Re: PyNGL/PyNIO on Mac OSX libc++ error?

Hi Mary,

I did a clean re-build of my GNU compiler library (libstdcxx) today with
the Macports +universal variant (
https://trac.macports.org/wiki/howto/buildUniversal) and now the downloaded
PyNGL binary is working. I'm not sure exactly why this worked, but perhaps
there was just something broken in my previous libstdcxx build.

Best,

Madeline

On Tue, Apr 30, 2013 at 7:24 AM, Mary Haley <haley@ucar.edu> wrote:

> Madeline,
>
> I think part of the problem is that the gcc/gfortran in /opt/local is
> newer than the one that PyNIO was built with.
>
> I don't want to tell you to downgrade your version of gcc/gfortran, so you
> may need to consider building PyNIO from source code.
>
> I can help with this if needed. Here's a link to help you get started:
>
> http://www.pyngl.ucar.edu/Download/build_pynio_from_src.shtml
>
> At a minimum, you will need to install NetCDF (4.1 or 4.2) before you
> build PyNIO. If you further want support for NetCDF-4, you will need to
> install HDF5 and szip. The instructions are all on this page.
>
> --Mary
>
>
> On Apr 23, 2013, at 10:54 PM, Madeline Miller wrote:
>
> > Hi Mary,
> >
> > I have several versions of gcc installed on my system. Some are the
> Apple defaults and the others are versions installed by Macports.
> >
> > The current default is:
> >
> > $which gcc
> > /opt/local/bin/gcc
> >
> > This is a softlink to
> > /opt/local/bin/gcc-mp-4.5
> >
> > which is gcc 4.5 installed by macports.
> >
> > $gcc --version:
> > gcc (MacPorts gcc45 4.5.4_6) 4.5.4
> >
> > $ ls /usr/local/lib/libgcc_*
> > /usr/local/lib/libgcc_ext.10.4.dylib
> /usr/local/lib/libgcc_s.10.5.dylib
> > /usr/local/lib/libgcc_ext.10.5.dylib
> /usr/local/lib/libgcc_s_ppc64.1.dylib
> > /usr/local/lib/libgcc_s.1.dylib
> /usr/local/lib/libgcc_s_x86_64.1.dylib
> > /usr/local/lib/libgcc_s.10.4.dylib
> >
> > The nm command reports nothing:
> >
> > $ nm /usr/local/lib/libgcc_s.1.dylib | grep ___emutls_get_address
> > $
> >
> >
> > Madeline
> >
> >
> >
> >
> >
> > On Tue, Apr 23, 2013 at 8:45 PM, Mary Haley <haley@ucar.edu> wrote:
> > Hi Madeline,
> >
> > Unfortunately I'm not certain of which version I used to build PyNIO,
> although 4.2.1 seems about right.
> >
> > The issue may be that you don't have gcc installed on your system, or
> it's out-of-date.
> >
> > What does the following report:
> >
> > which gcc
> > gcc --version
> > ls /usr/local/lib/libgcc_*
> >
> > If you have a file called "/usr/local/lib/libgcc_s.1.dylib", then what
> does the following report:
> >
> > nm /usr/local/lib/libgcc_s.1.dylib | grep ___emutls_get_address
> >
> > --Mary
> >
> > On Apr 23, 2013, at 7:16 PM, Madeline Miller wrote:
> >
> >> Hi Daryl,
> >>
> >> Thanks for this clarification; as you can tell I'm new to python. Now
> it seems the basic PyNGL examples are working so I just need to sort out
> PyNIO.
> >>
> >> Madeline
> >>
> >>
> >> On Tue, Apr 23, 2013 at 4:49 PM, daryl herzmann <akrherz@iastate.edu>
> wrote:
> >> Madeline,
> >>
> >> pynglex is a python script itself and can be run without invoking
> python first. You should be able to do simply this from the command line
> >>
> >> pynglex -l
> >>
> >> That assumes pynglex is in your $PATH variable and is set executable.
> >>
> >> The python triple prompt is for running python code interactively and
> not necessarily whole python scripts. Typically whole python scripts are
> run by:
> >>
> >> python myscript.py
> >>
> >> So you could try running pynglex like
> >>
> >> python pynglex -l
> >>
> >> daryl
> >>
> >>
> >> On Tue, 23 Apr 2013, Madeline Miller wrote:
> >>
> >> Oh, I had already switched the #!, but python still is not recognizing
> >> pynglex as a command. I am running python interactively and type the
> >> command "pynglex -l" at the prompt. It returns:
> >> pynglex -l
> >> Traceback (most recent call last):
> >> File "<stdin>", line 1, in <module>
> >> NameError: name 'pynglex' is not defined
> >>
> >> I tried doing this in the folder where pynglex resides, but that doesn't
> >> change the result.
> >>
> >>
> >> On Tue, Apr 23, 2013 at 3:13 PM, Mary Haley <haley@ucar.edu> wrote:
> >>
> >>
> >> Let me check on the version of gcc when I get home.
> >>
> >> I had a typo in my pynglex correction.
> >>
> >> It should be:
> >>
> >> #!/usr/bin/env python
> >>
> >>
> >> --Mary
> >>
> >> On Apr 23, 2013, at 4:08 PM, Madeline Miller wrote:
> >>
> >> Hi Mary,
> >>
> >> Is there a way to modify a path variable in one of the PyNGL/PyNIO files
> >> to point to another installed gcc version to run those functions, or
> does
> >> my version of Python need to be re-compiled with the newer gcc to make
> this
> >> work?
> >>
> >> Modifying that line in the pynglex file did not fix the problem; could
> >> this be related to the gcc issue as well?
> >>
> >> Thanks,
> >>
> >> Madeline
> >>
> >>
> >> On Tue, Apr 23, 2013 at 2:00 PM, Mary Haley <haley@ucar.edu> wrote:
> >> Hi Madeline,
> >>
> >> I believe this issue has to do with the version of gcc that PyNGL was
> >> compiled with.
> >>
> >> This was on my home Mac, so I can't verify which gcc this was built
> >> with. I *think* it was 4.5.0,
> >> which will certainly be an issue trying to link against your 4.2.1
> >> version.
> >>
> >> Do you have any other versions of gcc that you can point to on your
> >> system?
> >>
> >> The pynglex problem is a bug on my part.
> >>
> >> You should be able to edit this file directly and change the top line to
> >> read:
> >>
> >> !#/usr/bin/env python
> >>
> >>
> >> --Mary
> >>
> >> On Apr 23, 2013, at 10:46 AM, Madeline Miller wrote:
> >>
> >> Hi,
> >>
> >> I am having some issues getting PyNGL and PyNIO installed.
> >> I am using the most recent pre-compiled binaries for Mac OS X, Python
> >> 2.7 and NumPy 1.6.
> >>
> >> PyNIO-1.4.1.macos-10.6-x86_64-py271-numpy160-nodap.tar.gz
> >> PyNGL-1.4.0.macos-10.6-x86_64-py271-numpy160.tar.gz
> >>
> >>
> >> These are the details of my operating system/other installations:
> >>
> >> Mac OSX 10.6.8 (Snow Leopard)
> >>
> >> Python 2.7.3 installed with MacPorts, using GCC 4.2.1
> >>
> >> file `which python` returns:
> >> /opt/local/bin/python: Mach-O 64-bit executable x86_64
> >>
> >> After installing PyNIO and PyNGL in the python directories, I start
> >> python and try to import Nio and Ngl:
> >>
> >>
> >> import Nio
> >> Traceback (most recent call last):
> >> File "<stdin>", line 1, in <module>
> >> File
> >>
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/Nio.py",
> >> line 63, in <module>
> >> from nio import *
> >> ImportError:
> >>
> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so,
> >> 2): Symbol not found: ___emutls_get_address
> >> Referenced from: /usr/local/lib/libstdc++.6.dylib
> >> Expected in: /usr/local/lib/libgcc_s.1.dylib
> >> in /usr/local/lib/libstdc++.6.dylib
> >>
> >> Does anyone know what might be the issue or how to fix this?
> >>
> >>
> >> There are no errors for import Ngl, but
> >>
> >> pynglex -l
> >> Traceback (most recent call last):
> >> File "<stdin>", line 1, in <module>
> >> NameError: name 'pynglex' is not defined
> >>
> >> I put the binaries pynglex and pynglex 2.7 in the folder:
> >> $PYTHONPREFIX/bin
> >>
> >> Should they go somewhere else?
> >>
> >> Thanks,
> >>
> >> Madeline
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >>
> >>
> >>
> >>
> >>
> >>
> >> --
> >> /**
> >> * Daryl Herzmann
> >> * Assistant Scientist -- Iowa Environmental Mesonet
> >> * http://mesonet.agron.iastate.edu
> >> */
> >>
> >> _______________________________________________
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> >
> >
>
>
Received on Sun May 5 21:55:54 2013