[Nek5000-users] help with meshing a torus
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Mon Jun 2 11:42:25 CDT 2014
Hi all,
I'm trying to create a mesh for a torus (a doughnut).
In order to do so I create the mesh for a straight pipe and then I bend
it in usrdat2.
If I assign periodic boundary conditions on the two faces of the
straight pipe (that then coincide when I bend the pipe) everything works
fine.
If, instead, I assign E (as it should) nek stops after usrdat2 and
complains about unique labels shared (I attached a log). Why?
Best regards,
Jacopo
-------------- next part --------------
/----------------------------------------------------------\\
| _ __ ______ __ __ ______ ____ ____ ____ |
| / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ |
| / |/ // __/ / ,< /___ \\ / / / // / / // / / / |
| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |
| /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ |
| |
|----------------------------------------------------------|
| |
| NEK5000: Open Source Spectral Element Solver |
| COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC |
| Version: 1.0rc1 / SVN r1016 |
| Web: http://nek5000.mcs.anl.gov |
| |
\\----------------------------------------------------------/
Number of processors: 6
REAL wdsize : 8
INTEGER wdsize : 4
Beginning session:
/afs/mech.kth.se/home/mech/jcanton/scratch/DNSs/tests/test3-fullTorus-myMesh/b
timer accuracy: 1.1920929E-07 sec
read .rea file
read .re2 file
byte swap: F 6.54321003 -2.93127722E+35
nelgt/nelgv/lelt: 48 48 640
lx1 /lx2 /lx3 : 8 8 8
mapping elements to processors
0 8 8 48 48 NELV
2 8 8 48 48 NELV
1 8 8 48 48 NELV
4 8 8 48 48 NELV
5 8 8 48 48 NELV
3 8 8 48 48 NELV
RANK 0 IEG 25 26 27 37 38 39 41 42
element load imbalance: 0 8 8
done :: mapping elements to processors
reading mesh
reading curved sides
reading bc for ifld 1
done :: read .re2 file
0 objects found
done :: read .rea file 0.41709E-02 sec
Reset the target Courant number to .5
setup mesh topology
Right-handed check complete for 48 elements. OK.
setvert3d: 8 7525 17893 7525 7525
call usrsetvert
done :: usrsetvert
gs_setup: 2526 unique labels shared
pairwise times (avg, min, max): 8.15789e-06 7.98702e-06 8.32081e-06
crystal router : 1.40508e-05 1.34945e-05 1.44005e-05
all reduce : 2.36034e-05 2.35081e-05 2.36988e-05
used all_to_all method: pairwise
handle bytes (avg, min, max): 36537.3 34204 38436
buffer bytes (avg, min, max): 15104 12640 17104
setupds time 1.6498E-02 seconds 0 8 7525 48
8 max multiplicity
done :: setup mesh topology
call usrdat
Opening .rea.usr parameter file: /afs/mech.kth.se/home/mech/jcanton/scratch/DNSs/tests/test3-fullTorus-myMesh/bentPipe.rea.usr
UPARAM( 1) = 0.0000
UPARAM( 2) = 200.00
UPARAM( 3) = 0.0000
UPARAM( 4) = 1.0000
UPARAM( 5) = 0.30000
UPARAM( 6) = 360.00
UPARAM( 7) = 22.500
done :: usrdat
generate geometry data
vol_t,vol_v: 0.78539821905070573 0.78539821905070573
done :: generate geometry data
call usrdat2
writing hpts.in file
done :: usrdat2
regenerate geometry data 1
vol_t,vol_v: 8.2246709170395587 8.2246709170395587
NOTE: All elements deformed , param(59) ^=0
done :: regenerate geometry data 1
verify mesh topology
-2.1666666666666670 2.1666666666666670 Xrange
-2.1666666666666670 2.1666666666666670 Yrange
-0.50000000000000000 0.50000000000000000 Zrange
done :: verify mesh topology
118 Parameters from file:/afs/mech.kth.se/home/mech/jcanton/scratch/DNSs/tests/test3-fullTorus-myMesh/bentPipe.rea
1 1.00000 P001: DENSITY
2 -10. P002: VISCOS
7 1.00000 P007: RHOCP
8 1.00000 P008: CONDUCT
11 3 P011: NSTEPS
12 5.0E-03 P012: DT
15 1 P015: IOSTEP
17 1.00000 P017:
18 0.500000E-01 P018: GRID < 0 --> # cells on screen
19 -1.00000 P019: INTYPE
20 10.0000 P020: NORDER
21 0.100000E-08 P021: DIVERGENCE
22 0.100000E-08 P022: HELMHOLTZ
24 0.100000E-01 P024: TOLREL
25 0.100000E-01 P025: TOLABS
26 1.00000 P026: COURANT/NTAU
27 3.00000 P027: TORDER
28 0.00000 P028: TORDER: mesh velocity (0: p28=p27)
56 1.00000 P056: : :
59 0.00000 P059: !=0 --> full Jac. eval. for each el.
65 1.00000 P065: #iofiles (eg, 0 or 64); <0 --> sep. dirs
66 6.00000 P066: output : <0=ascii, else binary
67 6.00000 P067: restart: <0=ascii, else binary
68 20000 P068: iastep: freq for avg_all (0=iostep)
69 50000.0 P069: : : frequency of srf dump
93 20.0000 P093: Number of previous pressure solns saved
94 9.00000 P094: start projecting velocity after p94 step
95 9.00000 P095: start projecting pressure after p95 step
99 3.00000 P099: dealiasing: <0--> off/3--> old/4--> new
102 1.00000 P102: Dump out divergence at each time step
103 0.01000 P103: weight of stabilizing filter (.01)
IFTRAN = T
IFFLOW = T
IFHEAT = F
IFSPLIT = T
IFLOMACH = F
IFUSERVP = F
IFUSERMV = F
IFSTRS = F
IFCHAR = F
IFCYCLIC = T
IFAXIS = F
IFMVBD = F
IFMELT = F
IFMODEL = F
IFKEPS = F
IFMOAB = F
IFNEKNEK = F
IFSYNC = T
IFVCOR = T
IFINTQ = F
IFCWUZ = F
IFSWALL = 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= 12
Estimated eigenvalues
EIGAA = 3.6402682899481458
EIGGA = 109272.77145407666
EIGAE = 0.52560023437753967
EIGAS = 1.2032085561497324E-002
EIGGE = 109272.77145407666
EIGGS = 2.0000000000000000
verify mesh topology
-2.1666666666666670 2.1666666666666670 Xrange
-2.1666666666666670 2.1666666666666670 Yrange
-0.50000000000000000 0.50000000000000000 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: 60 unique labels shared
pairwise times (avg, min, max): 7.93139e-06 7.9155e-06 8.01086e-06
crystal router : 3.53654e-06 3.38554e-06 3.71933e-06
all reduce : 3.52065e-06 3.48091e-06 3.60012e-06
used all_to_all method: allreduce
handle bytes (avg, min, max): 1902.67 1756 2028
buffer bytes (avg, min, max): 960 960 960
setupds time 7.7677E-04 seconds 1 2 85 48
setvert3d: 4 1189 1573 1189 1189
call usrsetvert
done :: usrsetvert
gs_setup: 482 unique labels shared
pairwise times (avg, min, max): 5.97239e-06 5.6982e-06 6.10352e-06
crystal router : 5.74589e-06 5.6982e-06 5.79357e-06
all reduce : 9.81887e-06 9.5129e-06 1.01089e-05
used all_to_all method: crystal router
handle bytes (avg, min, max): 25184 18812 28900
buffer bytes (avg, min, max): 5962.67 5344 6288
setupds time 1.3289E-03 seconds 2 4 1189 48
setvert3d: 4 1189 1573 1189 1189
call usrsetvert
done :: usrsetvert
gs_setup: 482 unique labels shared
pairwise times (avg, min, max): 4.24385e-06 4.19617e-06 4.29153e-06
crystal router : 3.89814e-06 3.60012e-06 4.19617e-06
all reduce : 9.02017e-06 8.89301e-06 9.08375e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 25184 18812 28900
buffer bytes (avg, min, max): 5962.67 5344 6288
setupds time 1.2860E-03 seconds 3 4 1189 48
setvert3d: 6 3669 6741 3669 3669
call usrsetvert
done :: usrsetvert
gs_setup: 1304 unique labels shared
pairwise times (avg, min, max): 4.52201e-06 4.41074e-06 4.60148e-06
crystal router : 6.65188e-06 6.29425e-06 7.10487e-06
all reduce : 1.50323e-05 1.48058e-05 1.53065e-05
used all_to_all method: pairwise
handle bytes (avg, min, max): 19598.7 18332 20628
buffer bytes (avg, min, max): 8149.33 6816 9200
setupds time 2.0061E-03 seconds 4 6 3669 48
Error in generalev, info= 7 6 -1
Error in generalev, info= 7 6 -1
Error in generalev, info= 7 6 -1
Matrix: 0 aa 6 6 6
0 aa 3.29462E+00 -1.92870E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
Error in generalev, info= 12 6 -6
0 aa -1.92870E+00 3.42641E+00 -1.92870E+00 2.81394E-01 -6.58924E-02 0.00000E+00
0 aa 0.00000E+00 -1.92870E+00 3.29462E+00 -1.64731E+00 2.81394E-01 0.00000E+00
Error in generalev, info= 12 6 -6
0 aa 0.00000E+00 2.81394E-01 -1.64731E+00 3.29462E+00 -1.92870E+00 0.00000E+00
0 aa 0.00000E+00 -6.58924E-02 2.81394E-01 -1.92870E+00 Infinity -Infinity
0 aa 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -Infinity Infinity
Matrix: 0 bb 6 6 6
0 bb 1.05391E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0 bb 0.00000E+00 4.21563E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0 bb 0.00000E+00 0.00000E+00 1.05391E+00 0.00000E+00 0.00000E+00 0.00000E+00
0 bb 0.00000E+00 0.00000E+00 0.00000E+00 1.05391E+00 0.00000E+00 0.00000E+00
0 bb 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.10781E-01 0.00000E+00
0 bb 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
Matrix: 0 Aeig 6 6 6
0 Aeig 3.29462E+00 -1.92870E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0 Aeig -1.92870E+00 3.42641E+00 -1.92870E+00 2.81394E-01 -6.58924E-02 0.00000E+00
0 Aeig 0.00000E+00 -1.92870E+00 3.29462E+00 -1.64731E+00 2.81394E-01 0.00000E+00
0 Aeig 0.00000E+00 2.81394E-01 -1.64731E+00 3.29462E+00 -1.92870E+00 0.00000E+00
0 Aeig 0.00000E+00 -6.58924E-02 2.81394E-01 -1.92870E+00 Infinity -Infinity
0 Aeig 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -Infinity Infinity
Matrix: 0 Deig 1 6 6
0 Deig 2.81185E-01 1.10907E+00 2.47769E+00 3.98175E+00 1.00403E+01 1.11847E+01
Error in generalev, info= 12 6 -6
call exitt: dying ...
backtrace(): obtained 12 stack frames.
nek5000(print_stack_+0x1a) [0x509cfa]
nek5000(exitt_+0x24b) [0x5cbcbb]
nek5000(generalev_+0x172) [0x4a5d22]
nek5000(hsmg_setup_fast1d_+0xfb) [0x4d038b]
nek5000(hsmg_setup_fast_+0x5d7) [0x4d0a47]
nek5000(hsmg_setup_fdm_+0x10d) [0x4d0d1d]
nek5000(hsmg_setup_+0x3f) [0x4d1e1f]
nek5000(set_overlap_+0x1ae) [0x4f5ffe]
nek5000(nek_init_+0x82d) [0x421b0d]
nek5000(main+0x24) [0x41e294]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f954e52bead]
nek5000() [0x41e2d9]
total elapsed time : 6.08048E-02 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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