Author: bugman
Date: Wed Oct 15 00:43:39 2008
New Revision: 7704
URL: http://svn.gna.org/viewcvs/relax?rev=7704&view=rev
Log:
Modified the Modelfree4 system tests to work with the Portland C compiler
Linux version.
The modelfree4 Linux binary compiled with Gnu gcc gives different results,
sometimes quite large, to
the Linux binary compiled with the Portland C compiler. The tests now catch
this. There may be
problems with the Mac OS X Modelfree4 binary still.
Modified:
1.3/test_suite/system_tests/palmer.py
Modified: 1.3/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/palmer.py?rev=7704&r1=7703&r2=7704&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/palmer.py (original)
+++ 1.3/test_suite/system_tests/palmer.py Wed Oct 15 00:43:39 2008
@@ -70,14 +70,126 @@
# Execute the script.
self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/palmer.py')
+ # Determine if the Gnu gcc or Portland C compiler version is being
used.
+ spin = return_spin(':0', pipe='m2')
+ if spin.te == 1.951*1e-12:
+ compiler = 'gcc' # Gnu gcc modelfree4 version.
+ else:
+ compiler = 'pgf' # Portland C compiler modelfree4 version.
+
# Checks for model m1, m2, and m3 mfout file reading.
models = ['m1', 'm2', 'm3']
params = [['S2'], ['S2', 'te'], ['S2', 'Rex']]
spin_names = [':-2&:Gly', ':-1&:Gly', ':0&:Gly']
- s2 = [[0.869, 0.732, 0.802], [0.869, 0.730, 0.755], [0.715, 0.643,
0.734]]
- te = [[None, None, None], [0.0, 1.951, 1319.171], [None, None, None]]
- rex = [[None, None, None], [None, None, None], [4.308, 4.278, 1.017]]
+ if compiler == 'gcc':
+ s2 = [[0.869, 0.732, 0.802], [0.869, 0.730, 0.755], [0.715,
0.643, 0.734]]
+ te = [[None, None, None], [0.0, 1.951, 1319.171], [None, None,
None]] # Gnu gcc modelfree4 version.
+ rex = [[None, None, None], [None, None, None], [4.308, 4.278,
1.017]]
+ else:
+ s2 = [[0.869, 0.732, 0.802], [0.869, 0.730, 0.755], [0.715,
0.643, 0.732]]
+ te = [[None, None, None], [0.0, 1.952, 1319.172], [None, None,
None]] # Portland C compiler modelfree4 version.
+ rex = [[None, None, None], [None, None, None], [4.308, 4.278,
1.050]]
chi2 = [[36.6223, 20.3954, 5.2766], [36.6223, 20.3299, 0.0],
[1.9763, 0.6307, 5.2766]]
+ for model_index in xrange(3):
+ print "Model " + `models[model_index]`
+ for spin_index in xrange(3):
+ print "Spin " + `spin_names[spin_index]`
+
+ # Get the spin.
+ spin = return_spin(spin_names[spin_index],
pipe=models[model_index])
+
+ # Conversions.
+ if te[model_index][spin_index]:
+ te[model_index][spin_index] =
te[model_index][spin_index] * 1e-12
+ if rex[model_index][spin_index]:
+ rex[model_index][spin_index] =
rex[model_index][spin_index] / (2.0 * pi * spin.frq[0])**2
+
+ # Checks.
+ self.assertEqual(spin.model, models[model_index])
+ self.assertEqual(spin.params, params[model_index])
+ self.assertEqual(spin.s2, s2[model_index][spin_index])
+ self.assertEqual(spin.s2f, None)
+ self.assertEqual(spin.s2s, None)
+ if te[model_index][spin_index] == None:
+ self.assertEqual(spin.te, te[model_index][spin_index])
+ else:
+ self.assertAlmostEqual(spin.te,
te[model_index][spin_index])
+ self.assertEqual(spin.tf, None)
+ self.assertEqual(spin.ts, None)
+ self.assertEqual(spin.rex, rex[model_index][spin_index])
+ self.assertEqual(spin.chi2, chi2[model_index][spin_index])
+
+ # Checks for the final mfout file reading.
+ models = ['m3', 'm3', 'm2']
+ params = [['S2', 'Rex'], ['S2', 'Rex'], ['S2', 'te']]
+ s2 = [0.844, 0.760, 0.592]
+ te = [None, None, 1809.287]
+ rex = [0.0, 0.394, None]
+ chi2 = [1.7964, 0.7391, 0.0000]
+ for spin_index in xrange(3):
+ # Get the spin.
+ spin = return_spin(spin_names[spin_index], pipe='aic')
+
+ # Conversions.
+ if te[spin_index]:
+ te[spin_index] = te[spin_index] * 1e-12
+ if rex[spin_index]:
+ rex[spin_index] = rex[spin_index] / (2.0 * pi *
spin.frq[0])**2
+
+ # Checks.
+ self.assertEqual(spin.model, models[spin_index])
+ self.assertEqual(spin.params, params[spin_index])
+ self.assertEqual(spin.s2, s2[spin_index])
+ self.assertEqual(spin.s2f, None)
+ self.assertEqual(spin.s2s, None)
+ self.assertEqual(spin.te, te[spin_index])
+ self.assertEqual(spin.tf, None)
+ self.assertEqual(spin.ts, None)
+ self.assertEqual(spin.rex, rex[spin_index])
+ self.assertEqual(spin.chi2, chi2[spin_index])
+
+ # Final global values.
+ final_pipe = pipes.get_pipe('aic')
+ self.assertEqual(final_pipe.chi2, 2.5355)
+ self.assertEqual(final_pipe.diff_tensor.tm, 12.050)
+
+
+ def test_palmer_omp(self):
+ """Test a complete model-free analysis using 'Modelfree4' with the
OMP relaxation data, a PDB file, and a spheroid tensor."""
+
+ # Test for the presence of the Modelfree4 binary (skip the test if
not present).
+ try:
+ test_binary('modelfree4')
+ except:
+ return
+
+ # Execute the script.
+ self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/palmer_omp.py')
+
+ # Catch a the old, buggy modelfree4 versions and complain loudly!
+ spin = return_spin(':9', pipe='m2')
+ if spin.s2 == 0.855:
+ raise RelaxError, "You are using an old, buggy Modelfree4
version! You must upgrade to version 4.20 or later."
+
+ # Determine if the Gnu gcc or Portland C compiler version is being
used.
+ if spin.te == 20.043*1e-12:
+ compiler = 'gcc' # Gnu gcc modelfree4 version.
+ else:
+ compiler = 'pgf' # Portland C compiler modelfree4 version.
+
+ # Model m1, m2, and m3 mfout file data.
+ models = ['m1', 'm2', 'm3']
+ params = [['S2'], ['S2', 'te'], ['S2', 'Rex']]
+ spin_names = [':9', ':10', ':11']
+ s2 = [[0.822, 0.799, 0.823], [0.788, 0.777, 0.812], [0.822, 0.799,
0.823]]
+ if compiler == 'gcc':
+ te = [[None, None, None], [61.506, 36.084, 20.043], [None, None,
None]]
+ else:
+ te = [[None, None, None], [61.506, 36.087, 20.039], [None, None,
None]]
+ rex = [[None, None, None], [None, None, None], [0.0, 0.0, 0.0]]
+ chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 48.4927],
[143.6773, 105.1767, 61.6684]]
+
+ # Checks for model m1, m2, and m3 mfout file reading.
for model_index in xrange(3):
print "Model " + `models[model_index]`
for spin_index in xrange(3):
@@ -104,13 +216,19 @@
self.assertEqual(spin.rex, rex[model_index][spin_index])
self.assertEqual(spin.chi2, chi2[model_index][spin_index])
+ # Final mfout file data.
+ models = ['m2', 'm2', 'm2']
+ params = [['S2', 'te'], ['S2', 'te'], ['S2', 'te']]
+ if compiler == 'gcc':
+ s2 = [0.782, 0.760, 0.785]
+ te = [60.009, 29.134, 12.590]
+ chi2 = [24.0495, 8.1168, 0.5332]
+ else:
+ s2 = [0.755, 0.761, 0.787]
+ te = [52.197, 29.361, 12.677]
+ chi2 = [7.254, 8.0437, 0.5327]
+
# Checks for the final mfout file reading.
- models = ['m3', 'm3', 'm2']
- params = [['S2', 'Rex'], ['S2', 'Rex'], ['S2', 'te']]
- s2 = [0.844, 0.760, 0.592]
- te = [None, None, 1809.287]
- rex = [0.0, 0.394, None]
- chi2 = [1.7964, 0.7391, 0.0000]
for spin_index in xrange(3):
# Get the spin.
spin = return_spin(spin_names[spin_index], pipe='aic')
@@ -118,8 +236,6 @@
# Conversions.
if te[spin_index]:
te[spin_index] = te[spin_index] * 1e-12
- if rex[spin_index]:
- rex[spin_index] = rex[spin_index] / (2.0 * pi *
spin.frq[0])**2
# Checks.
self.assertEqual(spin.model, models[spin_index])
@@ -127,90 +243,7 @@
self.assertEqual(spin.s2, s2[spin_index])
self.assertEqual(spin.s2f, None)
self.assertEqual(spin.s2s, None)
- self.assertEqual(spin.te, te[spin_index])
- self.assertEqual(spin.tf, None)
- self.assertEqual(spin.ts, None)
- self.assertEqual(spin.rex, rex[spin_index])
- self.assertEqual(spin.chi2, chi2[spin_index])
-
- # Final global values.
- final_pipe = pipes.get_pipe('aic')
- self.assertEqual(final_pipe.chi2, 2.5355)
- self.assertEqual(final_pipe.diff_tensor.tm, 12.050)
-
-
- def test_palmer_omp(self):
- """Test a complete model-free analysis using 'Modelfree4' with the
OMP relaxation data, a PDB file, and a spheroid tensor."""
-
- # Test for the presence of the Modelfree4 binary (skip the test if
not present).
- try:
- test_binary('modelfree4')
- except:
- return
-
- # Execute the script.
- self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/palmer_omp.py')
-
- # Catch a the old, buggy modelfree4 versions and complain loudly!
- spin = return_spin(':9', pipe='m2')
- if spin.s2 == 0.855:
- raise RelaxError, "You are using an old, buggy Modelfree4
version! You must upgrade to version 4.20 or later."
-
- # Checks for model m1, m2, and m3 mfout file reading.
- models = ['m1', 'm2', 'm3']
- params = [['S2'], ['S2', 'te'], ['S2', 'Rex']]
- spin_names = [':9', ':10', ':11']
- s2 = [[0.822, 0.799, 0.823], [0.788, 0.777, 0.812], [0.822, 0.799,
0.823]]
- te = [[None, None, None], [61.506, 36.084, 20.043], [None, None,
None]]
- rex = [[None, None, None], [None, None, None], [0.0, 0.0, 0.0]]
- chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 48.4927],
[143.6773, 105.1767, 61.6684]]
- for model_index in xrange(3):
- print "Model " + `models[model_index]`
- for spin_index in xrange(3):
- print "Spin " + `spin_names[spin_index]`
-
- # Get the spin.
- spin = return_spin(spin_names[spin_index],
pipe=models[model_index])
-
- # Conversions.
- if te[model_index][spin_index]:
- te[model_index][spin_index] =
te[model_index][spin_index] * 1e-12
- if rex[model_index][spin_index]:
- rex[model_index][spin_index] =
rex[model_index][spin_index] / (2.0 * pi * spin.frq[0])**2
-
- # Checks.
- self.assertEqual(spin.model, models[model_index])
- self.assertEqual(spin.params, params[model_index])
- self.assertEqual(spin.s2, s2[model_index][spin_index])
- self.assertEqual(spin.s2f, None)
- self.assertEqual(spin.s2s, None)
- self.assertEqual(spin.te, te[model_index][spin_index])
- self.assertEqual(spin.tf, None)
- self.assertEqual(spin.ts, None)
- self.assertEqual(spin.rex, rex[model_index][spin_index])
- self.assertEqual(spin.chi2, chi2[model_index][spin_index])
-
- # Checks for the final mfout file reading.
- models = ['m2', 'm2', 'm2']
- params = [['S2', 'te'], ['S2', 'te'], ['S2', 'te']]
- s2 = [0.782, 0.760, 0.785]
- te = [60.009, 29.134, 12.590]
- chi2 = [24.0495, 8.1168, 0.5332]
- for spin_index in xrange(3):
- # Get the spin.
- spin = return_spin(spin_names[spin_index], pipe='aic')
-
- # Conversions.
- if te[spin_index]:
- te[spin_index] = te[spin_index] * 1e-12
-
- # Checks.
- self.assertEqual(spin.model, models[spin_index])
- self.assertEqual(spin.params, params[spin_index])
- self.assertEqual(spin.s2, s2[spin_index])
- self.assertEqual(spin.s2f, None)
- self.assertEqual(spin.s2s, None)
- self.assertEqual(spin.te, te[spin_index])
+ self.assertAlmostEqual(spin.te, te[spin_index])
self.assertEqual(spin.tf, None)
self.assertEqual(spin.ts, None)
self.assertEqual(spin.rex, None)
@@ -218,8 +251,15 @@
# Final global values.
final_pipe = pipes.get_pipe('aic')
- self.assertEqual(final_pipe.chi2, 32.6995)
- self.assertEqual(final_pipe.diff_tensor.tm, 8.964)
- self.assertEqual(final_pipe.diff_tensor.Dratio, 1.324)
- self.assertEqual(final_pipe.diff_tensor.theta, (-52.070 / 360.0) *
2.0 * pi + pi)
- self.assertEqual(final_pipe.diff_tensor.phi, (2.377 / 360.0) * 2.0 *
pi)
+ if compiler == 'gcc':
+ self.assertEqual(final_pipe.chi2, 32.6995)
+ self.assertEqual(final_pipe.diff_tensor.tm, 8.964)
+ self.assertEqual(final_pipe.diff_tensor.Dratio, 1.324)
+ self.assertEqual(final_pipe.diff_tensor.theta, (-52.070 / 360.0)
* 2.0 * pi + pi)
+ self.assertEqual(final_pipe.diff_tensor.phi, (2.377 / 360.0) *
2.0 * pi)
+ else:
+ self.assertEqual(final_pipe.chi2, 15.8304)
+ self.assertEqual(final_pipe.diff_tensor.tm, 8.443)
+ self.assertEqual(final_pipe.diff_tensor.Dratio, 1.053)
+ self.assertEqual(final_pipe.diff_tensor.theta, (68.864 / 360.0)
* 2.0 * pi)
+ self.assertEqual(final_pipe.diff_tensor.phi, (73.913 / 360.0) *
2.0 * pi)
r7704 - /1.3/test_suite/system_tests/palmer.py