Hi List,
I am trying to install numpy 1.0.1 on Linux. (Numeric and numarray have been
fine)
System info: Redhat Linux kernel 2.4 with gcc 3.2.3 but no separate FORTRAN
compiler.
It has a Fortran 77 compiler (the one which comes as part of gcc)
My questions:
1) install can't find ATLAS (*.a) that I specify.
Do they have to be *.so files? Do the *.a file sizes look right?
Where can I get libblas.so liblapack.so files?
2) do I need a FORTRAN compiler? Will Fortran 77 compiler do?
Thanks,
Shawn
Followings are error messages:
-----------------------------
When I type "python setup.py install > numpy.out", I get:
Screen display as follows:
-----------------------------
Running from numpy source directory.
/home/sgong/dev/numpy-1.0.1/numpy/distutils/system_info.py:934:
UserWarning:
*********************************************************************
Lapack library (from ATLAS) is probably incomplete:
size of /usr/lib/liblapack.so is 3676k (expected >4000k)
Follow the instructions in the KNOWN PROBLEMS section of the file
numpy/INSTALL.txt.
*********************************************************************
I then asked system admin people to install a complete ATLAS onto
/usr/local/lib/atlas
-rw-r--r-- 1 root root 8049172 May 15 08:49 libatlas.a
-rw-r--r-- 1 root root 279016 May 15 08:49 libcblas.a
-rw-r--r-- 1 root root 342062 May 15 08:49 libf77blas.a
-rw-r--r-- 1 root root 5314268 May 15 08:49 liblapack.a
-rw-r--r-- 1 root root 279590 May 15 08:49 libptcblas.a
-rw-r--r-- 1 root root 342430 May 15 08:49 libptf77blas.a
-rw-r--r-- 1 root root 320316 May 15 08:49 libtstatlas.a
System admin people said that he doesn't know how to get/install *.so. He can
only get *.a library.
I also changed site.cfg to enter
"library_dirs = /usr/local/lib/atlas/"
Please find the numpy.out.txt file. Some of the lines are:
--------------------------------
F2PY Version 2_3473
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in /home/sgong/dev/dist/lib
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack,blas not found in /usr/local/lib/atlas
libraries lapack,blas not found in /usr/local/lib/atlas/
libraries lapack,blas not found in /home/sgong/dev/dist/lib
libraries lapack,blas not found in /usr/local/lib/atlas
libraries lapack,blas not found in /usr/local/lib
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib']
language = c
Could not locate executable gfortran
Could not locate executable f95
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 -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes
-fPIC
compile options: '-c'
gcc: _configtest.c
gcc _configtest.o -L/usr/lib -llapack -lblas -o _configtest
_configtest.o(.text+0x15): In function `main':
/home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to
`ATL_buildinfo'
/usr/lib/liblapack.so: undefined reference to `e_wsfe'
/usr/lib/liblapack.so: undefined reference to `z_abs'
/usr/lib/liblapack.so: undefined reference to `c_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cmp'
/usr/lib/liblapack.so: undefined reference to `z_exp'
/usr/lib/liblapack.so: undefined reference to `c_exp'
/usr/lib/liblapack.so: undefined reference to `etime_'
/usr/lib/liblapack.so: undefined reference to `do_fio'
/usr/lib/liblapack.so: undefined reference to `z_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cat'
/usr/lib/liblapack.so: undefined reference to `s_stop'
/usr/lib/liblapack.so: undefined reference to `c_abs'
/usr/lib/liblapack.so: undefined reference to `s_wsfe'
/usr/lib/liblapack.so: undefined reference to `s_copy'
collect2: ld returned 1 exit status
_configtest.o(.text+0x15): In function `main':
/home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to
`ATL_buildinfo'
F2PY Version 2_3473
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in /home/sgong/dev/dist/lib
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack,blas not found in /usr/local/lib/atlas
libraries lapack,blas not found in /usr/local/lib/atlas/
libraries lapack,blas not found in /home/sgong/dev/dist/lib
libraries lapack,blas not found in /usr/local/lib/atlas
libraries lapack,blas not found in /usr/local/lib
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib']
language = c
Could not locate executable gfortran
Could not locate executable f95
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 -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes
-fPIC
compile options: '-c'
gcc: _configtest.c
gcc _configtest.o -L/usr/lib -llapack -lblas -o _configtest
_configtest.o(.text+0x15): In function `main':
/home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to
`ATL_buildinfo'
/usr/lib/liblapack.so: undefined reference to `e_wsfe'
/usr/lib/liblapack.so: undefined reference to `z_abs'
/usr/lib/liblapack.so: undefined reference to `c_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cmp'
/usr/lib/liblapack.so: undefined reference to `z_exp'
/usr/lib/liblapack.so: undefined reference to `c_exp'
/usr/lib/liblapack.so: undefined reference to `etime_'
/usr/lib/liblapack.so: undefined reference to `do_fio'
/usr/lib/liblapack.so: undefined reference to `z_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cat'
/usr/lib/liblapack.so: undefined reference to `s_stop'
/usr/lib/liblapack.so: undefined reference to `c_abs'
/usr/lib/liblapack.so: undefined reference to `s_wsfe'
/usr/lib/liblapack.so: undefined reference to `s_copy'
collect2: ld returned 1 exit status
_configtest.o(.text+0x15): In function `main':
/home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to
`ATL_buildinfo'
/usr/lib/liblapack.so: undefined reference to `e_wsfe'
/usr/lib/liblapack.so: undefined reference to `z_abs'
/usr/lib/liblapack.so: undefined reference to `c_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cmp'
/usr/lib/liblapack.so: undefined reference to `z_exp'
/usr/lib/liblapack.so: undefined reference to `c_exp'
/usr/lib/liblapack.so: undefined reference to `etime_'
/usr/lib/liblapack.so: undefined reference to `do_fio'
/usr/lib/liblapack.so: undefined reference to `z_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cat'
/usr/lib/liblapack.so: undefined reference to `s_stop'
/usr/lib/liblapack.so: undefined reference to `c_abs'
/usr/lib/liblapack.so: undefined reference to `s_wsfe'
/usr/lib/liblapack.so: undefined reference to `s_copy'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output:
FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib']
language = c
define_macros = [('NO_ATLAS_INFO', 2)]
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in /home/sgong/dev/dist/lib
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack,blas not found in /usr/local/lib/atlas
libraries lapack_atlas not found in /usr/local/lib/atlas
libraries lapack,blas not found in /usr/local/lib/atlas/
libraries lapack_atlas not found in /usr/local/lib/atlas/
libraries lapack,blas not found in /home/sgong/dev/dist/lib
libraries lapack_atlas not found in /home/sgong/dev/dist/lib
libraries lapack,blas not found in /usr/local/lib/atlas
libraries lapack_atlas not found in /usr/local/lib/atlas
libraries lapack,blas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'lapack', 'blas']
library_dirs = ['/usr/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 -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes
-fPIC
compile options: '-c'
gcc: _configtest.c
gcc _configtest.o -L/usr/lib -llapack -llapack -lblas -o _configtest
_configtest.o(.text+0x15): In function `main':
/home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to
`ATL_buildinfo'
/usr/lib/liblapack.so: undefined reference to `e_wsfe'
/usr/lib/liblapack.so: undefined reference to `z_abs'
/usr/lib/liblapack.so: undefined reference to `c_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cmp'
/usr/lib/liblapack.so: undefined reference to `z_exp'
/usr/lib/liblapack.so: undefined reference to `c_exp'
/usr/lib/liblapack.so: undefined reference to `etime_'
/usr/lib/liblapack.so: undefined reference to `do_fio'
/usr/lib/liblapack.so: undefined reference to `z_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cat'
/usr/lib/liblapack.so: undefined reference to `s_stop'
/usr/lib/liblapack.so: undefined reference to `c_abs'
/usr/lib/liblapack.so: undefined reference to `s_wsfe'
/usr/lib/liblapack.so: undefined reference to `s_copy'
collect2: ld returned 1 exit status
_configtest.o(.text+0x15): In function `main':
/home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to
`ATL_buildinfo'
/usr/lib/liblapack.so: undefined reference to `e_wsfe'
/usr/lib/liblapack.so: undefined reference to `z_abs'
/usr/lib/liblapack.so: undefined reference to `c_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cmp'
/usr/lib/liblapack.so: undefined reference to `z_exp'
/usr/lib/liblapack.so: undefined reference to `c_exp'
/usr/lib/liblapack.so: undefined reference to `etime_'
/usr/lib/liblapack.so: undefined reference to `do_fio'
/usr/lib/liblapack.so: undefined reference to `z_sqrt'
/usr/lib/liblapack.so: undefined reference to `s_cat'
/usr/lib/liblapack.so: undefined reference to `s_stop'
/usr/lib/liblapack.so: undefined reference to `c_abs'
/usr/lib/liblapack.so: undefined reference to `s_wsfe'
/usr/lib/liblapack.so: undefined reference to `s_copy'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output:
FOUND:
libraries = ['lapack', 'lapack', 'blas']
library_dirs = ['/usr/lib']
language = c
define_macros = [('NO_ATLAS_INFO', 2)]
running install
running build
running config_fc
running build_src
building py_modules sources
building extension "numpy.core.multiarray" sources
adding 'build/src.linux-i686-2.3/numpy/core/config.h' to sources.
executing numpy/core/code_generators/generate_array_api.py
adding 'build/src.linux-i686-2.3/numpy/core/__multiarray_api.h' to sources.
adding 'build/src.linux-i686-2.3/numpy/core/src' to include_dirs.
numpy.core - nothing done with h_files=
['build/src.linux-i686-2.3/numpy/core/src/scalartypes.inc',
'build/src.linux-i686-2.3/numpy/core/src/arraytypes.inc',
'build/src.linux-i686-2.3/numpy/core/config.h',
'build/src.linux-i686-2.3/numpy/core/__multiarray_api.h']
building extension "numpy.core.umath" sources
adding 'build/src.linux-i686-2.3/numpy/core/config.h' to sources.
executing numpy/core/code_generators/generate_ufunc_api.py
adding 'build/src.linux-i686-2.3/numpy/core/__ufunc_api.h' to sources.
adding 'build/src.linux-i686-2.3/numpy/core/src' to include_dirs.
numpy.core - nothing done with h_files=
['build/src.linux-i686-2.3/numpy/core/src/scalartypes.inc',
'build/src.linux-i686-2.3/numpy/core/src/arraytypes.inc',
'build/src.linux-i686-2.3/numpy/core/config.h',
'build/src.linux-i686-2.3/numpy/core/__ufunc_api.h']
building extension "numpy.core._sort" sources
adding 'build/src.linux-i686-2.3/numpy/core/config.h' to sources.
executing numpy/core/code_generators/generate_array_api.py
adding 'build/src.linux-i686-2.3/numpy/core/__multiarray_api.h' to sources.
numpy.core - nothing done with h_files=
['build/src.linux-i686-2.3/numpy/core/config.h',
'build/src.linux-i686-2.3/numpy/core/__multiarray_api.h']
building extension "numpy.core.scalarmath" sources
adding 'build/src.linux-i686-2.3/numpy/core/config.h' to sources.
executing numpy/core/code_generators/generate_array_api.py
adding 'build/src.linux-i686-2.3/numpy/core/__multiarray_api.h' to sources.
executing numpy/core/code_generators/generate_ufunc_api.py
adding 'build/src.linux-i686-2.3/numpy/core/__ufunc_api.h' to sources.
numpy.core - nothing done with h_files=
['build/src.linux-i686-2.3/numpy/core/config.h',
'build/src.linux-i686-2.3/numpy/core/__multiarray_api.h',
'build/src.linux-i686-2.3/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.numarray._capi" sources
building extension "numpy.fft.fftpack_lite" sources
building extension "numpy.linalg.lapack_lite" sources
adding 'numpy/linalg/lapack_litemodule.c' to sources.
building extension "numpy.random.mtrand" sources
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes
-fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/home/sgong/dev/dist/include/python2.3 -c'
gcc: _configtest.c
_configtest.c:7:2: #error No _WIN32
_configtest.c:7:2: #error No _WIN32
failure.
removing: _configtest.c _configtest.o
building data_files sources
running build_py
copying build/src.linux-i686-2.3/numpy/__config__.py ->
build/lib.linux-i686-2.3/numpy
copying build/src.linux-i686-2.3/numpy/distutils/__config__.py ->
build/lib.linux-i686-2.3/numpy/distutils
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running build_scripts
adding 'build/scripts.linux-i686-2.3/f2py' to scripts
running install_lib
copying build/lib.linux-i686-2.3/numpy/__config__.py ->
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy
copying build/lib.linux-i686-2.3/numpy/distutils/__config__.py ->
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/distutils
byte-compiling
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/__config__.py to
__config__.pyc
byte-compiling
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/distutils/__config__.py
to __config__.pyc
running install_scripts
changing mode of /home/sgong/dev/dist/bin/f2py to 755
running install_data
copying build/src.linux-i686-2.3/numpy/core/__multiarray_api.h ->
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/core/include/numpy
copying build/src.linux-i686-2.3/numpy/core/multiarray_api.txt ->
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/core/include/numpy
copying build/src.linux-i686-2.3/numpy/core/__ufunc_api.h ->
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/core/include/numpy
copying build/src.linux-i686-2.3/numpy/core/ufunc_api.txt ->
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/core/include/numpy
-rw-r--r-- 1 root root 8049172 May 15 08:49 libatlas.a
-rw-r--r-- 1 root root 279016 May 15 08:49 libcblas.a
-rw-r--r-- 1 root root 342062 May 15 08:49 libf77blas.a
-rw-r--r-- 1 root root 5314268 May 15 08:49 liblapack.a
-rw-r--r-- 1 root root 279590 May 15 08:49 libptcblas.a
-rw-r--r-- 1 root root 342430 May 15 08:49 libptf77blas.a
-rw-r--r-- 1 root root 320316 May 15 08:49 libtstatlas.a
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