Re: Problem in 3.6.2 on SL6 with hdf5

[Michael Martins]

Am 26.07.2012 14:47, schrieb Mike Miller:
> On Thu, Jul 26, 2012 at 6:37 AM, Michael Martins wrote:
> > Dear all
> >
> > I have a problem linking 3.6.2 on Scientific Linux 6 (SLD6, 64 bit) with the
> > hdf5 library. configure finds all libaries including hdf5 and compling is
> > now problem.
> How did you install hdf5 on your system? EPEL repository, another
> repo, or built from source? What is the output of "rpm -qa \*hdf5\*"?
> Also can you list the output of "grep -i hdf5 config.status" in your
> Octave source tree?

Here is the output from the commands above. Everything looks ok for me.

grep -i hdf5 config.status
"_H=1 -DHAVE_PCRE_COMPILE=1 -DHAVE_ZLIB_H=1 -DHAVE_Z=1 -DHAVE_HDF5_H=1 
-DHAVE_HDF5_18=1 -DHAVE_HDF5=1 -DHAVE_GL_GL_H=1 -DHAVE_GL_GLU_H=1 
-DHAVE_OPENG"\
S["TEXINFO_HDF5"]="@set HAVE_HDF5"
S["HDF5_LIBS"]="-lhdf5"
S["HDF5_LDFLAGS"]=""
S["HDF5_CPPFLAGS"]=""
D["HAVE_HDF5_H"]=" 1"
D["HAVE_HDF5_18"]=" 1"
D["HAVE_HDF5"]=" 1"

rpm -qa \*hdf5\*
hdf5-mpich2-1.8.5.patch1-7.el6.x86_64
hdf5-1.8.7-1.el6.rf.x86_64
hdf5-devel-1.8.7-1.el6.rf.x86_64

The libaries are taken from the EPEL repo as you did. Which version of 
hdf5 do you have on your CentOS

> I have a CentOS 6 64-bit with hdf5 installed from the EPEL repo and no
> problems linking Octave with their hdf5 build.
>
> > However in the linking process I am getting the following
> > errors
> >
> > ./.libs/liboctinterp.so: undefined reference to `H5Eset_auto2'
> > ./.libs/liboctinterp.so: undefined reference to `H5Gcreate2'
> > ./.libs/liboctinterp.so: undefined reference to `H5Dopen2'
> > ./.libs/liboctinterp.so: undefined reference to `H5Gopen2'
> > ./.libs/liboctinterp.so: undefined reference to `H5Dcreate2'
> > ./.libs/liboctinterp.so: undefined reference to `H5Eget_auto2'
> > ./.libs/liboctinterp.so: undefined reference to `H5Acreate2'
> >
> > This is somehow strange, because H5Eset_auto2 is not found in any part of
> > the octave sources. Only H5Eset_auto exists, e.g. in
> > src/ls-hdf5.cc:  H5Eset_auto (H5E_DEFAULT, 0, 0);
> These symbols show up for me as well, this is normal behavior for the library.

It seems to be, that they are not showing up in SL6, which is strange. 
Is there a lib missing ?

Thank you for your help!

Regards
Michael