Re: A great thank you from SBiNLab, Copenhagen University - (And a small system test fail in 3.1.5 related to python numpy:-) ) -- February 06, 2014 - 10:45

Hi Troels,


> Thank you for releasing version 3.1.5.

You're welcome!


> And I am happy to report that the use of relax in our lab is now spreading.

This is great to hear.


> A bachelor student have the last months extensively used relax to analyse
> recorded CPMG data sets, where I see that the data-flow and analysis have
> become much easier for us.
> Thank you!

All feedback is gladly welcomed, so if this student has ideas for
making the analysis even simpler, then please point them to the
mailing lists to communicate the ideas.  For example they may know how
to improve the relaxation dispersion chapter of the manual.  Although
this chapter is large, I would not call it complete.  Your student
would probably have lots of valuable ideas for improving the chapter
for others.


> And I am also happy to see that a post-doc is extremely happy for using the
> GUI interface for R1+R2 Relaxation curve-fitting analysis and NOE analysis.
>
> And from here I would like to express from several users, that your
> extensive manual is of absolute very very high value. That is fantastic.
> That is such a great amount of work.
>
> Thank you!
>
> Cheers from here!
> Troels Linnet
> On behalf of the NMR students in
> SBiNLab, BIOcenter, Copenhagen University

The manual is extensive but it could still be significantly improved.
And because it is so large, it is impossible for me to keep it
perfectly up to date.  I would also say that it is incomplete, as the
subject of dynamics in NMR is rather complicated.  Therefore if anyone
in your group has suggestions for improvements, these would be of
great benefit.  Just point them to the mailing lists.  If they have
suggested text to add or modify, that would be even better ;)

For the float16 bug, could you submit a bug report at
http://gna.org/bugs/?func=additem&group=relax.  This is to help other
users who encounter the same bug, and to improve the release notes by
pointing to a proper bug report.  It would be useful to include a link
to the original report
(http://thread.gmane.org/gmane.science.nmr.relax.devel/4958).  The
solution is very easy.  This bug is of very low significance as it
only affects that frame order test (as well as the frame order test
data generation scripts) on 32-bit systems where numpy.float16 is not
defined.

Cheers,

Edward


> -----------------
> I will finish off with a small report that I at the moment get a small
> system test fail in 3.1.5
>
> I think it is related to a numpy version?
> We have 1.4.1 from our Red-hat distribution.
>     from numpy import array, cross, dot, float16, float64, transpose, zeros
> ImportError: cannot import name float16
>
> Is there a requirement version number for numpy ?
>
> --------------------------------
> [software@haddock relax-3.1.5]$ ./relax -x
> Echoing of user function calls has been enabled.
>
>
> =============================
> = System / functional tests =
> =============================
>
> ....................................................................E...............................................................................................................................................................................................................................................................................................
> ======================================================================
> ERROR: Generate the rotor2 distribution of CaM.
> ----------------------------------------------------------------------
>
>
>
>                                             relax 3.1.5
>
>                               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.
>
> Processor fabric:  Uni-processor.
>
> Traceback (most recent call last):
>   File
> "/sbinlab2/software/NMR-relax/relax-3.1.5/test_suite/system_tests/frame_order.py",
> line 645, in test_generate_rotor2_distribution
>
> self.interpreter.run(script_file=self.cam_path+'generate_rotor2_distribution.py')
>   File "/sbinlab2/software/NMR-relax/relax-3.1.5/prompt/interpreter.py",
> line 278, in run
>     return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, quit=self.__quit_flag,
> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
>   File "/sbinlab2/software/NMR-relax/relax-3.1.5/prompt/interpreter.py",
> line 576, in run_script
>     return console.interact(intro, local, script_file, quit,
> show_script=show_script, raise_relax_error=raise_relax_error)
>   File "/sbinlab2/software/NMR-relax/relax-3.1.5/prompt/interpreter.py",
> line 468, in interact_script
>     exec_script(script_file, local)
>   File "/sbinlab2/software/NMR-relax/relax-3.1.5/prompt/interpreter.py",
> line 341, in exec_script
>     runpy.run_module(module, globals)
>   File "/usr/lib64/python2.6/runpy.py", line 140, in run_module
>     fname, loader, pkg_name)
>   File "/usr/lib64/python2.6/runpy.py", line 34, in _run_code
>     exec code in run_globals
>   File
> "/sbinlab2/software/NMR-relax/relax-3.1.5/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py",
> line 15, in <module>
>     from test_suite.shared_data.frame_order.cam.generate_base import Main
>   File
> "/sbinlab2/software/NMR-relax/relax-3.1.5/test_suite/shared_data/frame_order/cam/generate_base.py",
> line 27, in <module>
>     from numpy import array, cross, dot, float16, float64, transpose, zeros
> ImportError: cannot import name float16
>
> ----------------------------------------------------------------------
> Ran 356 tests in 922.788s
>
> FAILED (errors=1)
>
>
> ==============
> = Unit tests =
> ==============
>
> ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> ----------------------------------------------------------------------
> Ran 1272 tests in 18.364s
>
> OK
>
>
> =============
> = GUI tests =
> =============
>
> ....................................................................
> ----------------------------------------------------------------------
> Ran 68 tests in 200.113s
>
> OK
>
>
> ===================================
> = Summary of the relax test suite =
> ===================================
>
>
>
> Optional packages/modules
> =========================
>
> No tests skipped due to missing modules.
>
>
>
> Synopsis
> ========
>
> System/functional tests
> ................................................................. [ Failed ]
> Unit tests
> ..................................................................................
> [ OK ]
> GUI tests
> ...................................................................................
> [ OK ]
> Synopsis
> ................................................................................
> [ Failed ]
> -------------------------
>
> [software@haddock relax-3.1.5]$ ./relax -i
>
>
>
>                                             relax 3.1.5
>
>                               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.
>
> Processor fabric:  Uni-processor.
>
>
> Hardware information:
>     Machine:                 x86_64
>     Processor:               x86_64
>     Endianness:              little
>     Total RAM size:          24013 Mb
>     Total swap size:         26191 Mb
>
> Operating system information:
>     System:                  Linux
>     Release:                 2.6.32-431.el6.x86_64
>     Version:                 #1 SMP Sun Nov 10 22:19:54 EST 2013
>     GNU/Linux version:       Red Hat Enterprise Linux Server 6.5 Santiago
>     Distribution:            redhat 6.5 Santiago
>     Full platform string:
> Linux-2.6.32-431.el6.x86_64-x86_64-with-redhat-6.5-Santiago
>
> Python information:
>     Architecture:            64bit ELF
>     Python version:          2.6.6
>     Python branch:           tags/r266
>     Python build:            r266:84292, Sep  4 2013 07:46:00
>     Python compiler:         GCC 4.4.7 20120313 (Red Hat 4.4.7-3)
>     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:      ['/sbinlab2/software/NMR-relax/relax-3.1.5',
> '/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/share/python',
> '/sbinlab2/software/NMR-relax/relax-3.1.5',
> '/sbinlab2/software/x64/haddock2.1',
> '/sbinlab2/software/x64/lib64/python2.6/site-packages',
> '/sbinlab2/software/x64/ccpnmr/ccpnmr2.3/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/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/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info']
>
> Python packages and modules (most are optional):
>
> Name               Installed    Version                    Path
> minfx              True         1.0.5
> /sbinlab2/software/NMR-relax/relax-3.1.5/minfx
> bmrblib            True         1.0.3
> /sbinlab2/software/NMR-relax/relax-3.1.5/bmrblib
> numpy              True         1.4.1
> /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
> mpi4py             True         1.3.1
> /usr/lib64/python2.6/site-packages/mpi4py
> epydoc             False
> 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 (PyXML)
> /usr/lib64/python2.6/site-packages/_xmlplus/__init__.pyc
> xml.dom.minidom    True
> /usr/lib64/python2.6/site-packages/_xmlplus/dom/minidom.pyc
>
> relax information:
>     Version:                 3.1.5
>     Processor fabric:        Uni-processor.
>
> relax C modules:
>
> Module                        Compiled    File type
> Path
> target_functions.relax_fit    True        ELF 64-bit LSB shared object,
> x86-64, version 1 (SYSV), dynamically linked, not stripped
> /sbinlab2/software/NMR-relax/relax-3.1.5/target_functions/relax_fit.so
>
>
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