[Nek5000-users] mesh problems
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Thu Dec 27 05:13:33 CST 2012
Dear Neks,
I generated a big mesh with 7948800 elements for a cylindrical cell of aspect ratio 3, i.e.
x between -1.5 and 1.5
y between -1.5 and 1.5
z between 0 and 1
prex, n2to3, reatore2, amgdump and genmap worked. The AMG preconditioning with go.m worked as well (runtime 3.5 weeks).
prex started out of 3 basic elements which were refined with multi split into
Element1: 90, 90 subelements
Element2: 70, 90
Element3: 70, 90
stretch, r, factor 3
I started the job on BG/Q and get the following error messages in the output file:
bash-4.1$ m G3_96.out.0
/----------------------------------------------------------\
| _ __ ______ __ __ ______ ____ ____ ____ |
| / | / // ____// //_/ / ____/ / __ \ / __ \ / __ \ |
| / |/ // __/ / ,< /___ \ / / / // / / // / / / |
| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |
| /_/ |_//_____//_/ |_|/_____/ \____/ \____/ \____/ |
| |
|----------------------------------------------------------|
| |
| NEK5000: Open Source Spectral Element Solver |
| COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC |
| Version: 1.0rc1 / SVN r838 |
| Web: http://nek5000.mcs.anl.gov |
| |
\----------------------------------------------------------/
Number of processors: 65536
REAL wdsize : 8
INTEGER wdsize : 4
Beginning session:
/homec/hil02/hil020/nek5_svn/g396_r097_Lx1_08_Ra1e9/G3_96.rea
timer accuracy: 1.4962500E-07 sec
read .rea file
read .re2 file
byte swap: T -0.2931277218E+36 6.543210030
nelgt/nelgv/lelt: 7948800 7948800 150
lx1 /lx2 /lx3 : 4 2 4
mapping elements to processors
element load imbalance: 1 121 122
done :: mapping elements to processors
reading mesh
reading curved sides
reading bc for ifld 1
reading bc for ifld 2
done :: read .re2 file
0 objects found
done :: read .rea file 496.34 sec
Reset the target Courant number to .5
setup mesh topology
Right-handed check complete for 7948800 elements. OK.
setvert3d: 4 152084809 215675209 152084809 152084809
call usrsetvert
done :: usrsetvert
gs_setup: 50336837 unique labels shared
pairwise times (avg, min, max): 0.00330717 0.000218656 0.00853093
crystal router : 0.0077495 0.00761262 0.00818637
used all_to_all method: crystal router
setupds time 6.1645E-01 seconds 0 4 152084809 7948800
8 max multiplicity
done :: setup mesh topology
call usrdat
done :: usrdat
generate geomerty data
vol_t,vol_v: 7.06857958483581861 7.06857958483581861
done :: generate geomerty data
call usrdat2
done :: usrdat2
regenerate geomerty data 1
vol_t,vol_v: 7.06857958483581861 7.06857958483581861
done :: regenerate geomerty data 1
verify mesh topology
-1.50001142304138035 1.50001142290878886 Xrange
-1.50001142298026835 1.50001142292693612 Yrange
0.000000000000000000E+00 1.00000000000000000 Zrange
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
i,j,k,ie: 4 2 1 954634
i,j,k,ie: 1 2 1 916744
i,j,k,ie: 2 4 2 972970
i,j,k,ie: 2 1 1 931570
WARNING1 Element mesh mismatch at:
i,j,k,ie: 4 2 1 957874
WARNING1 Element mesh mismatch at:
i,j,k,ie: 4 2 1 996664
Near X = -.12308168E-01 -.34092836 .60036000E-01, d: .12947845E-04 .00000000E+00 81.225474
WARNING1 Element mesh mismatch at:
Near X = .11336871E-01 -.82826699 .61838637E-01, d: .00000000E+00 -.11766071E-04 88.069931
Near X = .97128875E-05 .82845591 .60036000E-01, d: .00000000E+00 -.20015559E-04 88.069931
i,j,k,ie: 2 1 1 981007
WARNING1 Element mesh mismatch at:
i,j,k,ie: 2 1 1 939607
i,j,k,ie: 4 2 4 995854
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
i,j,k,ie: 2 4 3 972989
WARNING1 Element mesh mismatch at:
i,j,k,ie: 2 4 4 931590
Near X = .12193251E-01 .42841310 .66558003E-01, d: .00000000E+00 -.12947474E-04 81.991313
WARNING1 Element mesh mismatch at:
i,j,k,ie: 4 2 4 916204
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
i,j,k,ie: 1 2 4 958144
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
Near X = .12320624E-01 .31593135 .73282003E-01, d: .12573222E-04 .00000000E+00 81.079569
i,j,k,ie: 3 2 4 541894
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
i,j,k,ie: 2 1 1 981003
WARNING1 Element mesh mismatch at:
i,j,k,ie: 2 4 1 939603
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
i,j,k,ie: 2 4 4 890151
WARNING1 Element mesh mismatch at:
Near X = -.62894639E-05 -1.1769232 .60036000E-01, d: .15284684E-04 .00000000E+00 92.459135
WARNING1 Element mesh mismatch at:
Near X = .63923475E-05 1.1769232 .60036000E-01, d: .00000000E+00 -.15284684E-04 92.458255
i,j,k,ie: 3 2 4 2524
i,j,k,ie: 3 2 4 624964
Near X = -.10302672E-04 .82845591 .60036000E-01, d: .20015559E-04 .00000000E+00 88.062609
i,j,k,ie: 2 4 4 62171
i,j,k,ie: 2 4 4 600363
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
WARNING1 Element mesh mismatch at:
---------------------------------------------------------
and so on…….
The job hangs at this position and does not continue. Can it be that the precision of the coordinate ranges is not sufficient?
For a job that runs well (here an aspect ratio one cell as an example) I got in the output file the following coordinates.
……
verify mesh topology
-0.500000000000000000 0.500000000000000000 Xrange
-0.500000000000000000 0.500000000000000000 Yrange
0.000000000000000000E+00 1.00000000000000000 Zrange
done :: verify mesh topology
……
i.e. precise bounds down to the last digit.
Note also that I had to adapt the programs n2to3 and reatore2, e.g.:
[josc1234 at reynolds n2to3]$ diff n2to3.f n2to3.f_orig
31c31
< parameter(nelm=99999)
---
> parameter(nelm=9999)
[josc1234 at reynolds reatore2]$ diff reatore2.f reatore2.f_orig
19c19
< parameter(lelt=10000000)
---
> parameter(lelt=1000000)
118c118
I wonder if you have an idea where things went wrong? Is it already the prex?
Thanks for your help in advance.
Best regards, Joerg.
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