<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div></div><div>Your mesh seems to be messed up (see zmax below).</div><div><br>On 12 Jan 2018, at 00:14, "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br><br></div><blockquote type="cite"><div><span>Im trying to make a turbulance flow 2d rectangular box and getting this </span><br><span>error</span><br><span></span><br><span>/----------------------------------------------------------\\</span><br><span>| _ __ ______ __ __ ______ ____ ____ ____ |</span><br><span>| / | / // ____// //_/ / ____/ / __ \\/ __ \\/ __ \\ |</span><br><span>| / |/ // __/ / ,< /___ \\ / / / // / / // / / / |</span><br><span>| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |</span><br><span>| /_/ |_//_____//_/ |_|/_____/ \\___/ \\___/ \\___/ |</span><br><span>| |</span><br><span>|----------------------------------------------------------|</span><br><span>| |</span><br><span>| NEK5000: Open Source Spectral Element Solver |</span><br><span>| COPYRIGHT (c) 2008-2017 UCHICAGO ARGONNE, LLC |</span><br><span>| Version: v17.0 |</span><br><span>| Web: <a href="http://nek5000.mcs.anl.gov">http://nek5000.mcs.anl.gov</a> |</span><br><span>| |</span><br><span>\\----------------------------------------------------------/</span><br><span></span><br><span></span><br><span> Number of processors: 8</span><br><span> REAL wdsize : 8</span><br><span> INTEGER wdsize : 4</span><br><span> Timer accuracy : 4.83E-08</span><br><span></span><br><span> Reading /home/Nek5000/run/git/NewBarc/NewBarc.rea</span><br><span> Reading /home/Nek5000/run/git/NewBarc/NewBarc.re2</span><br><span> mapping elements to processors</span><br><span> Reading /home/Nek5000/run/git/NewBarc/NewBarc.ma2</span><br><span> 0 91 91 730 730 NELV</span><br><span> 1 91 91 730 730 NELV</span><br><span> 2 91 91 730 730 NELV</span><br><span> 3 92 92 730 730 NELV</span><br><span> 4 91 91 730 730 NELV</span><br><span> 5 91 91 730 730 NELV</span><br><span> 6 91 91 730 730 NELV</span><br><span> 7 92 92 730 730 NELV</span><br><span> RANK 0 IEG 351 352 353 354 355 356 381 382</span><br><span> 383 384 385 386 387 388 389 391</span><br><span> 392 393 394 395 396 397 398 399</span><br><span> 401 402 403 404 405 406 407 408</span><br><span> 409 411 412 413 414 415 416 417</span><br><span> 418 419 421 422 423 424 425 426</span><br><span> 427 428 429 431 432 433 434 435</span><br><span> 436 437 438 441 442 443 444 445</span><br><span> 446 447 448 451 452 453 454 455</span><br><span> 456 457 458 461 462 463 464 465</span><br><span> 466 467 468 471 472 473 474 475</span><br><span> 476 477 478</span><br><span></span><br><span> element load imbalance: 1 91 92</span><br><span> done :: mapping 0.13924E-02 sec</span><br><span></span><br><span></span><br><span> preading mesh</span><br><span> preading bc for ifld 1</span><br><span> done :: read .re2 file 0.45E-02 sec</span><br><span></span><br><span> 0 objects found</span><br><span> 103 Parameters from file:</span><br><span> 1 1.000000 p01 DENSITY</span><br><span> 2 -40000.00 p02 VISCOS</span><br><span> 11 280000.000 p11 NSTEPS</span><br><span> 12 -.10000000E-04 p12 DT</span><br><span> 15 500.0000 p15 IOSTEP</span><br><span> 21 1.0000000E-05</span><br><span> 22 1.0000000E-08 p22 HELMHOLTZ</span><br><span> 24 1.0000000E-02 p24 TOLREL</span><br><span> 25 1.0000000E-02 p25 TOLABS</span><br><span> 26 2.000000 p26 COURANT/NTAU</span><br><span> 27 3.000000 p27 TORDER</span><br><span> 59 0.0000000E+00 p59 !=0 --> use std axhelm for all elem</span><br><span> 65 1.0000000E+00 p65 #iofile(eg,0 or 64); <0 --> sep. dirs</span><br><span> 66 6.000000 p66 write fmt:ONLY postx uses rea value</span><br><span> 67 6.000000 p67 read fmt: same modes as p66</span><br><span> 68 200000.00E+00 p68 iastep: freq for avg_all</span><br><span> 93 20.00000 p93 Numbr of prev pressure solns saved</span><br><span> 94 5.000000 p94 start projecting vel. after p94 step</span><br><span> 95 5.000000 p95 start projecting pr after p95 step</span><br><span> 99 4.000000 p99 dealiasing:if <0 disable</span><br><span> 101 2.0000000E+00 p101 No. of additional filter modes</span><br><span> 103 5.0000000E-01 p103 weight of stabilizing filter (.01)</span><br><span></span><br><span> done :: read .rea file 0.85864E-02 sec</span><br><span></span><br><span> nelgt/nelgv/lelt: 730 730 92</span><br><span> lx1 /lx2 /lx3 : 6 6 6</span><br><span> setup mesh topology</span><br><span> Right-handed check complete for 730 elements. OK.</span><br><span> setvert2d: 6 6880 18560 6880 6880</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 507 unique labels shared</span><br><span> pairwise times (avg, min, max): 4.50263e-06 4.3549e-06 4.572e-06</span><br><span> crystal router : 7.19253e-06 7.1082e-06 7.2708e-06</span><br><span> all reduce : 9.94137e-05 9.93523e-05 9.9448e-05</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 22683 22012 23620</span><br><span> buffer bytes (avg, min, max): 2084 1648 2720</span><br><span> setupds time 1.0156E-02 seconds 0 6 6880 730</span><br><span> 4 max multiplicity</span><br><span> done :: setup mesh topology</span><br><span></span><br><span> call usrdat</span><br><span> done :: usrdat</span><br><span></span><br><span> generate geometry data</span><br><span> NOTE: All elements deformed , param(59) ^=0</span><br><span> done :: generate geometry data</span><br><span></span><br><span> call usrdat2</span><br><span> done :: usrdat2</span><br><span></span><br><span> regenerate geometry data 1</span><br><span> NOTE: All elements deformed , param(59) ^=0</span><br><span> done :: regenerate geometry data 1</span><br><span></span><br><span> verify mesh topology</span><br><span> -2.3561944901923448 3.9269908169872418 Xrange</span><br><span> -1.0000000000000000 1.0000000000000000 Yrange</span><br><span> 9.9000000000000010E+021 -9.9000000000000010E+021 Zrange</span><br><span> done :: verify mesh topology</span><br><span></span><br><span> IFTRAN = T</span><br><span> IFFLOW = T</span><br><span> IFHEAT = F</span><br><span> IFSPLIT = T</span><br><span> IFLOMACH = F</span><br><span> IFUSERVP = F</span><br><span> IFUSERMV = F</span><br><span> IFPERT = F</span><br><span> IFADJ = F</span><br><span> IFSTRS = F</span><br><span> IFCHAR = T</span><br><span> IFCYCLIC = F</span><br><span> IFAXIS = F</span><br><span> IFMVBD = F</span><br><span> IFMELT = F</span><br><span> IFNEKNEK = F</span><br><span> IFSYNC = F</span><br><span></span><br><span> IFVCOR = F</span><br><span> IFINTQ = F</span><br><span> IFGEOM = F</span><br><span> IFSURT = F</span><br><span> IFWCNO = F</span><br><span></span><br><span> IFTMSH for field 1 = F</span><br><span> IFADVC for field 1 = T</span><br><span> IFNONL for field 1 = F</span><br><span></span><br><span> Dealiasing enabled, lxd= 9</span><br><span></span><br><span> Estimated eigenvalues</span><br><span> EIGAA = 1.3587005501361697</span><br><span> EIGGA = 1269143.4772368053</span><br><span> EIGAE = 0.25000000000000000</span><br><span> EIGAS = 2.2999917087593809E-002</span><br><span> EIGGE = 1269143.4772368053</span><br><span> EIGGS = 2.0000000000000000</span><br><span></span><br><span> verify mesh topology</span><br><span> -2.3561944901923448 3.9269908169872418 Xrange</span><br><span> -1.0000000000000000 1.0000000000000000 Yrange</span><br><span> 9.9000000000000010E+021 -9.9000000000000010E+021 Zrange</span><br><span> done :: verify mesh topology</span><br><span></span><br><span> E-solver strategy: 0 itr</span><br><span> mg_nx: 1 3 5</span><br><span> mg_ny: 1 3 5</span><br><span> mg_nz: 0 0 0</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 103 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.35579e-06 2.2701e-06 2.4383e-06</span><br><span> crystal router : 4.06828e-06 3.9056e-06 4.3852e-06</span><br><span> all reduce : 4.63608e-06 4.5825e-06 4.698e-06</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 4695 4540 4900</span><br><span> buffer bytes (avg, min, max): 468 368 608</span><br><span> setupds time 9.6015E-04 seconds 1 2 792 730</span><br><span> setvert2d: 4 3836 6756 3836 3836</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 305 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.88736e-06 2.7693e-06 2.9417e-06</span><br><span> crystal router : 5.67697e-06 5.5738e-06 5.7281e-06</span><br><span> all reduce : 1.5845e-05 7.419e-06 2.43007e-05</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 13689 13276 14260</span><br><span> buffer bytes (avg, min, max): 1276 1008 1664</span><br><span> setupds time 2.7936E-03 seconds 2 4 3836 730</span><br><span> setvert2d: 4 3836 6756 3836 3836</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 305 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.74806e-06 2.6386e-06 2.849e-06</span><br><span> crystal router : 5.45844e-06 5.3276e-06 5.5491e-06</span><br><span> all reduce : 7.42733e-06 7.3395e-06 7.5135e-06</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 13689 13276 14260</span><br><span> buffer bytes (avg, min, max): 1276 1008 1664</span><br><span> setupds time 1.7463E-03 seconds 3 4 3836 730</span><br><span> setvert2d: 6 6880 18560 6880 6880</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 507 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.98656e-06 2.8975e-06 3.0673e-06</span><br><span> crystal router : 1.37999e-05 1.36954e-05 1.38856e-05</span><br><span> all reduce : 1.64007e-05 1.62838e-05 1.65981e-05</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 22683 22012 23620</span><br><span> buffer bytes (avg, min, max): 2084 1648 2720</span><br><span> setupds time 2.4769E-03 seconds 4 6 6880 730</span><br><span> regenerate geometry data 1</span><br><span> NOTE: All elements deformed , param(59) ^=0</span><br><span> done :: regenerate geometry data 1</span><br><span></span><br><span> h1_mg_nx: 1 3 5</span><br><span> h1_mg_ny: 1 3 5</span><br><span> h1_mg_nz: 0 0 0</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 103 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.37065e-06 2.3153e-06 2.4607e-06</span><br><span> crystal router : 3.88401e-06 3.7749e-06 3.9709e-06</span><br><span> all reduce : 4.90976e-06 4.8233e-06 5.0116e-06</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 4695 4540 4900</span><br><span> buffer bytes (avg, min, max): 468 368 608</span><br><span> setupds time 9.4292E-04 seconds 5 2 792 730</span><br><span> setvert2d: 4 3836 6756 3836 3836</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 305 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.91439e-06 2.7588e-06 3.0219e-06</span><br><span> crystal router : 5.61719e-06 5.5624e-06 5.6535e-06</span><br><span> all reduce : 7.48192e-06 7.4368e-06 7.5201e-06</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 13689 13276 14260</span><br><span> buffer bytes (avg, min, max): 1276 1008 1664</span><br><span> setupds time 2.3787E-03 seconds 6 4 3836 730</span><br><span> setvert2d: 4 3836 6756 3836 3836</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 305 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.94944e-06 2.7296e-06 3.1507e-06</span><br><span> crystal router : 5.54658e-06 5.4843e-06 5.5919e-06</span><br><span> all reduce : 7.52008e-06 7.3959e-06 7.6057e-06</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 13689 13276 14260</span><br><span> buffer bytes (avg, min, max): 1276 1008 1664</span><br><span> setupds time 1.8404E-03 seconds 7 4 3836 730</span><br><span> setvert2d: 6 6880 18560 6880 6880</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 507 unique labels shared</span><br><span> pairwise times (avg, min, max): 3.04339e-06 2.9536e-06 3.1081e-06</span><br><span> crystal router : 7.14937e-06 7.0897e-06 7.1979e-06</span><br><span> all reduce : 1.48502e-05 1.47878e-05 1.49567e-05</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 22683 22012 23620</span><br><span> buffer bytes (avg, min, max): 2084 1648 2720</span><br><span> setupds time 2.3173E-03 seconds 8 6 6880 730</span><br><span> setvert2d: 6 6880 18560 6880 6880</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 507 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.87688e-06 2.7267e-06 2.9336e-06</span><br><span> crystal router : 7.30052e-06 7.2595e-06 7.3437e-06</span><br><span> all reduce : 1.4766e-05 1.46617e-05 1.48032e-05</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 22683 22012 23620</span><br><span> buffer bytes (avg, min, max): 2084 1648 2720</span><br><span> setupds time 2.2158E-03 seconds 9 6 6880 730</span><br><span> setvert2d: 8 9924 36204 9924 9924</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 709 unique labels shared</span><br><span> pairwise times (avg, min, max): 3.12636e-06 2.9746e-06 3.2381e-06</span><br><span> crystal router : 8.53711e-06 8.4963e-06 8.5871e-06</span><br><span> all reduce : 1.69634e-05 1.68605e-05 1.70839e-05</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 31677 30748 32980</span><br><span> buffer bytes (avg, min, max): 2892 2288 3776</span><br><span> setupds time 3.4194E-03 seconds 10 8 9924 730</span><br><span> setup h1 coarse grid, nx_crs= 2</span><br><span> call usrsetvert</span><br><span> done :: usrsetvert</span><br><span></span><br><span>gs_setup: 103 unique labels shared</span><br><span> pairwise times (avg, min, max): 2.45545e-06 2.3334e-06 2.5351e-06</span><br><span> crystal router : 3.81156e-06 3.7179e-06 3.8942e-06</span><br><span> all reduce : 4.5149e-06 4.4852e-06 4.5619e-06</span><br><span> used all_to_all method: pairwise</span><br><span> handle bytes (avg, min, max): 4695 4540 4900</span><br><span> buffer bytes (avg, min, max): 468 368 608</span><br><span> done :: setup h1 coarse grid 3.5807990061584860E-003 sec</span><br><span></span><br><span> call usrdat3</span><br><span> done :: usrdat3</span><br><span></span><br><span> set initial conditions</span><br><span> nekuic (1) for ifld 1</span><br><span> call nekuic for vel</span><br><span> xyz min -2.3562 -1.0000 0.99000E+22</span><br><span> uvwpt min 0.99000E+22 0.99000E+22 0.99000E+22 0.0000 0.0000</span><br><span> PS min 0.0000 0.99000E+22</span><br><span> xyz max 3.9270 1.0000 -0.99000E+22</span><br><span> uvwpt max -0.99000E+22 -0.99000E+22 -0.99000E+22 0.0000 0.0000</span><br><span> PS max 0.0000 -0.99000E+22</span><br><span> done :: set initial conditions</span><br><span></span><br><span> call userchk</span><br><span> 0.0000E+00 NaN NaN monitor</span><br><span> Start collecting statistics ...</span><br><span> done :: userchk</span><br><span></span><br><span>gridpoints unique/tot: 18560 26280</span><br><span> dofs: 18394 26280</span><br><span></span><br><span> Initialization successfully completed 0.76199E-01 sec</span><br><span></span><br><span>Starting time loop ...</span><br><span></span><br><span> DT/DTCFL/DTFS/DTINIT 0.100E-04 0.494-323 -0.558-261 0.100E-04</span><br><span>Step 1, time= 1.00000E-05, DT= 1.000E-05</span><br><span> Solving for fluid</span><br><span> 1 Helmh3 fluid unconverged! 201 NaN NaN 1.0000E-08</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span> ERROR: E-solver does not exist 0</span><br><span> Stop in ESOLVER</span><br><span></span><br><span>an error occured: dying ...</span><br><span></span><br><span></span><br><span>total elapsed time : 1.44827E-01 sec</span><br><span>total solver time w/o IO : 0.00000E+00 sec</span><br><span>time/timestep : 0.00000E+00 sec</span><br><span>avg throughput per timestep : 0.00000E+00 gridpts/CPUs</span><br><span>total max memory usage : 1.89690E-01 GB</span><br><span></span><br><span>-------------------------------------------------------</span><br><span>Primary job terminated normally, but 1 process returned</span><br><span>a non-zero exit code.. Per user-direction, the job has been aborted.</span><br><span>-------------------------------------------------------</span><br><span>--------------------------------------------------------------------------</span><br><span>mpiexec detected that one or more processes exited with non-zero status, </span><br><span>thus causing</span><br><span>the job to be terminated. The first process to do so was:</span><br><span></span><br><span> Process name: [[25844,1],0]</span><br><span> Exit code: 1</span><br><span>--------------------------------------------------------------------------</span><br><span></span><br><span>_______________________________________________</span><br><span>Nek5000-users mailing list</span><br><span><a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a></span><br><span><a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a></span><br></div></blockquote></body></html>