[Numpy-discussion] acml and numpy install problems

JJ josh8912 at yahoo.com
Thu Jun 15 00:13:06 CDT 2006


Hello.  I wrote to the list about a week ago regarding
slow speed of numpy relative to matlab.  Im fairly
sure that my installation of numpy had problems.  So I
am trying this time with the acml libraries for my AMD
Athelon 64 bit machine.  New machine with FC_5.  I was
able to install the acml libraries without much
trouble, and install UMFPACK and AMD without apparent
errors.  But I did have many errors when I tried to
install numpy.  My install messages are copied below. 
Apparently, numpy does see the acml libraries but
finds them faulty, or something.  I could use some
clues if anyone has any.  Also, I did set: 
setenv LD_LIBRARY_PATH /opt/acml3.1.0/gnu64/lib
# setenv LD_RUN_PATH /opt/acml3.1.0/gnu64/lib 

Here is my config file:
-----------------------------------
[atlas]
library_dirs = /opt/acml3.1.0/gnu64/lib
include_dirs = /opt/acml3.1.0/gnu64/include
atlas_libs = acml
language = f77

[blas]
library_dirs = /opt/acml3.1.0/gnu64/lib
include_dirs = /opt/acml3.1.0/gnu64/include
atlas_libs = acml
language = f77

[laplack]
library_dirs = /opt/acml3.1.0/gnu64/lib
include_dirs = /opt/acml3.1.0/gnu64/include
atlas_libs = acml
language = f77

[amd]
library_dirs = /usr/local/scipy/AMD/Lib
include_dirs = /usr/local/scipy/AMD/Include
amd_libs = amd
language =c

[umfpack]
library_dirs = /usr/local/scipy/UMFPACK/Lib
include_dirs = /usr/local/scipy/UMFPACK/Include
umfpack_libs = umfpack
language = c
------------------------------------
I have set symbolic links between lacml and libacml.

Here is the first half of the output, where most of
the errors are:
--------------------------------
[root at fedora-newamd numpy]# python setup.py install
Running from numpy source directory.
No module named __svn_version__
F2PY Version 2_2624
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not find in /usr/local/lib
  libraries mkl,vml,guide not find in /usr/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['acml']
    library_dirs = ['/opt/acml3.1.0/gnu64/lib']
    language = c

customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from
numpy_distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/opt/acml3.1.0/gnu64/lib
-lacml -o _configtest
_configtest.o: In function `main':
/usr/local/numpy/_configtest.c:5: undefined reference
to `ATL_buildinfo'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `do_lio'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `e_wsle'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `e_wsfe'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `z_abs'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined 
... <snip> ...
reference to `s_wsle'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_wsfe'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_copy'
collect2: ld returned 1 exit status
_configtest.o: In function `main':
/usr/local/numpy/_configtest.c:5: undefined reference
to `ATL_buildinfo'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `do_lio'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `e_wsle'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `e_wsfe'
... <snip> ...
reference to `s_wsle'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_wsfe'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_copy'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output:
  FOUND:
    libraries = ['acml']
    library_dirs = ['/opt/acml3.1.0/gnu64/lib']
    language = c
    define_macros = [('NO_ATLAS_INFO', 2)]

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not find in /usr/local/lib
  libraries mkl,vml,guide not find in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not find in
/opt/acml3.1.0/gnu64/lib
  libraries lapack not find in
/opt/acml3.1.0/gnu64/lib
  libraries acml not find in /usr/local/lib
  libraries lapack_atlas not find in /usr/local/lib
  libraries acml not find in /usr/lib
  libraries lapack_atlas not find in /usr/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
/usr/local/numpy/numpy/distutils/system_info.py:881:
UserWarning:
*********************************************************************
    Could not find lapack library within the ATLAS
installation.
*********************************************************************

  warnings.warn(message)
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['acml']
    library_dirs = ['/opt/acml3.1.0/gnu64/lib']
    language = c
    define_macros = [('ATLAS_WITHOUT_LAPACK', None)]

customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from
numpy_distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/opt/acml3.1.0/gnu64/lib
-lacml -o _configtest
_configtest.o: In function `main':
/usr/local/numpy/_configtest.c:5: undefined reference
to `ATL_buildinfo'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `do_lio'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `e_wsle'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `e_wsfe'

...<snip> ...
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `acos'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_wsle'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_wsfe'
/opt/acml3.1.0/gnu64/lib/libacml.so: undefined
reference to `s_copy'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output:
lapack_info:
  libraries lapack not find in /usr/local/lib
  libraries lapack not find in /usr/lib
  NOT AVAILABLE

/usr/local/numpy/numpy/distutils/system_info.py:1163:
UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries
not found.
    Directories to search for the libraries can be
specified in the
    numpy/distutils/site.cfg file (section [lapack])
or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
  NOT AVAILABLE

/usr/local/numpy/numpy/distutils/system_info.py:1166:
UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not
found.
    Directories to search for the sources can be
specified in the
    numpy/distutils/site.cfg file (section
[lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
  NOT AVAILABLE

running install
running build
running config_fc
running build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-2.4
creating build/src.linux-x86_64-2.4/numpy
creating build/src.linux-x86_64-2.4/numpy/distutils
building extension "numpy.core.multiarray" sources
creating build/src.linux-x86_64-2.4/numpy/core
Generating
build/src.linux-x86_64-2.4/numpy/core/config.h
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-I/usr/include/python2.4
-Inumpy/core/src -Inumpy/core/include 
-I/usr/include/python2.4 -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:50: warning: format ‘%d’ expects type
‘int’, but argument 4 has ty pe ‘long unsigned int’
_configtest.c:57: warning: format ‘%d’ expects type
‘int’, but argument 4 has ty pe ‘long unsigned int’
_configtest.c:72: warning: format ‘%d’ expects type
‘int’, but argument 4 has ty pe ‘long unsigned int’
gcc -pthread _configtest.o -L/usr/local/lib -L/usr/lib
-o _configtest
/usr/bin/ld: skipping incompatible
/usr/lib/libpthread.so when searching for -lp thread
/usr/bin/ld: skipping incompatible
/usr/lib/libpthread.a when searching for -lpt hread
/usr/bin/ld: skipping incompatible /usr/lib/libc.so
when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libc.a
when searching for -lc
_configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
_configtest.o: In function `main':
/usr/local/numpy/_configtest.c:5: undefined reference
to `exp'
collect2: ld returned 1 exit status
_configtest.o: In function `main':
/usr/local/numpy/_configtest.c:5: undefined reference
to `exp'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
gcc -pthread _configtest.o -lm -o _configtest
_configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D _FORTIFY_SOURCE=2
-fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fPIC

compile options: '-Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4  -c'
gcc: _configtest.c
_configtest.c: In function ‘main’:
_configtest.c:4: warning: statement with no effect
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
  adding
'build/src.linux-x86_64-2.4/numpy/core/config.h' to
sources.
executing
numpy/core/code_generators/generate_array_api.py
  adding
'build/src.linux-x86_64-2.4/numpy/core/__multiarray_api.h'
to sources.
creating build/src.linux-x86_64-2.4/numpy/core/src
conv_template:>
build/src.linux-x86_64-2.4/numpy/core/src/scalartypes.inc
  adding 'build/src.linux-x86_64-2.4/numpy/core/src'
to include_dirs.
conv_template:>
build/src.linux-x86_64-2.4/numpy/core/src/arraytypes.inc
numpy.core - nothing done with h_files=
['build/src.linux-x86_64-2.4/numpy/core/
src/scalartypes.inc',
'build/src.linux-x86_64-2.4/numpy/core/src/arraytypes.inc'
, 'build/src.linux-x86_64-2.4/numpy/core/config.h',
'build/src.linux-x86_64-2.4/
numpy/core/__multiarray_api.h']
building extension "numpy.core.umath" sources
  adding
'build/src.linux-x86_64-2.4/numpy/core/config.h' to
sources.
executing
numpy/core/code_generators/generate_ufunc_api.py
  adding
'build/src.linux-x86_64-2.4/numpy/core/__ufunc_api.h'
to sources.
conv_template:>
build/src.linux-x86_64-2.4/numpy/core/src/umathmodule.c
  adding 'build/src.linux-x86_64-2.4/numpy/core/src'
to include_dirs.
numpy.core - nothing done with h_files=
['build/src.linux-x86_64-2.4/numpy/core/
src/scalartypes.inc',
'build/src.linux-x86_64-2.4/numpy/core/src/arraytypes.inc'
, 'build/src.linux-x86_64-2.4/numpy/core/config.h',
'build/src.linux-x86_64-2.4/
numpy/core/__ufunc_api.h']
building extension "numpy.core._sort" sources
  adding
'build/src.linux-x86_64-2.4/numpy/core/config.h' to
sources.
  adding
'build/src.linux-x86_64-2.4/numpy/core/__multiarray_api.h'
to sources.
conv_template:>
build/src.linux-x86_64-2.4/numpy/core/src/_sortmodule.c
numpy.core - nothing done with h_files=
['build/src.linux-x86_64-2.4/numpy/core/ config.h',
'build/src.linux-x86_64-2.4/numpy/core/__multiarray_api.h']
building extension "numpy.core.scalarmath" sources
  adding
'build/src.linux-x86_64-2.4/numpy/core/config.h' to
sources.
  adding
'build/src.linux-x86_64-2.4/numpy/core/__multiarray_api.h'
to sources.
  adding
'build/src.linux-x86_64-2.4/numpy/core/__ufunc_api.h'
to sources.
conv_template:>
build/src.linux-x86_64-2.4/numpy/core/src/scalarmathmodule.c
numpy.core - nothing done with h_files=
['build/src.linux-x86_64-2.4/numpy/core/ config.h',
'build/src.linux-x86_64-2.4/numpy/core/__multiarray_api.h',
'build/sr
c.linux-x86_64-2.4/numpy/core/__ufunc_api.h']
building extension "numpy.core._dotblas" sources
  adding 'numpy/core/blasdot/_dotblas.c' to sources.
building extension "numpy.lib._compiled_base" sources
building extension "numpy.dft.fftpack_lite" sources
building extension "numpy.linalg.lapack_lite" sources
creating build/src.linux-x86_64-2.4/numpy/linalg
### Warning:  Using unoptimized lapack ###
---------------------------------------------
Any ideas?  I am still a novice and could use some
suggestions.  Thanks much.  JJ

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 




More information about the Numpy-discussion mailing list