[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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