Upstream bugs are rough. If you decide to report it to the libhdf5 developers,
note that even 1.8.13 has a new bug:
https://github.com/timholy/HDF5.jl/issues/172
Seems to be getting worse with each release.
--Tim
On Wednesday, November 19, 2014 10:35:47 AM Lanfeng Pan wrote:
> Wow, 1.8.13 works! I have been fighting with it for a whole night.
> Thanks!
>
> On Wednesday, November 19, 2014 12:15:16 PM UTC-6, Tim Holy wrote:
> > For the binary, which library version are you using? Can you test
> > something
> > different from 1.8.14? (I don't have any particular reason to suspect
> > 1.8.14 is
> > bad, I am just wondering...)
> >
> > --Tim
> >
> > On Wednesday, November 19, 2014 10:08:41 AM Lanfeng Pan wrote:
> > > Hi guys,
> > >
> > > I installed hdf5 manually on a linux server which I have no root
> >
> > privilege.
> >
> > > Pkg.add("HDF5") is fine but `using HDF5` will give me the following
> >
> > errors:
> > > julia> Pkg.add("HDF5")
> > > INFO: Installing BinDeps v0.3.6
> > > INFO: Installing HDF5 v0.4.6
> > > INFO: Installing SHA v0.0.3
> > > INFO: Installing URIParser v0.0.3
> > > INFO: Building HDF5
> > > INFO: Package database updated
> > >
> > > julia> using HDF5
> > >
> > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
> > > #000: H5P.c line 299 in H5Pcreate(): not a property list class
> > >
> > > major: Invalid arguments to routine
> > > minor: Inappropriate type
> > >
> > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
> > > #000: H5Pstrcpl.c line 159 in H5Pset_char_encoding(): can't find
> >
> > object
> >
> > > for ID
> > >
> > > major: Object atom
> > > minor: Unable to find atom information (already closed?)
> > >
> > > #001: H5Pint.c line 3381 in H5P_object_verify(): property list is not
> >
> > a
> >
> > > member of the class
> > >
> > > major: Property lists
> > > minor: Unable to register new atom
> > >
> > > #002: H5Pint.c line 3331 in H5P_isa_class(): not a property list
> > >
> > > major: Invalid arguments to routine
> > > minor: Inappropriate type
> > >
> > > ERROR: Error setting char encoding
> > >
> > > in h5p_set_char_encoding at
> >
> > /home/pan/.julia/v0.3/HDF5/src/plain.jl:1848
> >
> > > in include at ./boot.jl:245
> > > in include_from_node1 at ./loading.jl:128
> > > in include at ./boot.jl:245
> > > in include_from_node1 at ./loading.jl:128
> > > in reload_path at loading.jl:152
> > > in _require at loading.jl:67
> > > in require at loading.jl:51
> > >
> > > while loading /home/pan/.julia/v0.3/HDF5/src/plain.jl, in expression
> > > starting on line 2102
> > > while loading /home/pan/.julia/v0.3/HDF5/src/HDF5.jl, in expression
> > > starting on line 1
> > >
> > > julia> dlopen("libhdf5")
> > > Ptr{Void} @0x00000000057e89b0
> > >
> > >
> > >
> > >
> > > I also tried to use the binary hdf5 files, but the error persists. The
> > > system information:
> > >
> > > $ cat /etc/redhat-release
> > > CentOS release 6.6 (Final)
> > >
> > > $ gcc --version
> > > gcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15)
> > >
> > > $which gcc
> > > ~/gcc-4.8.2/bin/gcc
> > >
> > > $ julia --version
> > > julia version 0.3.2
