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

Hi Deepak,
I have tried the prebuild binaries, but only the 64bit ones, which lead to the
error discribed under my first point. I have not tried 32bit, but at least the
Enthought Python Distro is 64bit; I'm not sure about the standard Python
distro on my system. NCL itself is working fine with my source build, and
there are no errors related to it.
Ciao,
        Andre

On January 10, 2012 01:39:06 AM Deepak Chandan wrote:
> 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 23:56:42 2012