[FLASH-USERS] hdf5 library locally installed

[chris]

Hi Kyujin,

It does not matter where you install HDF5.  I suspect that you are
trying to link 32-bit FLASH object files against a 64-bit HDF5.  You
can check by running

 > file /home/kkwak/hdf5_serial/lib/libhdf5.so
and then
 > file Driver_evolveFlash.o
(where Driver_evolveFlash.o is in your FLASH object directory)


If they are different then you should build the HDF5 library with your
commercial compiler, e.g. for Intel C compiler

(serial)
 > CC=icc ./configure --prefix=/home/kkwak/hdf5/intel/serial

(parallel)
 > CC=mpicc ./configure --enable-parallel 
--prefix=/home/kkwak/hdf5/intel/parallel

where mpicc is in your PATH and is the MPI wrapper script for your
commercial compiler.

or if you have an exotic commercial compiler that fails to build HDF5
then you can try a 32-bit gcc build (no guarantees that this will
work) using:

 > CFLAGS='-O2 -m32' ./configure --prefix=/home/kkwak/hdf5/gcc-32/serial

Chris



On 04/04/2012 09:37 PM, kkwak at physast.uga.edu wrote:
> Hi all,
>
> I am trying to setup FLASH4_beta in the linux cluster which does not have
> hdf5 yet. The MPI part was compiled and run well, but I am struggling with
> hdf5. As a start, I installed both hdf5_1.8 and hdf5_1.6 locally, i.e., in
> my home directory. The source codes were compiled fine, but in the process
> of linking, I've got the following error message. I tried to build hdf5
> with various options either with serial or parallel and so on, but nothing
> worked. Is this because I installed hdf5 locally? If I installed hdf5 in
> /usr/local, could this be resolved? Some information is as follows.
>
> Thank you for your help in advance.
>
> Kyujin
>
>
> FLASH error link message
>
> ...
> /usr/bin/ld: skipping incompatible /home/kkwak/hdf5_serial/lib/libhdf5.so
> when searching for -lhdf5
> /usr/bin/ld: skipping incompatible /home/kkwak/hdf5_serial/lib/libhdf5.a
> when searching for -lhdf5
> /usr/bin/ld: cannot find -lhdf5
> collect2: ld returned 1 exit status
> make: *** [flash4] Error 1
>
> Info from libhdf5.settings (for hdf5_1.6)
>
> SUMMARY OF THE HDF5 CONFIGURATION
> =================================
>
> HDF5 Version:           1.6.10
> Configure mode:         production
> Host system:            x86_64-unknown-linux-gnu
> Byte sex:               little-endian
> Libraries:              static, shared
> Parallel support:       no
> Installation point:     /home/kkwak/hdf5_serial
> Compiler:               /usr/bin/gcc (gcc-4.1.2)
> Compiler switches:       -std=c99 -Wno-long-long -O -fomit-frame-pointer
> -finlin
> e-functions -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE
> -D_LARGEFILE64_SOURCE -D
> _FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE
> Extra libraries:         -lz -lm
> Archiver:               ar
> Ranlib:                 ranlib
> Debugged Packages:
> API Tracing:            no
>
> Configure Summary
> Compiling Options:
>                 Compilation Mode:  Production
>                       C Compiler:  gcc
>                           CFLAGS:   -std=c99 -Wno-long-long -O
> -fomit-frame-pointer -finline-functions
>                         CPPFLAGS:  -UH5_DEBUG_API -DNDEBUG
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
> -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE
> -D_BSD_SOURCE
>                          LDFLAGS:
>                       Debug Mode:  None
>                 Shared Libraries:  Yes
>                 Static Libraries:  Yes
>    Statically Linked Executables:  No
>                          Tracing:  No
>     Optimization Instrumentation:  No
>
> Languages:
> ----------
>                              C++:  No
>                          Fortran:  No
>
> Features:
> ---------
>                          dmalloc:  No
>           Function Stack Tracing:  Disabled
>                             GPFS:  No
>        Strict File Format Checks:  Disabled
>          HDF5 v1.4 Compatibility:  No
>           I/O filters (external):  deflate
>           I/O filters (internal):  shuffle,fletcher32
>   Linux Large File Support (LFS):  Enabled
>                              MPE:  No
>                    Parallel HDF5:  No
>                     Threadsafety:  Disabled
>               High Level library:  Enabled
>