[Nek5000-users] turbChannel compiling issue after adding more elements
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Jan 24 22:57:05 CST 2018
Hi Ming & everyone,
I tracked down the error to a part of the gslib code (Nek5000/3rd_party/gslib/gslib-1.0.1/src/amg.c:487). Unfortunately, I am not familiar with AMG or gslib code so I cannot help you with this problem.
If someone is familiar with this issue, please help Ming out.
Sincerely,
Kento
> On Jan 24, 2018, at 22:40, nek5000-users at lists.mcs.anl.gov wrote:
>
> Hello Kento,
>
> Thank you for your help! The compiler now works. But I ran into another issue; after it started to run, it soon stopped and reported an error saying:
>
> AMG: preading through rows ... done
> ERROR (proc 0000, src/amg.c:487): AMG: missing data for some rows
>
> an error occured: dying …
>
> Would you run into this issue earlier before?
>
> Again thanks a lot for the suggestions.
>
> Regards,
>
> Ming
>
> *********** complete logfile *********
> Reading /global/home/hpc4076/Nek5000/run/turbChannel/turbChannel.par
> general = [(null)]
> general:stopat = [endTime]
> general:endtime = [200]
> general:dt = [0]
> general:timestepper = [bdf2]
> general:extrapolation = [OIFS]
> general:variabledt = [yes]
> general:targetcfl = [2.0]
> general:writecontrol = [runTime]
> general:writeinterval = [200.0]
> general:userparam01 = [100]
> general:userparam02 = [20]
> general:userparam03 = [1]
> general:filtering = [hpfrt]
> general:filterweight = [10]
> general:filtercutoffratio = [0.9]
> problemtype = [(null)]
> problemtype:variableproperties = [no]
> problemtype:equation = [incompNS]
> pressure = [(null)]
> pressure:preconditioner = [semg_amg]
> pressure:residualtol = [1e-04]
> pressure:residualproj = [yes]
> velocity = [(null)]
> velocity:residualtol = [1e-07]
> velocity:density = [1]
> velocity:viscosity = [-10900]
> Reading /global/home/hpc4076/Nek5000/run/turbChannel/turbChannel.re2
> mapping elements to processors
> Reading /global/home/hpc4076/Nek5000/run/turbChannel/turbChannel.ma2
> 0 9216 9216 73728 73728 NELV
> 5 9216 9216 73728 73728 NELV
> 7 9216 9216 73728 73728 NELV
> 1 9216 9216 73728 73728 NELV
> 3 9216 9216 73728 73728 NELV
> 6 9216 9216 73728 73728 NELV
> 4 9216 9216 73728 73728 NELV
> 2 9216 9216 73728 73728 NELV
>
> element load imbalance: 0 9216 9216
> done :: mapping 0.66962E-01 sec
>
>
> preading mesh
> preading bc for ifld 1
> done :: read .re2 file 0.30 sec
>
> nelgt/nelgv/lelt: 73728 73728 18439
> lx1 /lx2 /lx3 : 8 8 8
> setup mesh topology
> Right-handed check complete for 73728 elements. OK.
> setvert3d: 8 9476352 25401600 9476352 9476352
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 413952 unique labels shared
> pairwise times (avg, min, max): 0.000140989 0.000133355 0.000146356
> crystal router : 0.0012817 0.00128028 0.00128291
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 3.26526e+07 32652644 32652644
> buffer bytes (avg, min, max): 1.68269e+06 1682688 1682688
> setupds time 1.9997E+00 seconds 0 8 9476352 73728
> 8 max multiplicity
> done :: setup mesh topology
>
> call usrdat
> done :: usrdat
>
> generate geometry data
> NOTE: All elements deformed , param(59) ^=0
> done :: generate geometry data
>
> call usrdat2
> done :: usrdat2
>
> regenerate geometry data 1
> NOTE: All elements deformed , param(59) ^=0
> done :: regenerate geometry data 1
>
> verify mesh topology
> 0.000000000000000E+000 6.28318530717959 Xrange
> -1.00000000000000 1.00000000000000 Yrange
> 0.000000000000000E+000 3.14159265358979 Zrange
> done :: verify mesh topology
>
> IFTRAN = T
> IFFLOW = T
> IFHEAT = F
> IFSPLIT = T
> IFLOMACH = F
> IFUSERVP = F
> IFUSERMV = F
> IFPERT = F
> IFADJ = F
> IFSTRS = F
> IFCHAR = T
> IFCYCLIC = F
> IFAXIS = F
> IFMVBD = F
> IFMELT = F
> IFNEKNEK = F
> IFSYNC = F
>
> IFVCOR = T
> IFINTQ = F
> IFGEOM = F
> IFSURT = F
> IFWCNO = F
>
> IFTMSH for field 1 = F
> IFADVC for field 1 = T
> IFNONL for field 1 = F
>
> Dealiasing enabled, lxd= 8
>
> Estimated eigenvalues
> EIGAA = 1.23913370009078
> EIGGA = 30588693.2337829
> EIGAE = 0.250000000000000
> EIGAS = 1.681282119258565E-002
> EIGGE = 30588693.2337829
> EIGGS = 2.00000000000000
>
> verify mesh topology
> 0.000000000000000E+000 6.28318530717959 Xrange
> -1.00000000000000 1.00000000000000 Yrange
> 0.000000000000000E+000 3.14159265358979 Zrange
> done :: verify mesh topology
>
> E-solver strategy: 0 itr
> mg_nx: 1 3 7
> mg_ny: 1 3 7
> mg_nz: 1 3 7
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 8448 unique labels shared
> pairwise times (avg, min, max): 1.21617e-05 1.1921e-05 1.24227e-05
> crystal router : 3.65702e-05 3.65344e-05 3.66269e-05
> all reduce : 0.00014386 0.000142943 0.000144376
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 728420 728420 728420
> buffer bytes (avg, min, max): 37632 37632 37632
> setupds time 2.0250E-02 seconds 1 2 76032 73728
> setvert3d: 4 1421568 2011392 1421568 1421568
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 76032 unique labels shared
> pairwise times (avg, min, max): 4.62178e-05 4.47887e-05 4.74119e-05
> crystal router : 0.000222897 0.000222723 0.000223086
> all reduce : 0.000974339 0.000967893 0.000979289
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956
> buffer bytes (avg, min, max): 315648 315648 315648
> setupds time 3.5739E-01 seconds 2 4 1421568 73728
> setvert3d: 4 1421568 2011392 1421568 1421568
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 76032 unique labels shared
> pairwise times (avg, min, max): 4.5131e-05 4.40137e-05 4.5883e-05
> crystal router : 0.000217508 0.00021732 0.000217639
> all reduce : 0.000978618 0.000972797 0.000983269
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956
> buffer bytes (avg, min, max): 315648 315648 315648
> setupds time 3.5094E-01 seconds 3 4 1421568 73728
> setvert3d: 6 4555008 9273600 4555008 4555008
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 211200 unique labels shared
> pairwise times (avg, min, max): 9.59221e-05 9.2321e-05 9.80701e-05
> crystal router : 0.000574208 0.000573776 0.000574501
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 1.65554e+07 16555364 16555364
> buffer bytes (avg, min, max): 864000 864000 864000
> setupds time 9.2152E-01 seconds 4 6 4555008 73728
> regenerate geometry data 1
> NOTE: All elements deformed , param(59) ^=0
> done :: regenerate geometry data 1
>
> h1_mg_nx: 1 3 7
> h1_mg_ny: 1 3 7
> h1_mg_nz: 1 3 7
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 8448 unique labels shared
> pairwise times (avg, min, max): 1.42743e-05 1.37607e-05 1.47085e-05
> crystal router : 3.54692e-05 3.53276e-05 3.56395e-05
> all reduce : 0.000145775 0.000145112 0.000146347
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 728420 728420 728420
> buffer bytes (avg, min, max): 37632 37632 37632
> setupds time 1.9277E-02 seconds 5 2 76032 73728
> setvert3d: 4 1421568 2011392 1421568 1421568
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 76032 unique labels shared
> pairwise times (avg, min, max): 4.74352e-05 4.61341e-05 4.8379e-05
> crystal router : 0.000219904 0.000219596 0.000220055
> all reduce : 0.00108293 0.00107907 0.00108614
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956
> buffer bytes (avg, min, max): 315648 315648 315648
> setupds time 3.5849E-01 seconds 6 4 1421568 73728
> setvert3d: 4 1421568 2011392 1421568 1421568
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 76032 unique labels shared
> pairwise times (avg, min, max): 4.99966e-05 4.93097e-05 5.04928e-05
> crystal router : 0.000220982 0.000220777 0.000221201
> all reduce : 0.000975639 0.000969762 0.000980587
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956
> buffer bytes (avg, min, max): 315648 315648 315648
> setupds time 3.5221E-01 seconds 7 4 1421568 73728
> setvert3d: 6 4555008 9273600 4555008 4555008
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 211200 unique labels shared
> pairwise times (avg, min, max): 9.7033e-05 9.53629e-05 9.89481e-05
> crystal router : 0.000575673 0.000575274 0.00057601
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 1.65554e+07 16555364 16555364
> buffer bytes (avg, min, max): 864000 864000 864000
> setupds time 9.0969E-01 seconds 8 6 4555008 73728
> setvert3d: 8 9476352 25401600 9476352 9476352
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 413952 unique labels shared
> pairwise times (avg, min, max): 0.000145018 0.00014225 0.000147666
> crystal router : 0.00127508 0.00127457 0.00127577
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 3.26526e+07 32652644 32652644
> buffer bytes (avg, min, max): 1.68269e+06 1682688 1682688
> setupds time 1.9358E+00 seconds 9 8 9476352 73728
> setvert3d: 10 16185600 53934336 16185600 16185600
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 684288 unique labels shared
> pairwise times (avg, min, max): 0.000185176 0.000182058 0.000188558
> crystal router : 0.00236343 0.00236093 0.00236685
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 5.42058e+07 54205796 54205796
> buffer bytes (avg, min, max): 2.77171e+06 2771712 2771712
> setupds time 3.2958E+00 seconds 10 10 16185600 73728
> setup h1 coarse grid, nx_crs= 2
> call usrsetvert
> done :: usrsetvert
>
> gs_setup: 8448 unique labels shared
> pairwise times (avg, min, max): 1.58059e-05 1.48741e-05 1.6321e-05
> crystal router : 3.54276e-05 3.51642e-05 3.56729e-05
> all reduce : 0.000144706 0.000143665 0.00014533
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 728420 728420 728420
> buffer bytes (avg, min, max): 37632 37632 37632
> gs_setup: 8448 unique labels shared
> pairwise times (avg, min, max): 1.56632e-05 1.53686e-05 1.61476e-05
> crystal router : 1.74988e-05 1.74323e-05 1.75631e-05
> all reduce : 0.000148094 0.00014731 0.000148594
> used all_to_all method: pairwise
> handle bytes (avg, min, max): 368228 368228 368228
> buffer bytes (avg, min, max): 17664 17664 17664
> AMG version 2.01
> AMG: 8 levels
> AMG Chebyshev smoother data:
> AMG level 1: 3 iterations with rho = 0.79256
> AMG level 2: 2 iterations with rho = 0.668297
> AMG level 3: 2 iterations with rho = 0.481307
> AMG level 4: 2 iterations with rho = 0.409707
> AMG level 5: 2 iterations with rho = 0.458605
> AMG level 6: 3 iterations with rho = 0.696293
> AMG level 7: 2 iterations with rho = 0.666743
> AMG: 1664 rows
> AMG: preading through rows ... done
> ERROR (proc 0000, src/amg.c:487): AMG: missing data for some rows
>
> an error occured: dying ...
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