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TypeError/AssertionError test failures on i686 and armv7hl due to dtype being int32 instead of int64 #1362

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rathann opened this issue May 23, 2017 · 9 comments · Fixed by #1410
Closed

TypeError/AssertionError test failures on i686 and armv7hl due to dtype being int32 instead of int64 #1362

rathann opened this issue May 23, 2017 · 9 comments · Fixed by #1410
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32 bit

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@rathann
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rathann commented May 23, 2017

Expected behaviour

All tests pass.

Actual behaviour

39 tests fail with:

TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

or with AssertionError due to dtype being int32 instead of int64.

Code to reproduce the behaviour

Note that I had to use nosetests instead of mda_nosetests due to testsuite execution just stopping silently like in #1360 . Do you run the testsuite on 32bit x86? Sorry for the large paste, but github is not letting me attach the full log.

On Fedora rawhide (27) running on i686:

$ nosetests -v --nologcapture --exe --process-timeout=240
...
======================================================================
ERROR: test_ces (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 295, in test_ces
    results, details = encore.ces([self.ens1, self.ens2])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1131, in ces
    ncores=ncores)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_ces_convergence (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 334, in test_ces_convergence
    results = encore.ces_convergence(self.ens1, 5)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1588, in ces_convergence
    original_ensemble, window_size, selection=selection)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 717, in prepare_ensembles_for_convergence_increasing_window
    format='fac').shape[0]
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_ces_error_estimation (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 369, in test_ces_error_estimation
    selection="name CA and resnum 1-10")
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1131, in ces
    ncores=ncores)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_ces_error_estimation_ensemble_bootstrap (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 391, in test_ces_error_estimation_ensemble_bootstrap
    selection="name CA and resnum 1-10")
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1194, in ces
    selection=selection)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 345, in clustering_ensemble_similarity
    format='fac')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_ces_to_self (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 288, in test_ces_to_self
    clustering_method=encore.AffinityPropagationNative(preference = -3.0))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1131, in ces
    ncores=ncores)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dres (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 313, in test_dres
    results, details = encore.dres([self.ens1, self.ens2], selection="name CA and resnum 1-10")
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1407, in dres
    ncores=ncores)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dres_convergence (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 344, in test_dres_convergence
    results = encore.dres_convergence(self.ens1, 10)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1698, in dres_convergence
    original_ensemble, window_size, selection=selection)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 717, in prepare_ensembles_for_convergence_increasing_window
    format='fac').shape[0]
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dres_error_estimation (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 408, in test_dres_error_estimation
    selection="name CA and resnum 1-10")
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1407, in dres
    ncores=ncores)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dres_to_self (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 304, in test_dres_to_self
    results, details = encore.dres([self.ens1, self.ens1])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 1407, in dres
    ncores=ncores)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dres_without_superimposition (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 324, in test_dres_without_superimposition
    superimpose=False)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_hes (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 262, in test_hes
    results, details = encore.hes([self.ens1, self.ens2], weights='mass')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 940, in hes
    format='fac')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_hes_align (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 279, in test_hes_align
    results, details = encore.hes([self.ens1, self.ens2], align=True)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 940, in hes
    format='fac')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_hes_custom_weights (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 269, in test_hes_custom_weights
    results, details = encore.hes([self.ens1, self.ens2], weights='mass')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 940, in hes
    format='fac')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_hes_error_estimation (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 352, in test_hes_error_estimation
    averages, stdevs = encore.hes([self.ens1, self.ens1], estimate_error = True, bootstrapping_samples=10, selection="name CA and resnum 1-10")
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 913, in hes
    format=('fac')),
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_hes_to_self (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 255, in test_hes_to_self
    results, details = encore.hes([self.ens1, self.ens1])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py", line 940, in hes
    format='fac')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_rmsd_matrix_with_superimposition (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 163, in test_rmsd_matrix_with_superimposition
    n_jobs=1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_rmsd_matrix_with_superimposition_custom_weights (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 179, in test_rmsd_matrix_with_superimposition_custom_weights
    n_jobs=1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_rmsd_matrix_without_superimposition (MDAnalysisTests.analysis.test_encore.TestEncore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 196, in test_rmsd_matrix_without_superimposition
    coordinates = self.ens1.trajectory.timeseries(selection, format='fac')
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_AffinityPropagationNative_direct (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 499, in test_clustering_AffinityPropagationNative_direct
    distance_matrix = encore.get_distance_matrix(self.ens1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_AffinityPropagation_direct (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 511, in test_clustering_AffinityPropagation_direct
    distance_matrix = encore.get_distance_matrix(self.ens1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_DBSCAN_direct (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 537, in test_clustering_DBSCAN_direct
    distance_matrix = encore.get_distance_matrix(self.ens1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_one_ensemble (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 468, in test_clustering_one_ensemble
    cluster_collection = encore.cluster(self.ens1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_three_ensembles_two_identical (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 482, in test_clustering_three_ensembles_two_identical
    cluster_collection = encore.cluster([self.ens1, self.ens2, self.ens1])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_two_different_methods (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 551, in test_clustering_two_different_methods
    encore.DBSCAN(min_samples=2)])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_two_ensembles (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 475, in test_clustering_two_ensembles
    cluster_collection = encore.cluster([self.ens1, self.ens2])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_two_methods (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 492, in test_clustering_two_methods
    encore.AffinityPropagationNative()])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_clustering_two_methods_one_w_no_distance_matrix (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 575, in test_clustering_two_methods_one_w_no_distance_matrix
    encore.AffinityPropagationNative()])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_sklearn_affinity_propagation (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 584, in test_sklearn_affinity_propagation
    cc1 = encore.cluster([self.ens1])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 199, in cluster
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_one (MDAnalysisTests.analysis.test_encore.TestEncoreClusteringSklearn)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 686, in test_one
    method=clustering_method)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py", line 219, in cluster
    results = pc.run()
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/utils.py", line 296, in run
    **self.kwargs[i])))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py", line 156, in __call__
    noise=int(self.add_noise))
  File "MDAnalysis/analysis/encore/clustering/affinityprop.pyx", line 101, in MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation.run (MDAnalysis/analysis/encore/clustering/affinityprop.c:2206)
    cdef numpy.ndarray[long,   ndim=1] clusters   = numpy.zeros((s.size),dtype=long)
ValueError: Buffer dtype mismatch, expected 'long' but got 'long long'

======================================================================
ERROR: test_dimensionality_reduction_SPENative_direct (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 777, in test_dimensionality_reduction_SPENative_direct
    distance_matrix = encore.get_distance_matrix(self.ens1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dimensionality_reduction_one_ensemble (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 742, in test_dimensionality_reduction_one_ensemble
    coordinates, details = encore.reduce_dimensionality(self.ens1)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py", line 197, in reduce_dimensionality
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dimensionality_reduction_specified_dimension (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 769, in test_dimensionality_reduction_specified_dimension
    method=encore.StochasticProximityEmbeddingNative(dimension=dimension))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py", line 197, in reduce_dimensionality
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dimensionality_reduction_three_ensembles_two_identical (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 758, in test_dimensionality_reduction_three_ensembles_two_identical
    encore.reduce_dimensionality([self.ens1, self.ens2, self.ens1])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py", line 197, in reduce_dimensionality
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dimensionality_reduction_two_different_methods (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 828, in test_dimensionality_reduction_two_different_methods
    encore.PrincipalComponentAnalysis(dims[1])])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py", line 197, in reduce_dimensionality
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dimensionality_reduction_two_ensembles (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 751, in test_dimensionality_reduction_two_ensembles
    encore.reduce_dimensionality([self.ens1, self.ens2])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py", line 197, in reduce_dimensionality
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: test_dimensionality_reduction_two_methods (MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/analysis/test_encore.py", line 816, in test_dimensionality_reduction_two_methods
    encore.StochasticProximityEmbeddingNative(dims[1])])
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py", line 197, in reduce_dimensionality
    **kwargs))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 358, in get_distance_matrix
    verbose=verbose)
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py", line 99, in conformational_distance_matrix
    ensemble.select_atoms(selection), format='fac'))
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
ERROR: MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_noview
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/coordinates/test_memory.py", line 156, in test_timeseries_noview
    asel=selection).base is self.reader.get_array(),
  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py", line 365, in timeseries
    return array.take(asel.indices, a_index)
TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

======================================================================
FAIL: MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_downshift_dtype_ragged
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/core/test_topology.py", line 484, in test_downshift_dtype_ragged
    assert_(out[0].dtype == np.int64)
  File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 92, in assert_
    raise AssertionError(smsg)
AssertionError

======================================================================
FAIL: MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_downshift_dtype_square
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/core/test_topology.py", line 479, in test_downshift_dtype_square
    assert_(out[0].dtype == np.int64)
  File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 92, in assert_
    raise AssertionError(smsg)
AssertionError

----------------------------------------------------------------------

Ran 4498 tests in 599.158s

FAILED (SKIP=15, errors=37, failures=2)

Currently version of MDAnalysis:

0.16.0
@rathann rathann changed the title TypeError/AssertioError test failures on i686 due to dtype being int32 instead of int64 TypeError/AssertionError test failures on i686 due to dtype being int32 instead of int64 May 23, 2017
@mnmelo
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mnmelo commented May 23, 2017

32-bit testing/development has historically been tough. I recall similar problems when developing the XTCReader offset indexing, which could overflow 32-bit for large trajectories. Back then we had a hard time finding devs readily working on 32-bit machines and I guess the same holds now.

@kain88-de
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I'm not very much in favour of supporting 32bit machines. For two reasons. None of the devs is using a 32bit machine and we can't CI test it on travis. So 32bit support could break with any release even if we fix it now.

It's to bad for packaging this up for some distributions but I don't see it as a good fit to spend our time.

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Another reason for not supporting 32bit is the memory limit. I regularly have python processes larger then 4GB during analysis.

@richardjgowers richardjgowers mentioned this issue May 26, 2017
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@rathann
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rathann commented Jun 8, 2017

I've just managed to build and run testsuite of 0.16.1 on armv7hl and the result is similar:

Ran 4554 tests in 669.207s
FAILED (SKIP=16, errors=38, failures=2)

Full build.log from Fedora build system. I updated the issue summary, too.

@rathann rathann changed the title TypeError/AssertionError test failures on i686 due to dtype being int32 instead of int64 TypeError/AssertionError test failures on i686 and armv7hl due to dtype being int32 instead of int64 Jun 8, 2017
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rathann commented Jun 9, 2017

It looks like it might be a bug in numpy: numpy/numpy#4384 . I have a patch that brings the number of failed tests down to:

Ran 4554 tests in 643.255s

FAILED (SKIP=16, errors=12)

but it still needs further refinement and testing on 64bit.

@rathann rathann mentioned this issue Jun 9, 2017
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rathann commented Jun 11, 2017 •
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The remaining 12 errors are:

ERROR: test_one (MDAnalysisTests.analysis.test_encore.TestEncoreClusteringSklearn)
ERROR: test_clustering_AffinityPropagationNative_direct (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_clustering_one_ensemble (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_clustering_three_ensembles_two_identical (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_clustering_two_ensembles (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_clustering_two_methods (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_clustering_two_methods_one_w_no_distance_matrix (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_sklearn_affinity_propagation (MDAnalysisTests.analysis.test_encore.TestEncoreClustering)
ERROR: test_ces (MDAnalysisTests.analysis.test_encore.TestEncore)
ERROR: test_ces_convergence (MDAnalysisTests.analysis.test_encore.TestEncore)
ERROR: test_ces_error_estimation (MDAnalysisTests.analysis.test_encore.TestEncore)
ERROR: test_ces_to_self (MDAnalysisTests.analysis.test_encore.TestEncore)

and the backtraces all end in:

  File "/builddir/build/BUILDROOT/python-MDAnalysis-0.16.1-1.fc27.i386/usr/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py", line 157, in __call__
    noise=int(self.add_noise))
  File "MDAnalysis/analysis/encore/clustering/affinityprop.pyx", line 101, in MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation.run (MDAnalysis/analysis/encore/clustering/affinityprop.c:2206)
ValueError: Buffer dtype mismatch, expected 'long' but got 'long long'

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rathann commented Jun 11, 2017

Here are detailed ERROR logs.
ERRORs.txt

@richardjgowers richardjgowers mentioned this issue Jun 12, 2017
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@mtiberti @wouterboomsma the failures here are also in ENCORE #1362 (comment). Please have a look – it might be something easily fixable in the ENCORE C code – probably #1390 but please double check. Thanks!

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Sure, on it!

orbeckst pushed a commit that referenced this issue Jun 13, 2017
@richardjgowers @orbeckst
More work on making indexing arrays use intp (#1362)
eed7761 
- Added tests for 32 bit index support
- added @rathann to AUTHORS
orbeckst added a commit that referenced this issue Jun 14, 2017
@orbeckst
Merge pull request #1393 from MDAnalysis/issue-1362-int_types
6e6aa9d 
Issue #1362 : use np.intp types for indexing instead of np.int64

- According to numpy/numpy#4384 (comment), `np.intp` is the recommended dtype for indexing:
   "... use np.intp as dtype whenever things have to do with indexing or are logically related to 
   indexing/array sizes. This is the natural dtype for it and it will normally also be the fastest one.
- see https://docs.scipy.org/doc/numpy/user/basics.types.html
- see also PR #1391 for discussion
- This change should go some way towards increasing compatibility with i386/i696 (32 bit) platforms.

NOTE: No dedicated testing on 32 bit yet (see WIP PR #1392 )
@rathann rathann mentioned this issue Jun 19, 2017
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@jbarnoud jbarnoud mentioned this issue Jun 19, 2017
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richardjgowers pushed a commit that referenced this issue Jun 19, 2017
@rathann @richardjgowers
fix int type in asserts in TestDownshiftArrays (#1410)
1f36502 
Fixes #1362

this was missed in eed7761
@orbeckst orbeckst mentioned this issue Jun 21, 2017
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@junghans junghans mentioned this issue Sep 5, 2019
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fix int type in asserts in TestDownshiftArrays
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@orbeckst @mtiberti @kain88-de @rathann @mnmelo