September 2017 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Warning : DIV(V)-QTL too large
by nek5000-users＠lists.mcs.anl.gov 21 Sep '17

21 Sep '17

Hi, As proposed by Stefan, I'm trying to use the PnPn LowMach configuration. To do that, I simply set the logical switch of IFLOMACH to "true". But it is not working. Could you please explain me, what other parameters I have to change to switch from a PnPn Boussinesq configuration to a PnPn LowMach one ? Thank you in advance, Samuel

1 2

very low calculation speed
by nek5000-users＠lists.mcs.anl.gov 21 Sep '17

21 Sep '17

This problem compiled with PPLIST="NEKNEK" /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r1115 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 192 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 7.87E-07 /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r1115 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 24 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 5.25E-07 Reading /home/itp/ryzhenkov/nek5_calculate/annular_jet/swirl_0.0/G7/pipe_per.rea Reading /home/itp/ryzhenkov/nek5_calculate/annular_jet/swirl_0.0/G7/pipe_per.re2 byte swap: F 6.543210 -2.9312772E+35 Reading /home/itp/ryzhenkov/nek5_calculate/annular_jet/swirl_0.0/G7/pipe.rea Reading /home/itp/ryzhenkov/nek5_calculate/annular_jet/swirl_0.0/G7/pipe.re2 byte swap: F 6.543210 -2.9312772E+35 mapping elements to processors Reading /home/itp/ryzhenkov/nek5_calculate/annular_jet/swirl_0.0/G7/pipe.map mapping elements to processors Reading /home/itp/ryzhenkov/nek5_calculate/annular_jet/swirl_0.0/G7/pipe_per.map 0 213 213 5120 5120 NELV 3 213 213 5120 5120 NELV 4 213 213 5120 5120 NELV 5 213 213 5120 5120 NELV 1 213 213 5120 5120 NELV 2 213 213 5120 5120 NELV 6 213 213 5120 5120 NELV 7 213 213 5120 5120 NELV 8 213 213 5120 5120 NELV 9 213 213 5120 5120 NELV 10 213 213 5120 5120 NELV 11 213 213 5120 5120 NELV element load imbalance: 1 418 419 done :: mapping elements to processors reading mesh 14 213 213 5120 5120 NELV RANK 0 IEG 3873 3874 3875 3876 3877 3878 3879 3880 3881 3882 3883 3884 3885 3886 3887 3888 3889 3890 3891 3892 3893 3894 3895 3896 3897 3898 3899 3900 3901 3902 3903 3904 4129 4130 4131 4132 4133 4134 4135 4136 4137 4138 4139 4140 4141 4142 4143 4144 4145 4146 4147 4148 4149 4150 4151 4152 16 214 214 5120 5120 NELV 4153 4154 4155 4156 4157 4158 4159 4160 4353 4354 4355 4356 4361 4362 4363 4364 4369 4370 4371 4372 4377 4378 4379 4380 4385 4386 4387 4388 4389 4390 4391 4392 4393 4394 4395 4396 4397 4398 4399 4400 4401 4402 4403 4404 4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4609 4610 4611 4612 4613 4617 4618 4619 4620 4621 4625 4626 4627 4628 4633 4634 4635 4636 4637 4638 4641 4642 4643 4644 4645 4646 4647 4648 4649 4650 4651 4652 17 214 214 5120 5120 NELV 4653 4654 4655 4656 4657 4658 4659 4660 4661 4662 4663 4664 4665 4666 4667 4668 4669 4670 4671 4672 4865 4866 4867 4868 4869 4873 4874 4875 4876 4877 4881 4882 4883 4884 4889 4890 4891 4897 4898 4899 4900 4901 4902 4903 4904 4905 4906 4907 12 213 213 5120 5120 NELV 4908 4909 4910 4911 4912 4913 4914 4915 4916 4917 4918 4919 4920 4921 4922 4923 4924 4925 4926 4927 4928 15 213 213 5120 5120 NELV element load imbalance: 1 213 214 done :: mapping elements to processors 18 214 214 5120 5120 NELV reading mesh 22 214 214 5120 5120 NELV reading curved sides 13 213 213 5120 5120 NELV reading bc for ifld 1 20 214 214 5120 5120 NELV done :: read .re2 file 21 214 214 5120 5120 NELV 0 objects found 23 214 214 5120 5120 NELV 118 Parameters from file: 1 1.00000 p001 DENSITY 2 -8900.00 p002 VISCOS 19 214 214 5120 5120 NELV 7 1.00000 p007 RHOCP 8 -8900.00 p008 CONDUCT 11 100000.0 p011 NSTEPS 12 -3.0E-04 p012 DT 15 1000.0 p015 IOSTEP 18 5.0E-02 p018 GRID < 0 --> # cells on screen 19 -1.00000 p019 INTYPE 20 4.00000 p020 NORDER 21 1.0E-06 p021 DIVERGENCE 22 1.0E-08 p022 HELMHOLTZ 24 1.0E-02 p024 TOLREL 25 1.0E-02 p025 TOLABS 26 0.50000 p026 COURANT/NTAU 27 2.00000 p027 TORDER 28 1.00000 p028 TORDER: mesh velocity (0: p28=p27) 66 0.00000 p066 output : <0=ascii, else binary 67 0.00000 p067 restart: <0=ascii, else binary 93 20.0000 p093 Number of previous pressure solns saved 95 5.00000 p095 start projecting pressure after p95 step 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new 101 1.00000 p101 Number of additional modes to filter 102 1.00000 p102 Dump out divergence at each time step 103 9.500000E-01 p103 weight of stabilizing filter (.01) nelgt/nelgv/lelt: 5120 5120 4000 lx1 /lx2 /lx3 : 12 12 12 done :: read .rea file 0.54454 sec setup mesh topology Right-handed check complete for 5120 elements. OK. setvert3d: 12 1772160 6892160 1772160 1772160 call usrsetvert done :: usrsetvert gs_setup: 340773 unique labels shared pairwise times (avg, min, max): 0.000373997 0.000350785 0.000392795 reading curved sides crystal router : 0.00137192 0.00134859 0.0013859 used all_to_all method: pairwise handle bytes (avg, min, max): 2.16376e+06 2106108 2251852 buffer bytes (avg, min, max): 476643 410800 577024 setupds time 3.9776E-01 seconds 0 12 1772160 5120 8 max multiplicity done :: setup mesh topology call usrdat done :: usrdat generate geometry data reading bc for ifld 1 done :: read .re2 file 0 objects found 118 Parameters from file: 1 1.00000 p001 DENSITY 2 -8900.00 p002 VISCOS 7 1.00000 p007 RHOCP 8 -8900.00 p008 CONDUCT 11 100000.0 p011 NSTEPS 12 -3.0E-04 p012 DT 15 1000.0 p015 IOSTEP 18 5.0E-02 p018 GRID < 0 --> # cells on screen 19 -1.00000 p019 INTYPE 20 4.00000 p020 NORDER 21 1.0E-06 p021 DIVERGENCE 22 1.0E-08 p022 HELMHOLTZ 24 1.0E-02 p024 TOLREL 25 1.0E-02 p025 TOLABS 26 0.50000 p026 COURANT/NTAU 27 2.00000 p027 TORDER 28 1.00000 p028 TORDER: mesh velocity (0: p28=p27) 66 0.00000 p066 output : <0=ascii, else binary 67 0.00000 p067 restart: <0=ascii, else binary 93 20.0000 p093 Number of previous pressure solns saved 95 5.00000 p095 start projecting pressure after p95 step 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new 101 1.00000 p101 Number of additional modes to filter 102 1.00000 p102 Dump out divergence at each time step 103 9.500000E-01 p103 weight of stabilizing filter (.01) nelgt/nelgv/lelt: 80320 80320 4000 lx1 /lx2 /lx3 : 12 12 12 done :: read .rea file 1.1102 sec setup mesh topology Right-handed check complete for 80320 elements. OK. setvert3d: 12 26906208 107226208 26906208 26906208 call usrsetvert done :: usrsetvert gs_setup: 5553221 unique labels shared pairwise times (avg, min, max): done :: generate geometry data call usrdat2 0.0016136 0.0012603 0.00186529 crystal router : 0.00763995 0.00749459 0.00784841 used all_to_all method: pairwise handle bytes (avg, min, max): 4.35947e+06 3848020 4681812 buffer bytes (avg, min, max): 976972 546496 1320848 setupds time 2.1430E+00 seconds 0 12 26906208 80320 8 max multiplicity done :: setup mesh topology call usrdat done :: usrdat generate geometry data done :: generate geometry data call usrdat2 initializing intpts(), tol= 1.000000000000000E-013 initializing intpts(), tol= 1.000000000000000E-013 found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 1536 pipe_per found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe done :: usrdat2 done :: usrdat2 found 0 pipe regenerate geometry data 1 regenerate geometry data 1 found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe found 0 pipe done :: regenerate geometry data 1 verify mesh topology -1.00000000000000 1.00000000000000 Xrange -1.00000000000000 1.00000000000000 Yrange 0.000000000000000E+000 4.50000000000000 Zrange done :: verify mesh topology IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = T IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = T IFCHAR = F IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFNEKNEK = T IFSYNC = T IFVCOR = T IFINTQ = F IFCWUZ = F IFSWALL = F IFGEOM = F IFSURT = F IFWCNO = F IFCMT = F IFVISC = F IFFLTR = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Dealiasing enabled, lxd= 18 done :: regenerate geometry data 1 verify mesh topology -12.0000000000000 12.0000000000000 Xrange -12.0000000000000 12.0000000000000 Yrange 0.000000000000000E+000 36.0000000000000 Zrange done :: verify mesh topology IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = T IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = T IFCHAR = F IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFNEKNEK = T IFSYNC = T IFVCOR = F IFINTQ = F IFCWUZ = F IFSWALL = F IFGEOM = F IFSURT = F IFWCNO = F IFCMT = F IFVISC = F IFFLTR = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Dealiasing enabled, lxd= 18 Estimated eigenvalues EIGAA = 1.80739669073447 EIGGA = 13884400.9520853 EIGAE = 0.487387871658733 EIGAS = 2.247191011235953E-002 EIGGE = 13884400.9520853 EIGGS = 2.00000000000000 verify mesh topology -1.00000000000000 1.00000000000000 Xrange -1.00000000000000 1.00000000000000 Yrange 0.000000000000000E+000 4.50000000000000 Zrange done :: verify mesh topology E-solver strategy: 0 itr mg_nx: 1 7 11 mg_ny: 1 7 11 mg_nz: 1 7 11 call usrsetvert done :: usrsetvert gs_setup: 2723 unique labels shared pairwise times (avg, min, max): 2.96265e-05 2.85149e-05 3.04937e-05 crystal router : 1.43409e-05 1.38998e-05 1.49012e-05 all reduce : 6.69807e-05 6.60896e-05 6.82116e-05 used all_to_all method: crystal router handle bytes (avg, min, max): 66207.7 54708 77100 buffer bytes (avg, min, max): 9284 7536 10800 setupds time 4.3750E-03 seconds 1 2 5760 5120 setvert3d: 4 103040 144000 103040 103040 call usrsetvert done :: usrsetvert gs_setup: 25165 unique labels shared pairwise times (avg, min, max): 2.84771e-05 2.72989e-05 2.95877e-05 crystal router : 4.75297e-05 4.67062e-05 4.81129e-05 all reduce : 0.00061613 0.000604296 0.000622106 used all_to_all method: pairwise handle bytes (avg, min, max): 171156 165372 179980 buffer bytes (avg, min, max): 39800 34608 47744 setupds time 2.7411E-02 seconds 2 4 103040 5120 setvert3d: 8 681600 1787520 681600 681600 call usrsetvert done :: usrsetvert gs_setup: 137801 unique labels shared pairwise times (avg, min, max): 8.8045e-05 8.38041e-05 9.10997e-05 crystal router : 0.000316096 0.00030961 0.000320601 used all_to_all method: pairwise handle bytes (avg, min, max): 886769 861564 925228 buffer bytes (avg, min, max): 197997 170992 239168 setupds time 1.0851E-01 seconds 3 8 681600 5120 setvert3d: 10 1162880 3784320 1162880 1162880 call usrsetvert done :: usrsetvert gs_setup: 227995 unique labels shared pairwise times (avg, min, max): 0.000147719 0.00013988 0.000153089 crystal router : 0.000699271 0.000687408 0.000709796 used all_to_all method: pairwise handle bytes (avg, min, max): 1.45509e+06 1415292 1515868 buffer bytes (avg, min, max): 322264 277968 389792 setupds time 1.9729E-01 seconds 4 10 1162880 5120 regenerate geometry data 1 NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 h1_mg_nx: 1 3 11 h1_mg_ny: 1 3 11 h1_mg_nz: 1 3 11 call usrsetvert done :: usrsetvert gs_setup: 2723 unique labels shared pairwise times (avg, min, max): 2.57045e-05 2.50816e-05 2.63929e-05 crystal router : 1.31597e-05 1.27077e-05 1.35183e-05 all reduce : 6.57449e-05 6.45876e-05 6.69956e-05 used all_to_all method: crystal router handle bytes (avg, min, max): 66207.7 54708 77100 buffer bytes (avg, min, max): 9284 7536 10800 setupds time 3.6449E-03 seconds 5 2 5760 5120 setvert3d: 4 103040 144000 103040 103040 call usrsetvert done :: usrsetvert gs_setup: 25165 unique labels shared pairwise times (avg, min, max): 2.73794e-05 2.62976e-05 2.83003e-05 crystal router : 4.36117e-05 4.29153e-05 4.42028e-05 all reduce : 0.000558805 0.000551605 0.000561714 used all_to_all method: pairwise handle bytes (avg, min, max): 171156 165372 179980 buffer bytes (avg, min, max): 39800 34608 47744 setupds time 2.3185E-02 seconds 6 4 103040 5120 setvert3d: 4 103040 144000 103040 103040 call usrsetvert done :: usrsetvert gs_setup: 25165 unique labels shared pairwise times (avg, min, max): 3.27577e-05 3.13044e-05 3.38078e-05 crystal router : 4.4166e-05 4.32968e-05 4.48942e-05 all reduce : 0.000555371 0.00054791 0.000558496 used all_to_all method: pairwise handle bytes (avg, min, max): 171156 165372 179980 buffer bytes (avg, min, max): 39800 34608 47744 setupds time 2.2302E-02 seconds 7 4 103040 5120 setvert3d: 6 328320 656000 328320 328320 call usrsetvert done :: usrsetvert gs_setup: 70191 unique labels shared pairwise times (avg, min, max): 5.42253e-05 5.29051e-05 5.60999e-05 crystal router : 0.000130047 0.000128007 0.000131607 all reduce : 0.00147395 0.0014652 0.00147929 used all_to_all method: pairwise handle bytes (avg, min, max): 458791 444924 479932 buffer bytes (avg, min, max): 103843 89872 125152 setupds time 6.3579E-02 seconds 8 6 328320 5120 setvert3d: 12 1772160 6892160 1772160 1772160 call usrsetvert done :: usrsetvert gs_setup: 340773 unique labels shared pairwise times (avg, min, max): 0.000211759 0.000206304 0.00021801 crystal router : 0.00135557 0.00133109 0.00137 used all_to_all method: pairwise handle bytes (avg, min, max): 2.16376e+06 2106108 2251852 buffer bytes (avg, min, max): 476643 410800 577024 setupds time 3.5228E-01 seconds 9 12 1772160 5120 setvert3d: 14 2509440 11356800 2509440 2509440 call usrsetvert done :: usrsetvert gs_setup: 476135 unique labels shared pairwise times (avg, min, max): 0.000281647 0.000266504 0.000291586 crystal router : 0.00225826 0.0022172 0.00228479 used all_to_all method: pairwise handle bytes (avg, min, max): 3.01277e+06 2934012 3133180 buffer bytes (avg, min, max): 661133 569488 800864 setupds time 6.1860E-01 seconds 10 14 2509440 5120 setup h1 coarse grid, nx_crs= 2 call usrsetvert done :: usrsetvert gs_setup: 2723 unique labels shared pairwise times (avg, min, max): 1.48118e-05 1.41859e-05 1.58072e-05 crystal router : 1.33614e-05 1.21117e-05 1.38044e-05 all reduce : 6.4381e-05 6.33001e-05 6.53982e-05 used all_to_all method: crystal router handle bytes (avg, min, max): 66207.7 54708 77100 buffer bytes (avg, min, max): 9284 7536 10800 Estimated eigenvalues EIGAA = 1.396163174022414E-002 EIGGA = 26467996.3219686 EIGAE = 7.615435494667707E-003 EIGAS = 4.545454545454543E-002 EIGGE = 26467996.3219686 EIGGS = 2.00000000000000 verify mesh topology -12.0000000000000 12.0000000000000 Xrange -12.0000000000000 12.0000000000000 Yrange 0.000000000000000E+000 36.0000000000000 Zrange done :: setup h1 coarse grid 0.402811050415039 sec call usrdat3 done :: usrdat3 set initial conditions Checking restart options: pipe_per0.f00010 nekuic (1) for ifld 1 Reading checkpoint data 0 0 OPEN: pipe_per0.f00010 byte swap: F 6.543210 -2.9312772E+35 done :: verify mesh topology E-solver strategy: 0 itr mg_nx: 1 7 11 mg_ny: 1 7 11 mg_nz: 1 7 11 call usrsetvert done :: usrsetvert gs_setup: 40651 unique labels shared pairwise times (avg, min, max): 0.000218946 0.00018239 0.000236607 crystal router : 5.72741e-05 5.60999e-05 5.85079e-05 all reduce : 0.00148923 0.00145738 0.0015028 used all_to_all method: crystal router handle bytes (avg, min, max): 171689 112124 221476 buffer bytes (avg, min, max): 18153.2 12304 23232 setupds time 7.1854E-02 seconds 1 2 83038 80320 setvert3d: 4 1550072 2192632 1550072 1550072 call usrsetvert done :: usrsetvert gs_setup: 400269 unique labels shared pairwise times (avg, min, max): 0.000248798 0.000221109 0.000264406 crystal router : 0.000225847 0.000221992 0.000230503 used all_to_all method: crystal router handle bytes (avg, min, max): 1.41297e+06 878540 1853668 buffer bytes (avg, min, max): 151639 98096 195920 setupds time 7.4004E-02 seconds 2 4 1550072 80320 setvert3d: 8 10330540 27679660 10330540 10330540 call usrsetvert done :: usrsetvert gs_setup: 2233849 unique labels shared pairwise times (avg, min, max): 0.000514414 0.000456595 0.000552988 crystal router : 0.00232402 0.00227511 0.00238209 used all_to_all method: pairwise handle bytes (avg, min, max): 1.77983e+06 1567956 1917012 buffer bytes (avg, min, max): 405180 225984 547728 setupds time 4.5856E-01 seconds 3 8 10330540 80320 setvert3d: 10 17643974 58767814 17643974 17643974 call usrsetvert done :: usrsetvert gs_setup: 3707811 unique labels shared pairwise times (avg, min, max): 0.00074541 0.000669909 0.000782418 0 2.8664E+02 done :: Read checkpoint data avg data-throughput = 84.5MBps io-nodes = 1 crystal router : xyz min -1.0000 -1.0000 0.0000 uvwpt min -0.34051 -0.37479 -0.16102E-01 -0.90090E-01 0.0000 PS min 0.0000 0.0000 0.99000E+22 xyz max 1.0000 1.0000 4.5000 uvwpt max 0.32898 0.39774 1.3656 0.78843E-01 0.0000 PS max 0.0000 0.0000 -0.99000E+22 Restart: recompute geom. factors. regenerate geometry data 1 0.00430806 0.00423291 0.00441771 used all_to_all method: pairwise handle bytes (avg, min, max): 2.92727e+06 2581844 3147348 buffer bytes (avg, min, max): 660122 368832 892432 setupds time 1.0661E+00 seconds 4 10 17643974 80320 NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 regenerate geometry data 1 done :: set initial conditions call userchk NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 h1_mg_nx: 1 3 11 h1_mg_ny: 1 3 11 h1_mg_nz: 1 3 11 call usrsetvert done :: usrsetvert gs_setup: 40651 unique labels shared pairwise times (avg, min, max): 0.000203656 0.000173688 0.000223613 crystal router : 5.95078e-05 5.80072e-05 6.10113e-05 all reduce : 0.00126102 0.0012404 0.00127389 used all_to_all method: crystal router handle bytes (avg, min, max): 171689 112124 221476 buffer bytes (avg, min, max): 18153.2 12304 23232 setupds time 2.9112E-02 seconds 5 2 83038 80320 setvert3d: 4 1550072 2192632 1550072 1550072 call usrsetvert done :: usrsetvert gs_setup: 400269 unique labels shared pairwise times (avg, min, max): 0.000249024 0.000214601 0.000264192 crystal router : 0.000207164 0.000203013 0.000212216 used all_to_all method: crystal router handle bytes (avg, min, max): 1.41297e+06 878540 1853668 buffer bytes (avg, min, max): 151639 98096 195920 setupds time 5.8844E-02 seconds 6 4 1550072 80320 setvert3d: 4 1550072 2192632 1550072 1550072 call usrsetvert done :: usrsetvert gs_setup: 400269 unique labels shared pairwise times (avg, min, max): 0.000250614 0.000216007 0.000266099 crystal router : 0.000206963 0.000201392 0.000213099 used all_to_all method: crystal router handle bytes (avg, min, max): 1.41297e+06 878540 1853668 buffer bytes (avg, min, max): 151639 98096 195920 setupds time 5.8632E-02 seconds 7 4 1550072 80320 setvert3d: 6 4965906 10106386 4965906 4965906 call usrsetvert done :: usrsetvert gs_setup: 1131335 unique labels shared pairwise times (avg, min, max): 0.000345911 0.000313807 0.000366807 crystal router : 0.000918429 0.000901699 0.000948811 used all_to_all method: pairwise handle bytes (avg, min, max): 917140 806356 990804 buffer bytes (avg, min, max): 212147 117952 286736 setupds time 1.7421E-01 seconds 8 6 4965906 80320 setvert3d: 12 26906208 107226208 26906208 26906208 call usrsetvert done :: usrsetvert gs_setup: 5553221 unique labels shared pairwise times (avg, min, max): 0.00103432 0.000936699 0.00110071 crystal router : 0.00765613 0.0074913 0.0078582 used all_to_all method: pairwise handle bytes (avg, min, max): 4.35947e+06 3848020 4681812 buffer bytes (avg, min, max): 976972 546496 1320848 setupds time 1.9455E+00 seconds 9 12 26906208 80320 setvert3d: 14 38117242 176910202 38117242 38117242 call usrsetvert done :: usrsetvert gs_setup: 7770079 unique labels shared pairwise times (avg, min, max): 0.00144147 0.00128691 0.0015306 crystal router : 0.0118797 0.011621 0.0121873 used all_to_all method: pairwise handle bytes (avg, min, max): 6.07641e+06 5366484 6520404 buffer bytes (avg, min, max): 1.35573e+06 758976 1832976 setupds time 2.9645E+00 seconds 10 14 38117242 80320 setup h1 coarse grid, nx_crs= 2 call usrsetvert done :: usrsetvert gs_setup: 40651 unique labels shared pairwise times (avg, min, max): 0.000223077 0.000198388 0.000240588 crystal router : 5.7518e-05 5.61953e-05 5.86987e-05 all reduce : 0.00124078 0.0012202 0.00125399 used all_to_all method: crystal router handle bytes (avg, min, max): 171689 112124 221476 buffer bytes (avg, min, max): 18153.2 12304 23232 done :: setup h1 coarse grid 22.2913181781769 sec call usrdat3 done :: usrdat3 set initial conditions Checking restart options: pipe0.f00010 nekuic (1) for ifld 1 Reading checkpoint data 0 0 OPEN: pipe0.f00010 byte swap: F 6.543210 -2.9312772E+35 0 2.8664E+02 done :: Read checkpoint data avg data-throughput = 98.5MBps io-nodes = 1 xyz min -12.000 -12.000 0.0000 uvwpt min -0.99492 -0.76080 -0.82980 -1.4131 0.0000 PS min 0.0000 0.0000 0.99000E+22 xyz max 12.000 12.000 36.000 uvwpt max 0.81959 0.91894 1.4289 0.99220 0.0000 PS max 0.0000 0.0000 -0.99000E+22 Restart: recompute geom. factors. regenerate geometry data 1 NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 done :: set initial conditions call userchk force z: 1.000000000000000E-005 done :: userchk gridpoints unique/tot: 6892160 8847360 dofs: 6737280 6892160 Initial time: 0.2866404E+03 Initialization successfully completed 71.437 sec Starting time loop ... DT/DTCFL/DTFS/DTINIT 0.300E-03 0.000E+00 0.233-309 0.300E-03 force z: 1.000000000000000E-005 dump history points reading hpts.in found 80 points initializing intpts(), tol= 1.000000000000000E-013 done :: dump history points Building mesh for avg Avg mesh builded initializing intpts(), tol= 1.000000000000000E-008 call intpts call findpts total number of points = 1920000 failed = 0 done :: intpts Writting interp data avg Interp data avg written call intpts call findpts total number of points = 1920000 failed = 0 done :: intpts Writting interp data avg Interp data avg written call intpts call findpts total number of points = 1920000 failed = 0 done :: intpts Writting interp data avg Interp data avg written Building the mesh for pod1 Mesh for pod1 builded call intpts call findpts total number of points = 21504000 failed = 0 done :: intpts Writting pod1 data pod1 data written Building the mesh for pod2 Mesh for pod2 builded call intpts call findpts total number of points = 21504000 failed = 0 done :: intpts Writting pod2 data pod2 data written done :: userchk gridpoints unique/tot: 107226208 138792960 dofs: 106989839 106823343 Initial time: 0.2866404E+03 Initialization successfully completed 4728.4 sec Starting time loop ... DT/DTCFL/DTFS/DTINIT 0.300E-03 0.000E+00 0.236-309 0.300E-03 Step 1, t= 2.8664073E+02, DT= 3.0000000E-04, C= 0.149 0.0000E+00 0.0000E+00 Step 1, t= 2.8664073E+02, DT= 3.0000000E-04, C= 0.438 0.0000E+00 0.0000E+00 Solving for fluid T T T filt amp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2375 0.9500 filt trn 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.7625 0.0500 1.000000000000000E-008 p22 1 1 1 1.00000E-06 3.08669E-03 5.12889E-03 6.01823E-01 1 Divergence 2 1.00000E-06 1.63507E-03 5.12889E-03 3.18795E-01 1 Divergence 3 1.00000E-06 5.70865E-04 5.12889E-03 1.11304E-01 1 Divergence 4 1.00000E-06 3.19087E-04 5.12889E-03 6.22137E-02 1 Divergence 5 1.00000E-06 1.67594E-04 5.12889E-03 3.26764E-02 1 Divergence 6 1.00000E-06 8.78601E-05 5.12889E-03 1.71304E-02 1 Divergence 7 1.00000E-06 4.10072E-05 5.12889E-03 7.99534E-03 1 Divergence 8 1.00000E-06 2.09226E-05 5.12889E-03 4.07936E-03 1 Divergence 9 1.00000E-06 1.17707E-05 5.12889E-03 2.29498E-03 1 Divergence 10 1.00000E-06 6.32563E-06 5.12889E-03 1.23333E-03 1 Divergence 11 1.00000E-06 3.53710E-06 5.12889E-03 6.89642E-04 1 Divergence 12 1.00000E-06 1.96804E-06 5.12889E-03 3.83716E-04 1 Divergence 13 1.00000E-06 1.14795E-06 5.12889E-03 2.23821E-04 1 Divergence 14 1.00000E-06 7.12487E-07 5.12889E-03 1.38916E-04 1 Divergence 1 PRES gmres: 14 7.1249E-07 1.0000E-06 5.1289E-03 1.8504E+00 4.1575E+00 F 0 1.0000E-08 3.4398E-07 1.0000E-08 tol,matmod 1 Helmholtz3/fluid: 7 0.1612E-08 0.1000E-07 0.1453E-01 L1/L2 DIV(V) : -3.3387E-15 4.5580E-04 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: -3.3387E-15 4.5580E-04 1 2.8664E+02 6.3868E+00 Fluid done Solving for fluid T T T filt amp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2375 0.9500 filt trn 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.7625 0.0500 > Can you please post your logfile otherwise it’s hard to tell what’s going wrong. > On 20 Sep 2017, at 12:20, "nek5000-users at lists.mcs.anl.gov <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <mailto:nek5000-users at lists.mcs.anl.gov <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> " <nek5000-users at lists.mcs.anl.gov <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <mailto:nek5000-users at lists.mcs.anl.gov <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > wrote: > Dear Nek devs > Usually I start some calculation with 100-150 processors and it runs with acceptable speed. But sometimes the speed of calculation is extremely low, something like 1 step per 10 hours with 50 million mesh points. It seems like all computational nodes fall on one processors, while the rest just stay without any job, despite that all requirements about nodes per processor are satisfied. > Have you ever seen something like that ? And how it can be fixed ? > Regards, Vatslav С уважением, Владимир Рыженьков

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Re: [Nek5000-users] Warning : DIV(V)-QTL too large
by nek5000-users＠lists.mcs.anl.gov 20 Sep '17

20 Sep '17

Hi Stefan, Thank you very much for your answers. I was using Boussinesq approximation because I thougth it will be easier to converge. I will try with LowMach, thank you for the advice. Samuel

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very low calculation speed
by nek5000-users＠lists.mcs.anl.gov 20 Sep '17

20 Sep '17

Dear Nek devs Usually I start some calculation with 100-150 processors and it runs with acceptable speed. But sometimes the speed of calculation is extremely low, something like 1 step per 10 hours with 50 million mesh points. It seems like all computational nodes fall on one processors, while the rest just stay without any job, despite that all requirements about nodes per processor are satisfied. Have you ever seen something like that ? And how it can be fixed ? Regards, Vatslav

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Re: [Nek5000-users] Volume integral time derivative vorticity
by nek5000-users＠lists.mcs.anl.gov 20 Sep '17

20 Sep '17

You'll find the previous velocity in the vxlag array. Integration is easy, just multiply by bm1 and sum up. The tricky part might be to identify your sub-domain i.e. the elements. -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Tuesday 19th September 2017 18:46 > To: nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > Subject: [Nek5000-users] Volume integral time derivative vorticity > > I performed some simulations around a plunging flat plate. > I have to compute the volume integral over a choosen domain (a rectangle around the body with a fixed geometrical dimension) of the eulerian time derivative of the vorticity field multiplied by the local position vector components. I found a subroutine to compute the vorticity. How should I compute vorticity at the previous timestep? And how can I perform the integrations? > > Thanks > Mario > > Mario Ostieri > > Ph.D. Student > University of Naples Federico II > Department of Industrial Engineering > Piazzale V. Tecchio 80 > 80125 Napoli, Italy > tel. +390817682184 > email: mario.ostieri(a)unina.it > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Warning : DIV(V)-QTL too large
by nek5000-users＠lists.mcs.anl.gov 19 Sep '17

19 Sep '17

Dear Nek experts, I'm trying to simulate a differentially heated cavity with a Rayleigh number of 10e9 (turbulent convection). I modified the tutorial of the Rayleigh Benard cell to build my case. I increased progessively the Rayleigh number. As my Ra increase, I get this warning "DIV(V)-QTL is too large" so I refined the mesh and the timestep as proposed in this thread https://lists.mcs.anl.gov/pipermail/nek5000-users/2016-January/003553.html. I have now still this warning even if my courant number is very low (around 0.05). So I would like to know if I could use a bigger time step keeping C below 0.5. My other question is the meaning of QTL, the thermal divergence. In my simulation it is equal to 0, this is partly why DIV(V)-QTL is too large. Should I specify a QTL ? Thank you in advance for your answers, Best, Samuel

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Re: [Nek5000-users] Warning : DIV(V)-QTL too large
by nek5000-users＠lists.mcs.anl.gov 19 Sep '17

19 Sep '17

In an incompressible flow, QTL (thermal divergence) is ZERO. In this case the error in divergence is essentially the divergence in velocity. The error depends on your spatial resolution (typically dominates), dt and pressure solver tolerance. You may want to visualize the error in divergence to get a feeling about the spatial location. Hope this helps Stefan -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Tuesday 19th September 2017 16:09 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Warning : DIV(V)-QTL too large > > Dear Nek experts, > > I'm trying to simulate a differentially heated cavity with a Rayleigh > number of 10e9 (turbulent convection). > I modified the tutorial of the Rayleigh Benard cell to build my case. > I increased progessively the Rayleigh number. As my Ra increase, I get > this warning "DIV(V)-QTL is too large" so I refined the mesh and the > timestep as proposed in this thread > https://lists.mcs.anl.gov/pipermail/nek5000-users/2016-January/003553.html. > > I have now still this warning even if my courant number is very low > (around 0.05). > So I would like to know if I could use a bigger time step keeping C > below 0.5. > > My other question is the meaning of QTL, the thermal divergence. In my > simulation it is equal to 0, this is partly why DIV(V)-QTL is too large. > Should I specify a QTL ? > > > Thank you in advance for your answers, > Best, > Samuel > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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Re: [Nek5000-users] Nek5000-users Digest, Vol 103, Issue 17: Managing post-processing of multiple box files
by nek5000-users＠lists.mcs.anl.gov 18 Sep '17

18 Sep '17

Hi Paul, Thanks for that, so you're saying that I can set up my box file by individually prescribing the coordinates of each element? I think I am able to do this, I still find, however, that when I post-process my results in Python and use the element map in the 0.f##### files that the elements are not mapped to the correct places. Are you saying that there's a way to pre-emptively fix this problem in the box file before I do my simulation? Cheers, Daniel ________________________________ From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 18 September 2017 13:04 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 103, Issue 17 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. Re: Nek5000-users Digest, Vol 103, Issue 12 (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Sep 2017 12:03:59 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 103, Issue 12 Message-ID: <mailman.953.1505736244.10190.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="us-ascii" Daniel, If you want a custom distribution in any of the directions, you just list a positive value, nel, for the number of elements in that direction, and then provide a list with nel+1 entries. Note, the list of entries must be shorter than 80 characters, so you have to wrap the line if it goes over 80 characters. This is because I wrote a parser to allow for comments in the box files and as such it only parses 80 character strings. Just so long as the sequence of strings has nel+1 values, it will keep reading the strings till satisfied. It will then go on to the next required read (e.g., the next list of element locations for the next direction). 2D example: -2 9 # 2 elements in x, 9 in y 0 1 0.5 x0,x1, ratio: element 2 is half the size of element 1 0 .1 .2 .3 .4 .5 .6 .7 .8 .9 coordinates for y (comments only on last string) etc Paul ________________________________ From: Nek5000-users <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: Monday, September 18, 2017 4:02:28 AM To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 103, Issue 12 Hi Paul, Sorry for not replying earlier, I didn't see your reply last week unfortunately. So in my case I'm creating a partition as follows: Box_1 -20 -50 nel_1, nel_2 0. 50. 0.8 x0, x1 0. 100. 1.1 y0, y1 W ,E ,W ,W (bc's) velocity (west, east, south, north) T ,E ,t ,W (bc's) temperature (west, east, south, north) Box_2 -20 -50 nel_1, nel_2 50. 100. 1.2 x0, x1 0. 100. 1.1 y0, y1 E ,W ,W ,W (bc's) velocity (west, east, south, north) E ,T ,t ,W (bc's) temperature (west, east, south, north) This makes two boxes, separated in the x-direction. Is what you're saying, then, that my two 20x50 boxes are stacked one on top of the other to, in effect, create one 20x100 box? If that's the case, how do I take my element map (which is just a list of 2000 numbers mapping local to global elements) and make sure that my two boxes are concatenated in the x-direction, instead of the z? Thanks in advance, Daniel ________________________________ From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 15 September 2017 13:05:25 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 103, Issue 12 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. Re: time integration scheme for temperature/scalar equations (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Nek5000-users Digest, Vol 103, Issue 9 (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 15 Sep 2017 13:02:20 +0200 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] time integration scheme for temperature/scalar equations Message-ID: <mailman.839.1505473384.10190.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi, To be more precise. Routines "makeabq" and "makebdq" are called if you use hemholtz solver for passive scalars. The other option is cvode, which uses slightly different scheme. I guess hemholtz is default and to use cvode you have to add CVODE to preprocessing flag. About the link to doxygen. This one is outdated so it could be dangerous to use it. There is doxygen showing current beta2 version under https://adampep.github.io/KTH_Framework/files.html Regards Adam On 15/09/17 12:11, nek5000-users(a)lists.mcs.anl.gov wrote: > > Hi Bolun Xu, > > Yes, > > you can see that in the conduct.f file( in which convection-diffusion > equation for temperature is solved): > http://www.mcs.anl.gov/research/projects/nek5/docs/html/conduct_8f_source.h… > > In the subroutine "makeabq" the same Adam-Bashforth coefficients AB() > are called and in the subroutine "makebdq", the BD() coefficients are > used again. > > best, > Pierre-Emmanuel > > > On 2017-09-15 11:47, nek5000-users(a)lists.mcs.anl.gov wrote: >> Hi! All, >> >> I learned from the subroutines makeabf and makebdf in navier1.f that the >> time integration scheme for momentum equation is the AB-CN scheme, that >> explicit schemes for nonlinear and forcing term, and implicit ones for >> viscous term. The prefactors of those schemes are stored in AB() and BD() >> arrays. Now my question is, whether the temperature/scalar equations also >> use the same schemes as momentum ones and also share the same prefactors in >> AB() / BD() arrays. >> >> Any help is appreciated. >> >> Regards. >> >> ---------------------------------------------------------------- >> >> Bolun Xu >> >> University of Science and Technology of China >> >> Department of Modern Mechanics >> >> Hefei, Anhui, China >> >> >> >> >> >> >> _______________________________________________ >> 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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Re: [Nek5000-users] Nek5000-users Digest, Vol 103, Issue 12
by nek5000-users＠lists.mcs.anl.gov 18 Sep '17

18 Sep '17

Hi Paul, Sorry for not replying earlier, I didn't see your reply last week unfortunately. So in my case I'm creating a partition as follows: Box_1 -20 -50 nel_1, nel_2 0. 50. 0.8 x0, x1 0. 100. 1.1 y0, y1 W ,E ,W ,W (bc's) velocity (west, east, south, north) T ,E ,t ,W (bc's) temperature (west, east, south, north) Box_2 -20 -50 nel_1, nel_2 50. 100. 1.2 x0, x1 0. 100. 1.1 y0, y1 E ,W ,W ,W (bc's) velocity (west, east, south, north) E ,T ,t ,W (bc's) temperature (west, east, south, north) This makes two boxes, separated in the x-direction. Is what you're saying, then, that my two 20x50 boxes are stacked one on top of the other to, in effect, create one 20x100 box? If that's the case, how do I take my element map (which is just a list of 2000 numbers mapping local to global elements) and make sure that my two boxes are concatenated in the x-direction, instead of the z? Thanks in advance, Daniel ________________________________ From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 15 September 2017 13:05:25 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 103, Issue 12 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. Re: time integration scheme for temperature/scalar equations (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Nek5000-users Digest, Vol 103, Issue 9 (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 15 Sep 2017 13:02:20 +0200 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] time integration scheme for temperature/scalar equations Message-ID: <mailman.839.1505473384.10190.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi, To be more precise. Routines "makeabq" and "makebdq" are called if you use hemholtz solver for passive scalars. The other option is cvode, which uses slightly different scheme. I guess hemholtz is default and to use cvode you have to add CVODE to preprocessing flag. About the link to doxygen. This one is outdated so it could be dangerous to use it. There is doxygen showing current beta2 version under https://adampep.github.io/KTH_Framework/files.html Regards Adam On 15/09/17 12:11, nek5000-users(a)lists.mcs.anl.gov wrote: > > Hi Bolun Xu, > > Yes, > > you can see that in the conduct.f file( in which convection-diffusion > equation for temperature is solved): > http://www.mcs.anl.gov/research/projects/nek5/docs/html/conduct_8f_source.h… > > In the subroutine "makeabq" the same Adam-Bashforth coefficients AB() > are called and in the subroutine "makebdq", the BD() coefficients are > used again. > > best, > Pierre-Emmanuel > > > On 2017-09-15 11:47, nek5000-users(a)lists.mcs.anl.gov wrote: >> Hi! All, >> >> I learned from the subroutines makeabf and makebdf in navier1.f that the >> time integration scheme for momentum equation is the AB-CN scheme, that >> explicit schemes for nonlinear and forcing term, and implicit ones for >> viscous term. The prefactors of those schemes are stored in AB() and BD() >> arrays. Now my question is, whether the temperature/scalar equations also >> use the same schemes as momentum ones and also share the same prefactors in >> AB() / BD() arrays. >> >> Any help is appreciated. >> >> Regards. >> >> ---------------------------------------------------------------- >> >> Bolun Xu >> >> University of Science and Technology of China >> >> Department of Modern Mechanics >> >> Hefei, Anhui, China >> >> >> >> >> >> >> _______________________________________________ >> 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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Convection velocity and outlet BC
by nek5000-users＠lists.mcs.anl.gov 17 Sep '17

17 Sep '17

Dear Neks, for different convective boundary conditions there is a parameter I need to calculate: the convection velocity, which can be aproximated as the mean streamwise velocity averaged at the exit plane. Is there a quick way to calculate Uc for each time step? Now I'm using Dong (2014) BC, but it also needs a convection velocity, and I'm using an aproximate number, but I'd like to calculate the right one. On the other hand, the BC I'd like to try now is: (du_i/dt)+Uc*(du_i/dy)=0 (dT/dt)+Uc*(dT/dy)=0 where the stramwise direction is y, since it is a free convection flow, and Uc is the convection velocity. And, any idea or help to implement those BC? Thank you very much, Juan Pablo.

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