Author: bugman
Date: Fri Oct 2 11:44:49 2015
New Revision: 27940
URL: http://svn.gna.org/viewcvs/relax?rev=27940&view=rev
Log:
Merged revisions 24514-24520 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24514 | bugman | 2014-07-10 18:12:07 +0200 (Thu, 10 Jul 2014) | 5 lines
Changed the minimisation in the frame order system tests where optimisation
is activated.
The number of iterations is now set to 1 for speed testing, and the
constraints are turned on.
........
r24515 | bugman | 2014-07-10 18:13:09 +0200 (Thu, 10 Jul 2014) | 5 lines
Turned on the optimisation flag for the Frame_order.test_cam_free_rotor
system test.
This is to activate code paths currently not tested by the test suite.
........
r24516 | bugman | 2014-07-10 18:27:10 +0200 (Thu, 10 Jul 2014) | 6 lines
Constraints are now properly turned off in the minimise user function for
the frame order analysis.
The A and b matrices from linear_constraints() are now set to None if they
are returned as empty
arrays.
........
r24517 | bugman | 2014-07-10 19:04:37 +0200 (Thu, 10 Jul 2014) | 26 lines
Parallelised the frame order optimisation code to run on clusters or
multi-core systems via OpenMPI.
The optimisation code has been split into the three standard parts of the
multi-processor:
- Frame_order_memo is the new Memo object used to store data on the master
for use when data is
returned from the slaves.
- Frame_order_minimise_command is the Slave_command which stored all
required data for the
optimisation, is pickled and sent to a slave, sets up the target function,
and then performs
optimisation.
- Frame_order_result_command is the Result_command initialised by the
Slave_command on the slave for
pickling and returning results to the master.
To avoid pickling the target function class, which is not possible, the
store_bc_data() and
target_fn_setup() functions of the
specific_analyses.frame_order.optimisation module have been
redesigned to work with basic data structures rather than the target
function class directly. The
target_fn_setup() function no longer returns an initialised target function
class, but rather all
the data assembled prior to the initialisation. And the target function
class was itself modified
so that pcs_theta and rdc_theta are always defined to allow the
store_bc_data() function to be used
successfully.
This parallelisation currently only allows the Monte Carlo simulations to
be run on slave
processors.
........
r24518 | bugman | 2014-07-11 09:07:01 +0200 (Fri, 11 Jul 2014) | 21 lines
Reverted r24495 as this is rubbish.
The pivot point needs to be initially guessed to centre the grid search for
the pivot to a
reasonable 20 Angstrom box in the PDB space.
The command used was:
svn merge -r24495:r24494 .
.....
r24495 | bugman | 2014-07-09 15:31:21 +0200 (Wed, 09 Jul 2014) | 7 lines
Changed paths:
M
/branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
Modified the specific_analyses.frame_order.parameters.update_model()
function.
The pivot parameters are now set to 0.0 if they do not currently exist.
They were previously
excluded from this initialisation, but this is required for the frame
order models if the pivot is
not initially fixed at a give location in the PDB space.
.....
........
r24519 | bugman | 2014-07-11 10:14:45 +0200 (Fri, 11 Jul 2014) | 5 lines
The frame order linear_constraints() function now returns None if no
constraints are present.
This allows the code using this to be simplified with respect to turning
off the constraints.
........
r24520 | bugman | 2014-07-11 10:33:48 +0200 (Fri, 11 Jul 2014) | 6 lines
Improvements for the printout at the start of optimisation of the frame
order models.
This is in the target_fn_setup() frame order method. All the printouts are
now in one place and
they are now better formatted and better controlled.
........
Modified:
trunk/ (props changed)
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/target_functions/frame_order.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27940&r1=27939&r2=27940&view=diff
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27940&r1=27939&r2=27940&view=diff
Modified: trunk/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameters.py?rev=27940&r1=27939&r2=27940&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27940&r1=27939&r2=27940&view=diff
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=27940&r1=27939&r2=27940&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=27940&r1=27939&r2=27940&view=diff
r27940 - in /trunk: ./ specific_analyses/frame_order/ target_functions/ test_suite/system_tests/ test_suite/system_tests/scr...