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6,358 bytes added, 14:18, 15 October 2015
Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.
__TOC__
 
== Download from ==
Download from:<br>
</source>
It will make a '''bash''' activation script in: '''$HOME/Enthought/Canopy_64bit/User/bin/activate'''
That will make an activation source file.
PATH="$VIRTUAL_ENV/bin:$PATH"
export PATH
 
# unset PYTHONHOME if set
The path to the Canopy installation is: '''/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64'''.
=== Install ===
<source lang="bash">
tcsh
canopy_cli --common-install --no-gui-setup --install-dir $PWD
</source>
 
=== Make tcsh activation script ===
 
Now we want to make a tcsh activation script.
<source lang="bash">
cat > cshr_epd cshrc_epd << 'EOF'
set VIRTUAL_ENV_DISABLE_PROMPT=1
endif
'EOF'
</source>
 
Then let us see it, and change the one important line.
<source lang="bash">
set EPDUSER=$PWD/Canopy_64bit/User
# Sed can use any separator instead of / in the s command. Just use something that is not encountered in the path: s+AAA+BBB+
sed -i "s+MYINSTALLDIR+$EPDUSER+g" cshrc_epd
grep "set VIRTUAL_ENV" cshrc_epd
</source>
 
=== Add to shared cshrc ===
Let the user ''software''' has a shared '''cshrc''' file, which all users with source from their own '''$HOME/.cshrc''' file.
 
<source lang="bash">
cat >> $HOME/cshrc << EOF
#--------------------------------------------------------------
# Enthought Python distribution
# Canopy
#--------------------------------------------------------------
# Alias 'ap' as activate python.
alias ap 'source $PWD/cshrc_epd'
EOF
</source>
 
=== Source shared cshrc for all users ===
Each user needs to put in their '''.cshrc''' file
 
<source lang="bash">
source /sbinlab2/software/cshrc
</source>
 
== Install Minfx and Bmrblib and mpi4py ==
 
# [[Minfx#Install | Minfx]]
# [[Bmrblib#Install | Bmrblib]]
# [[Mpi4py#Install | Mpi4py]]
 
== Scripts to run relax ==
See [[Installation_linux#mpi4py | linux mpi4py installtion]] if you want to run multi processor mode.
 
Here we have one computer, with 24 cores, called '''haddock'''.
We want to have the users logon on to haddock, when they want to do multi-core calculations.
 
Make these scripts available somewhere in PATH.
 
For private single computer
<source lang="bash">
#!/bin/tcsh
 
# Set the lax version used for this script.
set RELAX=/sbinlab2/software/NMR-relax/relax_trunk/relax
# Then see itRun relax in multi processor mode.cat cshr_epdset RELAXRUN="$RELAX $argv"
# Activate python
ap
$RELAX $argv
</source>
 
For multi core computations.
<source lang="bash">
#!/bin/tcsh
 
# Set the lax version used for this script.
set RELAX=/sbinlab2/software/NMR-relax/relax_trunk/relax
 
# Set number of available CPUs.
#set NPROC=`nproc`
set NPROC=5
set NP=`echo $NPROC + 1 | bc `
 
# Run relax in multi processor mode.
set RELAXRUN="/usr/lib64/openmpi/bin/mpirun -np $NP $RELAX --multi='mpi4py' $argv"
 
# Check machine, since only machine haddock have openmpi-devel installed
if ( $HOST != "haddock") then
echo "You have to run on haddock. I do it for you"
ssh haddock -Y -t "cd $PWD; ap; $RELAXRUN; /bin/tcsh"
else
# Activate python
ap
/usr/lib64/openmpi/bin/mpirun -np $NP $RELAX --multi='mpi4py' $argv
endif
</source>
 
== Compile program issues with scons ==
<source lang="bash">
# Go into install directory
tcsh
set IND=/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64
cd $IND
# setenv PYTHON_LIBRARY XXXXX/libpython2.7.so
# libpython2.7.so
find . -name libpython2.7.so -type f
./appdata/canopy-1.4.0.1938.rh5-x86_64/lib/libpython2.7.so
./appdata/canopy-1.4.0.1938.rh5-x86_64/lib/python2.7/config/libpython2.7.so
./Canopy_64bit/User/lib/libpython2.7.so
./Canopy_64bit/System/lib/libpython2.7.so
# setenv PYTHON_EXECUTABLE XXXXX/python2.7
# find . -name python\*
# find . -name python -type f
# find . -name python2.7 -type f
./appdata/canopy-1.4.0.1938.rh5-x86_64/bin/python2.7
./Canopy_64bit/User/bin/python
./Canopy_64bit/User/bin/python2.7
./Canopy_64bit/System/bin/python
./Canopy_64bit/System/bin/python2.7
# setenv PYTHON_INCLUDE_DIR XXXX/
# find . -name Python.h -type f
./appdata/canopy-1.4.0.1938.rh5-x86_64/include/python2.7/Python.h
</source>
 
=== Python.h ===
<source lang="bash">
[tlinnet@tomat disp_spin_speed]$ scons
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
gcc -o target_functions/relax_fit.os -c -I/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/include/python2.7 -fPIC target_functions/relax_fit.c
target_functions/relax_fit.c:21:20: error: Python.h: No such file or directory
target_functions/relax_fit.c:30: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
target_functions/relax_fit.c:79: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
target_functions/relax_fit.c:117: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
target_functions/relax_fit.c:142: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
target_functions/relax_fit.c:153: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
target_functions/relax_fit.c:171: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'relax_fit_methods'
target_functions/relax_fit.c: In function 'initrelax_fit':
target_functions/relax_fit.c:227: error: 'relax_fit_methods' undeclared (first use in this function)
target_functions/relax_fit.c:227: error: (Each undeclared identifier is reported only once
target_functions/relax_fit.c:227: error: for each function it appears in.)
scons: *** [target_functions/relax_fit.os] Error 1
scons: building terminated because of errors.
</source>
Then try
<source lang="bash">
#setenv PYTHON_LIBRARY $IND/appdata/canopy-1.4.0.1938.rh5-x86_64/lib/libpython2.7.so
#setenv PYTHON_EXECUTABLE $IND/appdata/canopy-1.4.0.1938.rh5-x86_64/bin/python2.7
setenv PYTHON_INCLUDE_DIR $IND/appdata/canopy-1.4.0.1938.rh5-x86_64/include/python2.7
</source>
 
Setting system environment variable '''PYTHON_INCLUDE_DIR''' to point to the dir with '''Python.h''' solved the problem.
 
=== For MAC ===
==== Python.h ====
<source lang="bash">
echo "PYTHON_INCLUDE_DIR=/Applications/Canopy.app/appdata/canopy-1.4.0.1938.macosx-x86_64/Canopy.app/Contents/include/python2.7" >> $HOME/.bash_profile
 
echo "export PYTHON_INCLUDE_DIR" >> $HOME/.bash_profile
</source>
 
==== Wx program running on Canopy 1.4 on OS X "Please run with a Framework build of python" ====
See https://support.enthought.com/entries/22601196-wxPython-2-8-and-2-9 to fix it.
 
=== For Linux ===
==== Python.h ====
<source lang="bash">
setenv PYTHON_INCLUDE_DIR /sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.1.1975.rh5-x86_64/include/python2.7
 
# Or
cd /sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.1.1975.rh5-x86_64/include
ln -s /sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/appdata/canopy-1.4.1.1975.rh5-x86_64/include/python2.7 python2.7
</source>
 
== See also ==
[[Category:Installation | Installation category]]
[[Category:Installation]]
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