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
