Author: bugman
Date: Thu Mar 15 20:07:09 2012
New Revision: 15489
URL: http://svn.gna.org/viewcvs/relax?rev=15489&view=rev
Log:
Merged revisions 15479-15483,15487 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r15479 | bugman | 2012-03-15 16:48:13 +0100 (Thu, 15 Mar 2012) | 5 lines
The extern and minfx.scipy_subset relax packages are now excluded form the
API documentation.
This will be updated at http://www.nmr-relax.com/api/ after the next relax
release.
........
r15480 | bugman | 2012-03-15 16:58:15 +0100 (Thu, 15 Mar 2012) | 3 lines
Epydoc docstring fix.
........
r15481 | bugman | 2012-03-15 17:05:18 +0100 (Thu, 15 Mar 2012) | 3 lines
The setup.py script can now be imported for the epydoc API documentation
system.
........
r15482 | bugman | 2012-03-15 17:06:12 +0100 (Thu, 15 Mar 2012) | 5 lines
The multi-processor test implementation scripts are now excluded from the
API documentation.
The import of the scripts was failing, and they are not part of the relax
API.
........
r15483 | bugman | 2012-03-15 17:21:14 +0100 (Thu, 15 Mar 2012) | 3 lines
Formatting of the epydoc exclusion list.
........
r15487 | bugman | 2012-03-15 20:05:40 +0100 (Thu, 15 Mar 2012) | 13 lines
Fix for bug #19528 (https://gna.org/bugs/?19528).
This bug was reported by Hugh Dannatt (h dott dannatt att sheffield dot ac
dot uk).
The problem was in the multi-processor code for the model-free
calculations, specifically for the
Monte Carlo simulations. Rather than processing the queue of slave
processor commands for the
model-free calculation for each spin system at the end of each simulation,
the processing of the
queue was happening at the end of all Monte Carlo simulations. This caused
memory usage to bloat!
A full description of the problem can be found at
https://mail.gna.org/public/relax-users/2012-03/msg00037.html (Message-id:
<CAED9pY_Z1wGEg3gZo3WCkhvYTBdqs-Feex5Og4vJFovgJkUOyw@xxxxxxxxxxxxxx>).
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/minimise.py
branches/frame_order_testing/multi/__init__.py
branches/frame_order_testing/scons/manuals.py
branches/frame_order_testing/setup.py
branches/frame_order_testing/specific_fns/model_free/mf_minimise.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Mar 15 20:07:09 2012
@@ -1,1 +1,1 @@
-/1.3:1-15474
+/1.3:1-15487
Modified: branches/frame_order_testing/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/minimise.py?rev=15489&r1=15488&r2=15489&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/minimise.py (original)
+++ branches/frame_order_testing/generic_fns/minimise.py Thu Mar 15 20:07:09
2012
@@ -29,7 +29,6 @@
# relax module imports.
from generic_fns.mol_res_spin import return_spin, spin_loop
from generic_fns import pipes
-from multi import Processor_box
from relax_errors import RelaxError
import specific_fns
from status import Status; status = Status()
@@ -138,12 +137,6 @@
# Grid search.
else:
grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
-
- # Get the Processor box singleton (it contains the Processor instance).
- processor_box = Processor_box()
-
- # Execute the queued elements.
- processor_box.processor.run_queue()
def minimise(min_algor=None, min_options=None, func_tol=None, grad_tol=None,
max_iterations=None, constraints=True, scaling=True, verbosity=1,
sim_index=None):
@@ -214,12 +207,6 @@
else:
minimise(min_algor=min_algor, min_options=min_options,
func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations,
constraints=constraints, scaling=scaling, verbosity=verbosity)
- # Get the Processor box singleton (it contains the Processor instance).
- processor_box = Processor_box()
-
- # Execute the queued elements.
- processor_box.processor.run_queue()
-
def reset_min_stats(data_pipe=None, spin=None):
"""Function for resetting the minimisation statistics.
Modified: branches/frame_order_testing/multi/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/multi/__init__.py?rev=15489&r1=15488&r2=15489&view=diff
==============================================================================
--- branches/frame_order_testing/multi/__init__.py (original)
+++ branches/frame_order_testing/multi/__init__.py Thu Mar 15 20:07:09 2012
@@ -157,7 +157,7 @@
@param processor_name: Name of the processor module/class to load.
@type processor_name: str
@keyword verbosity: The verbosity level at initialisation. This can
be changed during program execution. A value of 0 suppresses all output. A
value of 1 causes the basic multi-processor information to be printed. A
value of 2 will switch on a number of debugging print outs. Values greater
than 2 currently do nothing, though this might change in the future.
- @type keyword: int
+ @type verbosity: int
@return: A loaded processor object or None to indicate
failure.
@rtype: multi.processor.Processor instance
"""
Modified: branches/frame_order_testing/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/scons/manuals.py?rev=15489&r1=15488&r2=15489&view=diff
==============================================================================
--- branches/frame_order_testing/scons/manuals.py (original)
+++ branches/frame_order_testing/scons/manuals.py Thu Mar 15 20:07:09 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2011 Edward d'Auvergne
#
+# Copyright (C) 2006-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -93,7 +93,15 @@
# exclude
# The list of objects to exclude.
- exclude = ['graphics', 'sample_scripts', 'scripts']
+ exclude = [
+ 'extern',
+ 'graphics',
+ 'minfx.scipy_subset',
+ 'multi.test_implementation',
+ 'multi.test_implementation2',
+ 'sample_scripts',
+ 'scripts'
+ ]
# output
# The type of output that should be generated. Should be one
Modified: branches/frame_order_testing/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/setup.py?rev=15489&r1=15488&r2=15489&view=diff
==============================================================================
--- branches/frame_order_testing/setup.py (original)
+++ branches/frame_order_testing/setup.py Thu Mar 15 20:07:09 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2011 Edward d'Auvergne
#
+# Copyright (C) 2011-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -38,7 +38,10 @@
# Python module import.
from os import getcwd, listdir, sep
from re import search
-from setuptools import setup
+try:
+ from setuptools import setup
+except ImportError:
+ setup = None
import sys
# relax module imports.
Modified: branches/frame_order_testing/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/mf_minimise.py?rev=15489&r1=15488&r2=15489&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/model_free/mf_minimise.py
(original)
+++ branches/frame_order_testing/specific_fns/model_free/mf_minimise.py Thu
Mar 15 20:07:09 2012
@@ -1589,6 +1589,9 @@
num_data_sets = 0
data_store.num_spins = 1
+ # Get the Processor box singleton (it contains the Processor
instance) and alias the Processor.
+ processor_box = Processor_box()
+ processor = processor_box.processor
# Loop over the minimisation instances.
#######################################
@@ -1683,10 +1686,6 @@
if min_algor == 'back_calc':
return self.mf.calc_ri()
- # Get the Processor box singleton (it contains the Processor
instance) and alias the Processor.
- processor_box = Processor_box()
- processor = processor_box.processor
-
# Parallelised grid search for the diffusion parameter space.
if match('^[Gg]rid', min_algor) and data_store.model_type ==
'diff':
# Print out.
@@ -1707,6 +1706,9 @@
memo = MF_memo(model_free=self,
model_type=data_store.model_type, spin=spin, sim_index=sim_index,
scaling=scaling, scaling_matrix=data_store.scaling_matrix)
processor.add_to_queue(command, memo)
+ # Execute the queued elements.
+ processor.run_queue()
+
# Exit this method.
return
@@ -1724,3 +1726,6 @@
# Set up the model-free memo and add it to the processor queue.
memo = MF_memo(model_free=self,
model_type=data_store.model_type, spin=spin, sim_index=sim_index,
scaling=scaling, scaling_matrix=data_store.scaling_matrix)
processor.add_to_queue(command, memo)
+
+ # Execute the queued elements.
+ processor.run_queue()
r15489 - in /branches/frame_order_testing: ./ generic_fns/ multi/ scons/ specific_fns/model_free/