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<div>Hello Kento,</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>
<div>AMG: preading through rows ... done</div>
<div>ERROR (proc 0000, src/amg.c:487): AMG: missing data for some rows</div>
<div> </div>
<div>an error occured: dying …</div>
</div>
<div><br>
</div>
<div>Would you run into this issue earlier before?</div>
<div><br>
</div>
<div>Again thanks a lot for the suggestions.</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Ming</div>
<div><br>
</div>
<div>***********<span style="font-weight: bold;"> complete logfile *********</span>
<hr align="center" size=""3"" width=""95%"">
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<div>
<div>Reading /global/home/hpc4076/Nek5000/run/turbChannel/turbChannel.par </div>
<div>general = [(null)]</div>
<div>general:stopat = [endTime]</div>
<div>general:endtime = [200]</div>
<div>general:dt = [0]</div>
<div>general:timestepper = [bdf2]</div>
<div>general:extrapolation = [OIFS]</div>
<div>general:variabledt = [yes]</div>
<div>general:targetcfl = [2.0]</div>
<div>general:writecontrol = [runTime]</div>
<div>general:writeinterval = [200.0]</div>
<div>general:userparam01 = [100]</div>
<div>general:userparam02 = [20]</div>
<div>general:userparam03 = [1]</div>
<div>general:filtering = [hpfrt]</div>
<div>general:filterweight = [10]</div>
<div>general:filtercutoffratio = [0.9]</div>
<div>problemtype = [(null)]</div>
<div>problemtype:variableproperties = [no]</div>
<div>problemtype:equation = [incompNS]</div>
<div>pressure = [(null)]</div>
<div>pressure:preconditioner = [semg_amg]</div>
<div>pressure:residualtol = [1e-04]</div>
<div>pressure:residualproj = [yes]</div>
<div>velocity = [(null)]</div>
<div>velocity:residualtol = [1e-07]</div>
<div>velocity:density = [1]</div>
<div>velocity:viscosity = [-10900]</div>
<div> Reading /global/home/hpc4076/Nek5000/run/turbChannel/turbChannel.re2 </div>
<div> mapping elements to processors</div>
<div> Reading /global/home/hpc4076/Nek5000/run/turbChannel/turbChannel.ma2 </div>
<div> 0 9216 9216 73728 73728 NELV</div>
<div> 5 9216 9216 73728 73728 NELV</div>
<div> 7 9216 9216 73728 73728 NELV</div>
<div> 1 9216 9216 73728 73728 NELV</div>
<div> 3 9216 9216 73728 73728 NELV</div>
<div> 6 9216 9216 73728 73728 NELV</div>
<div> 4 9216 9216 73728 73728 NELV</div>
<div> 2 9216 9216 73728 73728 NELV</div>
<div> </div>
<div> element load imbalance: 0 9216 9216</div>
<div> done :: mapping 0.66962E-01 sec</div>
<div><br>
</div>
<div> </div>
<div> preading mesh </div>
<div> preading bc for ifld 1</div>
<div> done :: read .re2 file 0.30 sec</div>
<div><br>
</div>
<div> nelgt/nelgv/lelt: 73728 73728 18439</div>
<div> lx1 /lx2 /lx3 : 8 8 8</div>
<div> setup mesh topology</div>
<div> Right-handed check complete for 73728 elements. OK.</div>
<div> setvert3d: 8 9476352 25401600 9476352 9476352</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 413952 unique labels shared</div>
<div> pairwise times (avg, min, max): 0.000140989 0.000133355 0.000146356</div>
<div> crystal router : 0.0012817 0.00128028 0.00128291</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 3.26526e+07 32652644 32652644</div>
<div> buffer bytes (avg, min, max): 1.68269e+06 1682688 1682688</div>
<div> setupds time 1.9997E+00 seconds 0 8 9476352 73728</div>
<div> 8 max multiplicity</div>
<div> done :: setup mesh topology</div>
<div> </div>
<div> call usrdat</div>
<div> done :: usrdat</div>
<div><br>
</div>
<div> generate geometry data</div>
<div> NOTE: All elements deformed , param(59) ^=0</div>
<div> done :: generate geometry data</div>
<div> </div>
<div> call usrdat2</div>
<div> done :: usrdat2</div>
<div><br>
</div>
<div> regenerate geometry data 1</div>
<div> NOTE: All elements deformed , param(59) ^=0</div>
<div> done :: regenerate geometry data 1</div>
<div> </div>
<div> verify mesh topology</div>
<div> 0.000000000000000E+000 6.28318530717959 Xrange</div>
<div> -1.00000000000000 1.00000000000000 Yrange</div>
<div> 0.000000000000000E+000 3.14159265358979 Zrange</div>
<div> done :: verify mesh topology</div>
<div> </div>
<div> IFTRAN = T</div>
<div> IFFLOW = T</div>
<div> IFHEAT = F</div>
<div> IFSPLIT = T</div>
<div> IFLOMACH = F</div>
<div> IFUSERVP = F</div>
<div> IFUSERMV = F</div>
<div> IFPERT = F</div>
<div> IFADJ = F</div>
<div> IFSTRS = F</div>
<div> IFCHAR = T</div>
<div> IFCYCLIC = F</div>
<div> IFAXIS = F</div>
<div> IFMVBD = F</div>
<div> IFMELT = F</div>
<div> IFNEKNEK = F</div>
<div> IFSYNC = F</div>
<div> </div>
<div> IFVCOR = T</div>
<div> IFINTQ = F</div>
<div> IFGEOM = F</div>
<div> IFSURT = F</div>
<div> IFWCNO = F</div>
<div> </div>
<div> IFTMSH for field 1 = F</div>
<div> IFADVC for field 1 = T</div>
<div> IFNONL for field 1 = F</div>
<div> </div>
<div> Dealiasing enabled, lxd= 8</div>
<div> </div>
<div> Estimated eigenvalues</div>
<div> EIGAA = 1.23913370009078 </div>
<div> EIGGA = 30588693.2337829 </div>
<div> EIGAE = 0.250000000000000 </div>
<div> EIGAS = 1.681282119258565E-002</div>
<div> EIGGE = 30588693.2337829 </div>
<div> EIGGS = 2.00000000000000 </div>
<div> </div>
<div> verify mesh topology</div>
<div> 0.000000000000000E+000 6.28318530717959 Xrange</div>
<div> -1.00000000000000 1.00000000000000 Yrange</div>
<div> 0.000000000000000E+000 3.14159265358979 Zrange</div>
<div> done :: verify mesh topology</div>
<div> </div>
<div> E-solver strategy: 0 itr</div>
<div> mg_nx: 1 3 7</div>
<div> mg_ny: 1 3 7</div>
<div> mg_nz: 1 3 7</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 8448 unique labels shared</div>
<div> pairwise times (avg, min, max): 1.21617e-05 1.1921e-05 1.24227e-05</div>
<div> crystal router : 3.65702e-05 3.65344e-05 3.66269e-05</div>
<div> all reduce : 0.00014386 0.000142943 0.000144376</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 728420 728420 728420</div>
<div> buffer bytes (avg, min, max): 37632 37632 37632</div>
<div> setupds time 2.0250E-02 seconds 1 2 76032 73728</div>
<div> setvert3d: 4 1421568 2011392 1421568 1421568</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 76032 unique labels shared</div>
<div> pairwise times (avg, min, max): 4.62178e-05 4.47887e-05 4.74119e-05</div>
<div> crystal router : 0.000222897 0.000222723 0.000223086</div>
<div> all reduce : 0.000974339 0.000967893 0.000979289</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956</div>
<div> buffer bytes (avg, min, max): 315648 315648 315648</div>
<div> setupds time 3.5739E-01 seconds 2 4 1421568 73728</div>
<div> setvert3d: 4 1421568 2011392 1421568 1421568</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 76032 unique labels shared</div>
<div> pairwise times (avg, min, max): 4.5131e-05 4.40137e-05 4.5883e-05</div>
<div> crystal router : 0.000217508 0.00021732 0.000217639</div>
<div> all reduce : 0.000978618 0.000972797 0.000983269</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956</div>
<div> buffer bytes (avg, min, max): 315648 315648 315648</div>
<div> setupds time 3.5094E-01 seconds 3 4 1421568 73728</div>
<div> setvert3d: 6 4555008 9273600 4555008 4555008</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 211200 unique labels shared</div>
<div> pairwise times (avg, min, max): 9.59221e-05 9.2321e-05 9.80701e-05</div>
<div> crystal router : 0.000574208 0.000573776 0.000574501</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 1.65554e+07 16555364 16555364</div>
<div> buffer bytes (avg, min, max): 864000 864000 864000</div>
<div> setupds time 9.2152E-01 seconds 4 6 4555008 73728</div>
<div> regenerate geometry data 1</div>
<div> NOTE: All elements deformed , param(59) ^=0</div>
<div> done :: regenerate geometry data 1</div>
<div> </div>
<div> h1_mg_nx: 1 3 7</div>
<div> h1_mg_ny: 1 3 7</div>
<div> h1_mg_nz: 1 3 7</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 8448 unique labels shared</div>
<div> pairwise times (avg, min, max): 1.42743e-05 1.37607e-05 1.47085e-05</div>
<div> crystal router : 3.54692e-05 3.53276e-05 3.56395e-05</div>
<div> all reduce : 0.000145775 0.000145112 0.000146347</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 728420 728420 728420</div>
<div> buffer bytes (avg, min, max): 37632 37632 37632</div>
<div> setupds time 1.9277E-02 seconds 5 2 76032 73728</div>
<div> setvert3d: 4 1421568 2011392 1421568 1421568</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 76032 unique labels shared</div>
<div> pairwise times (avg, min, max): 4.74352e-05 4.61341e-05 4.8379e-05</div>
<div> crystal router : 0.000219904 0.000219596 0.000220055</div>
<div> all reduce : 0.00108293 0.00107907 0.00108614</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956</div>
<div> buffer bytes (avg, min, max): 315648 315648 315648</div>
<div> setupds time 3.5849E-01 seconds 6 4 1421568 73728</div>
<div> setvert3d: 4 1421568 2011392 1421568 1421568</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 76032 unique labels shared</div>
<div> pairwise times (avg, min, max): 4.99966e-05 4.93097e-05 5.04928e-05</div>
<div> crystal router : 0.000220982 0.000220777 0.000221201</div>
<div> all reduce : 0.000975639 0.000969762 0.000980587</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 5.91396e+06 5913956 5913956</div>
<div> buffer bytes (avg, min, max): 315648 315648 315648</div>
<div> setupds time 3.5221E-01 seconds 7 4 1421568 73728</div>
<div> setvert3d: 6 4555008 9273600 4555008 4555008</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 211200 unique labels shared</div>
<div> pairwise times (avg, min, max): 9.7033e-05 9.53629e-05 9.89481e-05</div>
<div> crystal router : 0.000575673 0.000575274 0.00057601</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 1.65554e+07 16555364 16555364</div>
<div> buffer bytes (avg, min, max): 864000 864000 864000</div>
<div> setupds time 9.0969E-01 seconds 8 6 4555008 73728</div>
<div> setvert3d: 8 9476352 25401600 9476352 9476352</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 413952 unique labels shared</div>
<div> pairwise times (avg, min, max): 0.000145018 0.00014225 0.000147666</div>
<div> crystal router : 0.00127508 0.00127457 0.00127577</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 3.26526e+07 32652644 32652644</div>
<div> buffer bytes (avg, min, max): 1.68269e+06 1682688 1682688</div>
<div> setupds time 1.9358E+00 seconds 9 8 9476352 73728</div>
<div> setvert3d: 10 16185600 53934336 16185600 16185600</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 684288 unique labels shared</div>
<div> pairwise times (avg, min, max): 0.000185176 0.000182058 0.000188558</div>
<div> crystal router : 0.00236343 0.00236093 0.00236685</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 5.42058e+07 54205796 54205796</div>
<div> buffer bytes (avg, min, max): 2.77171e+06 2771712 2771712</div>
<div> setupds time 3.2958E+00 seconds 10 10 16185600 73728</div>
<div> setup h1 coarse grid, nx_crs= 2</div>
<div> call usrsetvert</div>
<div> done :: usrsetvert</div>
<div><br>
</div>
<div>gs_setup: 8448 unique labels shared</div>
<div> pairwise times (avg, min, max): 1.58059e-05 1.48741e-05 1.6321e-05</div>
<div> crystal router : 3.54276e-05 3.51642e-05 3.56729e-05</div>
<div> all reduce : 0.000144706 0.000143665 0.00014533</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 728420 728420 728420</div>
<div> buffer bytes (avg, min, max): 37632 37632 37632</div>
<div>gs_setup: 8448 unique labels shared</div>
<div> pairwise times (avg, min, max): 1.56632e-05 1.53686e-05 1.61476e-05</div>
<div> crystal router : 1.74988e-05 1.74323e-05 1.75631e-05</div>
<div> all reduce : 0.000148094 0.00014731 0.000148594</div>
<div> used all_to_all method: pairwise</div>
<div> handle bytes (avg, min, max): 368228 368228 368228</div>
<div> buffer bytes (avg, min, max): 17664 17664 17664</div>
<div>AMG version 2.01</div>
<div>AMG: 8 levels</div>
<div>AMG Chebyshev smoother data:</div>
<div>AMG level 1: 3 iterations with rho = 0.79256</div>
<div>AMG level 2: 2 iterations with rho = 0.668297</div>
<div>AMG level 3: 2 iterations with rho = 0.481307</div>
<div>AMG level 4: 2 iterations with rho = 0.409707</div>
<div>AMG level 5: 2 iterations with rho = 0.458605</div>
<div>AMG level 6: 3 iterations with rho = 0.696293</div>
<div>AMG level 7: 2 iterations with rho = 0.666743</div>
<div>AMG: 1664 rows</div>
<div>AMG: preading through rows ... done</div>
<div>ERROR (proc 0000, src/amg.c:487): AMG: missing data for some rows</div>
<div> </div>
<div>an error occured: dying ...</div>
</div>
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