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List: relax-users
Subject: RE: C modules not compiled
From: "Maciejewski,Mark W." <markm () uchc ! edu>
Date: 2014-11-14 13:58:34
Message-ID: a95e10a9cf7d499c81c968401034ce57 () NSO-ITEXC-MB22 ! uchc ! net
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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@gmail.com [mailto:edward.dauvergne@gmail.com] On Behalf Of \
Edward d'Auvergne
Sent: Friday, November 14, 2014 4:20 AM
To: Troels Emtekær Linnet
Cc: Maciejewski,Mark W.; relax-users@gna.org
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@gmail.com> 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@uchc.edu> 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)
> >
> > This is the relax-users mailing list
> > relax-users@gna.org
> >
> > To unsubscribe from this list, get a password reminder, or change
> > your subscription options, visit the list information page at
> > https://mail.gna.org/listinfo/relax-users
> >
> _______________________________________________
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password reminder, or change your
> subscription options, visit the list information page at
> https://mail.gna.org/listinfo/relax-users
_______________________________________________
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