numpy installation as non root using site.cfg
Dear mailing list I am trying to install numpy-1.1.1 on a cluster where I do not have root permission. I have succesfully installed \ python2.5.2. I am using the cite.cfg file to include the blas and atlas libraries. I have done that by setting the\ defaults to: library_dirs = /usr/lib include_dirs = /usr/include where blas and atlas is located. Then I type: python setup.py install --home=$HOME and get the following output Running from numpy source directory. F2PY Version 2_5585 Traceback (most recent call last): File "setup.py", line 96, in <module> setup_package() File "setup.py", line 89, in setup_package configuration=configuration ) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/core.py", line 150, in setup config = configuration() File "setup.py", line 56, in configuration config.add_subpackage('numpy') File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/misc_util.py", line 850, in add_subpackage caller_level = 2) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/misc_util.py", line 833, in get_subpackage caller_level = caller_level + 1) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/misc_util.py", line 780, in _get_configuration_from_s\ etup_py config = setup_module.configuration(*args) File "numpy/setup.py", line 9, in configuration config.add_subpackage('core') File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/misc_util.py", line 850, in add_subpackage caller_level = 2) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/misc_util.py", line 833, in get_subpackage caller_level = caller_level + 1) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/misc_util.py", line 780, in _get_configuration_from_s\ etup_py config = setup_module.configuration(*args) File "numpy/core/setup.py", line 299, in configuration blas_info = get_info('blas_opt',0) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/system_info.py", line 267, in get_info return cl().get_info(notfound_action) File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/system_info.py", line 366, in __init__ self.parse_config_files() File "/data/pgmoses/SourceCode/numpy-1.1.1/numpy/distutils/system_info.py", line 372, in parse_config_files self.cp.read(self.files) File "/data/pgmoses/lib/python2.5/ConfigParser.py", line 267, in read self._read(fp, filename) File "/data/pgmoses/lib/python2.5/ConfigParser.py", line 462, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /data/pgmoses/SourceCode/numpy-1.1.1/site.cfg, line: 60 'library_dirs = /usr/lib\n' Do you have any suggestion to what I might be doing wrong Best regards, Poul Georg Moses -- View this message in context: http://www.nabble.com/numpy-installation-as-non-root-using-site.cfg-tp196977... Sent from the Numpy-discussion mailing list archive at Nabble.com.
On Fri, Sep 26, 2008 at 18:07, Poul Georg Moses <pgmoses@engineering.ucsb.edu> wrote:
Dear mailing list
I am trying to install numpy-1.1.1 on a cluster where I do not have root permission. I have succesfully installed \ python2.5.2. I am using the cite.cfg file to include the blas and atlas libraries. I have done that by setting the\ defaults to: library_dirs = /usr/lib include_dirs = /usr/include
You need [DEFAULT] library_dirs = /usr/lib include_dirs = /usr/include just like it is in the site.cfg.example -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
Thank you Robert It is now possible for me to install numpy. I get an error with the defaults libraries, which I have reported in a pending mail to the mailen list. Then I tried to use the intel mkl libraries in this way: [mkl] library_dirs = /opt/intel/mkl70/lib/32 mkl_libs = mkl, guide lapack_libs = mkl_lapack include_dirs = /opt/intel/mkl70/include I can still install numpy but when I import numpy I get an error. pgmoses@head ~]$ python Python 2.5.2 (r252:60911, Sep 26 2008, 14:15:17) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-53)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import numpy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/data/pgmoses/lib/python/numpy/__init__.py", line 103, in <module> import linalg File "/data/pgmoses/lib/python/numpy/linalg/__init__.py", line 4, in <module> from linalg import * File "/data/pgmoses/lib/python/numpy/linalg/linalg.py", line 29, in <module> from numpy.linalg import lapack_lite ImportError: /data/pgmoses/lib/python/numpy/linalg/lapack_lite.so: undefined symbol: dgesdd_
It seem like my inclusion of the mkl libraries did not work, since it is trying to use lapack_lite.so. I was my impression that it should work any way. What is the underlying problem here? Best regards, Poul Georg Moses On 4:15 pm 09/26/08 "Robert Kern" <robert.kern@gmail.com> wrote:
On Fri, Sep 26, 2008 at 18:07, Poul Georg Moses <pgmoses@engineering.ucsb.edu> wrote:
Dear mailing list
I am trying to install numpy-1.1.1 on a cluster where I do not have root permission. I have succesfully installed \ python2.5.2. I am using the cite.cfg file to include the blas and atlas libraries. I have done that by setting the\ defaults to: library_dirs = /usr/lib include_dirs = /usr/include
You need
[DEFAULT] library_dirs = /usr/lib include_dirs = /usr/include
just like it is in the site.cfg.example
-- Robert Kern
"I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco _______________________________________________ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
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Poul Georg Moses
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Robert Kern