[Numpy-discussion] acml and numpy install problems (original) (raw)

JJ josh8912 at yahoo.com
Thu Jun 15 01:13:06 EDT 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 ... ... 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' ... ... 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'

... ... /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

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