Dear Konrad, The program crashes on hdf5 because the refl-flux file you want to load does not exist. This makes sense because it is the reference from the straight waveguide. This file is created by running your program first with: unix% meep no-bend?=true bend-flux.ctl this calculation should be succesful and unix% meep bend-flux.ctl should run without any problems. At least it ran on my ubuntu box.
Martijn ------------------------------------------------------ ir. Martijn Schaafsma Surface Photonics Group FOM-Institute AMOLF c/o Philips Research Laboratories Eindhoven Room WAG 1.2.44 High Tech Campus 4 5656 AE EINDHOVEN The Netherlands Tel. : +31 - (0)40 27 49369 email : [email protected] [email protected] ------------------------------------------------------ ________________________________ Van: [email protected] [[email protected]] namens Konrad Michalczyk [[email protected]] Verzonden: dinsdag 19 april 2011 13:02 Aan: meep-discuss Onderwerp: [Meep-discuss] Meep on Ubuntu problem (part.2) Hi I've seen simmilar subject before, but it seems to me that no one had any idea how to solve this problem. Or I don's see it. Prrevious topic is here: http://www.mail-archive.com/[email protected]/msg03877.html So, what's going on... I'm trying to use meep on my PC under Ubuntu. There was no problem with installing it on my machine, but when I'm trying to execute simple ctl file (that one from the meep tutorial http://ab-initio.mit.edu/wiki/index.php/Meep_Tutorial | "Transmission spectrum around a waveguide bend" section). When I'm trying to run meep using this geometry I recive this: _______________________________________________________________________________ Initializing structure... Working in 2D dimensions. Computational cell is 16 x 32 x 0 with resolution 10 block, center = (-2,-11.5,0) size (12,1,1e+20) axes (1,0,0), (0,1,0), (0,0,1) dielectric constant epsilon diagonal = (12,12,12) block, center = (3.5,2,0) size (1,28,1e+20) axes (1,0,0), (0,1,0), (0,0,1) dielectric constant epsilon diagonal = (12,12,12) time for set_epsilon = 0.84895 s ----------- HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 3078211280: #000: ../../../src/H5F.c line 1514 in H5Fopen(): unable to open file major: File accessability minor: Unable to open file #001: ../../../src/H5F.c line 1218 in H5F_open(): unable to open file major: File accessability minor: Unable to open file #002: ../../../src/H5FD.c line 1079 in H5FD_open(): open failed major: Virtual File Layer minor: Unable to initialize object #003: ../../../src/H5FDsec2.c line 365 in H5FD_sec2_open(): unable to open file major: File accessability minor: Unable to open file #004: ../../../src/H5FDsec2.c line 365 in H5FD_sec2_open(): No such file or directory major: Internal error (too specific to document in detail) minor: System error message meep: error on line 252 of ../../../src/h5file.cpp: error opening HDF5 input file 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. _________________________________________________________________________________ At first i thought that there is a problem with shared libraries. But when I execute ldd command I recive this: user@cops:/usr/bin$ ldd ./meep linux-gate.so.1 => (0x009e1000) libmeep.so.6 => /usr/lib/libmeep.so.6 (0x00452000) libctl.so.3 => /usr/lib/libctl.so.3 (0x00828000) libguile.so.17 => /usr/lib/libguile.so.17 (0x00d3f000) libgmp.so.3 => /usr/lib/libgmp.so.3 (0x00f57000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x005dd000) libltdl.so.7 => /usr/lib/libltdl.so.7 (0x00110000) libdl.so.2 => /lib/libdl.so.2 (0x008a9000) libhdf5.so.6 => /usr/lib/libhdf5.so.6 (0x00fb8000) libpthread.so.0 => /lib/libpthread.so.0 (0x00325000) libz.so.1 => /lib/libz.so.1 (0x00119000) libgsl.so.0 => /usr/lib/libgsl.so.0 (0x0012e000) libharminv.so.2 => /usr/lib/libharminv.so.2 (0x0054f000) liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x055a7000) libcblas.so.3gf => /usr/lib/libcblas.so.3gf (0x0033f000) libf77blas.so.3gf => /usr/lib/libf77blas.so.3gf (0x00c1b000) libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x13f06000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00a21000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x007af000) libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00add000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0035f000) libm.so.6 => /lib/libm.so.6 (0x00508000) libc.so.6 => /lib/libc.so.6 (0x180a6000) /lib/ld-linux.so.2 (0x006e9000) libblas.so.3gf => /usr/lib/libblas.so.3gf (0x02273000) For me this looks like shell knows where to find demanded libraries. So after that I've tried to run few simmulations, starting only with geometry of "my" structure, and with each step adding new stuff (sorces, fluxes etc.) After that I've noticed that one line causes previous error. This line is: "if (not no-bend?) (load-minus-flux "refl-flux" refl))" I don't know if all of this it's helpful but... Ok... as a summary I'll say that, at the moment i don't have absolutely no idea what causes this problem. Any help or suggestion is expected, and I'll be grateful for it. Best reagards KOnrad ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. 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