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

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > 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. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> 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 > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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Error in generalev
by nek5000-users＠lists.mcs.anl.gov 02 Jul '14

02 Jul '14

Hello Neks, I've recently come across an error I haven't seen before. It occurs in the routine "generalev" at the beginning of my run. It looks like the matrix "a" and "b" being fed to the routine have an Infinity or NaN at position (0,0). Are there any ideas of what could cause this type of error? I have attached the logfile to this email. Thanks, -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

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MPI problems
by nek5000-users＠lists.mcs.anl.gov 28 Feb '14

28 Feb '14

Dear Nek’s I have a problem when running the code on more than one processor. The problem just appeared after a recent update of the system (debian) on our cluster. The code was working perfectly before the update but now I cannot run jobs in parallel anymore. MPI works with other softwares, but not with NEK. In particular I have the following problem: When I execute a parallel run using the script nekmpi eddy_uv 4 the command execute 4 different jobs running on a single processor rather than a single job running on 4 processors. I attach the log to this mail (log.out) . After a few second three jobs are killed and only one remains active. A similar problem was also found on a new machine with a fresh installation of debian. It seems that the scripts is not able to set the correct value of the variable np (or_np). Anyone found a similar problem ? Any explanation for such behavior ? Any advice to solve the problem ? Thanks in advance Flavio Platform uname -a Linux cfd 2.6.32-5-amd64 #1 SMP Mon Sep 23 22:14:43 UTC 2013 x86_64 GNU/Linux ompi_info Package: Open MPI manuel@ce170155 Distribution Open MPI: 1.4.2 Open MPI SVN revision: r23093 Open MPI release date: May 04, 2010 Open RTE: 1.4.2 Open RTE SVN revision: r23093 Open RTE release date: May 04, 2010 OPAL: 1.4.2 OPAL SVN revision: r23093 OPAL release date: May 04, 2010 Ident string: 1.4.2 Prefix: /usr Configured architecture: x86_64-pc-linux-gnu Configure host: ce170155 Configured by: manuel Configured on: Wed Sep 1 15:58:32 UTC 2010 Configure host: ce170155 Built by: root Built on: Wed Sep 1 16:01:42 UTC 2010 Built host: ce170155 C bindings: yes C++ bindings: yes Fortran77 bindings: yes (all) Fortran90 bindings: yes Fortran90 bindings size: small C compiler: gcc C compiler absolute: /usr/lib/ccache/gcc C++ compiler: g++ C++ compiler absolute: /usr/lib/ccache/g++ Fortran77 compiler: gfortran Fortran77 compiler abs: /usr/bin/gfortran Fortran90 compiler: gfortran Fortran90 compiler abs: /usr/bin/gfortran C profiling: yes C++ profiling: yes Fortran77 profiling: yes Fortran90 profiling: yes C++ exceptions: no Thread support: posix (mpi: no, progress: no) Sparse Groups: no Internal debug support: no MPI parameter check: runtime Memory profiling support: no Memory debugging support: no libltdl support: yes Heterogeneous support: yes mpirun default --prefix: no MPI I/O support: yes MPI_WTIME support: gettimeofday Symbol visibility support: yes FT Checkpoint support: yes (checkpoint thread: no) MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.2) MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.2) MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2) MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.4.2) MCA carto: file (MCA v2.0, API v2.0, Component v1.4.2) MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.4.2) MCA maffinity: libnuma (MCA v2.0, API v2.0, Component v1.4.2) MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.2) MCA installdirs: env (MCA v2.0, API v2.0, Component v1.4.2) MCA installdirs: config (MCA v2.0, API v2.0, Component v1.4.2) MCA crs: none (MCA v2.0, API v2.0, Component v1.4.2) MCA dpm: orte (MCA v2.0, API v2.0, Component v1.4.2) MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.4.2) MCA allocator: basic (MCA v2.0, API v2.0, Component v1.4.2) MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: basic (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: inter (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: self (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: sm (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: sync (MCA v2.0, API v2.0, Component v1.4.2) MCA coll: tuned (MCA v2.0, API v2.0, Component v1.4.2) MCA io: romio (MCA v2.0, API v2.0, Component v1.4.2) MCA mpool: fake (MCA v2.0, API v2.0, Component v1.4.2) MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.4.2) MCA mpool: sm (MCA v2.0, API v2.0, Component v1.4.2) MCA pml: cm (MCA v2.0, API v2.0, Component v1.4.2) MCA pml: crcpw (MCA v2.0, API v2.0, Component v1.4.2) MCA pml: csum (MCA v2.0, API v2.0, Component v1.4.2) MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.4.2) MCA pml: v (MCA v2.0, API v2.0, Component v1.4.2) MCA bml: r2 (MCA v2.0, API v2.0, Component v1.4.2) MCA rcache: vma (MCA v2.0, API v2.0, Component v1.4.2) MCA btl: ofud (MCA v2.0, API v2.0, Component v1.4.2) MCA btl: openib (MCA v2.0, API v2.0, Component v1.4.2) MCA btl: self (MCA v2.0, API v2.0, Component v1.4.2) MCA btl: sm (MCA v2.0, API v2.0, Component v1.4.2) MCA btl: tcp (MCA v2.0, API v2.0, Component v1.4.2) MCA topo: unity (MCA v2.0, API v2.0, Component v1.4.2) MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.4.2) MCA osc: rdma (MCA v2.0, API v2.0, Component v1.4.2) MCA crcp: bkmrk (MCA v2.0, API v2.0, Component v1.4.2) MCA iof: hnp (MCA v2.0, API v2.0, Component v1.4.2) MCA iof: orted (MCA v2.0, API v2.0, Component v1.4.2) MCA iof: tool (MCA v2.0, API v2.0, Component v1.4.2) MCA oob: tcp (MCA v2.0, API v2.0, Component v1.4.2) MCA odls: default (MCA v2.0, API v2.0, Component v1.4.2) MCA ras: slurm (MCA v2.0, API v2.0, Component v1.4.2) MCA ras: tm (MCA v2.0, API v2.0, Component v1.4.2) MCA rmaps: load_balance (MCA v2.0, API v2.0, Component v1.4.2) MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.4.2) MCA rmaps: round_robin (MCA v2.0, API v2.0, Component v1.4.2) MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.4.2) MCA rml: ftrm (MCA v2.0, API v2.0, Component v1.4.2) MCA rml: oob (MCA v2.0, API v2.0, Component v1.4.2) MCA routed: binomial (MCA v2.0, API v2.0, Component v1.4.2) MCA routed: direct (MCA v2.0, API v2.0, Component v1.4.2) MCA routed: linear (MCA v2.0, API v2.0, Component v1.4.2) MCA plm: rsh (MCA v2.0, API v2.0, Component v1.4.2) MCA plm: slurm (MCA v2.0, API v2.0, Component v1.4.2) MCA plm: tm (MCA v2.0, API v2.0, Component v1.4.2) MCA snapc: full (MCA v2.0, API v2.0, Component v1.4.2) MCA filem: rsh (MCA v2.0, API v2.0, Component v1.4.2) MCA errmgr: default (MCA v2.0, API v2.0, Component v1.4.2) MCA ess: env (MCA v2.0, API v2.0, Component v1.4.2) MCA ess: hnp (MCA v2.0, API v2.0, Component v1.4.2) MCA ess: singleton (MCA v2.0, API v2.0, Component v1.4.2) MCA ess: slurm (MCA v2.0, API v2.0, Component v1.4.2) MCA ess: tool (MCA v2.0, API v2.0, Component v1.4.2) MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.4.2) MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.4.2)

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set boundary condition on spectral element
by nek5000-users＠lists.mcs.anl.gov 25 Feb '14

25 Feb '14

Hello, I have a question about setting boundary condition on spectral element mesh when I am not sure that on the boundary condition I have spectral mesh or not?! like pipe with some extension in inlet/outlet that boundary condition is located at the beginning of pipe but the mesh started from extension. What I thought was using normal surface to specify spectral boundary condition there! Is that right?! my question is to how set the boundary condition on spectral element? Thank you, Ami

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subroutine for drag
by nek5000-users＠lists.mcs.anl.gov 25 Feb '14

25 Feb '14

Hi neks, I have three pipes attached together, I compute drag using the subroutine. I want to compute the drag only for two pipes, Could some one tell me how to change the routine just to take only the two pipes into account. Is nobj the control variable for it ? Thanks, Kamal.

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Lid driven cavity using nek5000
by nek5000-users＠lists.mcs.anl.gov 24 Feb '14

24 Feb '14

Hello, I'm trying to solve a simple lid driven cavity problem with nek5000. I set up a coarse 3d mesh and prescribed the velocity for the lid according to Bouffanis et al. 2008 PoF (to ensure that there is no discontinuity between the lid and the walls),I'm getting a vanishing jacobian error. I'm not sure how nek solves, but for the moving wall do I have to prescribe the mesh velocity equal to the lid velocity or is there a way to specify that the mesh doesn't really move in time? Thanks for your help! -- Regards Shriram

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Segmentation Error
by nek5000-users＠lists.mcs.anl.gov 21 Feb '14

21 Feb '14

Hi Neks, I have a setobj() subroutine which defines my wall surface of integral, This subroutine worked well on my local machine for a smaller mesh. Recently I launched a simulation with a big mesh, I found that using the setobj() subroutine gives a error which something looks like this, I have attached the complete error file with this mail along with logfile and .usr file. could some tell me what is going wrong ? *************************************************************** [lomc-itp-43:15165] *** Process received signal *** [lomc-itp-43:15159] *** Process received signal *** [lomc-itp-43:15159] Signal: Segmentation fault (11) [lomc-itp-43:15159] Signal code: Address not mapped (1) [lomc-itp-43:15159] Failing at address: (nil) [lomc-itp-43:15164] *** Process received signal *** [lomc-itp-43:15160] *** Process received signal *** [lomc-itp-43:15160] Signal: Segmentation fault (11) [lomc-itp-43:15160] Signal code: Address not mapped (1) [lomc-itp-43:15160] Failing at address: (nil) [lomc-itp-43:15162] *** Process received signal *** [lomc-itp-43:15162] Signal: Segmentation fault (11) [lomc-itp-43:15162] Signal code: Address not mapped (1) [lomc-itp-43:15162] Failing at address: (nil) [lomc-itp-43:15163] *** Process received signal *** [lomc-itp-43:15163] Signal: Segmentation fault (11) [lomc-itp-43:15163] Signal code: Address not mapped (1) [lomc-itp-43:15163] Failing at address: (nil) [lomc-itp-43:15164] Signal: Segmentation fault (11) [lomc-itp-43:15164] Signal code: Address not mapped (1) [lomc-itp-43:15164] Failing at address: (nil) ******************************************************************** Thanks, Kamal

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NEK with MOAB using MPI
by nek5000-users＠lists.mcs.anl.gov 19 Feb '14

19 Feb '14

Dear All, I am trying to run NEK with Moab and have done so successfully when launching the pipe example using one processor (i.e. running './nekmpi pipe 1' ). To then run the example with more processors I have partitioned the input.h5m mesh using mbpart (with Zoltan flags) and tested that HDF5 was compiled well to work with mpi. When I try to run the example on 4 ('./nekmpi pipe 4') processors I get the following error: ---------------------------------------------------------------------------------- read .rea file ASSERT ERROR: 21 in moab.f line 477 ASSERT ERROR: 21 in moab.f line 477 ASSERT ERROR: 21 in moab.f line 477 ASSERT ERROR: 21 in moab.f line 477 call exitt: dying ... backtrace(): obtained 10 stack frames. ./nek5000(print_stack_+0x1a) [0x58497a] ./nek5000(exitt_+0x24b) [0x64bd8b] ./nek5000(imesh_err_+0x170) [0x64b640] ./nek5000(nekmoab_load_+0xec) [0x649c1c] ./nek5000(nekmoab_import_+0x95) [0x64a425] ./nek5000(readat_+0x53f) [0x4cbdef] ./nek5000(nek_init_+0x57) [0x49c327] ./nek5000(main+0x24) [0x499184] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f56b4fad995] ./nek5000() [0x49bb87] ---------------------------------------------------------------------------------- Any idea on what I am doing wrong please? Regards, JP

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Building mass and stiffness matrices
by nek5000-users＠lists.mcs.anl.gov 18 Feb '14

18 Feb '14

Dear users and developers, I am using NEK5000 for a 3d unsteady simulation with mixed Dirichlet and periodic bc. For the post-processing (a POD-based dynamics) I need the global mass and stiffness matrices as built by NEK5000 on my mesh. I would also need the matrix having as entries (phi_i, grad(phi_j)) where phi are the basis polynomials. Is it possible to have NEK build these matrices and then save them on file? The ultimate goal is to import them on a PETSc program to perform some algebraic manipulations. I already found a way to import the simulations' results. Surfing the code, I have found some 1-d routines, but I don't know how to extend them to my needs. Thank you in advance for any help or hint. Best regards, Giuseppe

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Visco-elastic Models
by nek5000-users＠lists.mcs.anl.gov 18 Feb '14

18 Feb '14

Hi Neks, 1) Is there a subroutine which allows me to find the position of maximum velocity along a cross-section (pipe) ? 2) Is it possible to simulate a visco-elastic fluid using NEK5000 ? for example the Oldroyd-B model. Thanks, Kamal

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