Author: tlinnet
Date: Sat Jun 21 08:42:47 2014
New Revision: 24231
URL: http://svn.gna.org/viewcvs/relax?rev=24231&view=rev
Log:
Modified super profiling script, to allow input to script, where
alternative version of relax is positioned.
Collected the variables in a list of lists, for better overview.
Added a print out comment to IT99, to remember the bug.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py?rev=24231&r1=24230&r2=24231&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
Sat Jun 21 08:42:47 2014
@@ -41,53 +41,34 @@
# The number of iterations to run each script for the statistics.
N = 10
-# The models.
+# The models / The current scripts. / Iterations / Multiplication factors
(to scale for different nr_iter values).
models = [
- 'CR72 full',
- 'TSMFK01',
- 'B14 full',
- 'NS CPMG 2-site expanded',
- 'NS CPMG 2-site 3D full',
- 'M61',
- 'DPL94',
- 'TP02',
- 'TAP03',
- 'MP05',
- 'NS R1rho 2-site'
+ ['No Rex', 'profiling_norex.py', 100, 1],
+ ['LM63', 'profiling_lm63.py', 100, 1],
+ ['CR72', 'profiling_cr72.py', 100, 1],
+ ['CR72 full', 'profiling_cr72_full.py', 100, 1],
+ ['IT99', 'profiling_it99.py', 100, 1],
+ ['TSMFK01', 'profiling_tsmfk01.py', 100, 1],
+ ['B14', 'profiling_b14.py', 100, 1],
+ ['B14 full', 'profiling_b14_full.py', 100, 1],
+ ['NS CPMG 2-site 3D', 'profiling_ns_cpmg_2site_3D.py', 10, 10],
+ ['NS CPMG 2-site 3D full', 'profiling_ns_cpmg_2site_3D_full.py', 10,
10],
+ ['NS CPMG 2-site expanded', 'profiling_ns_cpmg_2site_expanded.py',
100, 1],
+ ['NS CPMG 2-site star', 'profiling_ns_cpmg_2site_star.py', 10, 10],
+ ['NS CPMG 2-site star full', 'profiling_ns_cpmg_2site_star_full.py',
10, 10],
+ ['M61', 'profiling_m61.py', 100, 1],
+ ['DPL94', 'profiling_dpl94.py', 100, 1],
+ ['TP02', 'profiling_tp02.py', 100, 1],
+ ['TAP03', 'profiling_tap03.py', 100, 1],
+ ['MP05', 'profiling_mp05.py', 100, 1],
+ ['NS R1rho 2-site', 'profiling_ns_r1rho_2site.py', 10, 10],
]
-# The current scripts.
-scripts = [
- 'profiling_cr72.py',
- 'profiling_tsmfk01.py',
- 'profiling_b14.py',
- 'profiling_ns_cpmg_2site_expanded.py',
- 'profiling_ns_cpmg_2site_3D.py',
- 'profiling_m61.py',
- 'profiling_dpl94.py',
- 'profiling_tp02.py',
- 'profiling_tap03.py',
- 'profiling_mp05.py',
- 'profiling_ns_r1rho_2site.py'
-]
-
-# Multiplication factors (to scale for different nr_iter values).
-scaling_factor = [
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 10.0,
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 10.0
-]
-
# Path to relax 3.2.2, or any other version.
-alt_path = '/data/relax/tags/3.2.2'
+if len(sys.argv) == 1:
+ alt_path = '/data/relax/tags/3.2.2'
+else:
+ alt_path = sys.argv[1]
# The Python executable name.
python = 'python'
@@ -99,13 +80,18 @@
sys.stdout.write("\n\n")
# Copy the current scripts to the base directory of the alternative relax
version.
-for script in scripts:
+for i in range(len(models)):
+ # Alias.
+ model, script, iter, scaling_factor = models[i]
+ print("Copying: model=%s script=%s iterations=%s scale=%s"%(model,
script, iter, scaling_factor))
copyfile(script, alt_path+sep+script)
# Initialise structures for the timing statistics.
timings_new = {}
timings_alt = {}
-for model in models:
+for i in range(len(models)):
+ # Alias.
+ model, script, iter, scaling_factor = models[i]
timings_new[model] = zeros((2, N), float64)
timings_alt[model] = zeros((2, N), float64)
timings = [timings_new, timings_alt]
@@ -117,10 +103,11 @@
# Loop over each model.
for i in range(len(models)):
+ model, script, iter, scaling_factor = models[i]
# The commands to run.
cmds = [
- "%s %s" % (python, scripts[i]),
- "%s %s %s" % (python, alt_path+sep+scripts[i], alt_path),
+ "%s %s" % (python, script),
+ "%s %s %s" % (python, alt_path+sep+script, alt_path),
]
# Loop over the commands.
@@ -162,7 +149,7 @@
row = line.split()
# The timing.
- timings[cmd_index][models[i]][index, exec_iter] =
float(row[3])
+ timings[cmd_index][model][index, exec_iter] = float(row[3])
# Increment the index.
index += 1
@@ -182,19 +169,19 @@
# Loop over the models.
for i in range(len(models)):
# Alias.
- model = models[i]
+ model, script, iter, scaling_factor = models[i]
# The averages (scaled for different nr_iter).
- ave_new[model] = average(timings_new[model][0]) * scaling_factor[i]
- ave_new_cluster[model] = average(timings_new[model][1]) *
scaling_factor[i]
- ave_alt[model] = average(timings_alt[model][0]) * scaling_factor[i]
- ave_alt_cluster[model] = average(timings_alt[model][1]) *
scaling_factor[i]
+ ave_new[model] = average(timings_new[model][0]) * scaling_factor
+ ave_new_cluster[model] = average(timings_new[model][1]) *
scaling_factor
+ ave_alt[model] = average(timings_alt[model][0]) * scaling_factor
+ ave_alt_cluster[model] = average(timings_alt[model][1]) *
scaling_factor
# The SD.
- sd_new[model] = std(timings_new[model][0]) * scaling_factor[i]
- sd_new_cluster[model] = std(timings_new[model][1]) * scaling_factor[i]
- sd_alt[model] = std(timings_alt[model][0]) * scaling_factor[i]
- sd_alt_cluster[model] = std(timings_alt[model][1]) * scaling_factor[i]
+ sd_new[model] = std(timings_new[model][0]) * scaling_factor
+ sd_new_cluster[model] = std(timings_new[model][1]) * scaling_factor
+ sd_alt[model] = std(timings_alt[model][0]) * scaling_factor
+ sd_alt_cluster[model] = std(timings_alt[model][1]) * scaling_factor
# The speed up.
speed_up[model] = ave_alt[model] / ave_new[model]
@@ -202,8 +189,17 @@
# Final printout.
print("\n\n100 single spins analysis:")
-for model in models:
+for i in range(len(models)):
+ # Alias.
+ model, script, iter, scaling_factor = models[i]
print("%-25s %7.3f+/-%.3f -> %7.3f+/-%.3f, %7.3fx faster." %
(model+':', ave_alt[model], sd_alt[model], ave_new[model], sd_new[model],
speed_up[model]))
+
print("\nCluster of 100 spins analysis:")
-for model in models:
- print("%-25s %7.3f+/-%.3f -> %7.3f+/-%.3f, %7.3fx faster." %
(model+':', ave_alt_cluster[model], sd_alt_cluster[model],
ave_new_cluster[model], sd_new_cluster[model], speed_up_cluster[model]))
+for i in range(len(models)):
+ # Alias.
+ model, script, iter, scaling_factor = models[i]
+ if model == 'IT99':
+ comment = "IT99: Cluster of only 1 spin analysis, since v. 3.2.2
had a bug with clustering analysis.:"
+ else:
+ comment = ""
+ print("%-25s %7.3f+/-%.3f -> %7.3f+/-%.3f, %7.3fx faster. %s" %
(model+':', ave_alt_cluster[model], sd_alt_cluster[model],
ave_new_cluster[model], sd_new_cluster[model], speed_up_cluster[model],
comment) )
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Re: r24231 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py