Author: bugman
Date: Thu Aug 15 11:55:06 2013
New Revision: 20597
URL: http://svn.gna.org/viewcvs/relax?rev=20597&view=rev
Log:
Merged revisions 20590-20596 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20590 | bugman | 2013-08-14 16:48:43 +0200 (Wed, 14 Aug 2013) | 8 lines
Reverted r20587 and r20588 as these were rubbish!
The command used was:
svn merge -rHEAD:r20586 .
There are gcc verses pdf Modelfree4 binary results for version 4.20.
........
r20591 | bugman | 2013-08-14 18:19:38 +0200 (Wed, 14 Aug 2013) | 6 lines
Proper fix for the Palmer.test_palmer_omp for the different Modelfree4
binaries.
The gcc and pdf binaries are now properly detected and the slightly
different results are now
correctly checked for.
........
r20592 | bugman | 2013-08-14 18:53:13 +0200 (Wed, 14 Aug 2013) | 3 lines
Updated the Mac Framework setup document to help with scipy compilation
problems.
........
r20593 | bugman | 2013-08-14 18:54:19 +0200 (Wed, 14 Aug 2013) | 5 lines
Improved the Python seeking and module version print out script for
symlinks.
This should now be much more capable of finding all Python versions on a
system.
........
r20594 | bugman | 2013-08-14 19:52:39 +0200 (Wed, 14 Aug 2013) | 8 lines
Added support for the Mac OS X Modelfree4 binary results to the Palmer.*
system tests.
The Mac OS X Modelfree 4.20 binary produces different results than the
Linux binaries, mainly due to
a compilation problem. In the Linux binaries, the results are written out
to 4 decimal places. In
the Mac binaries, the results are instead written out to 4 significant
figures. Therefore the
number of decimal places are much less than the Linux results.
........
r20595 | bugman | 2013-08-14 19:55:57 +0200 (Wed, 14 Aug 2013) | 5 lines
Fix for the Palmer.test_palmer system test for older Python versions.
This is a problem introduced in the previous commit (r20594).
........
r20596 | bugman | 2013-08-15 09:10:12 +0200 (Thu, 15 Aug 2013) | 24 lines
Syntax error fix for one of the unused scripts in the relax test suite
shared data directories.
This problem was encountered by Jack Howarth <howarth att bromo dott med
dott uc dott edu> and
communicated in a private message. The issue was found by fink. This
script is never used and will
never be used again - it is only there for reference. How a syntax error
was introduced is a
mystery. For reference, the full message is:
"""
While preparing fink packaging for the new relax 3.0.0 release, I
noticed an error
in the python scripts. When installing relax-py27-3.0.0, I get the
following error as
the the frame_order_pseudo_ellipse.py python script is compiled. What is
the correct
syntax for that particular call to pymol.command?
Setting up relax-py27 (3.0.0-1) ...
Compiling
/sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
...
File
"/sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py",
line 154
pymol.command('show spheres'_pseudo_ellipse)
^
SyntaxError: invalid syntax
Thanks in advance for any clarification.
"""
........
Modified:
branches/peak_intensities/ (props changed)
branches/peak_intensities/devel_scripts/python_seek.py
branches/peak_intensities/docs/Mac_framework_build_3way
branches/peak_intensities/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
branches/peak_intensities/test_suite/system_tests/palmer.py
Propchange: branches/peak_intensities/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Aug 15 11:55:06 2013
@@ -1,1 +1,1 @@
-/trunk:1-20588
+/trunk:1-20596
Modified: branches/peak_intensities/devel_scripts/python_seek.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/devel_scripts/python_seek.py?rev=20597&r1=20596&r2=20597&view=diff
==============================================================================
--- branches/peak_intensities/devel_scripts/python_seek.py (original)
+++ branches/peak_intensities/devel_scripts/python_seek.py Thu Aug 15
11:55:06 2013
@@ -5,8 +5,8 @@
# Python module imports.
-from os import X_OK, access, system
-from os.path import isfile, islink
+from os import X_OK, access, readlink, system
+from os.path import abspath, dirname, isabs, isfile, islink, join
from subprocess import PIPE, Popen
import sys
@@ -96,6 +96,17 @@
# The file name.
file = line[:-1]
+ # Recursively follow and expand links.
+ while 1:
+ if islink(file):
+ orig = readlink(file)
+ if not isabs(orig):
+ orig = join(dirname(file), orig)
+ file = orig
+ continue
+ else:
+ break
+
# Check if the path is a file.
if not isfile(file):
continue
@@ -104,12 +115,12 @@
if not access(file, X_OK):
continue
- # Check if the path is a link.
- if islink(file):
- continue
-
- # Add the file.
- binaries.append(file)
+ # Convert to an absolute path.
+ file = abspath(file)
+
+ # Add the file, avoiding duplicates.
+ if file not in binaries:
+ binaries.append(file)
# Return the file list.
return binaries
Modified: branches/peak_intensities/docs/Mac_framework_build_3way
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/docs/Mac_framework_build_3way?rev=20597&r1=20596&r2=20597&view=diff
==============================================================================
--- branches/peak_intensities/docs/Mac_framework_build_3way (original)
+++ branches/peak_intensities/docs/Mac_framework_build_3way Thu Aug 15
11:55:06 2013
@@ -34,7 +34,12 @@
$ PATH=/usr/local/bin/:$PATH C_INCLUDE_PATH=/sw/include/suitesparse/
~/bin/python2.7 setup.py install
-The PATH option is needed if gfortran is located in both /usr/local/bin/ and
/sw/bin/. The C_INCLUDE_PATH may be needed if the suitesparse header files
cannot be found.
+The PATH option is needed if gfortran is located in both /usr/local/bin/ and
/sw/bin/. The C_INCLUDE_PATH may be needed if the suitesparse header files
cannot be found. If you still encounter swig problems finding the
umfpack_*.h files, then manually type:
+
+$ swig -I/sw/include/suitesparse/ -python -o
build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c
-outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack
scipy/sparse/linalg/dsolve/umfpack/umfpack.i
+$ PATH=/usr/local/bin/:$PATH C_INCLUDE_PATH=/sw/include/suitesparse/
~/bin/python2.7 setup.py install
+
+The swig command will build the Scipy part requining the umfpack_*.h files,
and then the python command will continue happily.
Modified:
branches/peak_intensities/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py?rev=20597&r1=20596&r2=20597&view=diff
==============================================================================
---
branches/peak_intensities/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
(original)
+++
branches/peak_intensities/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
Thu Aug 15 11:55:06 2013
@@ -151,7 +151,7 @@
# PyMOL.
pymol.view()
- pymol.command('show spheres'_pseudo_ellipse)
+ pymol.command('show spheres')
pymol.cone_pdb('cone_pseudo_ellipse.pdb')
Modified: branches/peak_intensities/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/test_suite/system_tests/palmer.py?rev=20597&r1=20596&r2=20597&view=diff
==============================================================================
--- branches/peak_intensities/test_suite/system_tests/palmer.py (original)
+++ branches/peak_intensities/test_suite/system_tests/palmer.py Thu Aug 15
11:55:06 2013
@@ -74,14 +74,32 @@
# Execute the script.
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'palmer.py')
+ # Determine if the Gnu gcc or Portland C compiler version is being
used.
+ spin = return_spin(':0@N', pipe='m2')
+ if spin.te == 1.951*1e-12:
+ binary = 'linux-i386-gcc' # Linux Gnu gcc modelfree4 version.
+ else:
+ binary = 'linux-i386-pgf' # Linux Portland C compiler
modelfree4 version.
+ spin = return_spin(':-2@N', pipe='m1')
+ if spin.chi2 == 36.62:
+ binary = 'mac-i386' # Mac OS X intel binary.
+ if not binary:
+ raise RelaxError("The Modelfree4 binary cannot be identified,
therefore the parameters cannot be meaningfully checked.")
+ print("\nDetected the '%s' Modelfree4 binary." % binary)
+
# Checks for model m1, m2, and m3 mfout file reading.
models = ['m1', 'm2', 'm3']
params = [['s2'], ['s2', 'te'], ['s2', 'rex']]
spin_names = [':-2@N', ':-1@N', ':0@N']
s2 = [[0.869, 0.732, None], [0.869, 0.730, None], [0.715, 0.643,
None]]
- te = [[None, None, None], [0.0, 1.952, None], [None, None, None]]
+ if binary == 'linux-i386-gcc':
+ te = [[None, None, None], [0.0, 1.951, None], [None, None, None]]
+ else:
+ te = [[None, None, None], [0.0, 1.952, None], [None, None, None]]
rex = [[None, None, None], [None, None, None], [4.308, 4.278, None]]
chi2 = [[36.6223, 20.3954, None], [36.6223, 20.3299, None], [1.9763,
0.6307, None]]
+ if binary == 'mac-i386':
+ chi2 = [[36.62, 20.40, None], [36.62, 20.33, None], [1.976,
0.6307, None]]
for model_index in range(3):
print("Model " + repr(models[model_index]))
for spin_index in range(3):
@@ -118,6 +136,8 @@
te = [None, None]
rex = [0.005, 0.404]
chi2 = [1.7966, 0.7389]
+ if binary == 'mac-i386':
+ chi2 = [1.796, 0.7392]
for spin_index in range(3):
# Get the spin.
spin = return_spin(spin_names[spin_index], pipe='aic')
@@ -135,19 +155,26 @@
# Checks.
self.assertEqual(spin.model, models[spin_index])
self.assertEqual(spin.params, params[spin_index])
- self.assertEqual(spin.s2, s2[spin_index])
+ self.assertAlmostEqual(spin.s2, s2[spin_index])
self.assertEqual(spin.s2f, None)
self.assertEqual(spin.s2s, None)
- self.assertEqual(spin.te, te[spin_index])
+ if te[spin_index]:
+ self.assertAlmostEqual(spin.te, te[spin_index])
+ else:
+ self.assertEqual(spin.te, None)
self.assertEqual(spin.tf, None)
self.assertEqual(spin.ts, None)
- self.assertEqual(spin.rex, rex[spin_index])
+ self.assertAlmostEqual(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, 2.5356)
- self.assertEqual(final_pipe.diff_tensor.tm, 12.045)
+ if binary == 'mac-i386':
+ self.assertAlmostEqual(final_pipe.chi2, 2.5355)
+ self.assertAlmostEqual(final_pipe.diff_tensor.tm, 12.051)
+ else:
+ self.assertAlmostEqual(final_pipe.chi2, 2.5356)
+ self.assertAlmostEqual(final_pipe.diff_tensor.tm, 12.045)
def test_palmer_omp(self):
@@ -166,6 +193,20 @@
spin = return_spin(':9@N', 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 the Modelfree4 binary type used.
+ spin = return_spin(':9@N', pipe='aic')
+ binary = None
+ if spin.te * 1e12 == 52.195:
+ binary = 'linux-i386-gcc' # Linux Gnu gcc modelfree4 version.
+ elif spin.te * 1e12 == 52.197:
+ binary = 'linux-i386-pgf' # Linux Portland C compiler
modelfree4 version.
+ spin = return_spin(':9@N', pipe='m1')
+ if spin.chi2 == 143.7:
+ binary = 'mac-i386' # Mac OS X intel binary.
+ if not binary:
+ raise RelaxError("The Modelfree4 binary cannot be identified,
therefore the parameters cannot be meaningfully checked.")
+ print("\nDetected the '%s' Modelfree4 binary." % binary)
# Model m1, m2, and m3 mfout file data.
models = ['m1', 'm2', 'm3']
@@ -173,8 +214,12 @@
spin_names = [':9@N', ':10@N', ':11@N']
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, 36.087, 20.039], [None, None,
None]]
+ if binary == 'mac-i386':
+ te = [[None, None, None], [61.504, 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]]
+ if binary == 'mac-i386':
+ chi2 = [[143.7, 105.2, 61.67], [40.91, 57.16, 48.49], [143.7,
105.2, 61.67]]
# Checks for model m1, m2, and m3 mfout file reading.
for model_index in range(3):
@@ -184,20 +229,20 @@
# Get the spin.
spin = return_spin(spin_names[spin_index],
pipe=models[model_index])
+ print spin
# 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 *
cdp.spectrometer_frq[cdp.ri_ids[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.assertAlmostEqual(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])
+ if te[model_index][spin_index]:
+ self.assertAlmostEqual(spin.te * 1e12,
te[model_index][spin_index])
self.assertEqual(spin.tf, None)
self.assertEqual(spin.ts, None)
self.assertEqual(spin.rex, rex[model_index][spin_index])
@@ -207,34 +252,49 @@
models = ['m2', 'm2', 'm2']
params = [['s2', 'te'], ['s2', 'te'], ['s2', 'te']]
s2 = [0.755, 0.761, 0.787]
- te = [52.197, 29.361, 12.677]
+ if binary == 'linux-i386-gcc':
+ te = [52.195, 29.356, 12.678]
+ elif binary == 'linux-i386-pgf':
+ te = [52.197, 29.361, 12.677]
+ elif binary == 'mac-i386':
+ te = [52.197, 29.357, 12.676]
chi2 = [7.254, 8.0437, 0.5327]
+ if binary == 'mac-i386':
+ chi2 = [7.254, 8.044, 0.5327]
# Checks for the final mfout file reading.
for spin_index in range(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.assertAlmostEqual(spin.s2, s2[spin_index])
self.assertEqual(spin.s2f, None)
self.assertEqual(spin.s2s, None)
- self.assertAlmostEqual(spin.te, te[spin_index])
+ if te[spin_index]:
+ self.assertAlmostEqual(spin.te * 1e12, te[spin_index])
self.assertEqual(spin.tf, None)
self.assertEqual(spin.ts, None)
self.assertEqual(spin.rex, None)
- self.assertEqual(spin.chi2, chi2[spin_index])
+ self.assertAlmostEqual(spin.chi2, chi2[spin_index])
# Final global values.
final_pipe = pipes.get_pipe('aic')
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.assertAlmostEqual(final_pipe.diff_tensor.theta, (68.592 /
360.0) * 2.0 * pi)
- self.assertAlmostEqual(final_pipe.diff_tensor.phi, (73.756 / 360.0)
* 2.0 * pi)
+ if binary == 'linux-i386-gcc':
+ self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.443)
+ self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.053)
+ self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0
/ pi, 68.592)
+ self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 /
pi, 73.756)
+ elif binary == 'linux-i386-pgf':
+ self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.443)
+ self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.053)
+ self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0
/ pi, 68.864)
+ self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 /
pi, 73.913)
+ elif binary == 'mac-i386':
+ self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.459)
+ self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.049)
+ self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0
/ pi, 64.611)
+ self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 /
pi, 79.281)
r20597 - in /branches/peak_intensities: ./ devel_scripts/ docs/ test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_r...