[f2py] F90 Module Allocatable Arrays SegFault on Assignment using Intel ia64

[Howard Salis]

Hi again,
    I sent this to the mailing list back in June, but never found an 
answer. I figure I'd give it a second try. Thank you for any help!

Hi all,
   First off, let me say that f2py has automagically worked very well so 
far and this is the first serious bug I've run into. So kudos to the 
developers!

I did find a bug though related to running on a 64-bit machine. Here it is:

   I'm using an Intel Itanium2 (ia64) running Linux 2.4.21-27.0.2.EL. 
It's Python version v2.4.2 and numpy version v0.9.6 with the 
accompanying f2py. I copy & pasted the example from chapter 4.6.1 of the 
f2py documentation into "Test.f90". The example allocates a F90 module 
allocatable array and assigns a Numpy array to it.  I f2py'd it using 
"f2py -m Test -c --f90exec=ifort --f90flags='-O3'  --build-dir 
/home/es7000/salis/Py3S/f2py -I/home/es7000/salis/Py3S/f2py 
-L/opt/intel_fc_80/lib -lifcoremt -lcprts  Test.f90". For some reason, 
using "--fcompiler=intele" does not work. The output from f2py is pasted 
below (but it seems to work fine).

   After that, I try allocating and assigning data to the module 
variable, using "Test.mod.b = [[1, 2], [3, 4], [5, 6]]" and it 
segfaults. I also tried importing numpy ("from numpy import *") and 
using "a = array([[1,2], [3,4], [5,6]], 'f')" and "Test.mod.b = a". That 
also segfaults. In other tests, I was successful in assigning a numpy 
scalar or a python scalar to a scalar module variable. I was also 
successful in assigning a 1 dimensional numpy array to a module 
variable, but it will raise the exception "ValueError: negative 
dimensions are not allowed" when trying to read it.

Any suggestions or fixes (besides not using any module variables)?

Thank you,
   Howard Salis

   University of Minnesota

F90 file:

module mod

real, allocatable :: b(:,:)

contains

subroutine foo
IMPLICIT NONE
integer :: k

if (allocated(b)) then
 print*, "b=["
 do k = 1,size(b,1)
   print*, b(k,1:size(b,2))
 enddo

 print*, "]"
else
 print*, "b is not allocated"
endif

end subroutine foo

end module mod

F2py output:

running build
running config_fc
running build_src
building extension "Test" sources
f2py options: []
f2py:> /home/es7000/salis/Py3S/f2py/src/Testmodule.c
Reading fortran codes...
       Reading file 'Test.f90' (format:free)
Post-processing...
       Block: Test
               Block: mod
                       Block: foo
Post-processing (stage 2)...
       Block: Test
        Block: unknown_interface
               Block: mod
                       Block: foo
Building modules...
       Building module "Test"...
        Constructing F90 module support for "mod"...
          Variables: b
               Constructing wrapper function "mod.foo"...
                 foo()
       Wrote C/API module "Test" to file 
"/home/es7000/salis/Py3S/f2py/src/Testmodule.c"
       Fortran 90 wrappers are saved to 
"/home/es7000/salis/Py3S/f2py/src/Test-f2pywrappers2.f90"
 adding '/home/es7000/salis/Py3S/f2py/src/fortranobject.c' to sources.
 adding '/home/es7000/salis/Py3S/f2py/src' to include_dirs.
 adding '/home/es7000/salis/Py3S/f2py/src/Test-f2pywrappers2.f90' to 
sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
Could not locate executable gfortran
Could not locate executable f95
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using build_ext
building 'Test' extension
compiling C sources
gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC'
compile options: '-I/home/es7000/salis/Py3S/f2py 
-I/home/es7000/salis/Py3S/f2py/src 
-I/home/es7000/salis/Python/Python-2.4.2/Lib/site-packages/numpy/core/include 
-I/home/es7000/salis/Python/Python-2.4.2/Include 
-I/home/es7000/salis/Python/Python-2.4.2 -c'
gcc: /home/es7000/salis/Py3S/f2py/src/Testmodule.c
/home/es7000/salis/Py3S/f2py/src/Testmodule.c: In function 
`f2py_setup_mod':
/home/es7000/salis/Py3S/f2py/src/Testmodule.c:176: warning: assignment 
from incompatible pointer type
XXX: module_build_dir='/home/es7000/salis/Py3S/f2py/' option ignored
XXX: Fix module_dir_switch for  GnuFCompiler
XXX: module_dirs=[] option ignored
XXX: Fix module_include_switch for  GnuFCompiler
compiling Fortran 90 module sources
g77(f77) options: '-Wall -fno-second-underscore -fPIC -O2 -funroll-loops'
ifort(f90) options: '-O3 -fPIC -O2 -funroll-loops'
ifort(fix) options: '-O3 -fPIC -O2 -funroll-loops'
compile options: '-I/home/es7000/salis/Py3S/f2py 
-I/home/es7000/salis/Py3S/f2py/src 
-I/home/es7000/salis/Python/Python-2.4.2/Lib/site-packages/numpy/core/include 
-I/home/es7000/salis/Python/Python-2.4.2/Include 
-I/home/es7000/salis/Python/Python-2.4.2 -c'
ifort:f90: Test.f90
ifort: Command line warning: overriding '-O3' with '-O2'
ifort: Command line warning: ignoring unknown option '-funroll-loops'
moving mod.mod -> /home/es7000/salis/Py3S/f2py/
compiling Fortran sources
g77(f77) options: '-Wall -fno-second-underscore -fPIC -O2 -funroll-loops'
ifort(f90) options: '-O3 -fPIC -O2 -funroll-loops'
ifort(fix) options: '-O3 -fPIC -O2 -funroll-loops'
compile options: '-I/home/es7000/salis/Py3S/f2py 
-I/home/es7000/salis/Py3S/f2py/src 
-I/home/es7000/salis/Python/Python-2.4.2/Lib/site-packages/numpy/core/include 
-I/home/es7000/salis/Python/Python-2.4.2/Include 
-I/home/es7000/salis/Python/Python-2.4.2 -c'
ifort:f90: /home/es7000/salis/Py3S/f2py/src/Test-f2pywrappers2.f90
ifort: Command line warning: overriding '-O3' with '-O2'
ifort: Command line warning: ignoring unknown option '-funroll-loops'
/usr/bin/g77 -shared /home/es7000/salis/Py3S/f2py/Testmodule.o 
/home/es7000/salis/Py3S/f2py/fortranobject.o 
/home/es7000/salis/Py3S/f2py/Test.o 
/home/es7000/salis/Py3S/f2py/Test-f2pywrappers2.o -L/opt/intel_fc_80/lib 
-lifcoremt -lcprts -lg2c -o ./Test.so

Python IDE:

Python 2.4.2 (#1, Mar 18 2006, 15:42:52)
[GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-53)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import Test
 >>> from numpy import *
 >>> print Test.mod.__doc__
b - 'f'-array(-1,-1), not allocated
foo - Function signature:
 foo()
 >>> a = array([[ 1., 2., 3.],[4., 5., 6.]],'f')
 >>> Test.mod.b = a
Segmentation fault