Re: [Nek5000-users] simulation termination at istep=0 with NaN
Hello, Thanks for your help. Please see below for the log file. Ajay ####################### Number of processors: 8 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 7.87E-07 Reading /home/ajay/nek5_svn/runs/smallcylinder/simplecylinder.rea mapping elements to processors Reading /home/ajay/nek5_svn/runs/smallercylinder/simpleduct.map 0 2827 2827 22620 22620 NELV 1 2828 2828 22620 22620 NELV 2 2827 2827 22620 22620 NELV 3 2828 2828 22620 22620 NELV 4 2827 2827 22620 22620 NELV 5 2828 2828 22620 22620 NELV 6 2827 2827 22620 22620 NELV 7 2828 2828 22620 22620 NELV RANK 0 IEG 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 . . 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 element load imbalance: 1 2827 2828 done :: mapping elements to processors 0 objects found 103 Parameters from file: 1 1.00000 p1 DENSITY 2 -500.000 p2 VISCOS 7 1.00000 p7 RHOCP 8 1.00000 p8 CONDUCT 11 10000 p11 NSTEPS 12 0.10000E-05 p12 DT 15 5 p15 IOSTEP 18 -20.00000 p18 GRID 19 -1.00000 p19 INTYPE 20 10.0000 p20 NORDER 26 1.00000 p26 COURANT/NTAU 27 2.00000 p27 TORDER 65 1.00000 p65 #iofiles (eg, 0 or 64); <0 --> sep. dirs 66 4.00000 p66 output : <0=ascii, else binary 67 4.00000 p67 restart: <0=ascii, else binary 93 20.0000 p93 Number of previous pressure solns saved 94 3.00000 p94 start projecting velocity after p94 step 95 5.00000 p95 start projecting pressure after p95 step 99 0. p99 dealiasing: <0--> off/3--> old/4--> new 102 1.00000 p102 Dump out divergence at each time step 103 -1.00000 p103 weight of stabilizing filter (.01) nelgt/nelgv/lelt: 22620 22620 4800 lx1 /lx2 /lx3 : 4 2 4 done :: read .rea file 0.31992 sec Reset the target Courant number to .5 setup mesh topology Right-handed check complete for 22620 elements. OK. setvert3d: 4 442198 623158 442198 442198 call usrsetvert done :: usrsetvert gs_setup: 30559 unique labels shared pairwise times (avg, min, max): 0.000139931 0.000135946 0.000145721 crystal router : 0.000256464 0.000254369 0.000258589 all reduce : 0.00160212 0.00160019 0.00160458 used all_to_all method: pairwise handle bytes (avg, min, max): 1.84397e+06 1811380 1886892 buffer bytes (avg, min, max): 127744 104448 159248 setupds time 2.7611E-01 seconds 0 4 442198 22620 8 max multiplicity done :: setup mesh topology call usrdat done :: usrdat generate geometry data done :: generate geometry data call usrdat2 done :: usrdat2 regenerate geometry data 1 done :: regenerate geometry data 1 verify mesh topology 0.000000000000000E+000 40.0000037000000 Xrange -0.999999929000000 0.999999933000000 Yrange -0.999999934000000 0.999999930000000 Zrange done :: verify mesh topology IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = F IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = F IFCHAR = F IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFNEKNEK = F IFSYNC = T IFVCOR = F IFINTQ = F IFCWUZ = F IFSWALL = F IFGEOM = F IFSURT = F IFWCNO = F IFCMT = F IFVISC = F IFFLTR = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Dealiasing enabled, lxd= 6 Estimated eigenvalues EIGAA = 1.64699045940739 EIGGA = 96667.1875918256 EIGAE = 6.168501609507998E-003 EIGAS = 3.121097622977694E-004 EIGGE = 96667.1875918256 EIGGS = 2.00000000000000 verify mesh topology 0.000000000000000E+000 40.0000037000000 Xrange -0.999999929000000 0.999999933000000 Yrange -0.999999934000000 0.999999930000000 Zrange done :: verify mesh topology E-solver strategy: 1 itr Matrix: 0 aa 4 4 4 0 aa Infinity -4.08542E+02 7.41342E+01 0.00000E+00 0 aa -4.08542E+02 4.65569E+02 -1.31161E+02 0.00000E+00 0 aa 7.41342E+01 -1.31161E+02 7.04788E+01 0.00000E+00 0 aa 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 Matrix: 0 bb 4 4 4 0 bb NaN 0.00000E+00 0.00000E+00 0.00000E+00 0 bb 0.00000E+00 2.66276E-02 -5.47992E-03 0.00000E+00 0 bb 0.00000E+00 -5.47992E-03 2.45184E-02 0.00000E+00 0 bb 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 Error in generalev, info= 3 4 1 Matrix: 0 Aeig 4 4 4 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN Matrix: 0 Deig 1 4 4 0 Deig NaN NaN NaN NaN Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 call exitt: dying ... backtrace(): obtained 10 stack frames. ./nek5000() [0x6b38f9] ./nek5000() [0x8262fa] ./nek5000() [0x546de7] ./nek5000() [0x68bd34] ./nek5000() [0x66424d] ./nek5000() [0x40a834] ./nek5000() [0x408e17] ./nek5000() [0x408ca6] /lib64/libc.so.6(__libc_start_main+0xf0) [0x7fb5451ef9f0] ./nek5000() [0x408b29] total elapsed time : 2.33935E+00 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec #######################
Any reason why you use the old SVN version? You'll find a new one on GitHub. -----Original message-----
From:[email protected] <[email protected]> Sent: Wednesday 26th July 2017 23:12 To: [email protected] Subject: Re: [Nek5000-users] simulation termination at istep=0 with NaN
Hello, Thanks for your help. Please see below for the log file.
Ajay
####################### Number of processors: 8 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 7.87E-07 Reading /home/ajay/nek5_svn/runs/smallcylinder/simplecylinder.rea
mapping elements to processors Reading /home/ajay/nek5_svn/runs/smallercylinder/simpleduct.map 0 2827 2827 22620 22620 NELV 1 2828 2828 22620 22620 NELV 2 2827 2827 22620 22620 NELV 3 2828 2828 22620 22620 NELV 4 2827 2827 22620 22620 NELV 5 2828 2828 22620 22620 NELV 6 2827 2827 22620 22620 NELV 7 2828 2828 22620 22620 NELV RANK 0 IEG 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 . . 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 element load imbalance: 1 2827 2828 done :: mapping elements to processors 0 objects found 103 Parameters from file: 1 1.00000 p1 DENSITY 2 -500.000 p2 VISCOS 7 1.00000 p7 RHOCP 8 1.00000 p8 CONDUCT 11 10000 p11 NSTEPS 12 0.10000E-05 p12 DT 15 5 p15 IOSTEP 18 -20.00000 p18 GRID 19 -1.00000 p19 INTYPE 20 10.0000 p20 NORDER 26 1.00000 p26 COURANT/NTAU 27 2.00000 p27 TORDER 65 1.00000 p65 #iofiles (eg, 0 or 64); <0 --> sep. dirs 66 4.00000 p66 output : <0=ascii, else binary 67 4.00000 p67 restart: <0=ascii, else binary 93 20.0000 p93 Number of previous pressure solns saved 94 3.00000 p94 start projecting velocity after p94 step 95 5.00000 p95 start projecting pressure after p95 step 99 0. p99 dealiasing: <0--> off/3--> old/4--> new 102 1.00000 p102 Dump out divergence at each time step 103 -1.00000 p103 weight of stabilizing filter (.01) nelgt/nelgv/lelt: 22620 22620 4800 lx1 /lx2 /lx3 : 4 2 4 done :: read .rea file 0.31992 sec
Reset the target Courant number to .5 setup mesh topology Right-handed check complete for 22620 elements. OK. setvert3d: 4 442198 623158 442198 442198 call usrsetvert done :: usrsetvert
gs_setup: 30559 unique labels shared pairwise times (avg, min, max): 0.000139931 0.000135946 0.000145721 crystal router : 0.000256464 0.000254369 0.000258589 all reduce : 0.00160212 0.00160019 0.00160458 used all_to_all method: pairwise handle bytes (avg, min, max): 1.84397e+06 1811380 1886892 buffer bytes (avg, min, max): 127744 104448 159248 setupds time 2.7611E-01 seconds 0 4 442198 22620 8 max multiplicity done :: setup mesh topology call usrdat done :: usrdat
generate geometry data done :: generate geometry data call usrdat2 done :: usrdat2
regenerate geometry data 1 done :: regenerate geometry data 1 verify mesh topology 0.000000000000000E+000 40.0000037000000 Xrange -0.999999929000000 0.999999933000000 Yrange -0.999999934000000 0.999999930000000 Zrange done :: verify mesh topology IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = F IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = F IFCHAR = F IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFNEKNEK = F IFSYNC = T IFVCOR = F IFINTQ = F IFCWUZ = F IFSWALL = F IFGEOM = F IFSURT = F IFWCNO = F IFCMT = F IFVISC = F IFFLTR = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Dealiasing enabled, lxd= 6 Estimated eigenvalues EIGAA = 1.64699045940739 EIGGA = 96667.1875918256 EIGAE = 6.168501609507998E-003 EIGAS = 3.121097622977694E-004 EIGGE = 96667.1875918256 EIGGS = 2.00000000000000 verify mesh topology 0.000000000000000E+000 40.0000037000000 Xrange -0.999999929000000 0.999999933000000 Yrange -0.999999934000000 0.999999930000000 Zrange done :: verify mesh topology E-solver strategy: 1 itr
Matrix: 0 aa 4 4 4 0 aa Infinity -4.08542E+02 7.41342E+01 0.00000E+00 0 aa -4.08542E+02 4.65569E+02 -1.31161E+02 0.00000E+00 0 aa 7.41342E+01 -1.31161E+02 7.04788E+01 0.00000E+00 0 aa 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00
Matrix: 0 bb 4 4 4 0 bb NaN 0.00000E+00 0.00000E+00 0.00000E+00 0 bb 0.00000E+00 2.66276E-02 -5.47992E-03 0.00000E+00 0 bb 0.00000E+00 -5.47992E-03 2.45184E-02 0.00000E+00 0 bb 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 Error in generalev, info= 3 4 1
Matrix: 0 Aeig 4 4 4 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN
Matrix: 0 Deig 1 4 4 0 Deig NaN NaN NaN NaN Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 call exitt: dying ... backtrace(): obtained 10 stack frames. ./nek5000() [0x6b38f9] ./nek5000() [0x8262fa] ./nek5000() [0x546de7] ./nek5000() [0x68bd34] ./nek5000() [0x66424d] ./nek5000() [0x40a834] ./nek5000() [0x408e17] ./nek5000() [0x408ca6] /lib64/libc.so.6(__libc_start_main+0xf0) [0x7fb5451ef9f0] ./nek5000() [0x408b29] total elapsed time : 2.33935E+00 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec
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