[FLASH-USERS] hdf5 library locally installed

[kkwak at physast.uga.edu]

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