[Nek5000-users] Example 'turbChannel' Emergency exit

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Wed Apr 14 09:26:25 CDT 2010



I'm not too familiar with this particular setup, but in my past LES
experience I find one needs a significant reduction in dt in the passage
through transition to the fully turbulent state.   Looking at the e2
quanity  ( grep e2 logfile > t.2; gnuplot, plot 't.2' u 2:3 w l ), I
see that it looks like the simulation is getting to that point...

Just an observation...

Paul


On Wed, 14 Apr 2010, nek5000-users at lists.mcs.anl.gov wrote:

> Fred,
>
> for now just disable the dynamic Smagorinski model e.g. set param(30) = 0!
> Instead the simple filtering SGS model is used. Two parameters are important here:
>
> param(101) ... additional modes to filter
> param(103) ... filter weight of the last mode
>
> Typically a good starting point is p101=1 and p103=0.05.
>
> -Stefan
>
>
> On Apr 14, 2010, at 2:42 PM, nek5000-users at lists.mcs.anl.gov wrote:
>
>> Fred,
>>
>> we can reproduce your problem and we try to come up with a solution soon.
>>
>> Stefan
>>
>>
>> On Apr 14, 2010, at 10:37 AM, nek5000-users at lists.mcs.anl.gov wrote:
>>
>>> Hi Fred,
>>>
>>> please attach a full logfile.
>>>
>>> Stefan
>>>
>>>
>>> On Apr 14, 2010, at 10:25 AM, nek5000-users at lists.mcs.anl.gov wrote:
>>>
>>>> Hello NEKs,
>>>>
>>>> in the last day I had a couple of problems with my runs, so I started again the turbChannel example on our machine to get a better feeling for the parameters. When I run the turbChannel example, the run stopped after 5172 time steps with an 'emergency exit' cause the CFL number is getting to high. Do you know from where does this occur?? I just added the output of the last time steps.
>>>>
>>>> Best,
>>>> Fred
>>>>
>>>>
>>>> 5165  2.582500000E+01  3.916990657E-03  1.659821813E-03  3.694680560E-01 e2
>>>> Step   5166, t= 2.5830000E+01, DT= 5.0000000E-03, C=  2.079 3.4805E+04 1.3937E+01
>>>>          Solving for fluid
>>>>    5166    PRES alph1n  8.7741E+02  4.2415E+01  2.0687E+01    20
>>>>    5166    PRES halpha    20  1.1643E+01 -3.7137E+00  3.6211E-01 -2.0448E-01 -1.6916E+00  8.2524E-01  1.1625E+00  8.9342E-01 -1.6984E-01 -2.2222E-01
>>>>
>>>>    5166    PRES gmres:       75   8.8674E-06   1.0000E-05   8.5433E-02   4.1833E+00   9.7743E+00
>>>>    5166    Hmholtz VELX:     11   1.5456E-09   1.0149E+00   1.0000E-08
>>>>    5166    Hmholtz VELY:     11   3.0012E-09   1.9688E+00   1.0000E-08
>>>>    5166    Hmholtz VELZ:     11   2.5093E-09   1.8625E+00   1.0000E-08
>>>>            L1/L2 DIV(V)    :   4.9352E-18   9.2917E-01
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:   4.9352E-18   9.2917E-01
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5166   2.5830E+01  1.3669E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5166  2.583000000E+01  3.926052513E-03  1.662276122E-03  3.689963050E-01 e2
>>>> Step   5167, t= 2.5835000E+01, DT= 5.0000000E-03, C=  2.889 3.4820E+04 1.4982E+01
>>>>          Solving for fluid
>>>>    5167    PRES alph1n  1.5542E+03  7.1980E+02  2.1591E+00     1
>>>>    5167    PRES halpha     1  1.4480E+01
>>>>    5167    PRES gmres:       86   9.7160E-06   1.0000E-05   9.3445E-01   4.7986E+00   1.1231E+01
>>>>    5167    Hmholtz VELX:     12   5.8389E-09   1.3413E+00   1.0000E-08
>>>>    5167    Hmholtz VELY:     13   3.9482E-09   2.9638E+00   1.0000E-08
>>>>    5167    Hmholtz VELZ:     13   3.5924E-09   2.6194E+00   1.0000E-08
>>>>            L1/L2 DIV(V)    :   3.1068E-18   1.2785E+00
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:   3.1068E-18   1.2785E+00
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5167   2.5835E+01  1.5275E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5167  2.583500000E+01  3.993359862E-03  1.664692380E-03  3.685384235E-01 e2
>>>> Step   5168, t= 2.5840000E+01, DT= 5.0000000E-03, C=  3.423 3.4837E+04 1.6588E+01
>>>>          Solving for fluid
>>>>    5168    PRES alph1n  3.9778E+03  3.8710E+03  1.0276E+00     2
>>>>    5168    PRES halpha     2  1.2944E+01  6.2999E-01
>>>>    5168    PRES gmres:       79   9.2196E-06   1.0000E-05   4.3331E+00   4.4083E+00   1.0437E+01
>>>>    5168    Hmholtz VELX:     14   4.7243E-09   2.0176E+00   1.0000E-08
>>>>    5168    Hmholtz VELY:     14   6.8219E-09   4.6788E+00   1.0000E-08
>>>>    5168    Hmholtz VELZ:     15   1.8252E-09   4.0913E+00   1.0000E-08
>>>>            L1/L2 DIV(V)    :  -1.4831E-18   2.0942E+00
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:  -1.4831E-18   2.0942E+00
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5168   2.5840E+01  1.4678E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5168  2.584000000E+01  4.200707570E-03  1.667064185E-03  3.681057305E-01 e2
>>>> Step   5169, t= 2.5845000E+01, DT= 5.0000000E-03, C=  5.530 3.4853E+04 1.5991E+01
>>>>          Solving for fluid
>>>>    5169    PRES alph1n  7.2030E+03  3.1162E+03  2.3115E+00     3
>>>>    5169    PRES halpha     3 -6.0424E+01 -1.0653E+01 -8.4291E+00
>>>>    5169    PRES gmres:       97   9.6453E-06   1.0000E-05   3.9350E+00   5.4119E+00   1.2493E+01
>>>>    5169    Hmholtz VELX:     11   4.1711E-09   1.9124E+00   1.0000E-08
>>>>    5169    Hmholtz VELY:     11   7.0818E-09   3.3758E+00   1.0000E-08
>>>>    5169    Hmholtz VELZ:     11   9.3833E-09   4.3104E+00   1.0000E-08
>>>>            L1/L2 DIV(V)    :   5.4916E-18   2.0864E+00
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:   5.4916E-18   2.0864E+00
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5169   2.5845E+01  1.6361E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5169  2.584500000E+01  4.167598852E-03  1.701730652E-03  3.676193877E-01 e2
>>>> Step   5170, t= 2.5850000E+01, DT= 5.0000000E-03, C=  6.006 3.4871E+04 1.7673E+01
>>>>          Solving for fluid
>>>>    5170    PRES alph1n  3.8504E+03  2.1151E+03  1.8205E+00     4
>>>>    5170    PRES halpha     4 -4.5903E+00  2.8727E+00  1.4775E+00 -3.0313E+01
>>>>    5170    PRES gmres:       95   9.5031E-06   1.0000E-05   2.9323E+00   5.3008E+00   1.2248E+01
>>>>    5170    Hmholtz VELX:     11   2.9823E-09   2.3489E+00   1.0000E-08
>>>>    5170    Hmholtz VELY:     11   5.2939E-09   5.2327E+00   1.0000E-08
>>>>    5170    Hmholtz VELZ:     11   8.5864E-09   6.0722E+00   1.0000E-08
>>>>            L1/L2 DIV(V)    :  -1.3376E-19   1.6752E+00
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:  -1.3376E-19   1.6752E+00
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5170   2.5850E+01  1.6120E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5170  2.585000000E+01  4.085734913E-03  1.716209642E-03  3.671058529E-01 e2
>>>> Step   5171, t= 2.5855000E+01, DT= 5.0000000E-03, C=  4.227 3.4888E+04 1.7434E+01
>>>>          Solving for fluid
>>>>    5171    PRES alph1n  5.0358E+03  1.2448E+03  4.0456E+00     5
>>>>    5171    PRES halpha     5 -6.9028E+00 -1.4184E+00 -4.2028E+01 -1.2786E+01 -2.1059E+01
>>>>    5171    PRES gmres:       92   9.4249E-06   1.0000E-05   1.6822E+00   5.1338E+00   1.1887E+01
>>>>    5171    Hmholtz VELX:     11   2.1456E-09   2.9780E+00   1.0000E-08
>>>>    5171    Hmholtz VELY:     11   5.3606E-09   7.0811E+00   1.0000E-08
>>>>    5171    Hmholtz VELZ:     11   5.8359E-09   6.8710E+00   1.0000E-08
>>>>            L1/L2 DIV(V)    :  -1.6210E-17   3.1098E+00
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:  -1.6210E-17   3.1098E+00
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5171   2.5855E+01  1.5761E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5171  2.585500000E+01  4.389947285E-03  1.720108719E-03  3.665677180E-01 e2
>>>> Step   5172, t= 2.5860000E+01, DT= 5.0000000E-03, C= 14.041 3.4905E+04 1.7076E+01
>>>>          Solving for fluid
>>>>    5172    PRES alph1n  9.0973E+04  3.3755E+04  2.6951E+00     6
>>>>    5172    PRES halpha     6 -5.1818E+02 -1.4428E+02 -8.2239E+02 -5.2616E+01  6.5613E+01  2.1168E+02
>>>>    5172    PRES gmres:      132   9.6516E-06   1.0000E-05   4.3975E+01   7.3637E+00   1.7181E+01
>>>>    5172    Hmholtz VELX:     32   8.9325E-09   4.2902E+01   1.0000E-08
>>>>    5172    Hmholtz VELY:     33   6.7432E-09   1.0998E+02   1.0000E-08
>>>>    5172    Hmholtz VELZ:     33   8.7122E-09   9.2142E+01   1.0000E-08
>>>>            L1/L2 DIV(V)    :  -4.3714E-18   1.8897E+01
>>>>            L1/L2 QTL       :   0.0000E+00   0.0000E+00
>>>>            L1/L2 DIV(V)-QTL:  -4.3714E-18   1.8897E+01
>>>>            WARNING: DIV(V)-QTL too large!
>>>>    5172   2.5860E+01  2.3473E+01 Fluid done
>>>> Calculating eddy visosity
>>>> 5172  2.586000000E+01  4.640317048E-02  1.721776888E-03  3.660847580E-01 e2
>>>> CFL, Ctarg!   77.0972671240189        2.00000000000000
>>>>
>>>>  5173  2.5860E+01 Write checkpoint:
>>>>
>>>>  5173  2.5860E+01 OPEN: turbChannel.fld06
>>>>
>>>>        1  Emergency exit:        5173    time =   25.8599999999991
>>>> Latest solution and data are dumped for post-processing.
>>>> *** STOP ***
>>>>
>>>>        0  Emergency exit:        5173    time =   25.8599999999991
>>>> Latest solution and data are dumped for post-processing.
>>>> *** STOP ***
>>>>        0  opcount   7939907566848.00
>>>>        1  opcount   7939907566848.00
>>>> TOTAL OPCOUNT   15879815133696.0
>>>> opnode   0  subcl4      0.000000               0
>>>> opnode   0  ascol5      0.000000               0
>>>> opnode   0  invcl3     0.1355809E+10       10344
>>>> opnode   0  vlsum      0.1355809E+10     2648064
>>>> opnode   0  inver2     0.1355809E+10       10344
>>>> opnode   0  cadd2      0.2033713E+10       15516
>>>> opnode   0  admcol     0.2033713E+10        5172
>>>> opnode   0  invcl1     0.2033713E+10       15516
>>>> opnode   0  vsqrt      0.3389915E+10     2663583
>>>> opnode   0  opa2cl     0.4067426E+10        5172
>>>> opnode   0  subcl3     0.4067426E+10       15516
>>>> opnode   0  sub3       0.4747952E+10       37499
>>>> opnode   0  sub2       0.1152359E+11     8001078
>>>> opnode   0  opcv3c     0.1219992E+11       15513
>>>> opnode   0  add3s2     0.1220228E+11       31032
>>>> opnode   0  VLSC2      0.1285580E+11       49041
>>>> opnode   0  cadd       0.1391945E+11      106197
>>>> opnode   0  invcl2     0.1423639E+11    19891515
>>>> opnode   0  opcolv     0.2643827E+11       67236
>>>> opnode   0  add2s1     0.2927781E+11      111686
>>>> opnode   0  glsc2      0.3054948E+11      116537
>>>> opnode   0  ADD3       0.3129265E+11    61118464
>>>> opnode   0  cmult      0.4078676E+11    64159596
>>>> opnode   0  addcl4     0.4189481E+11      106544
>>>> opnode   0  col3       0.6824224E+11    32173287
>>>> opnode   0  ADD2       0.8181750E+11    85243418
>>>> opnode   0  glsc3      0.8983806E+11      228470
>>>> opnode   0  addcl3     0.1057688E+12    63724056
>>>> opnode   0  col2       0.2130625E+12   254874963
>>>> opnode   0  add2s2     0.3703272E+12     1412686
>>>> opnode   0  VLSC3      0.4606404E+12     1171469
>>>> opnode   0  mxm        0.6246592E+13 -1613811570
>>>> total time   34934.7607588768        34931.1205290364
>>>> copy time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> mxmf time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> inv3 time       10344   15.3735277652740       4.401097798307057E-004
>>>> invc time    19891515   146.002576589584       4.179727829464278E-003
>>>> mltd time       62064   4038.74821758270       0.115620345308577
>>>> cdtp time       15516   437.695099830627       1.253023359118396E-002
>>>> eslv time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> pres time        5172   14242.1249115467       0.407720241888833
>>>> crsl time       90681   47.9217271804810       1.371892068009847E-003
>>>> crsl min    47.9217271804810
>>>> crsl max    53.2970800399780
>>>> crsl avg    50.6094036102295
>>>> hmhz time       15521   15087.4339959621       0.431919553895237
>>>> usbc time        5173   85.1574075222015       2.437866470713835E-003
>>>> axhm time      238766   6975.35609674454       0.199688873162437
>>>> advc time -1333526528  2.332305834658064E-310  6.676870938527185E-315
>>>> gop  time      878153   62.8719458580017       1.799883453659598E-003
>>>> gop  min    62.8719387054443
>>>> gop  max    118.545093774796
>>>> gop  avg    90.7085191011429
>>>> vdss time       25861   108.827995061874       3.115502549407525E-003
>>>> vdss min    108.827995061874
>>>> vdss max    108.830206155777
>>>> vdss avg    108.829100608826
>>>> dsum time      334612   471.267515897751       1.349133691563118E-002
>>>> dsum min    440.130956649780
>>>> dsum max    471.267515897751
>>>> dsum avg    455.699236273766
>>>> gsum time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> dsnd time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> dadd time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> dsmx time           0  0.154825925827026       4.432320620757866E-006
>>>> dsmn time           0  1.043796539306641E-003  2.988156473363023E-008
>>>> slvb time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> ddsl time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> solv time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> sett time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> prep time        5173   12.7582430839539       3.652400178044276E-004
>>>> bsol time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> bso2 time           0  0.000000000000000E+000  0.000000000000000E+000
>>>> #  nid       tusbc       tdadd       tcrsl       tvdss       tdsum        tgop    qqq
>>>>     0  8.5157E+01  0.0000E+00  4.7922E+01  1.0883E+02  4.7127E+02  6.2872E+01 qqq
>>>>     1  8.8959E+01  0.0000E+00  5.3297E+01  1.0883E+02  4.4013E+02  1.1855E+02 qqq
>>>>
>>>> call exitt: dying ...
>>>>
>>>> backtrace(): obtained 11 stack frames.
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(print_stack_+0x26) [0x5d34ca]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(exitt_+0x34e) [0x6eb7ce]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(emerxit_+0x63c) [0x52deaa]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(setdt_+0xc9a) [0x52098a]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(settime_+0xb7) [0x4210a1]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(nek_advance_+0x27) [0x41d185]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(nek_solve_+0x2d1) [0x41d0d3]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(MAIN__+0x3b) [0x41bfaf]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(main+0x3c) [0x415b8c]
>>>> /lib/libc.so.6(__libc_start_main+0xda) [0x2aef191be4ca]
>>>> /data2/DATEN/frederik/nek5/examples/turbChannel/nek5000(for_write_seq_fmt_xmit+0x3a) [0x415aba]
>>>>
>>>> total elapsed time             :   3.49348E+04 sec
>>>> total solver time incl. I/O    :   3.49051E+04 sec
>>>> time/timestep                  :   6.74756E+00 sec
>>>> CPU seconds/timestep/DOF       :   7.82568E-05 sec
>>>>
>>>> _______________________________________________
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>>>> Nek5000-users at lists.mcs.anl.gov
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>>>
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>>
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