Bazaar branched tests fail

2013-03-04
2013-11-04
  • Hi,

    After successfully installing in Debian 7.0 with python 2.7 I proceeded to run the tests.
    I got the following error when running

     python basic_gen_tests_C.py
    

    Basic generator tests for C-based vector fields…
    In file included from /usr/include/stdio.h:28:0,
                     from /home/juanpi/Resources/PyDSTool/integrator/integration.h:6,
                     from /home/juanpi/Resources/PyDSTool/integrator/integration.c:1:
    /usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory
    compilation terminated.
    In file included from /usr/include/stdio.h:28:0,
                     from /home/juanpi/Resources/PyDSTool/integrator/integration.h:6,
                     from /home/juanpi/Resources/PyDSTool/integrator/integration.c:1:
    /usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory
    compilation terminated.

    Error occurred in generating Dopri system…
    <type 'exceptions.SystemExit'> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/pymodules/python2.7/numpy/core/include -I/usr/lib/pymodules/python2.7/numpy/numarray/include -I/home/juanpi/Resources/PyDSTool/tests -I/home/juanpi/Resources/PyDSTool/integrator -I/usr/lib/pymodules/python2.7/numpy/core/include -I/usr/include/python2.7 -c /home/juanpi/Resources/PyDSTool/integrator/integration.c -o dopri853_temp/home/juanpi/Resources/PyDSTool/integrator/integration.o -w -D__DOPRI__ -m32" failed with exit status 1
    Traceback (most recent call last):
      File "basic_gen_tests_C.py", line 20, in <module>
        tmm = Generator.Dopri_ODEsystem(DSargs)
      File "/home/juanpi/Resources/PyDSTool/Generator/Dopri_ODEsystem.py", line 400, in __init__
        self.compileLib()
      File "/home/juanpi/Resources/PyDSTool/Generator/Dopri_ODEsystem.py", line 774, in compileLib
        raise RuntimeError
    RuntimeError

    It seems that I cant find bits/predefs.h
    What is what I am missing?

    Thanks

    bzr info:


    revno: 365
    committer: Rob Clewley <rob.clewley@gmail.com>
    branch nick: PyDSTool
    timestamp: Fri 2013-02-22 17:30:28 -0500
    message:
      Improved error message when parameter or variables names are used as function arguments

     
  • Rob Clewley
    Rob Clewley
    2013-03-04

    Hi,

    That file is a system header, and from googling it seems that this problem might arise when trying to compile 32-bit versions of model code. The defaults are set to 32 bit. If that's the issue, and you want native 64 bit, you can try removing the -m32 flags in the python files that generate the C code, as described in the documentation for 64 bit systems. Let me know if that doesn't help.

     
  • Indeed,

    I just read the 64-bit part of the documentation and the FAQ. I am sorry I missed that. Removing -m2 from

    ./PyCont/ContClass.py:                                 extra_compile_args=['-w', '-D__PYTHON__', '-std=c99', '-m32'],
    ./PyCont/ContClass.py:                                 extra_link_args=['-w', '-m32'],
    ./Generator/Dopri_ODEsystem.py:                                 extra_compile_args=['-w', '-D__DOPRI__', '-m32'],
    ./Generator/Dopri_ODEsystem.py:                                 extra_link_args=['-w', '-m32'])])
    ./Generator/Radau_ODEsystem.py:                                 extra_compile_args=['-w', '-D__RADAU__', '-m32'],
    ./Generator/Radau_ODEsystem.py:                                 extra_link_args=['-w', '-m32'])],
    

    solves the problem.

    Thank you