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

Ryan Krauss ryanlists@gmail....
Wed Jun 10 17:03:57 CDT 2009


So, I found a thread on ubuntuforums that say that passing -std=legacy to
gfortran allows it to correctly complie files written for g77 or f77.  How
would I pass such a flag to f2py?

On Wed, Jun 10, 2009 at 4:50 PM, Ryan Krauss <ryanlists@gmail.com> wrote:

> I found this thread from a year ago:
> http://mail.scipy.org/pipermail/numpy-discussion/2008-June/035107.html
>
> The --fcompiler=gnu95 switch cleans up my output, but doesn't get rid of my
> problem:
>
>
> #------------------------------------
> ryan@ryan-duo-laptop:~/thesis/sym_control_design$ f2py -c -m
> fortran_model_bode1f --fcompiler=gnu95 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/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1fmodule.c
> creating /tmp/tmpocK64J
> creating /tmp/tmpocK64J/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/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1fmodule.c"
>     Fortran 77 wrappers are saved to
> "/tmp/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.f"
>   adding '/tmp/tmpocK64J/src.linux-i686-2.6/fortranobject.c' to sources.
>   adding '/tmp/tmpocK64J/src.linux-i686-2.6' to include_dirs.
> copying /usr/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.c ->
> /tmp/tmpocK64J/src.linux-i686-2.6
> copying /usr/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.h ->
> /tmp/tmpocK64J/src.linux-i686-2.6
>   adding
> '/tmp/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.f' to
> sources.
> running build_ext
> customize UnixCCompiler
> customize UnixCCompiler using build_ext
> customize Gnu95FCompiler
> Found executable /usr/bin/gfortran
> 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/tmpocK64J/tmp
> creating /tmp/tmpocK64J/tmp/tmpocK64J
> creating /tmp/tmpocK64J/tmp/tmpocK64J/src.linux-i686-2.6
> compile options: '-I/tmp/tmpocK64J/src.linux-i686-2.6
> -I/usr/lib/python2.6/dist-packages/numpy/core/include
> -I/usr/include/python2.6 -c'
> gcc: /tmp/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1fmodule.c
> gcc: /tmp/tmpocK64J/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/tmpocK64J/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/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.f
> /usr/bin/gfortran -Wall -Wall -shared
> /tmp/tmpocK64J/tmp/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1fmodule.o
> /tmp/tmpocK64J/tmp/tmpocK64J/src.linux-i686-2.6/fortranobject.o
> /tmp/tmpocK64J/fortran_model_bode1_out.o
> /tmp/tmpocK64J/tmp/tmpocK64J/src.linux-i686-2.6/fortran_model_bode1f-f2pywrappers.o
> -lgfortran -o ./fortran_model_bode1f.so
> running scons
> Removing build directory /tmp/tmpocK64J
>
> #--------------------------------
>
> In [2]: import fortran_model_bode1f
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
>
> /home/ryan/siue/Research/papers/noncolocated_TMM/expgraphs/symbolic_modeling.py
> in <module>()
> ----> 1
>       2
>       3
>       4
>       5
>
> ImportError: /home/ryan/thesis/sym_control_design/fortran_model_bode1f.so:
> failed to map segment from shared object: Operation not permitted
>
>
>
>
>
> On Wed, Jun 10, 2009 at 2:57 PM, Ryan Krauss <ryanlists@gmail.com> wrote:
>
>> 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@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
>>
>>
>
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