python 2.7.1
Download Packages
mkdir /usr/local/src/scipyBuildInstructions wget http://www.python.org/ftp/python/2.7.1/Python-2.7.1.tgz
pwd /usr/local/src/scipyBuildInstructions ls *.gz AMD-2.2.2.tar.gz fftw-3.2.2.tar.gz matplotlib-1.0.1.tar.gz numpy-1.5.1.tar.gz scipy-0.9.0.tar.gz UFconfig-3.6.0.tar.gz UMFPACK-5.5.1.tar.gz
build python 2.7.1
cd /usr/local/src/scipyBuildInstructions tar -zxvf Python-2.7.1.tgz cd Python-2.7.1 ./configure --prefix=/usr/local/src/apps/Python-2.7.1 --with-readline=gnu 2>&1 | tee log.configure.Python make -j8 2>&1 | tee log.makej8 make install 2>&1 | tee log.make_install_python
Test
/usr/local/src/apps/Python-2.7.1/bin/python Python 2.7.1 (r271:86832, Jun 29 2011, 09:08:45) [GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
Installation on the cluster users
scp -rp /usr/local/src/apps/Python-2.7.1/ admin:/sw/python/2.7.1
Module file for python 2.7.1
#%Module######################################################################
##
## python modulefile
##
proc ModulesHelp { } {
puts stderr "Sets up paths for python 2.7.1 "
}
module-whatis "adds python 2.7.1 directories to PATH etc. "
set base_path /sw/python
set python_base $base_path/2.7.1
prepend-path PATH $python_base/bin
prepend-path PYTHONPATH $python_base/lib/python2.7/site-packages
prepend-path LD_LIBRARY_PATH $python_base/lib/python2.7
prepend-path INCLUDE $python_base/include/python2.7
Module file usage
module load python/2.7.1
python 2.7.1-shared
CC="gcc -m64" cd //sw/python/2.7.1-shared cd /sw/python/2.7.1-shared/src tar -zxvf Python-2.7.1.tgz (cd Python-2.7.1) /sw/python/2.7.1-shared/src/Python-2.7.1 ./configure --enable-shared --prefix=/sw/python/2.7.1-shared/ 2>&1 | tee log.configure.Python make -j8 2>&1 | tee log.makej8 make install 2>&1 | tee log.make_install_python
Python 3.1.4
mkdir /tmp/python
cd /tmp/python
cp /tmp/Python-3.1.4.tgz .
tar -zxvf Python-3.1.4.tgz
module load intel-cc-11/11.1.072
module load intel-fc-11/11.1.072
module load intel-cmkl-11/11.1.072
module load intel-tools-11/11.1.072
module load intel-mpi/4.0.0.027
Test: which ifort
/sw/sdev/intel/Compiler/11.1/072/bin/intel64/ifort
./configure --prefix=/tmp/python --enable-zlib
[Python must also be compiled with the zlib module enabled for numpy]
make
make test
sudo make install
mv /tmp/python /sw/python/3.1.4/
cd /sw/python/3.1.4/bin
ln -s idel3 idle
ln -s pydoc3 pydoc
ln -s python3 python
Fixed the module file:
======================
pwd
/sw/com/modulefiles/python
[root@admin python]# more 3.1.4
#%Module######################################################################
##
## python modulefile
##
proc ModulesHelp { } {
puts stderr "Sets up paths for python and biopython"
}
module-whatis "adds python directories to PATH etc. "
set base_path /sw/python
set python_base $base_path/3.1.4
prepend-path PATH $python_base/bin
prepend-path PYTHONPATH $python_base/lib
./configure -help
`configure' configures python 3.1 to adapt to many kinds of systems.
Usage: ./configure [OPTION]... [VAR=VALUE]...
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
Defaults for the options are specified in brackets.
Configuration:
-h, --help display this help and exit
--help=short display options specific to this package
--help=recursive display the short help of all the included packages
-V, --version display version information and exit
-q, --quiet, --silent do not print `checking ...' messages
--cache-file=FILE cache test results in FILE [disabled]
-C, --config-cache alias for `--cache-file=config.cache'
-n, --no-create do not create output files
--srcdir=DIR find the sources in DIR [configure dir or `..']
Installation directories:
--prefix=PREFIX install architecture-independent files in PREFIX
[/usr/local]
--exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
[PREFIX]
By default, `make install' will install all the files in
`/usr/local/bin', `/usr/local/lib' etc. You can specify
an installation prefix other than `/usr/local' using `--prefix',
for instance `--prefix=$HOME'.
For better control, use the options below.
Fine tuning of the installation directories:
--bindir=DIR user executables [EPREFIX/bin]
--sbindir=DIR system admin executables [EPREFIX/sbin]
--libexecdir=DIR program executables [EPREFIX/libexec]
--sysconfdir=DIR read-only single-machine data [PREFIX/etc]
--sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
--localstatedir=DIR modifiable single-machine data [PREFIX/var]
--libdir=DIR object code libraries [EPREFIX/lib]
--includedir=DIR C header files [PREFIX/include]
--oldincludedir=DIR C header files for non-gcc [/usr/include]
--datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
--datadir=DIR read-only architecture-independent data [DATAROOTDIR]
--infodir=DIR info documentation [DATAROOTDIR/info]
--localedir=DIR locale-dependent data [DATAROOTDIR/locale]
--mandir=DIR man documentation [DATAROOTDIR/man]
--docdir=DIR documentation root [DATAROOTDIR/doc/python]
--htmldir=DIR html documentation [DOCDIR]
--dvidir=DIR dvi documentation [DOCDIR]
--pdfdir=DIR pdf documentation [DOCDIR]
--psdir=DIR ps documentation [DOCDIR]
Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
--enable-universalsdk[=SDKDIR]
Build against Mac OS X 10.4u SDK (ppc/i386)
--enable-framework[=INSTALLDIR]
Build (MacOSX|Darwin) framework
--enable-shared disable/enable building shared python library
--enable-profiling enable C-level code profiling
--enable-ipv6 Enable ipv6 (with ipv4) support
--disable-ipv6 Disable ipv6 support
--enable-big-digits[=BITS]
use big digits for Python longs [[BITS=30]]
Optional Packages:
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
--without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
--with-universal-archs=ARCH
select architectures for universal build ("32-bit",
"64-bit", "3-way", "intel" or "all")
--with-framework-name=FRAMEWORK
specify an alternate name of the framework built
with --enable-framework
--without-gcc never use gcc
--with-cxx-main=<compiler>
compile main() and link python executable with C++
compiler
--with-suffix=.exe set executable suffix
--with-pydebug build with Py_DEBUG defined
--with-libs='lib1 ...' link against additional libs
--with-system-ffi build _ctypes module using an installed ffi library
--with-dbmliborder=db1:db2:...
order to check db backends for dbm. Valid value is a
colon separated string with the backend names
`ndbm', `gdbm' and `bdb'.
--with-signal-module disable/enable signal module
--with-dec-threads use DEC Alpha/OSF1 thread-safe libraries
--with(out)-threads[=DIRECTORY]
disable/enable thread support
--with(out)-thread[=DIRECTORY]
deprecated; use --with(out)-threads
--with-pth use GNU pth threading libraries
--with(out)-doc-strings disable/enable documentation strings
--with(out)-tsc enable/disable timestamp counter profile
--with(out)-pymalloc disable/enable specialized mallocs
--with-wctype-functions use wctype.h functions
--with-fpectl enable SIGFPE catching
--with-libm=STRING math library
--with-libc=STRING C library
--with-wide-unicode Use 4-byte Unicode characters (default is 2 bytes)
--with-computed-gotos Use computed gotos / threaded dispatch in evaluation
loop (not available on all compilers)
Some influential environment variables:
CC C compiler command
CFLAGS C compiler flags
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CPP C preprocessor
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
Report bugs to <http://bugs.python.org/>.