I have also encountered this problem. My ctl file, which worked well under parallel version of meep 0.10, now came up with similar error when I updated meep to the 0.10.1 version and deleted the command (set! eps-averaging? false) in the ctl file. Anyone have some comments on this? Thank you!
Regards, Zhanghua 2007/11/23, [EMAIL PROTECTED] < [EMAIL PROTECTED]>: > > Send meep-discuss mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of meep-discuss digest..." > > > Today's Topics: > > 1. meep subpixel-averaging + MPI bug? (Ulrich Dobramysl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Nov 2007 14:49:00 +0100 > From: Ulrich Dobramysl <[EMAIL PROTECTED]> > Subject: [Meep-discuss] meep subpixel-averaging + MPI bug? > To: [email protected] > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-15 > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.7 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHRYjLvlTvENIKkvMRAq6BAJ9W8qtjWND9+J233HTudRW/OXWd3gCfYr/9 > Ga60+/AZj1xijjT9Qrx7Zpo= > =PHLz > -----END PGP SIGNATURE----- > > > > ------------------------------ > > _______________________________________________ > meep-discuss mailing list > [email protected] > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > > End of meep-discuss Digest, Vol 21, Issue 12 > ******************************************** >
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