I'm almost sure your instalation method is the problem. Are you using meep or meep-mpi? Did you install all packages from pre-compiled form? Or did you use pre-compiled some times and compile on hand other times?
2012/1/10 <[email protected]> > Hi Kajari: > > If you install a precompiled binary, you cannot link against this binary. > I think there is an issue related with your installation. A way to see your > current installation could be: > > 1. Please, can you post the output of?: > > apt-cache depends meep libmeep6 > > 2. and the output of?: > > dpkg -l \*meep\* \*hdf5\* > > This gives the details of your installation. There are serveral versions > of the hdf5 libraries as well as meep (parallel, serial, etc.) and this can > be a source of error... > > Regards, > > Rafael Gomez Alcala > > On 23:56 Tue 10 Jan , kajari chattopadhyay wrote: > > Hi, > > > > Thank you; but I had already installed HDF5. I have all those packages. > > Still I am getting the error. > > The HDF5 configuration is as mentioned below: > > > > root@kajari:/usr/lib# h5cc -showconfig > > SUMMARY OF THE HDF5 CONFIGURATION > > ================================= > > > > General Information: > > ------------------- > > HDF5 Version: 1.8.4-patch1 > > Configured on: Wed Feb 16 10:22:42 UTC 2011 > > Configured by: root@rothera > > Configure mode: production > > Host system: i686-pc-linux-gnu > > Uname information: Linux rothera 2.6.24-27-server #1 SMP Fri > Mar > > 12 01:45:06 UTC 2010 i686 i686 i386 GNU/Linux > > Byte sex: little-endian > > Libraries: > > Installation point: /usr > > > > Compiling Options: > > ------------------ > > Compilation Mode: production > > C Compiler: /usr/bin/gcc (gcc-4.5.2) > > CFLAGS: -O0 > > H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef > > -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align > > -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes > > -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls > > -Wnested-externs -Winline -Wno-long-long -Wfloat-equal > > -Wmissing-format-attribute -Wmissing-noreturn -Wpacked > > -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels > > -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch > > -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs > > -Wswitch-default -Wswitch-enum -Wunused-macros > -Wunsafe-loop-optimizations > > -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla > > -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O > > -fomit-frame-pointer -finline-functions > > AM_CFLAGS: > > CPPFLAGS: > > H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG > -UH5_DEBUG_API > > AM_CPPFLAGS: -D_LARGEFILE_SOURCE > -D_LARGEFILE64_SOURCE > > -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE > > Shared Libraries: yes > > Static Libraries: yes > > Statically Linked Executables: no > > LDFLAGS: -Wl,-Bsymbolic-functions > > AM_LDFLAGS: > > Extra libraries: -lpthread -lz -lm > > Archiver: ar > > Ranlib: ranlib > > Debugged Packages: > > API Tracing: no > > > > Languages: > > ---------- > > Fortran: yes > > Fortran Compiler: gfortran > > Fortran Flags: > > H5 Fortran Flags: > > AM Fortran Flags: -O0 > > C++: yes > > C++ Compiler: g++ > > C++ Flags: -O0 > > H5 C++ Flags: > > AM C++ Flags: > > > > Features: > > --------- > > Parallel HDF5: no > > High Level library: yes > > Threadsafety: yes > > Default API Mapping: v16 > > With Deprecated Public Symbols: yes > > I/O filters (external): deflate(zlib) > > I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset > > MPE: no > > Direct VFD: no > > dmalloc: no > > Clear file buffers before write: yes > > Using memory checker: no > > Function Stack Tracing: no > > GPFS: no > > Strict File Format Checks: no > > Optimization Instrumentation: no > > Linux Large File Support (LFS): yes > > > > Is it correct? > > How to link meep and HDF5? > > > > Thanking you > > Kajari > > > > On Tue, Jan 10, 2012 at 6:01 PM, Cícero Julião <[email protected] > >wrote: > > > > > Meep uses other softwares to do some things. You must to have them, > withou > > > meep don't work fine. So, like Rafael Gomez, "Have you compiled meep by > > > yourself or are you using a precompiled package from a Linux distro?" > If > > > you are using a Debian Like distro, run comand 'apt-cache depends > meep'. > > > This comand will show the packages meep depends. Install all the > packages. > > > > > > > > > > > > > > > 2012/1/10 <[email protected]> > > > > > >> Hi Kajari: > > >> > > >> Seems to me that you are using a meep version without HDF support. > > >> Have you compiled meep by yourself or are you using a precompiled > > >> package from a Linux distro? > > >> > > >> Kind regards, > > >> > > >> Rafael Gomez Alcala > > >> > > >> > > >> > > >> > > >> > > >> On 04:39 Tue 10 Jan , kajari wrote: > > >> > Hi, > > >> > > > >> > I start using meep for my final year project.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 | "Fields in > a > > >> waveguide" > > >> > 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 8 x 0 with resolution 10 > > >> > block, center = (0,0,0) > > >> > size (1e+20,1,1e+20) > > >> > axes (1,0,0), (0,1,0), (0,0,1) > > >> > dielectric constant epsilon diagonal = (12,12,12) > > >> > time for set_epsilon = 0.106434 s > > >> > ----------- > > >> > creating output file "./foo-eps-000000.00.h5"... > > >> > meep: not compiled with HDF5, required for HDF5 output > > >> > > > >> > 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. > > >> > > > >> > --------------------------------------------------------------------------------- > > >> > > > >> > I don't find any solution of this problem.Any help or suggestion is > > >> expected, > > >> > and I'll be grateful for it. > > >> > > > >> > Best regards > > >> > Kajari > > >> > > > >> > > > >> > _______________________________________________ > > >> > meep-discuss mailing list > > >> > [email protected] > > >> > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > > >> > > >> _______________________________________________ > > >> meep-discuss mailing list > > >> [email protected] > > >> http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > > >> > > > > > > > > > > > > -- > > > > > > Cícero Julião da Silva Junior > > > ____________________________________ > > > Institute of Physics - UFAL > > > www.ufal.br > > > > > > > > _______________________________________________ > meep-discuss mailing list > [email protected] > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > -- Cícero Julião da Silva Junior ____________________________________ Institute of Physics - UFAL www.ufal.br
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