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

Hi Mary,

Some progress. I had set the HAS_NETCDF4 environment variable but I wonder if the presence of the build directory was causing the software not to build. This time, after removing the build directory, I get::

[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 "Nio.py", line 61, in ?
    from nio import *
ImportError: /usr/lib/python2.4/site-packages/PyNIO/nio.so: undefined symbol: _gfortran_concat_string
>>>

I've attached the output of the build to this email.
Thanks!
Pat

-----Original Message-----
From: Mary Haley [mailto:haley_at_ucar.edu]
Sent: Wednesday, September 09, 2009 12:08 PM
To: Allen, Pat
Cc: pyngl-talk_at_ucar.edu
Subject: RE: [pyngl-talk] Building PyNIO on RHEL 5.3

Pat,

It's possible there's just an ordering problem with the libraries.
Did you also do the following:

    setenv HAS_NETCDF4 1

I assume you don't want GRIB2 or HDF-EOS2 support.

To answer your final question below:

     Initially you asked for the full output from the build. Is this
     with "python -v setup.py install" or is there some other information
     that would be helpful.

Yes, this is the information that would be helpful, and could you
remove the "build" directory before doing this so I get the full build
output?

Thanks,

--Mary

On Wed, 9 Sep 2009, Allen, Pat wrote:

> Hi Mary,
>
> Thanks for the pointers. I've been rebuilding everything this morning to make sure that I have everything the way that the documentation expects it. I had previously installed each package in their own directory under /usr/local but wondered if that might have been part of the problem. But here's the rundown on what I've done:
>
> 1. Rebuilt glib:
> ./configure --prefix=/usr/local
> 2. Rebuilt szip:
> ./configure --prefix=/usr/local --disable-shared
> 3. Rebuilt HDF4:
> ./configure --prefix=/usr/local --with-zlib=/usr/local --with-szlib=/usr/local \
> --includedir=/usr/local/include/hdf --disable-netcdf
> 4. Rebuilt HDF5:
> ./configure --with-zlib=/usr/local --with-szlib=/usr/local --prefix=/usr/local \
> --disable-shared
> 5. Rebuilt NetCDF-4.0.1:
> ./configure --with-hdf5=/usr/local --with-zlib=/usr/local --with-szlib=/usr/local \
> --prefix=/usr/local --disable-f90 --enable-netcdf-4
> 6. Rebuilt PyNIO:
> python setup.py install
>
> When I try to import Nio, I still get:
>
> [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 "Nio.py", line 61, in ?
> from nio import *
> ImportError: /usr/lib/python2.4/site-packages/PyNIO/nio.so: undefined symbol: SZ_BufftoBuffCompress
>>>>
>
> Initially you asked for the full output from the build. Is this with "python -v setup.py install" or is there some other information that would be helpful.
>
> Thanks again for all the help!
> Pat
>
>
> -----Original Message-----
> From: Mary Haley [mailto:haley_at_ucar.edu]
> Sent: Wednesday, September 09, 2009 7:48 AM
> To: Allen, Pat
> Cc: pyngl-talk_at_ucar.edu
> Subject: RE: [pyngl-talk] Building PyNIO on RHEL 5.3
>
>>
>> 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:
>
> http://www.pyngl.ucar.edu/Download/build_pynio_from_src.shtml#NetCDF4
>
> 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.
>
> --Mary
>
>> Hopefully this will take care of it.
>> Pat
>>
>> -----Original Message-----
>> From: Mary Haley [mailto:haley_at_ucar.edu]
>> Sent: Wednesday, September 09, 2009 7:04 AM
>> To: Allen, Pat
>> Cc: pyngl-talk_at_ucar.edu
>> 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 setup.py install
>>> ====> Installing Nio to the "PyNIO" site packages directory.
>>> running install
>>> running build
>>> running build_py
>>> copying ./pynio_version.py -> build/lib.linux-i686-2.4/PyNIO
>>> running build_ext
>>> running install_lib
>>> copying build/lib.linux-i686-2.4/PyNIO/pynio_version.py -> /usr/lib/python2.4/site-packages/PyNIO
>>> byte-compiling /usr/lib/python2.4/site-packages/PyNIO/pynio_version.py 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 "Nio.py", line 61, in ?
>>> from nio import *
>>> ImportError: /usr/lib/python2.4/site-packages/PyNIO/nio.so: 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
>>> HAS_NETCDF4=1
>>> 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.
>>> THANKS!
>>> Pat
>>> _______________________________________________
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>>>
>>
>