(1,1,1,1,i+1),ntot) endif enddo It was compiled without problem, but running the program yielded no change in hpts.out, as before there are only 5 columns # time vx vy [vz] pr T Please help

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how to turn off conductivity/diffusion
by nek5000-users＠lists.mcs.anl.gov 14 Jun '14

14 Jun '14

I would like to model scalar transport without diffusion. Now I model scalar transport with the help of temperature variable (as in examples.pdf). If I just set parameter p0008 to zero or less than e-7 I got exception (background scalar gradient is about 100), which is quite comprehensible because of the insulated boundary condition. Even e-7 is quite a lot for my problem. So is there a way to model scalar transport without diffusion, i.e. without RHS at all? Or may be some trick with boundary conditions, which allows to set diffusion coefficient to zero?

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PRENEK, how to set o change parameters ("input vales" like thermal conductivity)? Is there a manual with pictures?
by nek5000-users＠lists.mcs.anl.gov 11 Jun '14

11 Jun '14

According to manual http://www.mcs.anl.gov/~fischer/nek_manual_v0.pdf (which lacks for pictures) after you have set the [EQUATION TYPE] and switch [CONVECTION] you are prompted to enter [INPUT VALUES] where you can set parameter CONDUCT (the thermal conductivity), NORDER and so on but really in prex after you "Assemble form of equation to be solved" and "ACCEPT CURRENT SWITCHES", choose the switches "WITH CONVECTION" and "CHARACTERISTICS" you are to "BUILD FROM FILE" or "BUILD INTERACTIVELY" so there is no option to set material properties Then, after you have created the geometry you can set [SET MATL PROPS,Q] But when you try to assign a constant value you got a message "If properties in group zero are constants, they can be set in the SET PARAMETER menu. You cannot override those values here except with a FORTRAN FUNCTION. Please change them in the SET PARAMETER menu in a new session." I have looked for "SET PARAMETER" everywhere in the menu, but have not found. So how do I set and change thermal expansion, thermal conductivity, rho, cp, viscosity and so on? Thanks in advance Van

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problems running in parallel
by nek5000-users＠lists.mcs.anl.gov 11 Jun '14

11 Jun '14

Dear users, I am trying to simulate the flow past a cylinder. If I run my simulation with lelt=2000, lelg=2000 in 1 processor, everything works fine. However, if I increase the resolution to lelt=4200 I get a compilation error. Following this post: http://lists.mcs.anl.gov/pipermail/nek5000-users/2013-April/002101.html I have seen that if I use more processors, the code compiles fine. However, now I am not able to run the code using 4 processors. I get the following error: Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /SL/nek5_svn/test/cyl/cyl.rea timer accuracy: 1.1920929E-07 sec read .rea file Beginning session: /SL/nek5_svn/test/cyl/cyl.rea timer accuracy: 9.5367432E-08 sec read .rea file nelgt/nelgv/lelt: 4425 4425 2000 lx1 /lx2 /lx3 : 5 5 5 ABORT: Problem size too large! This solver has been compiled for: number of elements/proc (lelt): 2000 total number of elements (lelg): 5000 Recompile with the following SIZE parameters: lelt >= 4425 for np = 1 lelg >= 4425 I have a 3d mesh with 4425 elemnts. In the SIZE file I have set: parameter (ldim=3) parameter (lx1=5,ly1=lx1,lz1=lx1,lelt=2000,lelv=lelt) parameter (lxd=(3*lx1)/2,lyd=lxd,lzd=lxd) parameter (lelx=1,lely=lelx,lelz=lely) parameter (lx2=lx1-0) ! Pressure array dimensions parameter (ly2=ly1-0) parameter (lz2=lz1-0) parameter (lx3=lx2) parameter (ly3=ly2) parameter (lz3=lz2) parameter (lp = 4) ! Max # processors parameter (lelg = 5000) ! Max # elements, total parameter (lzl=3 + 2*(ldim-3)) I have tried to follow this post to solve the problem, but I couldn't: https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2013-December/002411.… Could you help me, please? Regards, SL

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Re: [Nek5000-users] volumetric heat source w/ inflow
by nek5000-users＠lists.mcs.anl.gov 10 Jun '14

10 Jun '14

Hi Aleks, As a follow up on the following post, I just wanted to note that the results of Nek's version of my setup agreed exactly with the MOAB counterpart, and so the aforementioned issue has different origin. Thanks, Mohsen On 10-Jun-14, at 1:55 PM, Mohsen Behzad wrote: > Thanks Aleks for your suggestion. > So you think it might be because of some issue with MOAB. I'll > check this out, though, apparently, I haven't had any problem > reading the mesh and sidesets into Nek via MOAB. > > Mohsen > > > On 10-Jun-14, at 12:27 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > >> Hi Mohsen, >> >> One way I usually check my MOAB setups is by running the Nek's >> version of it. >> >> For this one needs to get Mesh & BC by calling gen_rea(2) from say >> userchk, add the missing parameters to create .rea file, run >> genmap for .map file and fill q array in userq2() routine by >> calling the latter from userq() say once per timestep >> >> Aleks >> >> >> >> ________________________________________ >> From: nek5000-users-bounces(a)lists.mcs.anl.gov [nek5000-users- >> bounces(a)lists.mcs.anl.gov] on behalf of nek5000- >> users(a)lists.mcs.anl.gov [nek5000-users(a)lists.mcs.anl.gov] >> Sent: Tuesday, June 10, 2014 11:03 AM >> To: nek5000-users(a)lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] volumetric heat source w/ inflow >> >> Hi Aleks, >> I should have mentioned in my previous email that I am actually using >> MOAB. >> >> Thanks, >> Mohsen >> >> On 10-Jun-14, at 12:01 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: >> >>> Hi Mohsen, >>> >>> userq2 is used only with MOAB -- use qvol in userq instead -- see, >>> e.g. examples/conj_ht/conj_ht.usr but without condition on nelgv >>> >>> Best. >>> Aleks >>> >>> >>> ________________________________________ >>> From: nek5000-users-bounces(a)lists.mcs.anl.gov [nek5000-users- >>> bounces(a)lists.mcs.anl.gov] on behalf of nek5000- >>> users(a)lists.mcs.anl.gov [nek5000-users(a)lists.mcs.anl.gov] >>> Sent: Tuesday, June 10, 2014 10:16 AM >>> To: Nek 5000 >>> Subject: [Nek5000-users] volumetric heat source w/ inflow >>> >>> Hello all, >>> I am working on a problem consisting of an axially-horizontal >>> cylindrical tank with an inlet (an opening) at its top and a >>> connected pipe to its bottom as an outlet. The boundary conditions >>> are set accordingly, i.e., inflow and outflow, respectively. >>> There is >>> no problem with isothermal simulation of such configuration. >>> However, >>> when volumetric heat source is added to the fluid domain (via userq2 >>> subroutine), non-physical temperatures have been observed at the >>> walls (w/ adiabatic BC) in the immediate vicinity of the inflow (w/ >>> Dirichlet temperature BC). In fact, the element nodes close to the >>> inlet have very high or very low temperatures, which are no >>> expected. >>> >>> I am wondering if anyone has any experience/hint on this issue. >>> >>> Thanks, >>> Mohsen >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users(a)lists.mcs.anl.gov >>> 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 >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> 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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volumetric heat source w/ inflow
by nek5000-users＠lists.mcs.anl.gov 10 Jun '14

10 Jun '14

Hello all, I am working on a problem consisting of an axially-horizontal cylindrical tank with an inlet (an opening) at its top and a connected pipe to its bottom as an outlet. The boundary conditions are set accordingly, i.e., inflow and outflow, respectively. There is no problem with isothermal simulation of such configuration. However, when volumetric heat source is added to the fluid domain (via userq2 subroutine), non-physical temperatures have been observed at the walls (w/ adiabatic BC) in the immediate vicinity of the inflow (w/ Dirichlet temperature BC). In fact, the element nodes close to the inlet have very high or very low temperatures, which are no expected. I am wondering if anyone has any experience/hint on this issue. Thanks, Mohsen

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gmsh to nek converter
by nek5000-users＠lists.mcs.anl.gov 08 Jun '14

08 Jun '14

Dear neks Using a code from here https://bitbucket.org/mikael_mortensen/nek5000-tools we wrote a converter from gmsh to rea format. You can find it here https://bitbucket.org/cpraveen/nek5000 I would be very keen to have others try it out and tell us if there are any bugs. Currently it works only for 2d meshes. It can also create circular faces. See inside gmsh2nek directory. The karman.geo example can be tested together with the setup files from here https://code.google.com/p/cfdlab/source/browse/trunk/nek5000/cyl_turek/ Replace the mesh in cyl.rea with the mesh created in karman.rea To generate karman.rea do the following (use latest Gmsh software) gmsh -2 karman.geo python karman.py Best praveen

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