[SciPy-user] f2py problem: failed to map segment from shared object: Operation not permitted
Ryan Krauss
ryanlists at gmail.com
Wed Jun 10 18:03:57 EDT 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 at 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 at 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 at 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 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/f7b8d5ff/attachment.html>
More information about the SciPy-User
mailing list