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

Nek5000+MOAB
by nek5000-users＠lists.mcs.anl.gov 23 Sep '14

23 Sep '14

Hi NEKs, I am trying to use the MOAB enabled version of NEK. I looked at the pipe example in /examples/moab and it works. Than I recreated the .cub mesh using the journal file "pipe.jou" and Trelis. I converted the mesh using mbconvert blah.cub blah.h5m and it worked, even if there was a worrysome warning message " Element ids are not contiguous!". This is the mbsize result of the original input.h5m mesh: type count total minimum average rms maximum std.dev. ------- ------ ------- ----------------------- ----------------------- ----------------------- ----------------------- ----------------------- Edge 4952 5.1e+02 0.034623 0.10396 0.11844 0.19893 0.056762 Quad 2476 20 0.0017335 0.0082427 0.0086523 0.036989 0.0026306 Hex 5496 4.7 0.00014971 0.00085585 0.0023197 0.018287 0.0021561 1D Side 75856 7.8e+03 0.019193 0.1028 0.13066 0.50001 0.08065 Vertex 49005 an this is the same result for the new mesh: type count total minimum average rms maximum std.dev. ------- ------ ------- ----------------------- ----------------------- ----------------------- ----------------------- ----------------------- Edge 4952 5.1e+02 0.034623 0.10396 0.11844 0.19886 0.056762 Quad 2476 20 0.0017335 0.0082427 0.0086523 0.036969 0.0026306 Hex 5496 4.7 0.00014972 0.00085585 0.0023244 0.018468 0.0021611 1D Side 75856 8.3e+03 0.019195 0.11 0.14682 0.5 0.097238 Vertex 49005 If i try to use the new mesh in NEK I observe the following error: read .rea file ABORT: nelv is invalid in nekmoab_proc_map nelv, lelv = 0 5496 Probably it is more a MOAB related problem, but if anybody can give me any hints it will be great. Bests, Andrea

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SYM boundary conditions in MHD?
by nek5000-users＠lists.mcs.anl.gov 19 Sep '14

19 Sep '14

Hi, to my knowledge, the boundary conditions must be the same for the magnetic field and for the velocity field. My question is: Is it possible to use the SYM boundary conditions for both fields using the stress formulation (non-Cartesian mesh)? Many thanks, Benjamin.

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Re: [Nek5000-users] Nek5000 for Paraview
by nek5000-users＠lists.mcs.anl.gov 18 Sep '14

18 Sep '14

FYI, right now I am using Paraview 4.1 and presently the output of my Nek5000 is in the *.fld format with files named as "case_name.fld01, case_name.fld02, case_name.fld03 etc.." On Thu, Sep 18, 2014 at 1:01 PM, Pradeep Jha <pradeep.kumar.jha(a)gmail.com> wrote: > Hello, > > what should I change in the *.rea file so that Nek5000 outputs the result > in a file format readable by Paraview? > > Thanks. > Pradeep >

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Nek5000 for Paraview
by nek5000-users＠lists.mcs.anl.gov 18 Sep '14

18 Sep '14

Hello, what should I change in the *.rea file so that Nek5000 outputs the result in a file format readable by Paraview? Thanks. Pradeep

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Postx question
by nek5000-users＠lists.mcs.anl.gov 10 Sep '14

10 Sep '14

Hi, Neks I output my file with f00000 format and the number of my file is more than 10000. However I cannot open the file f10000 with postx. The error message is as below: opening file: 15 g10cond0.f0**** this is param(66): 6.0000000 WARNING: Could not open file. g10cond0.f0**** Unable to open dump number: 10000 Mu Xu

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Magnetoconvection setup
by nek5000-users＠lists.mcs.anl.gov 09 Sep '14

09 Sep '14

Dear NEK developers, We are trying to set up a magneto-convection case with NEK. Can you kindly give us pointers on how to do that? Also we would like to know the form of equations that are implemented in case of magneto-convection. with best wishes and regards, Supriyo Paul *********************************************************** *Dr. Supriyo Paul* CFD/CAE Centre for Development of Advanced Computing (C-DAC) Pune University Campus, Ganeshkhind, Pune - 411007 INDIA Phone:+91-202-570-4175 Mobile:+91-860-596-5538

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solving a helmholtz problem
by nek5000-users＠lists.mcs.anl.gov 09 Sep '14

09 Sep '14

Dear Neks, I want to solve the following Helmholtz problem: (A- c* B) f = g with functions f and g equal zero at the boundary c -- given positive real constant g -- given input field A -- mass matrix B -- discrete Laplacian How do I have to set up the .rea file to solve such a problem with nek. Thanks, Joerg.

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Outpost question
by nek5000-users＠lists.mcs.anl.gov 04 Sep '14

04 Sep '14

Howdy Nek's, I have a couple questions regarding the ouput of files: 1. How can force, within the code (say in usrchk), some files to be output in 64 bits for high-accuracy checkpointing and other in regular 8 bits for simple visualisation? 2. Say, during the first 1000 iterations, the code outpost a file every single iteration so that I have blah0.f00001 to blah0.f01000. How can I then force the code to outpost my new files (from istep = 1001 to 2000 say) rewriting on blah0.f00001 to blah0.f01000? Thanks a lot. Regards, JC -- Jean-Christophe Loiseau Homepage <https://sites.google.com/site/loiseaujc/>

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Wall Clock Time
by nek5000-users＠lists.mcs.anl.gov 04 Sep '14

04 Sep '14

Hello all, I'm interested in comparing the wall clock time for a same run with different number of CPU's. However, the time output seems to always give 0. I have tried using the mpi_wtime and dnekclock functions in the userchk subroutine and it has also been giving me 0 for each processor. I have included the end of my logfile in this email. The last 2 values of the first output line for a time step should give the total wall clock time and step wall clock time, but are both showing 0. At the end of the run, total elapsed time should be shown, but once again the value output is zero. Has anyone figured out a method permitting to obtain the total wall clock time? Thank you, Jï¿½rï¿½mie ----------------------- END OF LOGFILE ---------------------------------------------------------------------------- Step 20, t= 4.8774474E-02, DT= 2.4387237E-03, C= 0.501 0.0000E+00 0.0000E+00 Solving for fluid 20 1 4.7138E-02 1.7111E-07 2.7549E+05 15 alph1x 20 halpha 15 -1.1778E-03 1.2672E-01 6.1694E-02 1.1588E-01 5.4007E-02 5.1022E-02 3.1403E-02 2.4425E-02 1.0726E-02 6.0344E-03 20 Hmholtz VELX: 3 2.6011E-13 1.7111E-07 1.0000E-12 20 2 3.4534E-02 2.5050E-07 1.3786E+05 15 alph1x 20 halpha 15 1.8538E-02 1.0186E-01 4.5783E-02 4.5495E-02 4.2007E-02 4.7957E-02 3.7328E-02 2.8192E-02 2.2477E-02 9.2507E-03 20 Hmholtz VELY: 3 3.4751E-13 2.5050E-07 1.0000E-12 20 15 alpha: -2.7079E-06 -1.8713E-04 3.2842E-03 3.7249E-03 2.1355E-03 1.4731E-03 1.7188E-03 3.0469E-03 1.6907E-03 1.1608E-03 20 15 4.0387E-03 7.8105E-07 5.1708E+03 alph12 20 U-PRES gmres: 13 8.2682E-13 1.0000E-12 1.0390E-09 0.0000E+00 0.0000E+00 20 DNORM, DIVEX 8.2682338981824994E-013 8.2682352659334355E-013 20 4.8774E-02 0.0000E+00 Fluid done call outfld: ifpsco: F 20 4.8774E-02 Write checkpoint: 0 20 OPEN: naca24150.f00001 20 4.8774E-02 done :: Write checkpoint file size = 4.4 MB avg data-throughput = InfMB/s io-nodes = 1 end of time-step loop runtime statistics: total time 9.9999999999999995E-008 inv3 time 621 0.0000000000000000 0.0000000000000000 invc time 80 0.0000000000000000 0.0000000000000000 mltd time 1282 0.0000000000000000 0.0000000000000000 cdtp time 1282 0.0000000000000000 0.0000000000000000 eslv time 20 0.0000000000000000 0.0000000000000000 pres time 20 0.0000000000000000 0.0000000000000000 crsl time 565 0.0000000000000000 0.0000000000000000 crsl min 0.0000000000000000 crsl max 0.0000000000000000 crsl avg 0.0000000000000000 hmhz time 8 0.0000000000000000 0.0000000000000000 spro time 21 0.0000000000000000 0.0000000000000000 usbc time 21 0.0000000000000000 0.0000000000000000 usbc min 0.0000000000000000 usbc max 0.0000000000000000 usb avg 0.0000000000000000 axhm time 458 0.0000000000000000 0.0000000000000000 advc time 40 0.0000000000000000 0.0000000000000000 vdss time 622 0.0000000000000000 0.0000000000000000 vdss min 0.0000000000000000 vdss max 0.0000000000000000 vdss avg 0.0000000000000000 dsum time 2139 0.0000000000000000 0.0000000000000000 dsum min 0.0000000000000000 dsum max 0.0000000000000000 dsum avg 0.0000000000000000 dadd time 0 0.0000000000000000 0.0000000000000000 ddsl time 565 0.0000000000000000 0.0000000000000000 solv time 565 0.0000000000000000 0.0000000000000000 prep time 20 0.0000000000000000 0.0000000000000000 # nid tusbc tdadd tcrsl tvdss tdsum tgop qqq F 0 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 1 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 2 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 3 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 4 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 5 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq call exitt: dying ... backtrace(): obtained 5 stack frames. ./nek5000(print_stack_+0x1a) [0x4fa15a] ./nek5000(exitt_+0x1a6) [0x5e6b56] ./nek5000(main+0x39) [0x419489] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x2b7993c6076d] ./nek5000() [0x4194b9] total elapsed time : 0.00000E+00 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec

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Linking ESSL Lib to nek5000
by nek5000-users＠lists.mcs.anl.gov 04 Sep '14

04 Sep '14

Hi Aleks, I followed your suggestion and changed the path in makenek to # linking flags USR_LFLAGS="-L/bgsys/local/lib -lesslbg" This where ESSL lib is found on BG/Q Juqueen in Juelich. When I run makenek, I get the following error message. mpixlf77 -qsuppress=cmpmsg -o nek5000 obj/G1_96.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o obj/singlmesh.o obj/dsygv.o obj/ssygv.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_amg.o obj/jl_fcrs.o -L/bgsys/local/lib -lesslbg /bgsys/local/lib/libesslbg.a(emon.o):(.text+0x150): undefined reference to `_xlf_create_threadlocal' make: *** [nek5000] Error 1 Do you know what went wrong? Thanks, Joerg.

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