[SciPy-user] f2py problem: failed to map segment from shared object: Operation not permitted

Wed Jun 10 15:57:58 EDT 2009

I am trying to reuse some old code.  I am running into a problem importing a
module created by f2py.  Here is the traceback:

/home/ryan/pythonutil/rwkmisc.pyc in my_import(name)
    347
    348 def my_import(name):
--> 349     mod = __import__(name)
    350     components = name.split('.')
    351     for comp in components[1:]:

ImportError: /home/ryan/thesis/sym_control_design/fortran_model_bode1f.so:
failed to map segment from shared object: Operation not permitted
WARNING: Failure executing file: <symbolic_modeling.py>

I just tried recompiling the code.  The output of "f2py -c -m
fortran_model_bode1f fortran_model_bode1_out.f" is below.  Note that g77
doesn't show up in my Ubuntu 9.04 package manager.  I have gfortran
installed.  Can I safely ignore all the messages about not finding various
executeables since it eventually finds gfortran, or is this part of the
problem?  Recompiling did not fix my problem.  The fortran file is attached.

Thanks,

Ryan

ryan at ryan-duo-laptop:~/thesis/sym_control_design$ f2py -c -m
fortran_model_bode1f fortran_model_bode1_out.f
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler
options
running build_src
building extension "fortran_model_bode1f" sources
f2py options: []
f2py:> /tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1fmodule.c
creating /tmp/tmp3H0RSG
creating /tmp/tmp3H0RSG/src.linux-i686-2.6
Reading fortran codes...
    Reading file 'fortran_model_bode1_out.f' (format:fix,strict)
Post-processing...
    Block: fortran_model_bode1f
            Block: bodevect
            Block: invbodevect
            Block: invbode
            Block: zcosh
            Block: zsinh
            Block: bode
Post-processing (stage 2)...
Building modules...
    Building module "fortran_model_bode1f"...
        Constructing wrapper function "bodevect"...
          outvect = bodevect(svect,ucv)
        Constructing wrapper function "invbodevect"...
          outvect = invbodevect(svect,ucv)
        Creating wrapper for Fortran function "invbode"("invbode")...
        Constructing wrapper function "invbode"...
          invbode = invbode(s,ucv)
        Creating wrapper for Fortran function "zcosh"("zcosh")...
        Constructing wrapper function "zcosh"...
          zcosh = zcosh(z)
        Creating wrapper for Fortran function "zsinh"("zsinh")...
        Constructing wrapper function "zsinh"...
          zsinh = zsinh(z)
        Creating wrapper for Fortran function "bode"("bode")...
        Constructing wrapper function "bode"...
          bode = bode(s,ucv)
    Wrote C/API module "fortran_model_bode1f" to file
"/tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1fmodule.c"
    Fortran 77 wrappers are saved to
"/tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.f"
  adding '/tmp/tmp3H0RSG/src.linux-i686-2.6/fortranobject.c' to sources.
  adding '/tmp/tmp3H0RSG/src.linux-i686-2.6' to include_dirs.
copying /usr/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.c ->
/tmp/tmp3H0RSG/src.linux-i686-2.6
copying /usr/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.h ->
/tmp/tmp3H0RSG/src.linux-i686-2.6
  adding
'/tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.f' to
sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
Could not locate executable pgf77
customize AbsoftFCompiler
Could not locate executable f90
customize NAGFCompiler
Found executable /usr/bin/f95
customize VastFCompiler
customize GnuFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
Could not locate executable efort
Could not locate executable efc
customize IntelEM64TFCompiler
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'fortran_model_bode1f' extension
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC

creating /tmp/tmp3H0RSG/tmp
creating /tmp/tmp3H0RSG/tmp/tmp3H0RSG
creating /tmp/tmp3H0RSG/tmp/tmp3H0RSG/src.linux-i686-2.6
compile options: '-I/tmp/tmp3H0RSG/src.linux-i686-2.6
-I/usr/lib/python2.6/dist-packages/numpy/core/include
-I/usr/include/python2.6 -c'
gcc: /tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1fmodule.c
gcc: /tmp/tmp3H0RSG/src.linux-i686-2.6/fortranobject.c
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form
-fno-second-underscore -fPIC -O3 -funroll-loops -march=i686 -mmmx -msse2
-msse -msse3 -fomit-frame-pointer -malign-double
Fortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC
-O3 -funroll-loops -march=i686 -mmmx -msse2 -msse -msse3
-fomit-frame-pointer -malign-double
Fortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form
-fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops
-march=i686 -mmmx -msse2 -msse -msse3 -fomit-frame-pointer -malign-double
compile options: '-I/tmp/tmp3H0RSG/src.linux-i686-2.6
-I/usr/lib/python2.6/dist-packages/numpy/core/include
-I/usr/include/python2.6 -c'
gfortran:f77: fortran_model_bode1_out.f
gfortran:f77:
/tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.f
/usr/bin/gfortran -Wall -Wall -shared
/tmp/tmp3H0RSG/tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1fmodule.o
/tmp/tmp3H0RSG/tmp/tmp3H0RSG/src.linux-i686-2.6/fortranobject.o
/tmp/tmp3H0RSG/fortran_model_bode1_out.o
/tmp/tmp3H0RSG/tmp/tmp3H0RSG/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.o
-lgfortran -o ./fortran_model_bode1f.so
running scons
Removing build directory /tmp/tmp3H0RSG
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20090610/7f9aa0ec/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: fortran_model_bode1_out.f
Type: text/x-fortran
Size: 6127 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20090610/7f9aa0ec/attachment.bin>