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howto:compiling_python_2_7_3 [2012/09/17 15:04]
adymond [Berkley style databases] 		howto:compiling_python_2_7_3 [2021/12/09 16:42] (current)
Line 96: Line 96:
 Got quite a lot of failures here... Got quite a lot of failures here...
  
- +FIXME please...
-# +
 ===== Download and Configuration ===== ===== Download and Configuration =====
  
Line 130: Line 128:
 Where Where
   * dl is depreciated since Python 2.6, use ctypes instead.   * dl is depreciated since Python 2.6, use ctypes instead.
-  * Beginning in 2.3 some Unix versions of Python may have a bsddb185 +  * Beginning in 2.3 some Unix versions of Python may have a bsddb185 module. This is present only to allow backwards compatibility with systems which ship with the old Berkeley DB 1.85 database library. The bsddb185 module should never be used directly in new code. The module has been removed in Python 3. If you find you still need it look in PyPI.
-  module. This is present only to allow backwards compatibility with systems +
-  which ship with the old Berkeley DB 1.85 database library. The bsddb185 +
-  module should never be+
   * imageop and sunaudiodev, do not work on 64 bit systems.   * imageop and sunaudiodev, do not work on 64 bit systems.
-used directly in new code. The module has been removed in Python 3. If you find you still need it look in PyPI. 
-  * the audio and image operation modules, arent assumed unneeded. 
- 
 ===== Test ===== ===== Test =====
  
Line 166: Line 158:
 As for test_gdb, which i assume is the GNU debugger interfacing module, more As for test_gdb, which i assume is the GNU debugger interfacing module, more
 information on the error can be obtained by information on the error can be obtained by
-./python ../Lib/test/regrtest.py -v test_gdb+  $ ./python ../Lib/test/regrtest.py -v test_gdb
  
 If this is good enough for your applications proceed with the installation. If this is good enough for your applications proceed with the installation.
Line 241: Line 233:
   $ python setup.py install   $ python setup.py install
  
-==== Numpy ====+==== NumPy and SciPy====
  
 [[http://numpy.scipy.org/|NumPy]] is the fundamental package for scientific computing with Python. It [[http://numpy.scipy.org/|NumPy]] is the fundamental package for scientific computing with Python. It
Line 252: Line 244:
  
 Based on [[http://www.scipy.org/Installing_SciPy/Linux|installation guide]]. Based on [[http://www.scipy.org/Installing_SciPy/Linux|installation guide]].
- 
- 
-==== Build ATLAS(3.9.32) with complete Lapack(3.2.2) 
- 
-From a temporary director ( ie Scratch ) download the latest atlas from Source 
-forge 
-  $ wget http://www.netlib.org/lapack/lapack-3.4.0.tgz 
-  $ wget http://tenet.dl.sourceforge.net/project/math-atlas/Stable/3.10.0/atlas3.10.0.tar.bz2 
-  $ tar -xf atlas3.10.0.tar.bz2 
-  $ mkdir ATLAS/BUILD 
-  $ cd  ATLAS/BUILD 
-  $ ../configure -b 64 -Fa alg -fPIC --shared \ 
-  --with-netlib-lapack-tarfile=../../lapack-3.4.0.tgz --prefix=$HOME/usr  
-make 
-cd lib 
-make shared 
-make ptshared 
-cd .. 
-make install 
  
 === BLAS and LAPACK libraries === === BLAS and LAPACK libraries ===
Line 299: Line 272:
  -->   LAPACK TESTING SUMMARY  <--  -->   LAPACK TESTING SUMMARY  <--
        Processing LAPACK Testing output found in the TESTING  direcory        Processing LAPACK Testing output found in the TESTING  direcory
-SUMMARY        nb test run numerical error other error   +  SUMMARY        nb test run numerical error other error   
-================       =========== =================       ================   +  REAL         1077227 0 (0.000%) 0   (0.000%)  
-REAL   1077227 0 (0.000%) 0   (0.000%)  +  DOUBLE PRECISION 1078039 0 (0.000%) 0   (0.000%)  
-DOUBLE PRECISION 1078039 0 (0.000%) 0   (0.000%)  +  COMPLEX                 522814 0 (0.000%) 0   (0.000%)  
-COMPLEX 522814 0 (0.000%) 0   (0.000%)  +  COMPLEX16 552410 0 (0.000%) 0   (0.000%)  
-COMPLEX16 552410 0 (0.000%) 0   (0.000%)  +  --> ALL PRECISIONS 3230490 0 (0.000%) 0   (0.000%)
---> ALL PRECISIONS 3230490 0 (0.000%) 0   (0.000%)+
  
 if all went well if all went well
   $ cp -iv lib* $HOME/local/lib64   $ cp -iv lib* $HOME/local/lib64
 +  
 +To convert the built static libraries to dynamic libraries, the following bash
 +loop is used
 +  $ for LIB in *.a ; do
 +      DIR=${LIB}_contents
 +      SOLIB=${LIB%.*}.so
 +      echo $SOLIB
 +      mkdir $DIR
 +      cd $DIR
 +      ar -x ../$LIB
 +      cd -
 +      gfortran -shared -Wl,-soname=$SOLIB -o $SOLIB ${DIR}/*.o
 +    done;
 +  $ ln -snf librefblas.so libblas.so
  
-#Compile the shared object (so) or dynamic libraries for blas and lap#ack +Copy the shared object or dynamic libraries to your library folder 
-#  $ gcc -shared BLAS/SRC/*.o -o libblas.so +  $ cp -iv lib*.so $HOME/local/lib64 
-#  $ gcc -shared SRC/*.o -o liblapack.so +[warning dynamic libaries not fully tested] 
-#Basic library checks, +  
-#  $ ipython +
-#    $ from ctypes import * +
-#    $ blaslib = cdll.LoadLibrary('libblas.so') +
-#    $ array = (c_float*4)() +
-#    $ array[:] = [4.0, 3.14159, 4.1, 2.0] +
-#    $ print blaslib.isamax_(byref(c_int(len(array))), array, byref(c_int(1))) +
-#  The output should be 3. +
-#    $ lapacklib = cdll.LoadLibrary('liblapack.so') +
-#    $ n, info = 5, c_int() +
-#    $ diag, offdiag = (c_double*n)(), (c_double*(n-1))() +
-#    $ diag[:], offdiag[:] = [2.0]*n, [-1.0]*(n-1) +
-#    $ r=lapacklib.dsterf_(byref(c_int(n)), diag, offdiag, byref(info)) +
-#    $ print '[', ', '.join('%g'%v for v in diag[:]), ']' +
-#  You should get output like [ 0.267949, 1, 2, 3, 3.73205 ], the eigenvalues +
-#  for this special matrix.  +
- +
-#If so congratulations. Then copy the compiled libaries to your $HOME/usr +
-#directory +
-#  $ cp lib* $HOME/usr/lib +
 === Numpy building, testing and installation === === Numpy building, testing and installation ===
  
-#Download the last version of numpy source, in your scratch folder. 
-#  $ cd ~/scratch 
-#  $ easy_install --editable --build-directory . numpy 
-#  $ cd numpy 
-#Or alternatively 
 Download numpy Download numpy
   $ cd ~/scratch   $ cd ~/scratch
Line 347: Line 308:
   $ cd numpy-1.6.2   $ cd numpy-1.6.2
  
-#Before continuing read both INSTALL.txt and site.cfg.example +== build using shared object libraries == 
-#  $ echo '[DEFAULT]' > site.cfg +  $ echo "[DEFAULT]" > site.cfg 
-#  $ echo "library_dirs = $HOME/usr/lib64:$HOME/usr/lib" >> site.cfg +  $ echo "library_dirs = $HOME/local/lib64" >> site.cfg 
-#  $ echo "include_dirs = $HOME/usr/include:$HOME/usr/include/python2.7" >> site.cfg+  $ echo "include_dirs = $HOME/local/include"  >> site.cfg 
 +  $ python setup.py build --fcompiler=gnu95 
 +  $ python setup.py install
  
  
-#nun python setup.py install. +== build using static lapack and blas libraries (for interests sake only) ==
-#  $ python setup.py build --fcompiler=gnu95 +
-#  $ python setup.py install +
-#started at 09:25 +
- +
-#try unsetting CPPFLAGS , and setting include dirs in set.cfg, +
-#maybe this will avoid +
-#_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ +
-#[enabled by default] +
-#gcc -pthread _configtest.o -o _configtest +
-#_configtest.o: In function `main': +
-#/tmp/adymond/numpy-1.6.2/_configtest.c:6: undefined reference to `exp' +
-#while -lm (linking to math library should fix that, how do i add that to gcc +
- +
-#  $ unset CPPFLAGS +
-#  $ export CPPFLAGS='-lm' +
- +
- +
-#Sidenote: To compile with BLAS and LAPACK, set the following variables before +
- building +
-#  $ export ATLAS=None +
-#  $ export BLAS=None +
-#  $ export LAPACK=None+
  
 Set blas and lapack paths Set blas and lapack paths
Line 381: Line 322:
   $ export BLAS=$HOME/local/lib64/librefblas.a   $ export BLAS=$HOME/local/lib64/librefblas.a
   $ export LAPACK=$HOME/local/lib64/liblapack.a   $ export LAPACK=$HOME/local/lib64/liblapack.a
- 
 Build and install Build and install
   $ python setup.py build --fcompiler=gnu95   $ python setup.py build --fcompiler=gnu95
 +
 +NB to build without lapack and blas libraries, do the following
 +  $ export ATLAS=None
 +  $ export BLAS=None
 +  $ export LAPACK=None
 +then build
 +
 +speed difference: using LAPACK and BLAS libraries numpy testing takes between
 +10 and 12s, without the libraries numpy.test() takes exactly the same amount
 +of time?
 +
 +== testing ==
 +  $ mkdir -p /tmp/$USER/numpy-1.6.2_testing
 +  $ python setup.py install --prefix=/tmp/$USER/numpy-1.6.2_testing
 +  $ ipython
 +    $ import os, sys
 +    $ sys.path.insert(0,'/tmp/%s/numpy-1.6.2_testing/lib/python2.7/site-packages'  % os.environ['USER'])
 +    $ import numpy
 +    $ numpy.test()
 +If all the test were passed, rm the testing directory and install numpy
 +  $ rm -r /tmp/$USER/numpy-1.6.2_testing
   $ python setup.py install   $ python setup.py install
  
-Then test it (note this requires nose) +
-  $ cd ~ +
-  $ ipython +
-  $ import numpy +
-  $ numpy.test() +
-   +
- +
 === Scipy, minimal install === === Scipy, minimal install ===
  
   $ cd ~/scratch   $ cd ~/scratch
   $ wget http://tenet.dl.sourceforge.net/project/scipy/scipy/0.10.1/scipy-0.10.1.tar.gz   $ wget http://tenet.dl.sourceforge.net/project/scipy/scipy/0.10.1/scipy-0.10.1.tar.gz
-  $ tar -xf scipy-0.10.1.tar.gz +  $ tar -xf scipy-0.10.1.tar.gz
   $ cd scipy-0.10.1/   $ cd scipy-0.10.1/
-Set blas and lapack paths +  $ python setup.py build #takes about 10 minutes to build
-  $ export ATLAS=None +
-  $ export BLAS=$HOME/local/lib64/librefblas.a +
-  $ export LAPACK=$HOME/local/lib64/liblapack.a +
-Build it, which takes a while +
-  $ python setup.py build +
-Install it +
-  $ python setup.py install +
  
- +testing, 
-Once the build has been successfully completed, its time to install and test +  $ mkdir -p /tmp/$USER/scipy-0.10.1 
-scipy +  $ python setup.py install --prefix=/tmp/$USER/scipy-0.10.1_testing
-  $ python setup.py install +
-  $ cd ~+
   $ ipython   $ ipython
-  $ import scipy +    $ import os, sys 
-  $ scipy.test() +    $ sys.path.insert(0,'/tmp/%s/scipy-0.10.1_testing/lib/python2.7/site-packages'  % os.environ['USER']) 
 +    $ import scipy 
 +    $ scipy.test()
 which did not work 100 % :( which did not work 100 % :(
   FAILED (KNOWNFAIL=13, SKIP=41, failures=1)   FAILED (KNOWNFAIL=13, SKIP=41, failures=1)
   Out[2]: <nose.result.TextTestResult run=5101 errors=0 failures=1>   Out[2]: <nose.result.TextTestResult run=5101 errors=0 failures=1>
  
-=== matplotlib / pylab ===+If testing satisfactory, rm the testing directory and install scipy 
 +  $ rm -r /tmp/$USER/scipy-0.10.1_testing 
 +  $ python setup.py install 
 +==== matplotlib / pylab ====
  
   Download latest version from source forge (version 1.1 in this case)   Download latest version from source forge (version 1.1 in this case)
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