Re: relax installation with EPD -- July 29, 2013 - 17:39

Hi Mathilde,

I think Troels might be able to help you with this a bit better as he
has used the EPD (Enthought Python Distribution).  From memory, I
think he switched to standard Python as there were too many problems
with the EPD.  For example, this EPD bug that Troels reported:

http://gna.org/bugs/?20884

Can you use the standard Python in '/usr/bin/python'?  If you have
root access, as this is a fedora installation you can use all of the
'yum' commands at http://wiki.nmr-relax.com/Installation_linux.  Then
you need to make sure that when you type 'python' at the prompt that
you get the correct python at '/usr/bin/python'.  The EPD might have
played with paths or added aliases.  Try typing:

$ which python
/usr/bin/python
$ alias python
bash: alias: python: not found

This is what you should see.  Once you have the regular Python on your
system path, which you can see with:

$ echo $PATH

and you run the 'yum' commands in the relax wiki link above, then it
will be incredibly easy to compile the C modules!  Note that the scons
error you see is because scons is using /usr/bin/python but the
default Python in your shell environment is that from the EPD.  This
problem is eliminated when the standard Python is used.  Otherwise you
cannot use the standard scons but instead require a special scons for
the EPD.  I hope this helps.

Regards,

Edward



On 29 July 2013 13:32, mathilde lescanne <mathilde.lescanne@xxxxxxxxx> wrote:
> Hi all,
> I'am currently trying to install relax on my computer and I have some
> difficulties for compiling the C modules. I've tried to manually
> compile the modules but I failed... Notice that I use Enthough Python
> Distribution.
> Here is the output of the --info command:
>
> [mlescanne@localhost ~/relax_disp]$ relax --info
>
>
>
>                                   relax repository checkout r20477
>                           svn://svn.gna.org/svn/relax/branches/relax_disp
>
>                               Molecular dynamics by NMR data analysis
>
>                              Copyright (C) 2001-2006 Edward d'Auvergne
>                          Copyright (C) 2006-2013 the relax development team
>
> This is free software which you are welcome to modify and redistribute
> under the conditions of the
> GNU General Public License (GPL).  This program, including all
> modules, is licensed under the GPL
> and comes with absolutely no warranty.  For details type 'GPL' within
> the relax prompt.
>
> Assistance in using the relax prompt and scripting interface can be
> accessed by typing 'help' within
> the prompt.
>
> ImportError: relaxation curve fitting is unavailable, the
> corresponding C modules have not been compiled.
>
> Processor fabric:  Uni-processor.
>
>
> Hardware information:
>     Machine:                 i686
>     Processor:               i686
>     Endianness:              little
>     Total RAM size:          1967 Mb
>     Total swap size:         4102 Mb
>
> Operating system information:
>     System:                  Linux
>     Release:                 2.6.30.10-105.2.23.fc11.i686.PAE
>     Version:                 #1 SMP Thu Feb 11 07:05:37 UTC 2010
>     GNU/Linux version:       Fedora 11 Leonidas
>     Distribution:            fedora 11 Leonidas
>     Full platform string:
> Linux-2.6.30.10-105.2.23.fc11.i686.PAE-i686-with-fedora-11-Leonidas
>
> Python information:
>     Architecture:            32bit ELF
>     Python version:          2.7.3
>     Python branch:
>     Python build:            default, Apr 11 2012 18:02:54
>     Python compiler:         GCC 4.1.2 20080704 (Red Hat 4.1.2-44)
>     Libc version:            glibc 2.0
>     Python implementation:   CPython
>     Python revision:
>     Python executable:
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/bin/python
>     Python flags:            sys.flags(debug=0, py3k_warning=0,
> division_warning=0, division_new=0, inspect=0, interactive=0,
> optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0,
> ignore_environment=0, tabcheck=0, verbose=0, unicode=0,
> bytes_warning=0, hash_randomization=0)
>     Python float info:
> sys.float_info(max=1.7976931348623157e+308, max_exp=1024,
> max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
> radix=2, rounds=1)
>     Python module path:
> ['/data/people/mlescanne/fct_optimisation/relax/relax_disp',
> '/data/soft/ccpnmr_2.1.3_1/ccpnmr2.1/python',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python27.zip',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/plat-linux2',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/lib-tk',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/lib-old',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/lib-dynload',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages',
> '/data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/PIL']
>
> Python packages and modules (most are optional):
>
> Name               Installed    Version                    Path
> minfx              True         1.0.5
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/minfx
> bmrblib            True         1.0.3
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/bmrblib
> numpy              True         1.6.1
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/numpy
> scipy              True         0.10.1
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/scipy
> wxPython           True         2.8.10.1 (gtk2-unicode)
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/wx
> mpi4py             False
> epydoc             False
> optparse           True         1.5.3
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/optparse.pyc
> readline           True
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/lib-dynload/readline.so
> profile            True
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/profile.pyc
> bz2                True
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/lib-dynload/bz2.so
> gzip               True
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/gzip.pyc
> io                 True
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/io.pyc
> xml                True         0.8.4 (internal)
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/xml/__init__.pyc
> xml.dom.minidom    True
> /data/people/mlescanne/epd_free-7.3-2-rh5-x86/lib/python2.7/xml/dom/minidom.pyc
>
> relax information:
>     Version:                 repository checkout r20477
> svn://svn.gna.org/svn/relax/branches/relax_disp
>     Processor fabric:        Uni-processor.
>
> relax C modules:
>
> Module                        Compiled    File type    Path
> target_functions.relax_fit    False
>
> Here is the output when I type scons:
>
> [mlescanne@localhost ~/relax_disp]$  scons
> scons: Reading SConscript files ...
> The dependency 'minfx' has not been installed (see
> https://gna.org/projects/minfx/).
>
> I you dealt with this kind of problem I would be interested in the way
> you overcame it.
> Regards,
> Mathilde
>
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