Author: bugman
Date: Wed Mar 7 12:36:44 2012
New Revision: 15452
URL: http://svn.gna.org/viewcvs/relax?rev=15452&view=rev
Log:
Shifted the transfer of much of the data to the slave command to the
__init__() method.
This should improve the multi-processor scaling by reducing data transfer
times per function call.
However, from testing this currently does nothing! The structures now
pre-transfered include:
full_in_ref_frame
r_ln_pivot
A
Ri_prime
pcs_theta
pcs_theta_err
missing_pcs
Modified:
branches/frame_order_testing/maths_fns/frame_order.py
branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
Modified: branches/frame_order_testing/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order.py?rev=15452&r1=15451&r2=15452&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order.py Wed Mar 7 12:36:44
2012
@@ -51,7 +51,7 @@
class Frame_order:
"""Class containing the target function of the optimisation of Frame
Order matrix components."""
- def __init__(self, model=None, init_params=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_errors=None, rdc_weights=None,
rdc_vect=None, rdc_const=None, pcs=None, pcs_errors=None, pcs_weights=None,
pcs_atoms=None, temp=None, frq=None, paramag_centre=None,
scaling_matrix=None, num_int_pts=500, pivot=None, pivot_opt=False,
quad_int=True):
+ def __init__(self, model=None, init_params=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_errors=None, rdc_weights=None,
rdc_vect=None, rdc_const=None, pcs=None, pcs_errors=None, pcs_weights=None,
pcs_atoms=None, temp=None, frq=None, paramag_centre=zeros(3),
scaling_matrix=None, num_int_pts=500, pivot=zeros(3), pivot_opt=False,
quad_int=True):
"""Set up the target functions for the Frame Order theories.
@keyword model: The name of the Frame Order model.
@@ -250,7 +250,10 @@
self.pcs_const = zeros(self.num_align, float64)
self.r_pivot_atom = zeros((3, self.num_pcs), float64)
self.r_pivot_atom_rev = zeros((3, self.num_pcs), float64)
+ self.r_pivot_atom_rev = zeros((3, self.num_pcs), float64)
self.r_ln_pivot = zeros((3, self.num_pcs), float64)
+ for j in xrange(self.num_pcs):
+ self.r_ln_pivot[:, j] = pivot - self.paramag_centre
if self.paramag_centre == None:
self.paramag_centre = zeros(3, float64)
@@ -322,7 +325,7 @@
# Set up the slave processors.
self.slaves = []
for i in range(self.processor.processor_size()):
-
self.slaves.append(Slave_command_pcs_pseudo_ellipse_qrint(blocks[i]))
+
self.slaves.append(Slave_command_pcs_pseudo_ellipse_qrint(blocks[i],
full_in_ref_frame=self.full_in_ref_frame, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, Ri_prime=self.Ri_prime, pcs_theta=deepcopy(self.pcs_theta),
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs))
# The target function aliases (Scipy numerical integration).
else:
@@ -1180,7 +1183,11 @@
# Subdivide the points.
for i in range(self.processor.processor_size()):
# Initialise the slave command and memo.
- self.slaves[i].load_data(theta_x=cone_theta_x,
theta_y=cone_theta_x, sigma_max=cone_sigma_max,
full_in_ref_frame=self.full_in_ref_frame, r_pivot_atom=self.r_pivot_atom,
r_pivot_atom_rev=self.r_pivot_atom_rev, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime,
pcs_theta=deepcopy(self.pcs_theta), pcs_theta_err=self.pcs_theta_err,
missing_pcs=self.missing_pcs)
+ self.slaves[i].load_data(theta_x=cone_theta_x,
theta_y=cone_theta_x, sigma_max=cone_sigma_max,
r_pivot_atom=self.r_pivot_atom, r_pivot_atom_rev=self.r_pivot_atom_rev,
R_eigen=self.R_eigen, RT_eigen=RT_eigen)
+
+ # Update certain data structures.
+ if self.pivot_opt:
+ self.slaves[i].r_ln_pivot = self.r_ln_pivot
# Initialise the memo.
memo = Memo_pcs_pseudo_ellipse_qrint(data)
@@ -1761,7 +1768,8 @@
# The pivot to atom vectors.
for j in xrange(self.num_pcs):
# The lanthanide to pivot vector.
- self.r_ln_pivot[:, j] = pivot - self.paramag_centre
+ if self.pivot_opt:
+ self.r_ln_pivot[:, j] = pivot - self.paramag_centre
# The rotated vectors.
self.r_pivot_atom[:, j] = dot(R_ave, self.pcs_atoms[j] - pivot)
Modified: branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py?rev=15452&r1=15451&r2=15452&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
(original)
+++ branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py Wed Mar
7 12:36:44 2012
@@ -2416,40 +2416,17 @@
class Slave_command_pcs_pseudo_ellipse_qrint(Slave_command):
"""The slave command for the quasi-random pseudo-ellipse PCS numerical
integration."""
- def __init__(self, points=None):
+ def __init__(self, points=None, full_in_ref_frame=None, r_ln_pivot=None,
A=None, Ri_prime=None, pcs_theta=None, pcs_theta_err=None, missing_pcs=None):
"""Store the pre-target function invariable data.
@keyword points: The subdivision of points to process on
the slave processor.
@type points: numpy rank-2, 3D array
- """
-
- # Store the arguments.
- self.points = points
-
-
- def load_data(self, theta_x=None, theta_y=None, sigma_max=None,
full_in_ref_frame=None, r_pivot_atom=None, r_pivot_atom_rev=None,
r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None, Ri_prime=None,
pcs_theta=None, pcs_theta_err=None, missing_pcs=None):
- """Store the target function level variable data.
-
- @keyword theta_x: The x-axis half cone angle.
- @type theta_x: float
- @keyword theta_y: The y-axis half cone angle.
- @type theta_y: float
- @keyword sigma_max: The maximum torsion angle.
- @type sigma_max: float
@keyword full_in_ref_frame: An array of flags specifying if the
tensor in the reference frame is the full or reduced tensor.
@type full_in_ref_frame: numpy rank-1 array
- @keyword r_pivot_atom: The pivot point to atom vector.
- @type r_pivot_atom: numpy rank-2, 3D array
- @keyword r_pivot_atom_rev: The reversed pivot point to atom vector.
- @type r_pivot_atom_rev: numpy rank-2, 3D array
@keyword r_ln_pivot: The lanthanide position to pivot point
vector.
@type r_ln_pivot: numpy rank-2, 3D array
@keyword A: The full alignment tensor of the
non-moving domain.
@type A: numpy rank-2, 3D array
- @keyword R_eigen: The eigenframe rotation matrix.
- @type R_eigen: numpy rank-2, 3D array
- @keyword RT_eigen: The transpose of the eigenframe rotation
matrix (for faster calculations).
- @type RT_eigen: numpy rank-2, 3D array
@keyword Ri_prime: The empty rotation matrix for the
in-frame isotropic cone motion, used to calculate the PCS for each state i in
the numerical integration.
@type Ri_prime: numpy rank-2, 3D array
@keyword pcs_theta: The storage structure for the
back-calculated PCS values.
@@ -2461,20 +2438,43 @@
"""
# Store the arguments.
- self.theta_x = theta_x
- self.theta_y = theta_y
- self.sigma_max = sigma_max
+ self.points = points
self.full_in_ref_frame = full_in_ref_frame
- self.r_pivot_atom = r_pivot_atom
- self.r_pivot_atom_rev = r_pivot_atom_rev
self.r_ln_pivot = r_ln_pivot
self.A = A
- self.R_eigen = R_eigen
- self.RT_eigen = RT_eigen
self.Ri_prime = Ri_prime
self.pcs_theta = pcs_theta
self.pcs_theta_err = pcs_theta_err
self.missing_pcs = missing_pcs
+
+
+ def load_data(self, theta_x=None, theta_y=None, sigma_max=None,
r_pivot_atom=None, r_pivot_atom_rev=None, R_eigen=None, RT_eigen=None):
+ """Store the target function level variable data.
+
+ @keyword theta_x: The x-axis half cone angle.
+ @type theta_x: float
+ @keyword theta_y: The y-axis half cone angle.
+ @type theta_y: float
+ @keyword sigma_max: The maximum torsion angle.
+ @type sigma_max: float
+ @keyword r_pivot_atom: The pivot point to atom vector.
+ @type r_pivot_atom: numpy rank-2, 3D array
+ @keyword r_pivot_atom_rev: The reversed pivot point to atom vector.
+ @type r_pivot_atom_rev: numpy rank-2, 3D array
+ @keyword R_eigen: The eigenframe rotation matrix.
+ @type R_eigen: numpy rank-2, 3D array
+ @keyword RT_eigen: The transpose of the eigenframe rotation
matrix (for faster calculations).
+ @type RT_eigen: numpy rank-2, 3D array
+ """
+
+ # Store the arguments.
+ self.theta_x = theta_x
+ self.theta_y = theta_y
+ self.sigma_max = sigma_max
+ self.r_pivot_atom = r_pivot_atom
+ self.r_pivot_atom_rev = r_pivot_atom_rev
+ self.R_eigen = R_eigen
+ self.RT_eigen = RT_eigen
def run(self, processor, completed):
r15452 - in /branches/frame_order_testing/maths_fns: frame_order.py frame_order_matrix_ops.py