Re: PyNGL/PyNIO installation problems

From: Schwedler, Benjamin <bschwedl_at_nyahnyahspammersnyahnyah>
Date: Wed Sep 15 2010 - 07:17:34 MDT

Mary and Dave,

Thanks for your suggestions.
We have been trying to build this from source. We have been able to get
PyNgl to build properly. The problem seems to be that both Python 2.5.2
and 2.6.5 were build with gcc-4.4.0. We have now built Python 2.7 with
gcc-4.1.2, and

We are still having trouble with getting PyNio to compile correctly with
this version of python. I know that there seem to be a couple library
problems related to zlib, HDF, and NetCDF, but I don't know exactly what
versions of these are being used currently since the staff is trying to
get the libraries to link properly. I do know that when we tried to
build this on Python 2.5/2.6 the HDF4 library we were trying to use was
HDF4.2R4. Previously, I think the build for 2.5/2.6 was also linked to
the NetCDF header file included with CDAT-5.2 from LLNL because this
resolved some missing references like NC_CLASSIC_MODEL.

As mentioned previously, here is the system information
$ uname -a
Linux 2.6.18-194.3.1.el5rcac1 #1 SMP Sun May
16 16:03:15 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux

I will try to keep you updated with the progress, and any additional
suggestions are welcome.



On 09/09/2010 07:30 AM, Mary Haley wrote:
> Hi Ben,
> To follow-up on Dave's comments about PyNGL: if you are building from source code, you can also help the PyNGL installation find libgfortran.{a,so} by setting the F2CLIBS_PREFIX environment variable.
> See:
> for more information.
> If you are installing from a precompiled binary, then Dave's suggestion should help if you already have libgfortran installed.
> You might be able to find it with the "locate" command:
> locate libgfortran
> If you are still having problems, then please email us with more information, like whether you're building from source or using a precompiled binary, and what kind of system you have (uname -a).
> --Mary
> On Sep 8, 2010, at 3:37 PM, David Brown wrote:
>> I am not sure what is going on here, but it looks like there are
>> different problems for PyNIO and PyNGL. Do you know if PyNIO was build
>> from source or installed as a binary? This PyNIO problem looks like it
>> related to the HDF4 library. Normally if the HDF4 library is build
>> according to the instructions on
>> it will be compiled statically. Your version seems to be linked with
>> a shared version of the HDF library (called It is
>> possible that you could get this to work by setting LD_LIBRARY_PATH to
>> the location of But we always recommend that libraries
>> be linked statically as much as possible.
>> PyNGL does not seem to be able to find the gfortran library. This
>> might also be fixed by setting LD_LIBRARY_PATH.
>> Just as a general point, just because the build and install complete
>> without erros, that does not necessarily indicate a successful
>> install. Because the shared object is loaded dynamically, it is
>> impossible to tell if the build was successful until you can import
>> the module and use it. You will only have a pretty good idea the
>> install was successful if you can run the test scripts.
>> -dave
>> On Sep 3, 2010, at 12:41 PM, Schwedler, Benjamin wrote:
>>> A sysadmin for a cluster that I am working on has been trying to
>>> install
>>> PyNGL-1.3.1 and PyNIO-1.4.0. He was able to successfully build the
>>> packages, but upon importing Nio and Ngl, I receive the following
>>> errors:
>>> Python 2.5.2 (r252:60911, Apr 8 2010, 10:22:54)
>>> [GCC 4.4.0] on linux2
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> import numpy
>>>>>> numpy.__version__
>>> ''
>>>>>> import Nio
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File
>>> "/apps/coates/Python-2.5.2/lib/python2.5/site-packages/PyNIO/",
>>> line 63, in <module>
>>> from nio import *
>>> ImportError: cannot open shared object file: No such
>>> file
>>> or directory
>>>>>> import Ngl
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File
>>> "/apps/coates/Python-2.5.2/lib/python2.5/site-packages/PyNGL/",
>>> line 38, in <module>
>>> import fplib
>>> ImportError:
>>> /apps/coates/Python-2.5.2/lib/python2.5/site-packages/PyNGL/
>>> undefined symbol: _gfortran_pow_r8_i4
>>> Builds were attempted with Python-2.5.2 with numpy-1.5.0dev and
>>> Python-2.6.5 with numpy-2.0.0dev
>>> $ uname -a
>>> Linux 2.6.18-194.3.1.el5rcac1 #1 SMP Sun
>>> May
>>> 16 16:03:15 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
>>> Are there any suggestions for how we may able to get around this?
>>> Since
>>> I didn't perform the installation myself, I don't know the exact
>>> versions of all libraries that were used, but I should be able to find
>>> that out.
>>> Cheers,
>>> Ben
>>> --
>>> Benjamin R. J. Schwedler
>>> _______________________________________________
>>> pyngl-talk mailing list
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Benjamin R. J. Schwedler
Received on Wed Sep 15 07:17:53 2010

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