In a project I work on we use a Python C module compiled from Fortran with f2py. I’ve had no issues building it on Windows 7 32bit (using mingw32) and on the servers it’s built on 32bit Linux.
But I’ve recently installed Ubuntu 10.04 LTS 64bit on my laptop that I use for development, and when I build it I get a lot of warnings (even though I’ve apparently installed all gcc/fortran libraries/compilers), but it does finish the build. However when I try to use the built module in the application, most of it seems to run well but then it crashes with an error:
* glibc detected * /home/botondus/Envs/gasit/bin/python: free(): invalid next size (fast): 0x0000000006a44760 ***
Warnings on running f2py -c -m module_name ./fortran/source.f90
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize GnuFCompiler
Could not locate executable g77
Found executable /usr/bin/f77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
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
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
customize NAGFCompiler
Found executable /usr/bin/f95
customize VastFCompiler
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
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
I have tried building a 32bit version by installing the gfortran multilib packages and running f2py with -m32 option (but with no success):
f2py -c -m module_name ./fortran/source.f90 –f77flags=”-m32″ –f90flags=”-m32″
Any suggestions on what I could try to either build 32bit version or correctly build the 64bit version?
Edit: It looks like it crashes right at the end of a subroutine. The ‘write’ executes fine… which is strange.
write(6,*)'Eh=',Eh
end subroutine calcolo_involucro
The full backtrace is very long and I’m not sure if it’s any help, but here it is:
*** glibc detected *** /home/botondus/Envs/gasit/bin/python: free(): invalid next size (fast): 0x0000000007884690 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7fe24f8f05b6]
/lib/libc.so.6(cfree+0x73)[0x7fe24f8f6e53]
/usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x4183c)[0x7fe24a18183c]
/home/botondus/Envs/gasit/bin/python[0x46a50d]
/usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x4fbd8)[0x7fe24a18fbd8]
/usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x5aded)[0x7fe24a19aded]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x516e)[0x4a7c5e]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/home/botondus/Envs/gasit/bin/python[0x537620]
/home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7]
/home/botondus/Envs/gasit/bin/python[0x427dff]
/home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7]
/home/botondus/Envs/gasit/bin/python[0x477bff]
/home/botondus/Envs/gasit/bin/python[0x46f47f]
/home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4888)[0x4a7378]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/home/botondus/Envs/gasit/bin/python[0x537620]
/home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7]
/home/botondus/Envs/gasit/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x4a1b03]
/usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x2ee94)[0x7fe24a16ee94]
/home/botondus/Envs/gasit/bin/python(_PyObject_Str+0x61)[0x454a81]
/home/botondus/Envs/gasit/bin/python(PyObject_Str+0xa)[0x454b3a]
/home/botondus/Envs/gasit/bin/python[0x461ad3]
/home/botondus/Envs/gasit/bin/python[0x46f3b3]
/home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4888)[0x4a7378]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809]
/home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550]
======= Memory map: ========
00400000-0061c000 r-xp 00000000 08:05 399145 /home/botondus/Envs/gasit/bin/python
0081b000-0081c000 r--p 0021b000 08:05 399145 /home/botondus/Envs/gasit/bin/python
0081c000-0087e000 rw-p 0021c000 08:05 399145 /home/botondus/Envs/gasit/bin/python
0087e000-0088d000 rw-p 00000000 00:00 0
01877000-07a83000 rw-p 00000000 00:00 0 [heap]
7fe240000000-7fe240021000 rw-p 00000000 00:00 0
7fe240021000-7fe244000000 ---p 00000000 00:00 0
7fe247631000-7fe2476b1000 r-xp 00000000 08:03 140646 /usr/lib/libfreetype.so.6.3.22
7fe2476b1000-7fe2478b1000 ---p 00080000 08:03 140646 /usr/lib/libfreetype.so.6.3.22
7fe2478b1000-7fe2478b6000 r--p 00080000 08:03 140646 /usr/lib/libfreetype.so.6.3.22
7fe2478b6000-7fe2478b7000 rw-p 00085000 08:03 140646 /usr/lib/libfreetype.so.6.3.22
7fe2478b7000-7fe2478bb000 r-xp 00000000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fe2478bb000-7fe247aba000 ---p 00004000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fe247aba000-7fe247abb000 r--p 00003000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fe247abb000-7fe247abc000 rw-p 00004000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fe247abc000-7fe247abf000 r-xp 00000000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so
7fe247abf000-7fe247cbf000 ---p 00003000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so
7fe247cbf000-7fe247cc0000 r--p 00003000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so
7fe247cc0000-7fe247cc1000 rw-p 00004000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so
7fe247cc1000-7fe247cc5000 r-xp 00000000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so
7fe247cc5000-7fe247ec4000 ---p 00004000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so
7fe247ec4000-7fe247ec5000 r--p 00003000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so
7fe247ec5000-7fe247ec6000 rw-p 00004000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so
7fe247ec6000-7fe24800c000 r-xp 00000000 08:03 141358 /usr/lib/libxml2.so.2.7.6
7fe24800c000-7fe24820b000 ---p 00146000 08:03 141358 /usr/lib/libxml2.so.2.7.6
7fe24820b000-7fe248213000 r--p 00145000 08:03 141358 /usr/lib/libxml2.so.2.7.6
7fe248213000-7fe248215000 rw-p 0014d000 08:03 141358 /usr/lib/libxml2.so.2.7.6
7fe248215000-7fe248216000 rw-p 00000000 00:00 0
7fe248216000-7fe248229000 r-xp 00000000 08:03 140632 /usr/lib/libexslt.so.0.8.15
7fe248229000-7fe248428000 ---p 00013000 08:03 140632 /usr/lib/libexslt.so.0.8.15
7fe248428000-7fe248429000 r--p 00012000 08:03 140632 /usr/lib/libexslt.so.0.8.15
7fe248429000-7fe24842a000 rw-p 00013000 08:03 140632 /usr/lib/libexslt.so.0.8.15
7fe24842a000-7fe248464000 r-xp 00000000 08:03 141360 /usr/lib/libxslt.so.1.1.26
7fe248464000-7fe248663000 ---p 0003a000 08:03 141360 /usr/lib/libxslt.so.1.1.26
7fe248663000-7fe248664000 r--p 00039000 08:03 141360 /usr/lib/libxslt.so.1.1.26
7fe248664000-7fe248665000 rw-p 0003a000 08:03 141360 /usr/lib/libxslt.so.1.1.26
7fe248665000-7fe24876e000 r-xp 00000000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so
7fe24876e000-7fe24896d000 ---p 00109000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so
7fe24896d000-7fe24896e000 r--p 00108000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so
7fe24896e000-7fe248999000 rw-p 00109000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so
7fe248999000-7fe2489a7000 rw-p 00000000 00:00 0
7fe2489a7000-7fe2489bd000 r-xp 00000000 08:03 132934 /lib/libgcc_s.so.1
Fortunately managed to solve this.
It seems I didn’t notice that the numpy package version in the repositories for Ubuntu 10.04 are only v1.3.0. I removed numpy, then built v1.4.1 from source.
After that re-running f2py did give the same warnings, however using the module does not produce the crash anymore.