Re: [SciPy-user] Release of SciPy Core 0.4 (Beta)

Oct. 4, 2005


      Looks like I have BLAS but not ATLAS.  Here's the entire output from running 
setup.py:
root@sojourner:/home/steve/dl/python/scipy/scipy_core-0.4.1# python setup.py 
install
Assuming default configuration 
(scipy/distutils/command/{setup_command,setup}.py was not found)
Appending scipy.distutils.command configuration to scipy.distutils
Assuming default configuration 
(scipy/distutils/fcompiler/{setup_fcompiler,setup}.py was not found)
Appending scipy.distutils.fcompiler configuration to scipy.distutils
Appending scipy.distutils configuration to scipy
Assuming default configuration (scipy/weave/{setup_weave,setup}.py was not 
found)
Appending scipy.weave configuration to scipy
Assuming default configuration (scipy/test/{setup_test,setup}.py was not found)
Appending scipy.test configuration to scipy
F2PY Version 2_1126
Appending scipy.f2py configuration to scipy
Appending scipy.base configuration to scipy
blas_opt_info:
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
   NOT AVAILABLE

atlas_blas_info:
   NOT AVAILABLE

/home/steve/dl/python/scipy/scipy_core-0.4.1/scipy/distutils/system_info.py:1046: 
UserWarning:
     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
     Directories to search for the libraries can be specified in the
     scipy_distutils/site.cfg file (section [atlas]) or by setting
     the ATLAS environment variable.
   warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
   FOUND:
     libraries = ['blas']
     library_dirs = ['/usr/lib']
     language = f77

   FOUND:
     libraries = ['blas']
     library_dirs = ['/usr/lib']
     define_macros = [('NO_ATLAS_INFO', 1)]
     language = f77

lapack_opt_info:
atlas_threads_info:
Setting PTATLAS=ATLAS
scipy.distutils.system_info.atlas_threads_info
   NOT AVAILABLE

atlas_info:
scipy.distutils.system_info.atlas_info
   NOT AVAILABLE

/home/steve/dl/python/scipy/scipy_core-0.4.1/scipy/distutils/system_info.py:970: 
UserWarning:
     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
     Directories to search for the libraries can be specified in the
     scipy_distutils/site.cfg file (section [atlas]) or by setting
     the ATLAS environment variable.
   warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
   FOUND:
     libraries = ['lapack']
     library_dirs = ['/usr/lib']
     language = f77

   FOUND:
     libraries = ['lapack', 'blas']
     library_dirs = ['/usr/lib']
     define_macros = [('NO_ATLAS_INFO', 1)]
     language = f77

Appending scipy.lib configuration to scipy
Assuming default configuration (scipy/fftpack/{setup_fftpack,setup}.py was 
not found)
Appending scipy.fftpack configuration to scipy
Assuming default configuration (scipy/linalg/{setup_linalg,setup}.py was not 
found)
Appending scipy.linalg configuration to scipy
Assuming default configuration (scipy/stats/{setup_stats,setup}.py was not 
found)
Appending scipy.stats configuration to scipy
Appending scipy configuration to
scipy_core version 0.4.1
running install
running build
running config_fc
running build_src
building extension "scipy.base.multiarray" sources
   adding 'build/src/scipy/base/config.h' to sources.
   adding 'build/src/scipy/base/__multiarray_api.h' to sources.
   adding 'build/src/scipy/base/src' to include_dirs.
building extension "scipy.base.umath" sources
   adding 'build/src/scipy/base/config.h' to sources.
   adding 'build/src/scipy/base/__ufunc_api.h' to sources.
   adding 'build/src/scipy/base/src' to include_dirs.
building extension "scipy.base._compiled_base" sources
   adding 'build/src/scipy/base/config.h' to sources.
   adding 'build/src/scipy/base/__multiarray_api.h' to sources.
building extension "scipy.lib._dotblas" sources
building extension "scipy.lib.fftpack_lite" sources
building extension "scipy.lib.mtrand" sources
building extension "scipy.lib.lapack_lite" sources
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using build_ext
building 'scipy.lib._dotblas' extension
compiling C sources
gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC'
compile options: '-DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base
-Iscipy/base/src -I/usr/local/include/python2.4 -c'
gcc: scipy/corelib/blasdot/_dotblas.c
In file included from scipy/corelib/blasdot/_dotblas.c:6:
scipy/base/include/scipy/arrayobject.h:84: warning: redefinition of `ushort'
/usr/include/sys/types.h:152: warning: `ushort' previously declared here
scipy/base/include/scipy/arrayobject.h:85: warning: redefinition of `uint'
/usr/include/sys/types.h:153: warning: `uint' previously declared here
scipy/base/include/scipy/arrayobject.h:86: warning: redefinition of `ulong'
/usr/include/sys/types.h:151: warning: `ulong' previously declared here
scipy/corelib/blasdot/_dotblas.c:10:22: cblas.h: No such file or directory
scipy/corelib/blasdot/_dotblas.c: In function `FLOAT_dot':
scipy/corelib/blasdot/_dotblas.c:21: warning: implicit declaration of 
function `cblas_sdot'
scipy/corelib/blasdot/_dotblas.c: In function `DOUBLE_dot':
scipy/corelib/blasdot/_dotblas.c:31: warning: implicit declaration of 
function `cblas_ddot'
scipy/corelib/blasdot/_dotblas.c: In function `CFLOAT_dot':
scipy/corelib/blasdot/_dotblas.c:42: warning: implicit declaration of 
function `cblas_cdotu_sub'
scipy/corelib/blasdot/_dotblas.c: In function `CDOUBLE_dot':
scipy/corelib/blasdot/_dotblas.c:52: warning: implicit declaration of 
function `cblas_zdotu_sub'
scipy/corelib/blasdot/_dotblas.c: In function `dotblas_matrixproduct':
scipy/corelib/blasdot/_dotblas.c:235: warning: implicit declaration of function
`cblas_daxpy'
scipy/corelib/blasdot/_dotblas.c:239: warning: implicit declaration of function
`cblas_saxpy'
scipy/corelib/blasdot/_dotblas.c:243: warning: implicit declaration of function
`cblas_zaxpy'
scipy/corelib/blasdot/_dotblas.c:247: warning: implicit declaration of function
`cblas_caxpy'
scipy/corelib/blasdot/_dotblas.c:277: warning: implicit declaration of function
`cblas_dgemv'
scipy/corelib/blasdot/_dotblas.c:277: `CblasRowMajor' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:277: (Each undeclared identifier is 
reported only once
scipy/corelib/blasdot/_dotblas.c:277: for each function it appears in.)
scipy/corelib/blasdot/_dotblas.c:278: `CblasNoTrans' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:283: warning: implicit declaration of function
`cblas_sgemv'
scipy/corelib/blasdot/_dotblas.c:289: warning: implicit declaration of function
`cblas_zgemv'
scipy/corelib/blasdot/_dotblas.c:295: warning: implicit declaration of function
`cblas_cgemv'
scipy/corelib/blasdot/_dotblas.c:306: `CblasTrans' undeclared (first use in 
this function)
scipy/corelib/blasdot/_dotblas.c:334: warning: implicit declaration of function
`cblas_dgemm'
scipy/corelib/blasdot/_dotblas.c:341: warning: implicit declaration of function
`cblas_sgemm'
scipy/corelib/blasdot/_dotblas.c:348: warning: implicit declaration of function
`cblas_zgemm'
scipy/corelib/blasdot/_dotblas.c:355: warning: implicit declaration of function
`cblas_cgemm'
scipy/corelib/blasdot/_dotblas.c: In function `dotblas_innerproduct':
scipy/corelib/blasdot/_dotblas.c:522: `CblasRowMajor' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:523: `CblasNoTrans' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:579: `CblasTrans' undeclared (first use in 
this function)
scipy/corelib/blasdot/_dotblas.c: In function `dotblas_vdot':
scipy/corelib/blasdot/_dotblas.c:699: warning: implicit declaration of function
`cblas_zdotc_sub'
scipy/corelib/blasdot/_dotblas.c:703: warning: implicit declaration of function
`cblas_cdotc_sub'
In file included from scipy/corelib/blasdot/_dotblas.c:6:
scipy/base/include/scipy/arrayobject.h:84: warning: redefinition of `ushort'
/usr/include/sys/types.h:152: warning: `ushort' previously declared here
scipy/base/include/scipy/arrayobject.h:85: warning: redefinition of `uint'
/usr/include/sys/types.h:153: warning: `uint' previously declared here
scipy/base/include/scipy/arrayobject.h:86: warning: redefinition of `ulong'
/usr/include/sys/types.h:151: warning: `ulong' previously declared here
scipy/corelib/blasdot/_dotblas.c:10:22: cblas.h: No such file or directory
scipy/corelib/blasdot/_dotblas.c: In function `FLOAT_dot':
scipy/corelib/blasdot/_dotblas.c:21: warning: implicit declaration of 
function `cblas_sdot'
scipy/corelib/blasdot/_dotblas.c: In function `DOUBLE_dot':
scipy/corelib/blasdot/_dotblas.c:31: warning: implicit declaration of 
function `cblas_ddot'
scipy/corelib/blasdot/_dotblas.c: In function `CFLOAT_dot':
scipy/corelib/blasdot/_dotblas.c:42: warning: implicit declaration of 
function `cblas_cdotu_sub'
scipy/corelib/blasdot/_dotblas.c: In function `CDOUBLE_dot':
scipy/corelib/blasdot/_dotblas.c:52: warning: implicit declaration of 
function `cblas_zdotu_sub'
scipy/corelib/blasdot/_dotblas.c: In function `dotblas_matrixproduct':
scipy/corelib/blasdot/_dotblas.c:235: warning: implicit declaration of function
`cblas_daxpy'
scipy/corelib/blasdot/_dotblas.c:239: warning: implicit declaration of function
`cblas_saxpy'
scipy/corelib/blasdot/_dotblas.c:243: warning: implicit declaration of function
`cblas_zaxpy'
scipy/corelib/blasdot/_dotblas.c:247: warning: implicit declaration of function
`cblas_caxpy'
scipy/corelib/blasdot/_dotblas.c:277: warning: implicit declaration of function
`cblas_dgemv'
scipy/corelib/blasdot/_dotblas.c:277: `CblasRowMajor' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:277: (Each undeclared identifier is 
reported only once
scipy/corelib/blasdot/_dotblas.c:277: for each function it appears in.)
scipy/corelib/blasdot/_dotblas.c:278: `CblasNoTrans' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:283: warning: implicit declaration of function
`cblas_sgemv'
scipy/corelib/blasdot/_dotblas.c:289: warning: implicit declaration of function
`cblas_zgemv'
scipy/corelib/blasdot/_dotblas.c:295: warning: implicit declaration of function
`cblas_cgemv'
scipy/corelib/blasdot/_dotblas.c:306: `CblasTrans' undeclared (first use in 
this function)
scipy/corelib/blasdot/_dotblas.c:334: warning: implicit declaration of function
`cblas_dgemm'
scipy/corelib/blasdot/_dotblas.c:341: warning: implicit declaration of function
`cblas_sgemm'
scipy/corelib/blasdot/_dotblas.c:348: warning: implicit declaration of function
`cblas_zgemm'
scipy/corelib/blasdot/_dotblas.c:355: warning: implicit declaration of function
`cblas_cgemm'
scipy/corelib/blasdot/_dotblas.c: In function `dotblas_innerproduct':
scipy/corelib/blasdot/_dotblas.c:522: `CblasRowMajor' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:523: `CblasNoTrans' undeclared (first use 
in this function)
scipy/corelib/blasdot/_dotblas.c:579: `CblasTrans' undeclared (first use in 
this function)
scipy/corelib/blasdot/_dotblas.c: In function `dotblas_vdot':
scipy/corelib/blasdot/_dotblas.c:699: warning: implicit declaration of function
`cblas_zdotc_sub'
scipy/corelib/blasdot/_dotblas.c:703: warning: implicit declaration of function
`cblas_cdotc_sub'
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include 
-Ibuild/src/scipy/base
-Iscipy/base/src -I/usr/local/include/python2.4 -c 
scipy/corelib/blasdot/_dotblas.c -o 
build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit 
status 1

Thanks,
Steve

Travis Oliphant wrote:
...
Steven H. Rogers wrote:
...
"python setup.py install" for scipy_core 0.4.1 fails to build with:
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 
-Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include 
-Ibuild/src/scipy/base
-Iscipy/base/src -I/usr/local/include/python2.4 -c 
scipy/corelib/blasdot/_dotblas.c -o 
build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed 
with exit status 1
Hmm.  This is definitely a blas-related problem.    What other errors do 
you see.
A quick fix is to uncomment the blas_info=0 (line 15 of 
scipy/corelib/setup.py) and rerun setup (this will not try to build 
_dotblas.c
I'd like to track down what the real problem is though.
Do you see any output below
blas_opt_info:
when you run setup.py
For example,  my system shows.
blas_opt_info:
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
 NOT AVAILABLE
atlas_blas_info:
 FOUND:
   libraries = ['f77blas', 'cblas', 'atlas']
   library_dirs = ['/usr/lib/atlas']
   language = c
   include_dirs = ['/usr/include/atlas']
These include_dirs are needed to pick up cblas.h
-Travis
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Steven H. Rogers, Ph.D., steve@shrogers.com
Weblog: http://shrogers.com/weblog
"He who refuses to do arithmetic is doomed to talk nonsense."
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