October 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 when creating own mesh
by nek5000-users＠lists.mcs.anl.gov 01 Mar '16

01 Mar '16

Dear Neks, I am have attempted to use nek5000, firstly by following some of the examples etc. Now I am trying to create my own simulation, which is based upon the ocyl examples. My efforts simply include creating my own grid points in the .rea file to create a slightly different dimension... I believe I have understood how to define the problem however I continually receive errors when creating the genmap it reads as follows.... Input (.rea) file name: ocyl Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.2 reading .rea file data ... ERROR: error reading 1 11 24 aborting 510 in routine rdbdry. 1 quit All I have done again is change the dimensions of the elements in the .rea file so I do not see why it would now not work? Thank you for any help in advance, Friedrich.

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Submitting Job Nek Enabled Moab
by nek5000-users＠lists.mcs.anl.gov 02 Nov '14

02 Nov '14

Hi Vijay, Firstly thank you for your response! I have attempted all you suggested and this still does not seem to fix my issues. When I run ldd nek5000 I see: linux-vdso.so.1 => (0x00007fff635ff000) libz.so.1 => /home/eng/esumgy/pre-moab/zlib/zlib-1.2.8/libz.so.1 (0x00007fdd5a627000) libm.so.6 => /lib64/libm.so.6 (0x00007fdd5a37a000) libsz.so.2 => /home/eng/esumgy/pre-moab/szip/szip-2.1/gcc/lib/libsz.so.2 (0x00007fdd5a166000) libgpfs.so => /usr/lib64/libgpfs.so (0x00007fdd5a05a000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fdd59e55000) libmpi_f77.so.0 => /hpcwarwick/ompi/1.4.5/intel/11.1/lib/libmpi_f77.so.0 (0x00007fdd59c19000) libmpi.so.0 => /hpcwarwick/ompi/1.4.5/intel/11.1/lib/libmpi.so.0 (0x00007fdd59945000) libopen-rte.so.0 => /hpcwarwick/ompi/1.4.5/intel/11.1/lib/libopen-rte.so.0 (0x00007fdd596dc000) libopen-pal.so.0 => /hpcwarwick/ompi/1.4.5/intel/11.1/lib/libopen-pal.so.0 (0x00007fdd5945e000) libnsl.so.1 => /lib64/libnsl.so.1 (0x00007fdd59246000) libutil.so.1 => /lib64/libutil.so.1 (0x00007fdd59042000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fdd58d3c000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fdd58b26000) libintlc.so.5 => /gpfs/hpcwarwick/intel/Compiler/11.1/059/lib/intel64/libintlc.so.5 (0x00007fdd589e8000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fdd587cb000) libc.so.6 => /lib64/libc.so.6 (0x00007fdd58452000) librt.so.1 => /lib64/librt.so.1 (0x00007fdd58248000) /lib64/ld-linux-x86-64.so.2 (0x00007fdd5a83f000) libimf.so => /gpfs/hpcwarwick/intel/Compiler/11.1/059/lib/intel64/libimf.so (0x00007fdd57eb5000) libsvml.so => /gpfs/hpcwarwick/intel/Compiler/11.1/059/lib/intel64/libsvml.so (0x00007fdd57c9d000) The compiler being used is ompi/1.4.5/intel/11.1 See also the moab and hdf5 config.log attached! System information can be found - http://www2.warwick.ac.uk/fac/sci/csc/local/hpc Thank you for your help I am happy maybe to finally solve this issue Friedrich

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Submitting Job Nek Enabled Moab
by nek5000-users＠lists.mcs.anl.gov 29 Oct '14

29 Oct '14

Hi Again, I just wanted to update that although I have added the szip library to the LD_LIBRARY_PATH I still receive the same error: mv: cannot stat `pipe.log.12': No such file or directory mv: cannot stat `pipe.sch': No such file or directory ./nek5000: error while loading shared libraries: libintlc.so.5: failed to map segment from shared object: Cannot allocate memory ./nek5000: error while loading shared libraries: libintlc.so.5: failed to map segment from shared object: Cannot allocate memory ./nek5000: error while loading shared libraries: libintlc.so.5: failed to map segment from shared object: Cannot allocate memory ./nek5000: error while loading shared libraries: libintlc.so.5: failed to map segment from shared object: Cannot allocate memory Should I consider loading zlib etc in the same way or is this something else? Regards, Friedrich.

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Submitting Job Nek Enabled Moab
by nek5000-users＠lists.mcs.anl.gov 29 Oct '14

29 Oct '14

Hi Vijay, Ok I have done this, thank you for the advice! As I am submitting from a batch script should I consider running using nekpbs? If so what edits to the script would this entail etc. Friedrich

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Submitting Job Nek Enabled Moab
by nek5000-users＠lists.mcs.anl.gov 28 Oct '14

28 Oct '14

Hi All, I am currently experiencing issues when trying to run jobs on my hpc system. I have installed moab (with hdf5 and zoltan) as recommended on the nek5000 webpages - https://nek5000.mcs.anl.gov/index.php/Building_and_Using_Nek_/_MOAB. When I do this the simulation will run if I acquire resources form the system and then run the job using nekmpi [casename] [np]. However if I then attempt to submit this same simulation to the queue using: #!/bin/bash #PBS -l nodes=1:ppn=12,pvmem=1900mb,walltime=01:00:00 #PBS -V cd $PBS_O_WORKDIR nekmpi pipe 8 > log exit 0 I submit the job and it fails citing: mv: cannot stat `pipe.log.8': No such file or directory mv: cannot stat `pipe.sch': No such file or directory node6.8452Error re-mmapping shared memory: Cannot allocate memory (err=9) node6.8452Error re-mmapping shared memory: Cannot allocate memory [node6:08452] Open MPI detected an unexpected PSM error in opening an endpoint: Error re-mmapping shared memory: Cannot allocate memory -------------------------------------------------------------------------- mpiexec has exited due to process rank 7 with PID 8452 on node node6 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). -------------------------------------------------------------------------- I thus decided there may be issues with moab so I installed according to the moab webpages - http://trac.mcs.anl.gov/projects/ITAPS/wiki/BuildingAndUsingMOAB.<http://trac.mcs.anl.gov/projects/ITAPS/wiki/BuildingAndUsingMOAB> When I submit the job now I see a different error: mv: cannot stat `pipe.log.8': No such file or directory mv: cannot stat `pipe.sch': No such file or directory ./nek5000: error while loading shared libraries: libsz.so.2: cannot open shared object file: No such file or directory The above error I feel is somehow linked to either netcdf or hdf5 but I cannot see how or why as they both installed correctly (as far as I can tell). Thank you for any help, Friedrich

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Interfacing with Arpack
by nek5000-users＠lists.mcs.anl.gov 27 Oct '14

27 Oct '14

Dear users and developers, I would like to solve a generalized eigenvalue problem with Arpack, based on Nek subroutines. Using reverse communication interface, I only need to express the action of the matrices on the vectors, but I am not sure on how to apply the mass matrix and the inverse mass matrix in the Pn-Pn formulation. Is it sufficient to write: call col2(p1,bm1,n) !apply mass matrix to vector p1 ... call invcol2(p1,bm1,n) ! apply inverse mass matrix to vector p1 or should I do: call rzero(h1,n) call rone(h2,n) call hmholtz('vel',p,p1,h1,h2,pmask,vmult,imsh,tolh,maxiter,isd) to apply inverse mass matrix to p1, or should I do something else? Also, from a related question from a couple of years ago, should I call col2(v,vmask,n) after each matrix-vector product? Thank you in advance. Best, Giuseppe

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Curved GLL Points on Airfoil
by nek5000-users＠lists.mcs.anl.gov 27 Oct '14

27 Oct '14

Hello Neks, I am trying to simulate the flow around an interpolated airfoil with curved boundaries. To do so I am generating the collocation points separately and writing them into an input file, which is read in the usrdat2 subroutine before geometry re-initialization. The only curved elements in the mesh are located at the airfoil boundary. I am not getting any errors during geometry re-initialization. However, the calculation starts off with a large courant number (around 7), which ends up diverging after 5 times steps. Along the element edges near the airfoil, there seems to be discontinuities in the flow which cause the solution to diverge. However, when inputting non-curvilinear collocation points, written in the exact same order to the input file, the simulation runs flawlessly. Are there any switches that must be activated in the rea file for curved elements? If not, are there any general guidelines to using curved elements in this manner? Thanks, Jeremie

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Restarting simulation in same run
by nek5000-users＠lists.mcs.anl.gov 27 Oct '14

27 Oct '14

Dear neks I want to perform several simulations each with different initial condition in the same run of nek5000. This is for eigenvalue/vector computation with ARPACK and using time-stepping approach. I plan to do all of this in userchk. The call to ARPACK will be in userchk. Whenever ARPACK gives me a vector, I want to start a simulation with this vector as initial condition. I have to perform certain number of time-steps and return the result to ARPACK. What all do I need to do to initialize a simulation given the initial condition vector ? Thanks praveen

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outpost parallel error
by nek5000-users＠lists.mcs.anl.gov 26 Oct '14

26 Oct '14

Dear Neks, in the usr file, after doing some manipulations on a known solution (loaded from file with load_fld(...)), I save the computed values with a call to outpost, like: call outpost2(u1(1,1,1,1),v1(1,1,1,1), & w1(1,1,1,1),p1(1,1,1,1), & p1(1,1,1,1),1,'arp') While this is working correctly with 1 rank, in parallel it fails, returning only the error message: schfile:/.../myrun.sch then it hangs for a while, with all processes consuming all the cpu time until they are killed (so the .sch file is empty). Does anybody have an idea on how this could be solved? Best, Giuseppe

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