Hi,
That's great that you have time, to have this working properly is
quite important. I didn't realise how much of an issue the merging of
the multi-processor code and GUI code would be. I have now merged the
multi-processor branch into the main 1.3 line, as well as the new GUI
branch, and that is where the problems are. I think there are at
least 2 problems currently occurring. The first has to do with the
GUI tests:
$ relax --gui-test
I looks like that there is a clash of the wxPython App.MainLoop() and
how the master processors of the multi package interact. There
appears to be race conditions, even in the uni-processor fabric. This
only occurs in the test-suite, I have just tested manual operation of
the GUI which works, so this makes things more difficult. The problem
was not existent in the gui_testing branch (svn co
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/gui_testing/@14200)
until after the multi-processor code was merged.
The second problem is IO redirection. This occurs in a number of
places in relax. These include:
1) The --log command line flag which causes STDOUT and STDERR to be
sent to file.
2) The --tee command line flag which causes STDOUT and STDERR to be
sent both to file and to the terminal.
3) The test suite. The STDOUT and STDERR streams are caught and only
sent to STDERR if there is an error or failure in a test.
4) The relax controller (part of the GUI). This is a window to which
STDOUT and STDERR are directed. In the test-suite mode, the streams
also output to the terminal.
5) The multi-processor package. There are two parts. The first is
essentially a pre-filter which prepends certain tokens to the IO
stream (i.e. the 'M |', 'M E|', and 'S 1|' text). I cannot see how
we can do this as 4) is always set up after 5). So I am considering
removing this part. It will make it more difficult with debugging,
but I can see no other way.
6) The second part for the multi-processor package, which is
currently non-functional, is the catching of the IO streams of the
slave processes to send back to the master. I will try to mimic the
relax controller code here and store all slave text as a list with
flags specifying whether it is STDOUT or STDERR. Then the list can be
returned to the master at which point the text can be sent to the two
streams.
The problem is that at each point here, sys.stdout and sys.stderr are
replaced and the order in which this happens is impossible to change.
Well 4) will always be last.
Regards,
Edward
On 25 August 2011 14:51, Gary Thompson <garyt@xxxxxxxxxxxxxxx> wrote:
On 08/25/2011 11:40 AM, Edward d'Auvergne wrote:
Hi,
I'm working on this at the moment. Unfortunately the main 1.3 line is
severely broken at the moment! The new multi-processor package is
clashing with and causing relax to die hard on the test-suite and the
GUI. The main cause is IO redirection of sys.stdout and sys.stderr.
The multi-processor code (even in uni-processor mode) is hijacking the
streams and the test suite and GUI do not know what to do anymore.
Once I eliminate all the IO redirection of the multi package, apart
from the IO capture on the slave processes which is non-functional
anyway, then the test-suite should be back in order. I noticed you
performed an svnmerge, and this is likely causing the breakages in
your branch.
Regards,
Edward
Hi Ed
I do at last have time to work on this, would you like me to have a look
at what is going on?
which branch do I need to look at? and what are the specific problems
with the io redirect that need to be addressed?
regards
gary
On 25 August 2011 12:23, Sébastien Morin<sebastien.morin@xxxxxxxxx>
wrote:
Hi Ed,
While working on "inversion-recovery" branch, I realized that the system
tests "Relax_fit.check_curve_fitting__exp_2param_neg" and
"Relax_fit.check_curve_fitting__exp_3param_inv_neg" were failing. In
order
to pin point the problem, I checked on the main 1.3 branch (514439) and
system test "Relax_fit.check_curve_fitting" also failed, with the same
error:
==========
======================================================================
ERROR: check_curve_fitting (test_suite.system_tests.relax_fit.Relax_fit)
Check the results of the curve-fitting.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
Traceback (most recent call last):
File
"/Users/semor/Documents/pse-4/collaborations/relax/relax-1.3/test_suite/system_tests/relax_fit.py",
line 60, in check_curve_fitting
self.assertEqual(cdp.curve_type, 'exp')
AttributeError: 'PipeContainer' object has no attribute 'curve_type'
----------------------------------------------------------------------
Ran 1 test in 0.001s
FAILED (errors=1)
==========
I tried changing the pipe type from "mf" to "relax_fit" (as it should
be).
This did not solve the issue...
Any idea ?
Thanks !
Séb :)
--
Sébastien Morin, Ph.D.
Postdoctoral Fellow, S. Grzesiek NMR Laboratory
Department of Structural Biology
Biozentrum, Universität Basel
Klingelbergstrasse 70
4056 Basel
Switzerland
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--
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Dr Gary Thompson [Homans Lab Research Coordinator]
Astbury Centre for Structural Molecular Biology,
University of Leeds,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: garyt@xxxxxxxxxxxxxxx Fax +44-113-3431935
-------------------------------------------------------------------
Re: System test "Relax_fit.check_curve_fitting"