On Apr 25, 2008, at 12:06 PM, Ian Buss wrote:
>
> I am having a problem configuring h5utils on Mac OS X 10.5. I have
> installed meep-mpi with no problems with hdf5 support, and have tested
> the meep installation with the examples given, but on configuring
> h5utils it can't seem to find the hdf5 libraries. I have pasted the
> configure echo and the config.log files to http://pastebin.com/
> m6496e8ec and http://pastebin.com/m43a35b19 to save space here. There
> are lots of references to h5 there but not sure what it is telling
> me. Thanks for any help.
The key errors are:
configure:4213: checking for H5Fopen in -lhdf5
configure:4243: gcc -o conftest -g -O2 conftest.c -lhdf5 -lz -lm >&5
Undefined symbols:
"_ompi_mpi_info_null", referenced from:
_ompi_mpi_info_null$non_lazy_ptr in libhdf5.a(H5FDmpi.o)
_ompi_mpi_info_null$non_lazy_ptr in libhdf5.a(H5FDmpio.o)
"_ompi_mpi_comm_world", referenced from:
etcetera.
The problem is that you compiled HDF5 with MPI, but you are compiling
h5utils with gcc and is not linking the MPI libraries. (You need to
link them, even though h5utils won't actually call MPI.) The solution
is to compile h5utils with the MPI compiler:
./configure CC=mpicc
(I wish that the HDF5 people had figured out a way to put all the MPI
stuff into a separate small library, so that the serial and MPI
libraries could coexist more peacefully on the same system, but
unfortunately this isn't the case.)
Steven
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