Re: trouble installing PyNIO/PyNGL with binaries and source build with Intel

Hi Andre,
Have you tried to get a working installation by using pre-built NCL binaries? Furthermore, have you tried to install PyNGL and PyNIO with a 32 bit python? I have successfully installed PyNGL distributions on various system in both 64 and 32 bit modes, but on all these systems PyNGL and NCL are pre-built binaries.

Cheers,
Deepak

PhD Candidate
Department of Physics, University of Toronto
60 St. George Street
Toronto, ON, M5S1A7, Canada
Office: MP 619A
dchandan@atmosp.physics.utoronto.ca

On 2012-01-09, at 11:50 PM, Andre R. Erler wrote:

> Hi,
> I'm new to PyNGL and the whole NCAR software collection.
> I'm trying to install PyNIO and PyNGL; I tried both, the binaries and to build
> from source. Both were unsuccessful.
> I have already installed NCL and NCAR Graphics successfully from source, using
> the Intel Compiler Suite (after some tweaking).
> I'm installing all this on a (k)ubuntu 11.04 64bit system.
>
> 1) Binaries distributions: I've installed them to /usr/local:
>
> $ ls /usr/local/lib/python2.7/site-packages/
> Ngl.pth Nio.pth PyNGL PyNGL-1.4.0-py2.7.egg-info PyNIO PyNIO-1.4.1-
> py2.7.egg-info
>
> Apparently the *.pth files have no effect at all. The packages can be imported
> by path names (eg. PyNGL), but seem to be empty. Here is an example with
> resulting error:
>
> $ epd
> Enthought Python Distribution -- www.enthought.com
> Version: 7.1-1 (64-bit)
>
> Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul 3 2011, 15:17:51)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
> Type "packages", "demo" or "enthought" for more information.
>>>> import Ngl
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ImportError: No module named Ngl
>>>> import PyNGL
>>>> x = [10., 20.00, 30., 40.0, 50.000, 60.00, 70., 80.00, 90.000]
>>>> y = [ 0., 0.71, 1., 0.7, 0.002, -0.71, -1., -0.71, -0.003]
>>>> wks_type = "ps"
>>>> wks = PyNGL.open_wks(wks_type,"ngl01p") # Open a workstation.
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> AttributeError: 'module' object has no attribute 'open_wks'
>>>>
>
> I'm using the Enthought Python distribution here, but the same thing happens
> with the regular Python distro.
> The environment variable PYNGL_NCARG is set to /usr/local/lib/python2.7/site-
> packages/PyNGL/ncarg/.
>
> The binary version of PyNIO has the same problem.
>
> 2) Now source builds: I'm using the Intel compilers and the Enthought Python
> Distro, again. PyNIO compiles alright, but when I try to import the package, I
> get this error:
>
>>>> import nio
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ImportError: /opt/EPD/epd-7.1-1-rh5-x86_64/lib/python2.7/site-
> packages/PyNIO/nio.so: undefined symbol: for_cpystr
>>>>
>
> The symbol 'for_cpystr' is actually defined in a Fortran library related to
> the Intel compiler suite:
>
> $ nm /opt/intel/composerxe-2011.4.191/compiler/lib/intel64/libifcore.so | grep
> 'for_cpystr'
> 00000000000cfc60 T for_cpystr
>
> The library is in my LD_LIBRARY_PATH and adding it to /etc/ld.so.conf.d/
> doesn't help either. The source install resides in /opt/EPD/epd-7.1-1-rh5-
> x86_64/lib/python2.7/site-packages/ and
> $ ldd /opt/EPD/epd-7.1-1-rh5-x86_64/lib/python2.7/site-packages/PyNIO/nio.so |
> grep 'libifcore.so'
> turns up nothing, so it seems these libraries are not correctly linked in.
> Which leads me to suspect that the F2CLIBS and F2CLIBS_PREFIX environment
> variables are not properly read by the setup.py script.
> I have defined them in the following way:
>
> export F2CLIBS='m ifcore irc ifport'
> export F2CLIBS_PREFIX=/opt/intel/composerxe-2011.4.191/compiler/lib/intel64/
>
> With this combination (although different syntax) I was able to successfully
> build NCL. From my limited understanding of what the setup.py script does,
> this should produce a list of the required libraries required by f2py. But
> obviously it does not work that way.
> In fact none of the above libraries are actually linked in to 'nio.so', except
> 'libm.so' which points to the standard GNU/Linux version.
>
> The setup.py script for PyNGL crashes in the linking stage with the following
> error:
>
> gcc -pthread -shared -g -L/usr/local/lib -O2 -I/usr/local/include
> build/temp.linux-x86_64-2.7/Helper.o build/temp.linux-x86_64-2.7/hlu_wrap.o
> build/temp.linux-x86_64-2.7/gsun.o -L/usr/local/ncarg/lib -
> L/opt/intel/composerxe-2011.4.191/compiler/lib/intel64/ -L/opt/EPD/epd-7.1-1-
> rh5-x86_64/lib -lnfpfort -lhlu -lncarg -lncarg_gks -lncarg_c -lngmath -lX11 -
> lm -lifcore -lirc -lifport -lpython2.7 -o build/lib.linux-
> x86_64-2.7/PyNGL/_hlu.so
> /usr/bin/ld: /usr/local/ncarg/lib/libnfpfort.a(dmapgci.o): relocation
> R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared
> object; recompile with -fPIC
> /usr/local/ncarg/lib/libnfpfort.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
>
> (I don't know why gcc is used for linking... otherwise the Intel compilers are
> used.) NCL is installed in /usr/local/ncarg/ and this package were compiled
> with '-fPIC'. I don't know what the meaning of this is.
>
> Sorry for this lengthy post, but I wanted to provide as much information as
> possible. I'm really stuck now. Any help would be greatly appreciated!
>
> Thanks!
> Andre
>
>
>
>
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Received on Mon Jan 9 23:39:16 2012