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.dauver...@gmail.com [mailto:edward.dauver...@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 <tlin...@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." <ma...@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 _______________________________________________ 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
