r19609 - /trunk/devel_scripts/memory_leak_test_relax_fit.py -- April 29, 2013 - 12:01

Author: bugman
Date: Mon Apr 29 12:01:20 2013
New Revision: 19609

URL: http://svn.gna.org/viewcvs/relax?rev=19609&view=rev
Log:
Added a developer script for testing of memory leaks in the relax_fit C 
modules.


Added:
    trunk/devel_scripts/memory_leak_test_relax_fit.py

Added: trunk/devel_scripts/memory_leak_test_relax_fit.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/memory_leak_test_relax_fit.py?rev=19609&view=auto
==============================================================================
--- trunk/devel_scripts/memory_leak_test_relax_fit.py (added)
+++ trunk/devel_scripts/memory_leak_test_relax_fit.py Mon Apr 29 12:01:20 2013
@@ -1,0 +1,119 @@
+"""Script for relaxation curve fitting.
+
+Run with a debugging compiled version of Python, eg:
+
+/data/python/pydebug/bin/python relax relax_fit.py
+
+and build the C module with:
+
+gcc -o target_functions/c_chi2.os -c 
-I/data/python/pydebug/include/python2.7/ -fPIC target_functions/c_chi2.c
+gcc -o target_functions/exponential.os -c 
-I/data/python/pydebug/include/python2.7/ -fPIC target_functions/exponential.c
+gcc -o target_functions/relax_fit.os -c 
-I/data/python/pydebug/include/python2.7/ -fPIC target_functions/relax_fit.c
+gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os 
target_functions/exponential.os target_functions/relax_fit.os
+"""
+
+
+# Python module imports.
+from os import sep
+import sys
+
+# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Missing intensity type (allow this script to run outside of the system 
test framework).
+if not hasattr(ds, 'int_type'):
+    ds.int_type = 'height'
+
+# Missing temporary directory.
+if not hasattr(ds, 'tmpdir'):
+    ds.tmpdir = 'temp'
+
+# Create the data pipe.
+pipe.create('rx', 'relax_fit')
+
+# The path to the data files.
+data_path = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
+
+# Load the sequence.
+sequence.read('Ap4Aase.seq', dir=status.install_path + 
sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2)
+
+# Deselect unresolved spins.
+deselect.read(file='unresolved', dir=data_path, res_num_col=1)
+
+# Name the spins so they can be matched to the assignments.
+spin.name(name='N')
+
+# Spectrum names.
+names = [
+    'T2_ncyc1_ave',
+    'T2_ncyc1b_ave',
+    'T2_ncyc2_ave',
+    'T2_ncyc4_ave',
+    'T2_ncyc4b_ave',
+    'T2_ncyc6_ave',
+    'T2_ncyc9_ave',
+    'T2_ncyc9b_ave',
+    'T2_ncyc11_ave',
+    'T2_ncyc11b_ave'
+]
+
+# Relaxation times (in seconds).
+times = [
+    0.0176,
+    0.0176,
+    0.0352,
+    0.0704,
+    0.0704,
+    0.1056,
+    0.1584,
+    0.1584,
+    0.1936,
+    0.1936
+]
+
+# Load the data twice to test data deletion.
+for iter in range(2):
+    # Loop over the spectra.
+    for i in range(len(names)):
+        # Load the peak intensities.
+        spectrum.read_intensities(file=names[i]+'.list', dir=data_path, 
spectrum_id=names[i], int_method=ds.int_type)
+
+        # Set the relaxation times.
+        relax_fit.relax_time(time=times[i], spectrum_id=names[i])
+
+    # Specify the duplicated spectra.
+    spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
+    spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
+    spectrum.replicated(spectrum_ids=['T2_ncyc9b_ave', 'T2_ncyc9_ave'])
+    spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
+
+    # Peak intensity error analysis.
+    spectrum.error_analysis()
+
+    # Delete the data.
+    if iter == 0:
+        for i in range(len(names)):
+            spectrum.delete(names[i])
+
+# Set the relaxation curve type.
+relax_fit.select_model('exp')
+
+# Grid search.
+grid_search(inc=11)
+
+# Minimise.
+from guppy import hpy
+file = open('guppy_log', 'w')
+for i in range(10000):
+    minimise('simplex', constraints=False)
+    if not i % 100:
+        file.write("Iteration %i\n" % i)
+        file.write("Reference counts:\n%s\n\n" % sys.gettotalrefcount())
+        h = hpy()
+        file.write("Guppy heap:\n%s\n\n\n" % h.heap())
+        file.flush()
+
+
+print("Finished :)")