Re: Building PyNIO on RHEL 5.3

From: Mary Haley <haley_at_nyahnyahspammersnyahnyah>
Date: Wed, 9 Sep 2009 08:47:46 -0600 (MDT)

> On Wed, 9 Sep 2009, Allen, Pat wrote:
> Ahhh, perhaps I see the problem. I already had the NetCDF-4.0
> libraries on the system so I ignored that section of the INSTALL
> document. Your email mentioned the HDF5 libraries being required so I
> went back and looked and noticed that those are required if you have
> the NetCDF-4 libraries. So I'll build that and give it a try. But
> before I do, I have a question regarding the HDF libraries. Will this
> overwrite the HDF4.2 installation or do I need to be careful to
> install them in separate places? The install document implies that
> they both have a /usr/local prefix but the version 4 instructions have
> special notes regarding the --includedir option.

This is a good question, and you should be safe as is.

The HDF5 build will not overwrite the HDF4 build. You still need
to do the special "--includedir" part for the HDF4 build, but
the HDF5 build should be done just as it is described at:

The HDF5 libraries all have "hdf5" as part of the name, and the
include files are all prefixed with "H5"; hence no HDF4 or NetCDF
files will be overwritten.


> Hopefully this will take care of it.
> Pat
> -----Original Message-----
> From: Mary Haley []
> Sent: Wednesday, September 09, 2009 7:04 AM
> To: Allen, Pat
> Cc:
> Subject: Re: Building PyNIO on RHEL 5.3
> Hi Pat,
> Since you set HAS_NETCDF4 to 1, this implies that you want classic
> NetCDF4 support. To build this into PyNIO requires the HDF5 libraries,
> which in turn requires the szip library. So even though you
> build HDF4 with compression off, you still need szip for the HDF5
> libraries (it's not optional).
> The PyNIO build should be including "-lsz" on the compile line
> already, so I'm surprised to see this undefined reference.
> Can you set the full output from the PyNIO build?
> Thanks,
> --Mary
> On Wed, 9 Sep 2009, Allen, Pat wrote:
>> Good morning! I've built PyNIO on RHEL 5.3:
>> [root_at_elvis PyNIO-1.3.0b1]# python install
>> ====> Installing Nio to the "PyNIO" site packages directory.
>> running install
>> running build
>> running build_py
>> copying ./ -> build/lib.linux-i686-2.4/PyNIO
>> running build_ext
>> running install_lib
>> copying build/lib.linux-i686-2.4/PyNIO/ -> /usr/lib/python2.4/site-packages/PyNIO
>> byte-compiling /usr/lib/python2.4/site-packages/PyNIO/ to pynio_version.pyc
>> running install_data
>> Unfortunately, I'm getting the following error when trying to import Nio:
>> [root_at_elvis PyNIO-1.3.0b1]# python
>> Python 2.4.3 (#1, Jul 16 2009, 06:21:14)
>> [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> import Nio
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in ?
>> File "", line 61, in ?
>> from nio import *
>> ImportError: /usr/lib/python2.4/site-packages/PyNIO/ undefined symbol: SZ_BufftoBuffCompress
>> Here's what my environment variables look like:
>> F2CLIBS=g2c
>> F2CLIBS_PREFIX=/usr/lib/gcc/i386-redhat-linux/3.4.6
>> HDF_PREFIX=/usr/local/HDF
>> NCARG_ROOT=/usr/local/ncl
>> NETCDF4_PREFIX=/usr/local
>> In googling "undefined symbol: SZ_BufftoBuffCompress", I've figured out that it's the szip libraries. The most relevant hit that I found indicated that it was due to building the HDF libraries with the --with-szlib option. I rebuilt the libraries without szlib support and reinstalled them and got the same error. I'm at a loss. The only thing that I didn't build from scratch was NCL. Does that rely on the szip libraries? Does it expect to find them in a standard location?
>> Any help is GREATLY appreciated.
>> Pat
>> _______________________________________________
>> pyngl-talk mailing list
>> List instructions, subscriber options, unsubscribe:
pyngl-talk mailing list
List instructions, subscriber options, unsubscribe:
Received on Wed Sep 09 2009 - 08:47:46 MDT

This archive was generated by hypermail 2.2.0 : Thu Sep 10 2009 - 15:06:39 MDT