On Fri, Dec 9, 2011 at 8:02 PM, Russell E. Owen <rowen@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