I am new to hdf and am trying to get h5py
http://code.google.com/p/h5py/ installed. I think my problem is that I
don't know how to install hdf.
I downloaded the hdf5-1.8.5-macosx64-static.tar.gz
But reading through the README I don't really understand what I need
to do to install it.
This is the error I get when I try to install h5py
MacBookPro-new-2:h5py-read-only vmd$ python setup.py build --hdf5=/Library/hdf5
···
******************************************
Configure: Autodetecting HDF5 settings...
Custom HDF5 dir: /Library/hdf5
Custom API level: None
Undefined symbols:
"_inflateEnd", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
"_SZ_encoder_enabled", referenced from:
_H5Z_init_interface in libhdf5.a(H5Z.o)
"_compress2", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
"_inflateInit_", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
"_SZ_BufftoBuffDecompress", referenced from:
_H5Z_filter_szip in libhdf5.a(H5Zszip.o)
"_SZ_BufftoBuffCompress", referenced from:
_H5Z_filter_szip in libhdf5.a(H5Zszip.o)
"_inflate", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
Failed to compile HDF5 test program. Please check to make sure:
* You have a C compiler installed
* A development version of Python is installed (including header files)
* A development version of HDF5 is installed (including header files)
* If HDF5 is not in a default location, supply the argument --hdf5=<path>
******************************************
error: command 'cc' failed with exit status 1
Thanks
Vincent
Vincent,
The HDF5 library was built with szip and gzip compressions enabled. You will need to link with libsz.a and libz.a. You probably have libz.a on your system, but you will definitely need libsz.a. Both libraries were provided in a tar ball; please check the hdf5-1.8.5-macosx64-static/lib directory for them.
Also please check if h5py requires HDF5 shared libraries. If so, then you should build HDF5 from the source:
In the source directory run
./configure --prefix=<install_path>
make
make check
make install
make check-install
You will get C HDF5 shared libraries with gzip compression enabled. If you really need SZIP, please check information about szip (see http://www.hdfgroup.org/HDF5/release/obtain5.html - External Libraries Used by HDF5 section) and build it before configuring HDF5, then use
--with-szlib=<path to szip> configure flag.
Elena
···
On Jun 20, 2010, at 10:13 AM, Vincent Davis wrote:
I am new to hdf and am trying to get h5py
http://code.google.com/p/h5py/ installed. I think my problem is that I
don't know how to install hdf.
I downloaded the hdf5-1.8.5-macosx64-static.tar.gz
But reading through the README I don't really understand what I need
to do to install it.
This is the error I get when I try to install h5py
MacBookPro-new-2:h5py-read-only vmd$ python setup.py build --hdf5=/Library/hdf5
******************************************
Configure: Autodetecting HDF5 settings...
Custom HDF5 dir: /Library/hdf5
Custom API level: None
Undefined symbols:
"_inflateEnd", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
"_SZ_encoder_enabled", referenced from:
_H5Z_init_interface in libhdf5.a(H5Z.o)
"_compress2", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
"_inflateInit_", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
"_SZ_BufftoBuffDecompress", referenced from:
_H5Z_filter_szip in libhdf5.a(H5Zszip.o)
"_SZ_BufftoBuffCompress", referenced from:
_H5Z_filter_szip in libhdf5.a(H5Zszip.o)
"_inflate", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
Failed to compile HDF5 test program. Please check to make sure:
* You have a C compiler installed
* A development version of Python is installed (including header files)
* A development version of HDF5 is installed (including header files)
* If HDF5 is not in a default location, supply the argument --hdf5=<path>
******************************************
error: command 'cc' failed with exit status 1
Thanks
Vincent
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
I installed from source and everything seemed to work. I am still
having problems with h5py If you have any ideas on this great but I
will try to ask the h5py community
Thanks
Vincent
···
On Mon, Jun 21, 2010 at 8:18 AM, Elena Pourmal <epourmal@hdfgroup.org> wrote:
Vincent,
The HDF5 library was built with szip and gzip compressions enabled. You will need to link with libsz.a and libz.a. You probably have libz.a on your system, but you will definitely need libsz.a. Both libraries were provided in a tar ball; please check the hdf5-1.8.5-macosx64-static/lib directory for them.
Also please check if h5py requires HDF5 shared libraries. If so, then you should build HDF5 from the source:
In the source directory run
./configure --prefix=<install_path>
make
make check
make install
make check-install
You will get C HDF5 shared libraries with gzip compression enabled. If you really need SZIP, please check information about szip (see http://www.hdfgroup.org/HDF5/release/obtain5.html - External Libraries Used by HDF5 section) and build it before configuring HDF5, then use
--with-szlib=<path to szip> configure flag.
I installed h5py using macports: http://www.macports.org/. I don't know if
it will be a sufficiently up to date version for you and it may take a while
to build all the dependencies (including some you may already have
non-macports versions of). It was very easy to use though. One command,
wait a couple hours, and h5py was ready to go.
Cheers,
Ethan
···
On Mon, Jun 21, 2010 at 8:29 AM, Vincent Davis <vincent@vincentdavis.net>wrote:
On Mon, Jun 21, 2010 at 8:18 AM, Elena Pourmal <epourmal@hdfgroup.org> > wrote:
> Vincent,
>
> The HDF5 library was built with szip and gzip compressions enabled. You
will need to link with libsz.a and libz.a. You probably have libz.a on your
system, but you will definitely need libsz.a. Both libraries were provided
in a tar ball; please check the hdf5-1.8.5-macosx64-static/lib directory for
them.
>
> Also please check if h5py requires HDF5 shared libraries. If so, then you
should build HDF5 from the source:
> In the source directory run
>
> ./configure --prefix=<install_path>
> make
> make check
> make install
> make check-install
>
> You will get C HDF5 shared libraries with gzip compression enabled. If
you really need SZIP, please check information about szip (see
http://www.hdfgroup.org/HDF5/release/obtain5.html - External Libraries
Used by HDF5 section) and build it before configuring HDF5, then use
> --with-szlib=<path to szip> configure flag.
I installed from source and everything seemed to work. I am still
having problems with h5py If you have any ideas on this great but I
will try to ask the h5py community
Thanks
Vincent
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
