RE: [pyngl-talk] Building PyNIO on RHEL 5.3

From: Allen, Pat <pat_at_nyahnyahspammersnyahnyah>
Date: Wed, 9 Sep 2009 07:27:13 -0700

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.

Hopefully this will take care of it.

-----Original Message-----
From: Mary Haley []
Sent: Wednesday, September 09, 2009 7:04 AM
To: Allen, Pat
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?



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
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Received on Wed Sep 09 2009 - 08:27:13 MDT

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