Hello, list!
First of all, this will be a long message, due to the complexity of
our environment.
So, please be patient with my question.
I am trying to run a simple django application in a cluster
environment.
And, my application hangs while it imports scipy.linalg, and both
scipy and apache do not write out error messages.
When I run my application in my local python shell, it imports
scipy.linalg. But, somehow it does not when it is run by apache.
So, after reading this message, please share any ideas about how to
debug this problem or new solutions to address this issue or deploy my
application.
Now, let me explain our current setup.
1. OS
-- The server is a compute cluster where each node runs centos 6 that
was installed from a clean version of centos6 minimal.
2. Apache
-- Apache 2.2 was also manually installed from one of default linux
repository.
To be specific, it was installed from its source code together with
httpd-dev.
3. Python
-- Python 2.7.2 was also installed from its source code across all
nodes in the cluster. Its source code was downloaded from python.org's
ftp.
4. Python packages: nose, numpy, scipy
-- Nose 1.1.2 was downloaded from pypi.python.org and installed from
its source code.
-- numpy 1.6.1 was downloaded and installed from a linux repository.
When building numpy, gnu95 fortran complier was used.
-- To install scipy, we installed atlas-3.8.4, lapack-3.3.1, and blas
from their source code.
----- atlas was from sourceforge's 3.8.4 stable version. To compile
altas, gcc was used.
----- lapack and blas was obtained from netlib.org's repository. To
compile the package of lapack and blas, gforan was used.
----- Finally, after exporting paths to blas, lapack, and atlas,
scipy-0.9.0 was installed from its source code.
scipy was obtained from sourceforge.net's repository.
All of the above were installed in the same way across all nodes in
our cluster.
Since I am the only user of the cluster who needs to run python web
applications,
I installed python virtualenv package in my local directory.
Within my virtual environment, django-1.3 and pysal-1.2 (our own
package) were installed.
To deploy my web applications, we used mod_wsgi.
mod-wsgi was compiled with python-2.7.2 and loaded into apache-2.2.
My application is as follows:
import os, sys, site, time
print >> sys.stderr, str(time.time()) + ':' + str(time.ctime())
root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__),
'..'))
root_dir += '/myunghwa_python2'
print >> sys.stderr, root_dir
print >> sys.stderr, os.listdir(root_dir)
site.addsitedir(os.path.join(root_dir, 'lib/python2.7/site-packages'))
sys.path.append(root_dir)
print >> sys.stderr, sys.path
print >> sys.stderr, os.listdir(sys.path[-2])
os.environ['PYTHON_EGG_CACHE'] = '/home/mhwang3/repos/django/python-
eggs'
os.environ['DJANGO_SETTINGS_MODULE'] = 'wsgi.settings'
def application(environ, start_response):
status = '200 OK'
output = 'Hello!'
try:
t1 = time.time()
print >> sys.stderr, "Going to import numpy: " +
str(time.time()) + ":" + str(time.time() - t1)
import numpy
print >> sys.stderr, "imported numpy"
print >> sys.stderr, "Going to import scipy"
import scipy
print >> sys.stderr, "imported scipy
from:"+str(scipy.__path__)
print >> sys.stderr, "Going to import scipy.linalg" +
str(time.time()) + ':' + str(time.time() - t1)
import scipy.stats
print >> sys.stderr, "imported scipy.linalg: " +
str(time.time()) + ':' + str(time.time() - t1)
print >> sys.stderr, "Going to import pysal"
import pysal
print >> sys.stderr, "imported pysal"
except:
print >> sys.stderr, "exception"
raise
response_headers = [('Content-type', 'text/plain'),
('Content-Length', str(len(output)))]
start_response(status, response_headers)
return [output]
Basically, it is a 'hello world' application that tests if numpy,
scipy, and pysal can be imported.
In the attached file, lines 4-9 are just adding paths to django and
pysal so that apache knows where to find these packages.
Also, to let apache know where to find atlas-related packages, the
path to those packages was added to the LD_LIBRARY_PATH environment
variable in the /etc/sysconfig/httpd file.
When I first ran my application, it just hung and wrote no message.
So, across scipy.linalg modules, I added print out statements to
figure out at which point the import was broken.
Here is the messages I got when I imported scipy.linalg in my local
python shell.
########################
starting linalg.__init__
pre __init__.__doc__
pre __init__.__version__
pre __init__.misc
pre __init__.basic
#######################
Starting basic
pre basic.flinalg
pre basic.lapack
pre basic.misc
pre basic.scipy.linalg
pre basic.decomp_svd
pre __init__.decomp
################
starting decomp
pre decomp.array et al.
pre decomp.calc_lwork
pre decomp.LinAlgError
pre decomp.get_lapack_funcs
pre decomp.get_blas_funcs
####################
Starting blas
pre blas.scipy.linalg.fblas
pre blas.scipy.linalg.cblas
pre __init__.decomp_lu
pre __init__.decomp_cholesky
pre __init__.decomp_qr
#################
Starting special_matrices
pre special_matrices.math
pre special_matrices.np
pre __init__.decomp_svd
pre __init__.decomp_schur
##################
starting schur...
pre decomp_schur.misc
pre decomp_schur.LinAlgError
pre decomp_schur.get_lapack_funcs
pre decomp_schur.eigvals:1320454147.23Fri Nov 4 17:49:07 2011
schur testing
pre __init__.matfuncs
#####################
Starting matfuncs
pre matfuncs. asarray et al
pre matfuncs.matrix
pre matfuncs.np
pre matfuncs.misc
pre matfuncs.basic
pre matfuncs.special_matrices
pre matfuncs.decomp
pre matfuncs.decomp_svd
pre matfuncs.decomp_schur
pre __init__.blas
pre __init__.special_matrices
When scipy.linalg is successfully imported, I should get these
messages.
But, when my web application tried to import scipy.linalg, the output
messages stop at line 41.
At line 41, decomp_schur.py tries to import decomp.py. Since decomp.py
was already imported at line 16, scipy ignores it and continues to
import other modules in my local shell.
But, somehow, in apache-mod_wsgi environment, scipy failed to ignore
or reload decomp.py and seems to kill my web application.
This is really odd, because python does not give any message about
this error and neither does apache. apache just hangs without sending
out any response.
Since lapack and blas functions were imported successfully, the
problem seems not related to path setup.
If anyone in the list has any insights into or experience into this
kind of symptom,
please share your insights and experience. In particular, debugging
techniques or less-known installation/compilation problems would be
helpful.
I feel like I am at a dead end. So, please help me.
Thanks for reading this post.
I will look forward to your responses.
-- Myunghwa-Hwang Hwang
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