RE: C modules not compiled -- November 14, 2014 - 15:04

Troels and Edward,

Thanks for your assistance. Everything is working fine now.

I was using the source code to install (relax-3.3.2.src) and the relax_fit.so 
file was not present causing the problem.
From the base directory I typed "scons", which created the relax_fit.so file, 
and then "scons install " to install the program in /usr/local/relax and 
create the byte-compiled *.pyc files and everything was fine. I did not 
realize that I needed  to perform the "scons" command first before the "scons 
install" command.

I also downloaded the pre-build relax-3.3.2.GNU-Linux.x86_64 package and it 
ran fine as well.

Thanks again,

Mark

-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On 
Behalf Of Edward d'Auvergne
Sent: Friday, November 14, 2014 4:20 AM
To: Troels Emtekær Linnet
Cc: Maciejewski,Mark W.; relax-users@xxxxxxx
Subject: Re: C modules not compiled

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
> > _______________________________________________
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> >
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> >
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