[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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