Author: bugman
Date: Fri Sep 25 14:13:22 2015
New Revision: 27873
URL: http://svn.gna.org/viewcvs/relax?rev=27873&view=rev
Log:
Merged revisions 27848 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27848 | tlinnet | 2015-06-11 13:15:54 +0200 (Thu, 11 Jun 2015) | 45 lines
Reverted r27840-r27845, related to Bug #23618, queuing system for multi
processors is not well designed.
The changes has not been proven to increase the minimisation time, and some
of the fixes introduces unintentional bugs.
The command used was:
svn merge -r27845:r27839 .
.....
------------------------------------------------------------------------------------------------------------------
r27840 | tlinnet | 2015-05-27 03:09:48 +0200 (Wed, 27 May 2015) | 3
lines
Adding keyword for verbosity for multi processor mode.
Task #7826 (https://gna.org/task/?7826): Write an python class for the
repeated analysis of dispersion data.
------------------------------------------------------------------------------------------------------------------
r27841 | tlinnet | 2015-05-27 03:09:50 +0200 (Wed, 27 May 2015) | 2
lines
Adding to user function minimise.execute() the keyword "mp_verbosity",
to control the amount
of information to print when running multi processors.
------------------------------------------------------------------------------------------------------------------
r27842 | tlinnet | 2015-05-27 03:09:52 +0200 (Wed, 27 May 2015) | 1 line
In multi.processor(), moving up the debugging print-out of running sets
of calculatation.
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r27843 | tlinnet | 2015-05-27 03:09:55 +0200 (Wed, 27 May 2015) | 1 line
In pipe_control of minimise, adding the possibility to control
verbosity in multi processor mode.
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r27844 | tlinnet | 2015-05-27 03:09:57 +0200 (Wed, 27 May 2015) | 6
lines
Suggestion Fix 1, in multi.processor.run_queue().
This fix changes, that the amount of simulations is not chunked up
before sending each chunk to a CPU.
Rather, all jobs are to be submitted after each other, and finished for
themselves.
Bug #23618: (https://gna.org/bugs/index.php?23618): queuing system for
multi processors is not well designed.
------------------------------------------------------------------------------------------------------------------
r27845 | tlinnet | 2015-05-27 03:09:59 +0200 (Wed, 27 May 2015) | 3
lines
Suggestion for fix 2, where jobs are continously replenished when other
jobs are finished.
Bug #23618: (https://gna.org/bugs/index.php?23618): queuing system for
multi processors is not well designed.
------------------------------------------------------------------------------------------------------------------
.....
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
branches/frame_order_cleanup/multi/processor.py
branches/frame_order_cleanup/pipe_control/minimise.py
branches/frame_order_cleanup/user_functions/minimisation.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Sep 25 14:13:22 2015
@@ -1 +1 @@
-/trunk:1-27797,27800-27847
+/trunk:1-27797,27800-27848
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py?rev=27873&r1=27872&r2=27873&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
(original)
+++ branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
Fri Sep 25 14:13:22 2015
@@ -781,7 +781,7 @@
print("Clustered spins are:", cdp.clustering)
- def minimise_execute(self, verbosity=1, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False, mc_err_analysis=False, mp_verbosity=0):
+ def minimise_execute(self, verbosity=1, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False, mc_err_analysis=False):
"""Use value.set on all pipes."""
# Set default
@@ -826,7 +826,7 @@
subsection(file=sys.stdout, text="Performing Monte-Carlo
minimisations on %i simulations"%(getattr(cdp, "sim_number")), prespace=0)
# Do the minimisation.
- self.interpreter.minimise.execute(min_algor=self.min_algor,
func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations,
constraints=self.constraints, scaling=True, verbosity=verbosity,
mp_verbosity=mp_verbosity)
+ self.interpreter.minimise.execute(min_algor=self.min_algor,
func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations,
constraints=self.constraints, scaling=True, verbosity=verbosity)
# Do Monte-Carlo error analysis
if mc_err_analysis:
Modified: branches/frame_order_cleanup/multi/processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/multi/processor.py?rev=27873&r1=27872&r2=27873&view=diff
==============================================================================
--- branches/frame_order_cleanup/multi/processor.py (original)
+++ branches/frame_order_cleanup/multi/processor.py Fri Sep 25 14:13:22
2015
@@ -585,8 +585,6 @@
running_set = set()
idle_set = set([i for i in range(1, self.processor_size()+1)])
- all_jobs = list(reversed(xrange(1, len(queue)+1)))
- completed_jobs = []
if self.threaded_result_processing:
result_queue = Threaded_result_queue(self)
@@ -606,26 +604,18 @@
# Loop until the queue of calculations is depleted.
while len(running_set) != 0:
+ # Get the result.
+ result = self.master_receive_result()
+
# Debugging printout.
if verbosity.level():
- print('\n')
- print('Running nr of jobs: %i' % len(running_set))
- print('Completed jobs: %s' % len(completed_jobs))
-
- # Get the result.
- result = self.master_receive_result()
+ print('\nIdle set: %s' % idle_set)
+ print('Running set: %s' % running_set)
# Shift the processor rank to the idle set.
if result.completed:
idle_set.add(result.rank)
running_set.remove(result.rank)
- completed_jobs.append(all_jobs.pop())
- if len(queue) != 0:
- # Add new to que
- command = queue.pop()
- dest = result.rank
- self.master_queue_command(command=command, dest=dest)
- running_set.add(dest)
# Add to the result queue for instant or threaded processing.
result_queue.put(result)
@@ -643,8 +633,8 @@
"""
#FIXME: need a finally here to cleanup exceptions states
- #lqueue = self.chunk_queue(self.command_queue)
- self.run_command_queue(self.command_queue)
+ lqueue = self.chunk_queue(self.command_queue)
+ self.run_command_queue(lqueue)
del self.command_queue[:]
self.memo_map.clear()
Modified: branches/frame_order_cleanup/pipe_control/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/minimise.py?rev=27873&r1=27872&r2=27873&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/minimise.py (original)
+++ branches/frame_order_cleanup/pipe_control/minimise.py Fri Sep 25
14:13:22 2015
@@ -31,7 +31,6 @@
from lib.float import isNaN
from lib.io import write_data
from multi import Processor_box
-from multi.misc import Verbosity; mverbosity = Verbosity()
from pipe_control.mol_res_spin import return_spin, spin_loop
from pipe_control import pipes
from pipe_control.pipes import check_pipe
@@ -429,7 +428,7 @@
cdp.grid_zoom_level = level
-def minimise(min_algor=None, line_search=None, hessian_mod=None,
hessian_type=None, func_tol=None, grad_tol=None, max_iter=None,
constraints=True, scaling=True, verbosity=1, mp_verbosity=0, sim_index=None):
+def minimise(min_algor=None, line_search=None, hessian_mod=None,
hessian_type=None, func_tol=None, grad_tol=None, max_iter=None,
constraints=True, scaling=True, verbosity=1, sim_index=None):
"""Minimisation function.
@keyword min_algor: The minimisation algorithm to use.
@@ -452,8 +451,6 @@
@type scaling: bool
@keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
@type verbosity: int
- @keyword mp_verbosity: The amount of information to print from the
multi processor module. The higher the value, the greater the verbosity.
- @type mp_verbosity: int
@keyword sim_index: The index of the simulation to optimise.
This should be None if normal optimisation is desired.
@type sim_index: None or int
"""
@@ -490,9 +487,6 @@
processor_box = Processor_box()
processor = processor_box.processor
- # Store the verbosity level for the multiprocessor.
- mverbosity.set(mp_verbosity)
-
# Single Monte Carlo simulation.
if sim_index != None:
# Reset the minimisation statistics.
@@ -517,8 +511,8 @@
api.minimise(min_algor=min_algor, min_options=min_options,
func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iter,
constraints=constraints, scaling_matrix=scaling_matrix,
verbosity=verbosity-1, sim_index=i)
# Print out.
- if verbosity and processor.is_queued():
- print("Queueing Simulation nr:" + repr(i+1))
+ if verbosity and not processor.is_queued():
+ print("Simulation " + repr(i+1))
# Unset the status.
if status.current_analysis:
Modified: branches/frame_order_cleanup/user_functions/minimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/minimisation.py?rev=27873&r1=27872&r2=27873&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/minimisation.py (original)
+++ branches/frame_order_cleanup/user_functions/minimisation.py Fri Sep 25
14:13:22 2015
@@ -217,13 +217,6 @@
desc_short = "verbosity level",
desc = "The amount of information to print to screen. Zero corresponds
to minimal output while higher values increase the amount of output. The
default value is 1."
)
-uf.add_keyarg(
- name = "mp_verbosity",
- default = 0,
- py_type = "int",
- desc_short = "multi processor verbosity level",
- desc = "The amount of information to print to screen when running multi
processors. Zero corresponds to minimal output while higher values increase
the amount of output. The default value is 0."
-)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will perform an optimisation starting from
the current parameter values. This is only suitable for data pipe types
which have target functions and hence support optimisation.")
r27873 - in /branches/frame_order_cleanup: ./ auto_analyses/ multi/ pipe_control/ user_functions/