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Hi!
I don't know if I'm doing something wrong here, but I narrowed down my
problem to the following few lines of code (using meep-0.10.1 and the
SGI-MPI libraries):
(set! geometry-lattice (make lattice (size 2 2 1)))
(set! geometry (list
(make cylinder (center 0 0 0) (radius 1) (height 0.3)
(material (make dielectric (index 1.8))))
(make cylinder (center 0 0 0) (radius 0.5) (height 1)
(material (make dielectric (index 1.45))))))
(run-until 1)
When I try and run this with at least 2 processors (mpirun -np 2) it
crashes with meep outputting a few lines like this (the whole output is
at the end of the email):
meep: invalid point (-0.1,-0.45,-0.1)
followed by a MPI stacktrace. Since this output message is in the
subpixel-averaging code I tried setting eps-averaging? to false and this
doesn't show the problem. When I run the above code with using only one
processor it also finishes without problems. So it seems to be a
combination of subpixel-averaging and MPI that causes this.
Regards,
Uli
- -----------------
Output from meep:
$ mpirun -np 2 ${HOME}/inst/bin/meep-mpi meepdebug.ctl
Using MPI version 1.2, 2 processes
- -----------
Initializing structure...
Working in 3D dimensions.
cylinder, center = (0,0,0)
radius 1, height 0.3, axis (0, 0, 1)
dielectric constant epsilon = 3.24
cylinder, center = (0,0,0)
radius 0.5, height 1, axis (0, 0, 1)
dielectric constant epsilon = 2.1025
meep: invalid point (-0.1,-0.45,-0.1)
MPI: On host lilli, Program /S120S/home/k3503/k358643/inst/bin/meep-mpi,
Rank 1, Process 3253 called MPI_Abort(<communicator>, 1)
MPI: --------stack traceback-------
meep: invalid point (0.15,-0.5,-0.1)
Internal Error: Can't read/write file "/dev/mmtimer", (errno = 22)
Warning: bad source correlation found. Further instances ignored.
Info: Optimized variables show as <no value> when no location is allocated.
Assertion failed: spellingsrc/st/mem/pil_fileid.C54
This is an unexpected condition and may indicate the presence of a defect.
If you wish to report this, please include the stack trace that follows.
1 : 0x4000000001232770
2 : 0x4000000001a4cc80
3 : 0x4000000001950980
4 : 0x4000000001893550
5 : 0x40000000018aa860
6 : 0x400000000188e970
7 : 0x4000000001897a20
8 : 0x4000000001897240
9 : 0x400000000186c190
10 : 0x400000000186d530
11 : 0x4000000001933ab0
12 : 0x40000000018fac20
13 : 0x4000000001910590
14 : 0x4000000000f9c090
15 : 0x4000000000dea0a0
16 : 0x4000000000df1800
17 : 0x4000000000dedb60
18 : 0x400000000110e890
19 : 0x40000000011266c0
20 : 0x40000000011184a0
21 : 0x40000000010d1bf0
22 : 0x4000000001227ef0
23 : 0x4000000001226ef0
24 : 0x40000000012268f0
25 : 0x40000000012252d0
26 : 0x4000000000f4e300
27 : 0x200000000054b630
28 : 0x40000000004e4c00
- --------------
MPI: Intel(R) Debugger for applications running on IA-64, Version
9.1-28, Build 20070305
MPI: Reading symbolic information from
/S120S/home/k3503/k358643/inst/bin/meep-mpi...done
MPI: Attached to process id 3253 ....
MPI: stopped at [0xa000000000010621]
MPI: >0 0xa000000000010621
MPI: #1 0x2000000006287360 in waitpid(...) in /lib/libpthread-2.4.so
MPI: #2 0x2000000000928170 in MPI_SGI_stacktraceback(...) in
/usr/lib/libmpi.so
MPI: #3 0x20000000009648d0 in PMPI_Abort(...) in /usr/lib/libmpi.so
MPI: #4 0x40000000001e6030 in
meep::abort(fmt=0x400000000032fa28="invalid point (%g,%g,%g)\n", ...=<no
value>) "mympi.cpp":113
MPI: #5 0x4000000000011840 in
((geom_epsilon*)0x40000000003408c0)->geom_epsilon::eps(r=& struct vec {
... }) "structure.cpp":229
MPI: #6 0x400000000015c500 in
((material_function*)0x607fffffffb73ac8)->material_function::normal_vector(gv=&
struct geometric_volume { ... }) "anisotropic_averaging.cpp":57
MPI: #7 0x4000000000013fe0 in
((geom_epsilon*)0xccccccccccccd000)->geom_epsilon::meaneps(meps=& 0,
minveps=& 0, n=& struct vec { ... }, gv=& struct geometric_volume { ...
}, tol=0, maxeval=-4769608) "structure.cpp":384
MPI: #8 0x400000000014d3f0 in meep::anisoaverage(epsilon=<no value>,
dV=<no value>, ec=<no value>, invepsrow=<no value>, tol=<no value>,
maxeval=<no value>) "anisotropic_averaging.cpp":153
MPI: #9 0x4000000000157b50 in
((structure_chunk*)0x0)->structure_chunk::set_epsilon(epsilon=<no
value>, use_anisotropic_averaging=<no value>, tol=<no value>,
maxeval=<no value>) "anisotropic_averaging.cpp":258
MPI: #10 0x400000000024dde0 in
((structure*)0x2b021004a015008)->structure::set_epsilon(eps=& struct
material_function { ... }, use_anisotropic_averaging=.FALSE. (16),
tol=2.3267574194080845e+120, maxeval=1375733762) "structure.cpp":329
MPI: #11 0x400000000024e130 in
((structure*)0x2b021004a015008)->structure::set_materials(mat=& struct
material_function { ... }, use_anisotropic_averaging=.FALSE. (16),
tol=2.3267574194080845e+120, maxeval=1375733762) "structure.cpp":317
MPI: #12 0x4000000000257390 in
((structure*)0xffffffffffffffff)->structure::structure(thev=& struct
volume { ... }, eps=& struct material_function { ... }, br=& struct
boundary_region { ... }, s=& struct symmetry { ... }, num=0,
Courant=nan, use_anisotropic_averaging=.FALSE. (0),
tol=1.4916681463395389e-154, maxeval=106462336) "structure.cpp":51
MPI: #13 0x4000000000019490 in make_structure(dims=0, size=struct ._128
{ ... }, center=struct ._128 { ... }, resolution=2.0000000015145005,
enable_averaging=.FALSE. (112), subpixel_tol=1.4916681815021624e-154,
subpixel_maxeval=4873664, ensure_periodicity_p=.FALSE. (32),
geometry=struct ._137 { ... }, default_mat=struct material_type_struct {
... }, pml_layers=struct ._149 { ... }, symmetries=struct ._150 { ... },
num_chunks=8865148, Courant=1.4916681478632451e-154) "structure.cpp":809
MPI: #14 0x400000000004a080 in
_wrap_make_structure(s_0=0x607fffffffb738b8, s_1=0xbfb999999999999b,
s_2=0x400000000032fa28, s_3=0xbfb999999999999a, s_4=0x607fffffffb73ac8,
s_5=0xbfb999999999999b, s_6=0xbfdccccccccccccd, s_7=0xbfb999999999999a,
s_8=0x2, s_9=0x3fb999999999999b, s_10=0x3, s_11=0x2000000000000003,
s_12=0x600000000101e700, s_13=0x607fffffffb739f0) "meep_wrap.cxx":39343
MPI: #15 0x400000000004a310 in _wrap_make_structure_rest(rest=<no
value>) "meep_wrap.cxx":39359
MPI: -----stack traceback ends-----
Some deprecated features have been used. Set the environment
variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
program to get more information. Set it to "no" to suppress
this message.
MPI: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
MPI: aborting job
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