Author: bugman
Date: Fri Oct 2 11:59:06 2015
New Revision: 27942
URL: http://svn.gna.org/viewcvs/relax?rev=27942&view=rev
Log:
Merged revisions 24530-24534,24538-24539 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24530 | bugman | 2014-07-11 16:48:43 +0200 (Fri, 11 Jul 2014) | 7 lines
Sent the verbosity argument to the minfx.grid.grid_split() function for the
frame order analysis.
This matches the relax trunk changes for the model-free analysis. The
minfx function in the next
release (1.0.8) will now be more verbose, so this will help with user
feedback when running the
model-free analysis on a cluster or multi-core system using MPI.
........
r24531 | bugman | 2014-07-11 17:21:44 +0200 (Fri, 11 Jul 2014) | 9 lines
Improvements for the parallelised grid search for the frame order analysis.
As each grid point can take wildly different numbers of CPU cycles to
calculate the chi-squared
value for, the result of subdividing the grid search was that some
subdivisions where incredibly
quick while others required much larger amounts of time. To avoid this bad
slave management, the
grid points are now randomised. This means that the subdivisions will
require about the same amount
of time to optimise.
........
r24532 | bugman | 2014-07-11 17:47:01 +0200 (Fri, 11 Jul 2014) | 10 lines
Moved the setup of the target function data structures in the frame order
analysis.
This is for the grid_search and minimise user functions. The target
function data setup function
has been renamed to target_fn_data_setup(). This is now called before the
Frame_order_grid_command
and Frame_order_minimise_command multi-processor objects are initialised,
and all of the data is now
passed into these functions. Although the code is uglier, this has the
benefit that the
target_fn_data_setup() function will only be called once. This data setup
requires a lot of time,
so for a large cluster, this can be a large time saving for the grid search.
........
r24533 | bugman | 2014-07-14 12:17:07 +0200 (Mon, 14 Jul 2014) | 3 lines
Modified the frame_order_free_start.py script to better mimic the frame
order auto-analysis.
........
r24534 | bugman | 2014-07-15 11:14:39 +0200 (Tue, 15 Jul 2014) | 8 lines
Updated the frame order optimisation results for the 2nd CaM free rotor
test data.
The optimisation in the frame_order.py is now of higher precision with the
number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo
simulations. The new
frame order representation files have been added to the repository, as well
as the intermediate
state files.
........
r24538 | bugman | 2014-07-16 11:32:25 +0200 (Wed, 16 Jul 2014) | 8 lines
Updated the frame order optimisation results for the CaM free rotor test
data.
The optimisation in the frame_order.py is now of higher precision with the
number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo
simulations. The new
frame order representation files have been added to the repository, as well
as the intermediate
state files.
........
r24539 | bugman | 2014-07-16 15:38:08 +0200 (Wed, 16 Jul 2014) | 8 lines
Updated the frame order optimisation results for the CaM missing data free
rotor test data.
The optimisation in the frame_order.py is now of higher precision with the
number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo
simulations. The new
frame order representation files have been added to the repository, as well
as the intermediate
state files.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_sim.pdb.gz
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_fixed_piv.bz2
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_fixed_piv.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_sim.pdb.gz
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_true.bz2
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_true.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_sim.pdb.gz
- copied unchanged from r24534,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_fixed_piv.bz2
- copied unchanged from r24534,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_fixed_piv.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_sim.pdb.gz
- copied unchanged from r24534,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_true.bz2
- copied unchanged from r24534,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_true.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_sim.pdb.gz
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_fixed_piv.bz2
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_fixed_piv.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_sim.pdb.gz
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_true.bz2
- copied unchanged from r24539,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_true.bz2
Modified:
trunk/ (props changed)
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.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=27942&r1=27941&r2=27942&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=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_fixed_piv.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos_true.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.bz2?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.log.bz2?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_fixed_piv.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order_true.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_fixed_piv.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos_true.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.bz2?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.log.bz2?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_fixed_piv.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_true.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_fixed_piv.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/ave_pos_true.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.bz2?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.log.bz2?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_fixed_piv.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_true.pdb.gz?rev=27942&r1=27941&r2=27942&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py?rev=27942&r1=27941&r2=27942&view=diff
r27942 - in /trunk: ./ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam/free_rotor/ test_suite/shared_d...