[Numpy-discussion] trouble building numpy 1.6.1 on Scientific Linux 5

[Ralf Gommers]

On Fri, Dec 9, 2011 at 8:02 PM, Russell E. Owen <rowen at uw.edu> wrote:

> I'm trying to build numpy 1.6.1 on Scientific Linux 5 but the unit tests
> claim the wrong version of fortran was used. I thought I knew how to
> avoid that, but it's not working.
>
> I don't have atlas (this needs to run on a lot of
> similar-but-not-identical machines). I believe blas and lapack were
> built against gfortran:
> -bash-3.2$ ldd /usr/lib64/libblas.so
>   linux-vdso.so.1 =>  (0x00007fff4bffd000)
>   libm.so.6 => /lib64/libm.so.6 (0x00002ab26a0c8000)
>   libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002ab26a34c000)
>   libc.so.6 => /lib64/libc.so.6 (0x00002ab26a5e3000)
>   /lib64/ld-linux-x86-64.so.2 (0x0000003b2ba00000)
> -bash-3.2$ ldd /usr/lib64/liblapack.so
>   linux-vdso.so.1 =>  (0x00007fffe97fd000)
>   libblas.so.3 => /usr/lib64/libblas.so.3 (0x00002b6438d75000)
>   libm.so.6 => /lib64/libm.so.6 (0x00002b6438fca000)
>   libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002b643924d000)
>   libc.so.6 => /lib64/libc.so.6 (0x00002b64394e4000)
>   /lib64/ld-linux-x86-64.so.2 (0x0000003b2ba00000)
>
> The sysadmins have provided a gcc 4.4.0 compiler that I access using
> symlinks on my $PATH:
> -bash-3.2$ which gcc g++ gfortran
> ~/local/bin/gcc
> ~/local/bin/g++
> ~/local/bin/gfortran
> -bash-3.2$ ls -l ~/local/bin
> lrwxrwxrwx 1 rowen astro 14 Oct 28  2010 g++ -> /usr/bin/g++44
> lrwxrwxrwx 1 rowen astro 14 Oct 28  2010 gcc -> /usr/bin/gcc44
> lrwxrwxrwx 1 rowen astro 19 Dec  5 16:40 gfortran -> /usr/bin/gfortran44
> -bash-3.2$ gfortran --version
> GNU Fortran (GCC) 4.4.0 20090514 (Red Hat 4.4.0-6)
> Copyright (C) 2009 Free Software Foundation, Inc.
>
> For this log I used a home-bulit python 2.6.5 that is widely used.
> However, I've tried it with other builds of python that are on our
> system, as well, with no better success (including a Python 2.7.2).
> -bash-3.2$ which python
> /astro/apps/pkg/python64/bin/python
> -bash-3.2$ python
> Python 2.6.5 (r265:79063, Aug  4 2010, 11:27:53)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>
>
>
> numpy seems to see gfortran when it builds:
>
> -bash-3.2$ python setup.py build --fcompiler=gnu95
>
> Running from numpy source directory.non-existing path in
> 'numpy/distutils': 'site.cfg'
> F2PY Version 2
> blas_opt_info:
> blas_mkl_info:
> ... NOT AVAILABLE
>
> atlas_blas_threads_info:
> ... NOT AVAILABLE
>
> atlas_blas_info:
> ... NOT AVAILABLE
>
> blas_info:
> ... FOUND:
>    libraries = ['blas']
>    library_dirs = ['/usr/lib64']
>    language = f77
>
>  FOUND:
>    libraries = ['blas']
>    library_dirs = ['/usr/lib64']
>    define_macros = [('NO_ATLAS_INFO', 1)]
>    language = f77
>
> lapack_opt_info:
> lapack_mkl_info:
> mkl_info:
> ... NOT AVAILABLE
>
>  NOT AVAILABLE
>
> atlas_threads_info:
> ... NOT AVAILABLE
>
> atlas_info:
> ... NOT AVAILABLE
>
> /astro/users/rowen/build/numpy-1.6.1/numpy/distutils/system_info.py:1330:
>  UserWarning:
>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>    the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> lapack_info:
>  libraries lapack not found in
> /astro/apps/lsst_w12_sl5/Linux64/external/python/2.7.2+2/lib
> ... FOUND:
>    libraries = ['lapack']
>    library_dirs = ['/usr/lib64']
>    language = f77
>
>  FOUND:
>    libraries = ['lapack', 'blas']
>    library_dirs = ['/usr/lib64']
>    define_macros = [('NO_ATLAS_INFO', 1)]
>    language = f77
>
> 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
> build_src
> building py_modules sources
> creating build
> creating build/src.linux-x86_64-2.7
> creating build/src.linux-x86_64-2.7/numpy
> creating build/src.linux-x86_64-2.7/numpy/distutils
> building library "npymath" sources
> customize Gnu95FCompiler
> Found executable /astro/users/rowen/local/bin/gfortran
>
>
> # I install it in an out-of-the-way location just so I can test it
> -bash-3.2$ python setup.py install  --home=~/local
> ...
> -bash-3.2$ cd
> -bash-3.2$ python
> >>> import numpy
> >>> numpy.__path__
> ['/astro/users/rowen/local/lib/python/numpy']
> >>> numpy.test()
> Running unit tests for numpy
> NumPy version 1.6.1
> NumPy is installed in /astro/users/rowen/local/lib/python/numpy
> Python version 2.6.5 (r265:79063, Aug  4 2010, 11:27:53) [GCC 4.1.2
> 20080704 (Red Hat 4.1.2-46)]
> nose version 0.11.4
> ....
> ======================================================================
> FAIL: test_lapack (test_build.TestF77Mismatch)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/astro/users/rowen/local/lib/python/numpy/testing/decorators.py", line
> 146, in skipper_func
>    return f(*args, **kwargs)
>  File
> "/astro/users/rowen/local/lib/python/numpy/linalg/tests/test_build.py",
> line 50, in test_lapack
>    information.""")
> AssertionError: Both g77 and gfortran runtimes linked in lapack_lite !
> This is likely to
> cause random crashes and wrong results. See numpy INSTALL.txt for more
> information.
>
> ----------------------------------------------------------------------
> Ran 3533 tests in 13.400s
>
>
> Any suggestions on how to fix this?
>

I assume you have g77 installed and on your PATH. If so, try moving it off
your path.

Ralf
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