Re: install PyNGL on ubuntu 12.04 and solution

Hi Joel,

Sorry you had problems compiling PyNGL.

I think the gfortran dependency may be in the _hlu.so file, and not fplib.so.

Anyway, I *think* you have might have also been able to solve your problem by settng F2CLIBS_PREFIX to the path to the libgfortran.so file.

The issue may also be that Python doesn't put the -lgfortran in the right place on the final load line to create the *.so file. Really, though, if you are using gcc/gfortran that go together, I think the gcc should automatically find and load libgfortran.so.

I will look into using "depend" in the Extension module. This may be just what I need to get the -lgfortran to appear in the correct location. Thanks so much for the info.

--Mary

On Dec 17, 2012, at 6:11 AM, CHAVAS Joel wrote:

> I am working with ubuntu 12.04 LTS; I have installed ncl. I have installed PyNIO. I didn't have any problems with these. It was slightly more challenging with PyNGL:
>
> I am using PyNGL-1.4.0. I have the standard ubuntu installations, meaning that I have gcc version 4.6.3, python version 2.7.3, and gfortran version 4.6.3
>
> I compiled fine. But, on the use of PyNGL by running a python script,
> import numpy as np
> import Ngl
>
> I have an ImportError, stating
> undefined symbol: _gfortran_stop_numeric
> we note that the command (launched in the terminal from the directory PyGNL-1.4.0)
> ldd build/lib.linux-x86_64-2.7/PyNGL/fplib.so
> indicates no dependence on the library libgfortran.so.
> there lies the problem.
>
> Solution:
> 1) In PyGNL-1.4.0 obtained after the tar xvzf, remove by hand the build directory:
> rm -rf build
>
>
> 2) in the file setup.py, add a dependency on the gfortran library (it was not enough to modify LIBRARITES in my case):
> you replace:
> #########################################################"
> # Instructions for compiling the "_hlu.so" and "fplib.so" files.
> EXT_MODULES = [Extension('_hlu',
> ['Helper.c','hlu_wrap.c','gsun.c'],
> define_macros = DMACROS,
> include_dirs = INC_DIRS,
> library_dirs = LIB_DIRS,
> libraries = LIBRARIES,
> extra_objects = EXTRA_OBJECTS),
> Extension('fplib',
> [os.path.join('paft','fplibmodule.c')],
> define_macros = DMACROS,
> include_dirs = INC_DIRS,
> library_dirs = LIB_DIRS,
> libraries = LIBRARIES,
> extra_objects = EXTRA_OBJECTS
> )]
> ##########################################################
>
> with:
> (replace /usr/lib/gcc/x86_64-linux-gnu/4.6/ with the path of libgfortran.so on your computer)
>
> #########################################################"
> # Instructions for compiling the "_hlu.so" and "fplib.so" files.
> EXT_MODULES = [Extension('_hlu',
> ['Helper.c','hlu_wrap.c','gsun.c'],
> define_macros = DMACROS,
> include_dirs = INC_DIRS,
> library_dirs = LIB_DIRS,
> libraries = LIBRARIES,
> extra_objects = EXTRA_OBJECTS,
> depends = [('/usr/lib/gcc/x86_64-linux-gnu/4.6/libgfortran.so')]),
> Extension('fplib',
> [os.path.join('paft','fplibmodule.c')],
> define_macros = DMACROS,
> include_dirs = INC_DIRS,
> library_dirs = LIB_DIRS,
> libraries = LIBRARIES,
> extra_objects = EXTRA_OBJECTS,
> depends = [('/usr/lib/gcc/x86_64-linux-gnu/4.6/libgfortran.so')]
> )]
> ##########################################################
>
> 3) you compile using
> python setup --verbose build
> strangely, it will stop by giving a file/directory not present. I had not time to correct this bug.
> Just launch the last gcc command given before the error. In my case, I had to launch something like these (don't be afraid, it is just a copy/paste of the last log you see in the screen):
>
> gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -O2 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/ncl/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -lnfpfort -lhlu -lncarg -lncarg_gks -lncarg_c -lngmath -lX11 -lgfortran -o build/lib.linux-x86_64-2.7/PyNGL/_hlu.so
>
> gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -O2 build/temp.linux-x86_64-2.7/paft/fplibmodule.o -L/usr/local/ncl/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -lnfpfort -lhlu -lncarg -lncarg_gks -lncarg_c -lngmath -lX11 -lgfortran -o build/lib.linux-x86_64-2.7/PyNGL/fplib.so
>
> 4) python setup --verbose install
>
> 5) say how the find the ncl python library
> export PYNGL_NCARG=/usr/local/ncl/lib (in my case. Put it for example in .bashrc)
>
> 6) Then, the python script importing 'import Ngl' 'works!
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Received on Wed Dec 19 11:52:15 2012