Author: bugman
Date: Mon Mar 19 10:13:21 2012
New Revision: 15537
URL: http://svn.gna.org/viewcvs/relax?rev=15537&view=rev
Log:
Started to create a second script to demonstrate a working implementation of
the multi package.
Added:
1.3/multi/test_implementation2.py
- copied, changed from r15475, 1.3/multi/test_implementation.py
Modified:
1.3/test_suite/unit_tests/_multi/test___init__.py
Copied: 1.3/multi/test_implementation2.py (from r15475,
1.3/multi/test_implementation.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/multi/test_implementation2.py?p2=1.3/multi/test_implementation2.py&p1=1.3/multi/test_implementation.py&r1=15475&r2=15537&rev=15537&view=diff
==============================================================================
--- 1.3/multi/test_implementation.py (original)
+++ 1.3/multi/test_implementation2.py Mon Mar 19 10:13:21 2012
@@ -1,47 +1,28 @@
-"""A reference implementation of the multi-processor package.
+"""A reference implementation of the multi-processor package demonstrating
pre-sending of data.
Description
===========
-This is a basic but full implementation of the multi-processor package to
demonstrate how it is used.
+This implementation of the multi-processor package is used to demonstrate
how to pre-send invariant data once to all slaves to minimise the data
transfer for each parallelised calculation block.
Testing
=======
-To run in uni-processor mode on a dual core system, change the MULTI
variable to False and type::
-
-$ python test_implementation.py
-
-
-To run in mpi4py multi-processor mode with one master and two slave
processors on minimally a dual core system, change the MULTI variable to True
and type::
-
-$ mpiexec -n 3 python test_implementation.py
-
-For a single dual core CPU (Intel Core 2 Duo E8400 at 3.00GHz), the total
times averaged over 5 runs are:
- - Uni-processor: 51.548 seconds
(51.054+52.224+51.257+51.112+52.093)
- - Mpi4py-processor: 28.008 seconds
(30.719+27.218+27.799+26.343+27.961)
- - Scaling efficiency: 1.840
-
-
-Linux
------
-
-For multi-core systems and Linux 2.6, the following might be required to
prevent the master processor from taking 100% of one CPU core while waiting
for the slaves:
-
-# echo "1" > /proc/sys/kernel/sched_compat_yield
-
-This appears to be an OpenMPI problem with late 2.6 Linux kernels.
+To run in mpi4py multi-processor mode with one master and two slave
processors, type::
+
+$ mpiexec -n 3 python test_implementation2.py
"""
# Python module imports.
-from numpy import dot, float64, zeros
+from numpy import array, dot, float64, zeros
+from numpy.linalg import norm
try:
import cProfile as profile
except ImportError:
import profile
import pstats
-from random import uniform
+from random import gauss
import sys
# Modify the module path.
@@ -52,14 +33,8 @@
# Module variables.
-PROFILE = True
-MULTI = True
-if MULTI:
- FABRIC = 'mpi4py'
- PROCESSOR_NUM = 2
-else:
- FABRIC = 'uni'
- PROCESSOR_NUM = 1
+FABRIC = 'mpi4py'
+PROCESSOR_NUM = 2
def print_stats(stats, status=0):
@@ -69,6 +44,72 @@
pstats.Stats(stats).sort_stats('cumulative').print_stats()
+def quaternion_to_R(quat, R):
+ """Convert a quaternion into rotation matrix form.
+
+ This is from Wikipedia
(http://en.wikipedia.org/wiki/Rotation_matrix#Quaternion), where::
+
+ | 1 - 2y**2 - 2z**2 2xy - 2zw 2xz + 2yw |
+ Q = | 2xy + 2zw 1 - 2x**2 - 2z**2 2yz - 2xw |,
+ | 2xz - 2yw 2yz + 2xw 1 - 2x**2 - 2y**2 |
+
+ and where the quaternion is defined as q = (w, x, y, z). This has been
verified using Simo
+ Saerkkae's "Notes on Quaternions" at http://www.lce.hut.fi/~ssarkka/.
+
+
+ @param quat: The quaternion.
+ @type quat: numpy 4D, rank-1 array
+ @param R: A 3D matrix to convert to the rotation matrix.
+ @type R: numpy 3D, rank-2 array
+ """
+
+ # Alias.
+ (w, x, y, z) = quat
+
+ # Repetitive calculations.
+ x2 = 2.0 * x**2
+ y2 = 2.0 * y**2
+ z2 = 2.0 * z**2
+ xw = 2.0 * x*w
+ xy = 2.0 * x*y
+ xz = 2.0 * x*z
+ yw = 2.0 * y*w
+ yz = 2.0 * y*z
+ zw = 2.0 * z*w
+
+ # The diagonal.
+ R[0, 0] = 1.0 - y2 - z2
+ R[1, 1] = 1.0 - x2 - z2
+ R[2, 2] = 1.0 - x2 - y2
+
+ # The off-diagonal.
+ R[0, 1] = xy - zw
+ R[0, 2] = xz + yw
+ R[1, 2] = yz - xw
+
+ R[1, 0] = xy + zw
+ R[2, 0] = xz - yw
+ R[2, 1] = yz + xw
+
+
+def R_random_hypersphere(R):
+ """Generate a random rotation matrix using 4D hypersphere point picking.
+
+ A quaternion is generated by creating a 4D vector with each value
randomly selected from a
+ Gaussian distribution, and then normalising.
+
+ @param R: A 3D matrix to convert to the rotation matrix.
+ @type R: numpy 3D, rank-2 array
+ """
+
+ # The quaternion.
+ quat = array([gauss(0, 1), gauss(0, 1), gauss(0, 1), gauss(0, 1)],
float64)
+ quat = quat / norm(quat)
+
+ # Convert the quaternion to a rotation matrix.
+ quaternion_to_R(quat, R)
+
+
class Main:
"""The program."""
@@ -77,17 +118,24 @@
"""Set up some initial variables."""
# The total number of calculations to perform by all slave
processors.
- self.N = 2000000
+ self.N = 20000
# Variable for counting the completed calculations (to demonstrate
slave->master communication).
self.num = 0
+ # The invariant data to pass to the slaves once.
+ self.real_length = 2.0
+ self.vect = array([1, 2, 3], float64)
+ self.vect = self.vect / norm(self.vect) * self.real_length
+
def run(self):
"""This required method executes the entire program."""
# Initialise the Processor box singleton.
processor_box = Processor_box()
+
+ print "\n\nHELLO: ", processor_box.processor.rank(), self.vect
# Loop over the slaves.
num = processor_box.processor.processor_size()
@@ -181,26 +229,22 @@
-class Test_slave_command(Slave_command):
- """The slave command for use by the slave processor."""
-
- def __init__(self, N=0):
+class Test_slave_command_presend(Slave_command):
+ """The slave command used to pre-send data to the slave processors."""
+
+ def __init__(self, vect=None):
"""Set up the slave command object for the slave processor.
- @keyword N: The number of calculations for the slave to perform.
- @type N: int
+ @keyword vect: The invariant vector used in all the slave
calculations.
+ @type vect: int
"""
# Store the argument.
- self.N = N
-
- # Initialise some matrices.
- self.A = zeros((3, 3), float64)
- self.B = zeros((3, 3), float64)
+ self.vect = vect
def run(self, processor, completed=False):
- """Essential method for performing calculations on the slave
processors.
+ """Do nothing.
@param processor: The slave processor object.
@type processor: Processor instance
@@ -208,17 +252,46 @@
@type completed: bool
"""
+
+
+class Test_slave_command(Slave_command):
+ """The slave command for use by the slave processor."""
+
+ def __init__(self, N=0):
+ """Set up the slave command object for the slave processor.
+
+ @keyword N: The number of calculations for the slave to perform.
+ @type N: int
+ """
+
+ # Store the argument.
+ self.N = N
+
+ # Initialise the rotation matrix.
+ self.R = zeros((3, 3), float64)
+
+
+ def run(self, processor, completed=False):
+ """Essential method for performing calculations on the slave
processors.
+
+ @param processor: The slave processor object.
+ @type processor: Processor instance
+ @keyword completed: A flag specifying if the slave calculation is
completed. This is currently meaningless, but will be passed to this run()
method anyway so it needs to be present.
+ @type completed: bool
+ """
+
# Perform some random useless time-consuming stuff.
num_calcs = 0
for i in range(self.N):
- # Randomise the matrices.
- for j in range(3):
- for k in range(3):
- self.A[j, k] = uniform(0, 1)
- self.B[j, k] = uniform(0, 1)
-
- # Perform some linear algebra.
- dot(self.A, self.B)
+ # Random rotation matrix.
+ R_random_hypersphere(self.R)
+
+ continue
+ # Rotate the vector.
+ new_vect = dot(self.R, self.vect)
+
+ # The length sum.
+ self.length += norm(new_vect)
# Keep track of the number of calculations.
num_calcs += 1
@@ -231,14 +304,10 @@
# Set up the processor.
processor = load_multiprocessor(FABRIC, Application_callback(master=Main()),
processor_size=PROCESSOR_NUM, verbosity=1)
-# Run in multi-processor mode.
-if not PROFILE:
- processor.run()
-
-# Run in multi-processor mode with profiling.
-else:
- # Replace the default profiling print out function.
- profile.Profile.print_stats = print_stats
-
- # Execute with profiling.
- profile.runctx('processor.run()', globals(), locals())
+processor.run()
+
+# Replace the default profiling print out function.
+profile.Profile.print_stats = print_stats
+
+# Execute with profiling.
+#profile.runctx('processor.run()', globals(), locals())
Modified: 1.3/test_suite/unit_tests/_multi/test___init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_multi/test___init__.py?rev=15537&r1=15536&r2=15537&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/_multi/test___init__.py (original)
+++ 1.3/test_suite/unit_tests/_multi/test___init__.py Mon Mar 19 10:13:21 2012
@@ -40,4 +40,4 @@
self.package_path = sys.path[0] + sep + 'multi'
# Blacklisted scripts.
- self.blacklist = ['test_implementation.py']
+ self.blacklist = ['test_implementation.py',
'test_implementation2.py']
r15537 - in /1.3: multi/test_implementation2.py test_suite/unit_tests/_multi/test___init__.py