bugrelax - Bugs: bug #21605, Small system test fail in 3.1.5...

 
 
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bug #21605: Small system test fail in 3.1.5 related to python numpy import of float16

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Thu 06 Feb 2014 10:51:55 AM UTC  
 
Category: Test suiteSpecific analysis category: Frame order
Priority: 3 - LowSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 3.1.5Operating System: 64-bit GNU/Linux

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Fri 07 Feb 2014 10:32:09 AM UTC, SVN revision 22146:

Merged revisions 22138 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22138 | bugman | 2014-02-06 12:33:29 +0100 (Thu, 06 Feb 2014) | 7 lines

Fix for bug #21605, the failure of the Frame_order.test_generate_rotor2_distribution system test.

The bug at http://gna.org/bugs/?21605 is due to the fact that numpy.float16 is not defined on all
systems. Older numpy versions do not have this. Therefore the float16 value is now imported from
lib.check_types where it is aliased to float32 when not defined.
........

(Browse SVN revision 22146)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 06 Feb 2014 11:33:30 AM UTC, SVN revision 22138:

Fix for bug #21605, the failure of the Frame_order.test_generate_rotor2_distribution system test.

The bug at http://gna.org/bugs/?21605 is due to the fact that numpy.float16 is not defined on all
systems. Older numpy versions do not have this. Therefore the float16 value is now imported from
lib.check_types where it is aliased to float32 when not defined.

(Browse SVN revision 22138)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 06 Feb 2014 10:51:55 AM UTC, original submission:

This bug has been reported here: http://thread.gmane.org/gmane.science.nmr.relax.devel/4958

Small system test fail in 3.1.5

I think it is related to numpy float16 on 64 bit machines.

We have numpy 1.4.1 from our Red-hat distribution.


from numpy import float16
ImportError: cannot import name float16


---------------- System test -----------

[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 ]
-------------------------

---------------- System info -----------

[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

Troels E. Linnet <tlinnet>
Project Member

 

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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 11 Feb 2014 08:18:38 AM UTCbugmanStatusNone=>Fixed
      Assigned toNone=>bugman
      Open/ClosedOpen=>Closed
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