Re: C modules not compiled -- November 14, 2014 - 10:37

Hi Mark,

I would also recommend that you sign up for the relax-announce mailing
list (https://mail.gna.org/listinfo/relax-announce/).  This list only
receives a few emails per year (see
http://news.gmane.org/gmane.science.nmr.relax.announce), and it is
used almost exclusively for announcing new relax versions, for example
relax 3.3.2 which I am in the process of releasing now (see
http://www.nmr-relax.com/download.html).  Since relax 3.2.3, there
have been the following releases:

http://wiki.nmr-relax.com/Relax_3.3.0
http://wiki.nmr-relax.com/Relax_3.3.1
http://wiki.nmr-relax.com/Relax_3.3.2

That last link will appear later today.  If you are performing either
a model-free or relaxation dispersion analysis, I would highly
recommend that you upgrade to relax 3.3.2 to obtain all the bug fixes
and Troels' huge relaxation dispersion speed ups
(http://wiki.nmr-relax.com/Relax_3.3.0).

Regards,

Edward


On 14 November 2014 10:19, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi Mark,
>
> Welcome to the relax mailing lists!  The problem you see could be due
> to a number of factors.  Firstly, could you check if you have the
> compiled file present on your system:
>
> $ ls -alh /usr/local/relax/target_functions/relax_fit.so
> $ file /usr/local/relax/target_functions/relax_fit.so
>
>
> If the file is there, then maybe you have a Python version problem.
> The C module was compiled using Python 2.7.  Normally this will then
> work for Python 2.5, 2.6 and 2.7 but not Python >= 3.1 (I have a Linux
> set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4
> that I regularly check this with).  You can check this by running
> relax and typing:
>
> relax> import target_functions.relax_fit
>
>
> For example in Python 3, this gives the error:
>
> relax> import target_functions.relax_fit
> Traceback (most recent call last):
>   File "<console>", line 1, in <module>
> ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so:
> undefined symbol: Py_InitModule4_64
>
>
> Maybe you will see something similar.  In any case you have two
> alternatives.  The first is to upgrade Python, if the relax_fit.so
> file exists, though this can be a painful and dangerous task on Linux
> systems (you can change the base 'relax' file to point to a different
> alternative Python version if you wish).  The second is as Troels
> suggests.  Install the scons program, the Python headers, and then
> just run 'scons' as root in the /usr/local/relax directory to compile
> the module yourself.
>
> Note that you only need this C module for fitting exponential curves
> for the R1, R2, or relaxation dispersion analyses.
>
> Regards,
>
> Edward
>
>
>
>
>
> On 14 November 2014 01:05, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
> > Hi.
> >
> > Try just write scons
> >
> > But this should only be for the source code.
> >
> > The packaged versions should already have the compiled C code in it.
> >
> > So this is weird.
> >
> > Can you run
> > relax - d
> > and post it here?
> >
> > Best
> > Troels
> > On 13 Nov 2014 22:34, "Maciejewski,Mark W." <markm@xxxxxxxx> wrote:
> >
> > > Hello,
> > >
> > > I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine
> > > except for the error:
> > > "ImportError: relaxation curve fitting is unavailable, the corresponding C
> > > modules have not been compiled."
> > >
> > > I installed relax using the command:
> > > scons install
> > >
> > > I have searched the archives and see that others have had similar
> > > problems, but cannot find a solution that works for me.
> > >
> > > Any suggestions on how to install or compile the C modules?
> > >
> > > Below is the output from "relax -info"
> > >
> > > Thanks,
> > > Mark
> > >
> > >
> > > [nmradmin@nmrbox_wisc ~]$ relax --info
> > >
> > >
> > >
> > >                                             relax 3.2.3
> > >
> > >                               Molecular dynamics by NMR data analysis
> > >
> > >                              Copyright (C) 2001-2006 Edward d'Auvergne
> > >                          Copyright (C) 2006-2014 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:                 x86_64
> > >     Processor:               x86_64
> > >     Processor name:          Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
> > >     Endianness:              little
> > >     Total RAM size:          3832 Mb
> > >     Total swap size:         3967 Mb
> > >
> > > Operating system information:
> > >     System:                  Linux
> > >     Release:                 2.6.32-504.1.3.el6.x86_64
> > >     Version:                 #1 SMP Tue Nov 11 17:57:25 UTC 2014
> > >     GNU/Linux version:       CentOS 6.6 Final
> > >     Distribution:            centos 6.6 Final
> > >     Full platform string:
> > > Linux-2.6.32-504.1.3.el6.x86_64-x86_64-with-centos-6.6-Final
> > >
> > > Python information:
> > >     Architecture:            64bit ELF
> > >     Python version:          2.6.6
> > >     Python branch:           tags/r266
> > >     Python build:            r266:84292, Jan 22 2014 09:42:36
> > >     Python compiler:         GCC 4.4.7 20120313 (Red Hat 4.4.7-4)
> > >     Libc version:            glibc 2.2.5
> > >     Python implementation:   CPython
> > >     Python revision:         84292
> > >     Python executable:       /usr/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.floatinfo(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=2.2204460492503131e-16,
> > > radix=2, rounds=1)
> > >     Python module path:      ['/usr/local/relax',
> > > '/usr/lib/python2.6/site-packages/requests-2.4.3-py2.6.egg',
> > > '/usr/lib/python2.6/site-packages/pip-1.5.6-py2.6.egg',
> > > '/usr/lib/python2.6/site-packages/distribute-0.7.3-py2.6.egg',
> > > '/usr/lib/python2.6/site-packages/setuptools-7.0-py2.6.egg',
> > > '/home/nmradmin', '/usr/local/ccpnmr/ccpnmr2.4/python',
> > > '/usr/lib64/python26.zip', '/usr/lib64/python2.6',
> > > '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk',
> > > '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload',
> > > '/usr/lib64/python2.6/site-packages',
> > > '/usr/lib64/python2.6/site-packages/PIL',
> > > '/usr/lib64/python2.6/site-packages/gst-0.10',
> > > '/usr/lib64/python2.6/site-packages/gtk-2.0',
> > > '/usr/lib64/python2.6/site-packages/webkit-1.0',
> > > '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode',
> > > '/usr/lib/python2.6/site-packages',
> > > '/usr/lib64/python2.6/site-packages/Scientific/linux2']
> > >
> > > Python packages and modules (most are optional):
> > >
> > > Name               Installed    Version                    Path
> > > minfx              True         1.0.7
> > > /usr/local/relax/minfx
> > > bmrblib            True         1.0.3
> > > /usr/local/relax/bmrblib
> > > numpy              True         1.9.1
> > > /usr/lib64/python2.6/site-packages/numpy
> > > scipy              True         0.7.2
> > > /usr/lib64/python2.6/site-packages/scipy
> > > wxPython           True         2.8.12.0 (gtk2-unicode)
> > > /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx
> > > matplotlib         True         0.99.1.1
> > >  /usr/lib64/python2.6/site-packages/matplotlib
> > > mpi4py             False
> > > epydoc             True         3.0.1
> > > /usr/lib/python2.6/site-packages/epydoc
> > > optparse           True         1.5.3
> > > /usr/lib64/python2.6/optparse.pyc
> > > readline           True
> > > /usr/lib64/python2.6/lib-dynload/readline.so
> > > profile            True
> > > /usr/lib64/python2.6/profile.pyc
> > > bz2                True
> > > /usr/lib64/python2.6/lib-dynload/bz2.so
> > > gzip               True
> > > /usr/lib64/python2.6/gzip.pyc
> > > io                 True
> > > /usr/lib64/python2.6/io.pyc
> > > xml                True         0.8.4 (internal)
> > >  /usr/lib64/python2.6/xml/__init__.pyc
> > > xml.dom.minidom    True
> > > /usr/lib64/python2.6/xml/dom/minidom.pyc
> > >
> > > relax information:
> > >     Version:                 3.2.3
> > >     Processor fabric:        Uni-processor.
> > >
> > > relax C modules:
> > >
> > > Module                        Compiled    File type    Path
> > > target_functions.relax_fit    False
> > > _______________________________________________
> > > relax (http://www.nmr-relax.com)
> > >
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