[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 22:40:45 CST 2018


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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