Fix errors when running tests in debug mode

[astrofrog]

If I compile Hyperion with --enable-debug and then run the tests, there are a few failures that need to be investigated:

=================================== FAILURES ===================================
________________________ test_point_source_outside_grid ________________________

tmpdir = local('/tmp/tmp8ee8ggsh/test_point_source_outside_grid0')

    def test_point_source_outside_grid(tmpdir):
    
        dust = get_test_dust()
    
        m = Model()
        m.set_cartesian_grid([-1., 1.], [-1., 1.], [-1., 1.])
        m.add_density_grid(np.array([[[1.]]]), dust)
        m.set_n_photons(initial=100, imaging=0)
        s = m.add_point_source()
        s.position = (-1.5, 0., 0.)
        s.temperature = 5000.
        s.luminosity = 1.
        m.write(tmpdir.join(random_id()).strpath)
        log_file = tmpdir.join(random_id()).strpath
        with pytest.raises(SystemExit) as exc:
            m.run(tmpdir.join(random_id()).strpath, logfile=log_file)
        assert exc.value.args[0] == 'An error occurred, and the run did not ' + \
                                    'complete'
        with open(log_file) as f:
            log_file_contents = f.read()
        print(log_file_contents)
>       assert 'photon was not emitted inside a cell' in log_file_contents
E       assert 'photon was not emitted inside a cell' in "At line 186 of file src/grid/grid_geometry_cartesian_3d.f90\nFortran runtime error: Index '-1' of dimension 1 of arra...place_in_cell failed - killing [place_in_cell]\nRun did not complete successfully: output file appears to be corrupt\n"

hyperion/model/tests/test_fortran.py:33: AssertionError
----------------------------- Captured stdout call -----------------------------
At line 186 of file src/grid/grid_geometry_cartesian_3d.f90
Fortran runtime error: Index '-1' of dimension 1 of array 'geo%w1' below lower bound of 1

Error termination. Backtrace:
#0  0x7f2502bd62da in ???
#1  0x7f2502bd6ec5 in ???
#2  0x7f2502bd7297 in ???
#3  0x557b8f434d21 in adjust_wall
	at src/grid/grid_geometry_cartesian_3d.f90:186
#4  0x557b8f434c7d in __grid_geometry_specific_MOD_place_in_cell
	at src/grid/grid_geometry_cartesian_3d.f90:255
#5  0x557b8f4590d4 in __sources_MOD_emit
	at src/sources/source.f90:176
#6  0x557b8f48cc94 in __iteration_lucy_MOD_do_lucy
	at src/main/iter_lucy.f90:130
#7  0x557b8f4903ae in MAIN__
	at src/main/main.f90:183
#8  0x557b8f490f22 in main
	at src/main/main.f90:3
 ------------------------------------------------------------
 Hyperion v1.0.0
 Started on 05 February 2019 at 14:57:40
 Input:  /tmp/tmp8ee8ggsh/test_point_source_outside_grid0/CnRSrkVXiI6su7bhZejmz3wHWExv1FUJ
 Output: /tmp/tmp8ee8ggsh/test_point_source_outside_grid0/1HZ6zx9KJ3PWfsatgFYprRBGu2lOoyjI
 ------------------------------------------------------------
 [main] using random seed = -124902
 [dust] reading dust_001
 [setup_grid_geometry] Reading cartesian grid
 [grid_physics] reading density grid
 [grid_physics] reading minimum_specific_energy
 [grid_physics] checking energy_abs
 WARNING: specific_energy below minimum allowed in some cells - resetting [update_energy_abs]
 [grid_physics] updating energy_abs_tot
 [sources] setting up sources
 [main] starting Lucy iteration 1
 [grid_physics] pre-computing jnu_var

        # Photons    CPU time (sec)    Photons/sec  
      ----------------------------------------------
 WARNING: photon not in grid (in x direction) [find_cell]
 WARNING: place_in_cell failed - killing [place_in_cell]
Run did not complete successfully: output file appears to be corrupt

----------------------------- Captured stderr call -----------------------------
WARNING: Planck function for lowest temperature not completely covered by opacity function [hyperion.dust.mean_opacities]
WARNING: Planck function for lowest temperature not completely covered by opacity function [hyperion.dust.emissivities]
------------------------------ Captured log call -------------------------------
mean_opacities.py           54 WARNING  Planck function for lowest temperature not completely covered by opacity function
emissivities.py             46 WARNING  Planck function for lowest temperature not completely covered by opacity function
_____________________________ test_voronoi_basics ______________________________

tmpdir = local('/tmp/tmp8ee8ggsh/test_voronoi_basics0')

    def test_voronoi_basics(tmpdir):
        # A test to check the interaction between C++, Fortran and Python,
        # and to test the internal consistency of the Voronoi gridding.
    
        from ...util.constants import au
    
        np.random.seed(12343)
    
        # Generate random points
        N = 1000
        x = np.random.uniform(-100 * au, 100 * au, N)
        y = np.random.uniform(-100 * au, 100 * au, N)
        z = np.random.uniform(-100 * au, 100 * au, N)
    
        # Set up model
        m = Model()
        m.set_voronoi_grid(x, y, z)
        kmh_dust = SphericalDust(os.path.join(DATA, 'kmh_lite.hdf5'))
        m.add_density_grid(np.repeat(1.e-17, N), kmh_dust)
    
        # Set up fly-around images
        i = m.add_peeled_images()
        i.set_wavelength_range(1, 900., 1000)
        i.set_viewing_angles(np.repeat(85, 9), np.linspace(0., 60., 10)[:-1])
        i.set_image_limits(-150 * au, 150 * au, -150 * au, 150 * au)
        i.set_image_size(512, 512)
    
        # We are just simulating a cube with a constant temperature of 20K
        m.set_n_initial_iterations(0)
        m.set_minimum_temperature(20.)
    
        # Use raytracing for optimal signal-to-noise
        m.set_raytracing(True)
        m.set_n_photons(imaging=0, raytracing_sources=0, raytracing_dust=1e5)
    
        m.write(tmpdir.join(random_id()).strpath)
>       m.run(tmpdir.join(random_id()).strpath)

hyperion/model/tests/test_model.py:338: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <hyperion.model.model.Model object at 0x7f72474472b0>
filename = '/tmp/tmp8ee8ggsh/test_voronoi_basics0/tyvnkIPUNmOYlzTDxawX4BS06AsbCZep'
logfile = None, mpi = False, n_processes = 36, overwrite = False

    def run(self, filename=None, logfile=None, mpi=False, n_processes=multiprocessing.cpu_count(), overwrite=False):
        """
        Run the model (should be called after `write()`).
    
        Parameters
        ----------
        filename : str, optional
            The output filename for the model. If not specified, then if the
            input file name contains ``.rtin``, then this is replaced with
            ``.rtout``, and otherwise ``.rtout`` is appended to the input
            filename.
        logfile : str, optional
            If specified, the standard output and errors will be output to
            this log file
        mpi : bool, optional
            Whether to run the model using the parallel (MPI) version of
            Hyperion.
        n_processes : int, optional
            If ``mpi`` is set to ``True``, this can be used to specify the
            number of processes to run Hyperion on.
        overwrite : bool, optional
            If set to ``True``, the output file is overwritten without
            warning.
        """
    
        if self.filename is None:
            raise ValueError("Input file does not exist - write() needs to be called before run()")
    
        if mpi:
            option = '-m {0}'.format(n_processes)
        else:
            option = ''
    
        input_file = self.filename
        if filename is None:
            if '.rtin' in self.filename:
                output_file = self.filename.replace('.rtin', '.rtout')
            else:
                output_file = self.filename + '.rtout'
        else:
            output_file = filename
    
        if overwrite and os.path.exists(output_file):
            os.remove(output_file)
    
        if logfile:
            flog = open(logfile, 'wb')
            returncode = subprocess.call('hyperion %s %s %s' % (option, input_file, output_file), stdout=flog, stderr=flog, shell=True)
        else:
            returncode = subprocess.call('hyperion %s %s %s' % (option, input_file, output_file), shell=True)
    
        if returncode != 0:
>           raise SystemExit("An error occurred, and the run did not complete")
E           SystemExit: An error occurred, and the run did not complete

hyperion/model/model.py:1066: SystemExit
----------------------------- Captured stdout call -----------------------------
INFO: Updating Voronoi Tesselation [hyperion.grid.voronoi_grid]
INFO: Computing the tessellation via voro++ [hyperion.grid.voronoi_helpers]
 ------------------------------------------------------------
 Hyperion v1.0.0
 Started on 05 February 2019 at 14:58:01
 Input:  /tmp/tmp8ee8ggsh/test_voronoi_basics0/UPQv05YK9kSq34sFIybmGfajM21LHDNR
 Output: /tmp/tmp8ee8ggsh/test_voronoi_basics0/tyvnkIPUNmOYlzTDxawX4BS06AsbCZep
 ------------------------------------------------------------
 [main] using random seed = -124902
 [dust] reading dust_001
Run did not complete successfully: output file appears to be corrupt
----------------------------- Captured stderr call -----------------------------
WARNING: Version 1 dust file detected - discarding mean opacities and recomputing them [hyperion.dust.dust_type]
At line 147 of file src/grid/grid_geometry_voronoi.f90
Fortran runtime error: Array bound mismatch for dimension 1 of array 'geo' (14/15)

Error termination. Backtrace:
#0  0x7ffb8c4282da in ???
#1  0x7ffb8c428ec5 in ???
#2  0x7ffb8c429297 in ???
#3  0x561fd13acb80 in __grid_geometry_specific_MOD_setup_grid_geometry
	at src/grid/grid_geometry_voronoi.f90:147
#4  0x561fd1401e9d in __setup_MOD_setup_initial
	at src/main/setup_rt.f90:172
#5  0x561fd140642e in MAIN__
	at src/main/main.f90:167
#6  0x561fd1407081 in main
	at src/main/main.f90:3
------------------------------ Captured log call -------------------------------
dust_type.py               339 WARNING  Version 1 dust file detected - discarding mean opacities and recomputing them
voronoi_grid.py            235 INFO     Updating Voronoi Tesselation
voronoi_helpers.py         123 INFO     Computing the tessellation via voro++
__________________ TestCylindricalBase.test_ptsource_vertices __________________

self = <hyperion.model.tests.test_propagation.TestCylindricalBase object at 0x7f72461dc080>
tmpdir = local('/tmp/tmp8ee8ggsh/test_ptsource_vertices4')

    def test_ptsource_vertices(self, tmpdir):
        '''Point sources exactly on the vertices'''
    
        for iw in range(len(self.w) - 1):
            for iz in range(len(self.z)):
                for ip in range(len(self.p)):
                    s = self.m.add_point_source()
                    x = self.w[iw] * np.cos(self.p[ip])
                    y = self.w[iw] * np.sin(self.p[ip])
                    z = self.z[iz]
                    # Clip to w=0 (necessary due to numerical precision)
                    x = 0 if abs(x) < 1.e-10 else x
                    y = 0 if abs(y) < 1.e-10 else y
                    s.position = (x, y, z)
                    s.luminosity = 1
                    s.temperature = 5000.
    
        s = self.m.add_point_source()
        s.position = (0., 0., 0.)
        s.luminosity = 1
        s.temperature = 5000.
    
        self.m.set_n_initial_iterations(1)
        self.m.set_n_photons(initial=100000, imaging=0)
    
        self.m.write(tmpdir.join(random_id()).strpath)
        file_out = tmpdir.join(random_id()).strpath
>       self.m.run(file_out)

hyperion/model/tests/test_propagation.py:411: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <hyperion.model.model.Model object at 0x7f72461dcd68>
filename = '/tmp/tmp8ee8ggsh/test_ptsource_vertices4/HfA5sQXvBumgykOYJj8WErZbKlzMe9Dc'
logfile = None, mpi = False, n_processes = 36, overwrite = False

    def run(self, filename=None, logfile=None, mpi=False, n_processes=multiprocessing.cpu_count(), overwrite=False):
        """
        Run the model (should be called after `write()`).
    
        Parameters
        ----------
        filename : str, optional
            The output filename for the model. If not specified, then if the
            input file name contains ``.rtin``, then this is replaced with
            ``.rtout``, and otherwise ``.rtout`` is appended to the input
            filename.
        logfile : str, optional
            If specified, the standard output and errors will be output to
            this log file
        mpi : bool, optional
            Whether to run the model using the parallel (MPI) version of
            Hyperion.
        n_processes : int, optional
            If ``mpi`` is set to ``True``, this can be used to specify the
            number of processes to run Hyperion on.
        overwrite : bool, optional
            If set to ``True``, the output file is overwritten without
            warning.
        """
    
        if self.filename is None:
            raise ValueError("Input file does not exist - write() needs to be called before run()")
    
        if mpi:
            option = '-m {0}'.format(n_processes)
        else:
            option = ''
    
        input_file = self.filename
        if filename is None:
            if '.rtin' in self.filename:
                output_file = self.filename.replace('.rtin', '.rtout')
            else:
                output_file = self.filename + '.rtout'
        else:
            output_file = filename
    
        if overwrite and os.path.exists(output_file):
            os.remove(output_file)
    
        if logfile:
            flog = open(logfile, 'wb')
            returncode = subprocess.call('hyperion %s %s %s' % (option, input_file, output_file), stdout=flog, stderr=flog, shell=True)
        else:
            returncode = subprocess.call('hyperion %s %s %s' % (option, input_file, output_file), shell=True)
    
        if returncode != 0:
>           raise SystemExit("An error occurred, and the run did not complete")
E           SystemExit: An error occurred, and the run did not complete

hyperion/model/model.py:1066: SystemExit
---------------------------- Captured stderr setup -----------------------------
WARNING: Planck function for lowest temperature not completely covered by opacity function [hyperion.dust.mean_opacities]
WARNING: Planck function for lowest temperature not completely covered by opacity function [hyperion.dust.emissivities]
------------------------------ Captured log setup ------------------------------
mean_opacities.py           54 WARNING  Planck function for lowest temperature not completely covered by opacity function
emissivities.py             46 WARNING  Planck function for lowest temperature not completely covered by opacity function
----------------------------- Captured stdout call -----------------------------
 ------------------------------------------------------------
 Hyperion v1.0.0
 Started on 05 February 2019 at 15:00:38
 Input:  /tmp/tmp8ee8ggsh/test_ptsource_vertices4/pUO0rb2YCZNPTEwXGQKcIxy6fFt5iqn1
 Output: /tmp/tmp8ee8ggsh/test_ptsource_vertices4/HfA5sQXvBumgykOYJj8WErZbKlzMe9Dc
 ------------------------------------------------------------
 [main] using random seed = -124902
 [dust] reading dust_001
 [setup_grid_geometry] Reading cylindrical polar grid
 [grid_physics] reading density grid
 [grid_physics] reading minimum_specific_energy
 [grid_physics] checking energy_abs
 WARNING: specific_energy below minimum allowed in some cells - resetting [update_energy_abs]
 [grid_physics] updating energy_abs_tot
 [sources] setting up sources
 [main] starting Lucy iteration 1
 [grid_physics] pre-computing jnu_var

        # Photons    CPU time (sec)    Photons/sec  
      ----------------------------------------------
Run did not complete successfully: output file appears to be corrupt
----------------------------- Captured stderr call -----------------------------
At line 683 of file src/grid/grid_geometry_cylindrical_3d.f90
Fortran runtime error: Index '18' of dimension 1 of array 'geo%w2' above upper bound of 17

Error termination. Backtrace:
#0  0x7fbb73aad2da in ???
#1  0x7fbb73aadec5 in ???
#2  0x7fbb73aae297 in ???
#3  0x55f375abd831 in __grid_geometry_specific_MOD_find_wall
	at src/grid/grid_geometry_cylindrical_3d.f90:683
#4  0x55f375afb0e9 in __grid_propagate_MOD_grid_integrate
	at src/grid/grid_propagate_3d.f90:103
#5  0x55f375b1b131 in __iteration_lucy_MOD_do_lucy
	at src/main/iter_lucy.f90:156
#6  0x55f375b1e72c in MAIN__
	at src/main/main.f90:183
#7  0x55f375b1f2a0 in main
	at src/main/main.f90:3
______________ TestCylindricalBase.test_ptsource_vertices_noclip _______________

self = <hyperion.model.tests.test_propagation.TestCylindricalBase object at 0x7f7245fdb128>
tmpdir = local('/tmp/tmp8ee8ggsh/test_ptsource_vertices_noclip1')

    def test_ptsource_vertices_noclip(self, tmpdir):
        '''Point sources on vertices, but without clipping'''
    
        for iw in range(len(self.w) - 1):
            for iz in range(len(self.z)):
                for ip in range(len(self.p)):
                    s = self.m.add_point_source()
                    x = self.w[iw] * np.cos(self.p[ip])
                    y = self.w[iw] * np.sin(self.p[ip])
                    z = self.z[iz]
                    s.position = (x, y, z)
                    s.luminosity = 1
                    s.temperature = 5000.
    
        s = self.m.add_point_source()
        s.position = (0., 0., 0.)
        s.luminosity = 1
        s.temperature = 5000.
    
        self.m.set_n_initial_iterations(1)
        self.m.set_n_photons(initial=100000, imaging=0)
    
        self.m.write(tmpdir.join(random_id()).strpath)
        file_out = tmpdir.join(random_id()).strpath
>       self.m.run(file_out)

hyperion/model/tests/test_propagation.py:466: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <hyperion.model.model.Model object at 0x7f7245fdbef0>
filename = '/tmp/tmp8ee8ggsh/test_ptsource_vertices_noclip1/xd6RoNaWA3IUKe8lSFZ0jsM4zhLPQJHG'
logfile = None, mpi = False, n_processes = 36, overwrite = False

    def run(self, filename=None, logfile=None, mpi=False, n_processes=multiprocessing.cpu_count(), overwrite=False):
        """
        Run the model (should be called after `write()`).
    
        Parameters
        ----------
        filename : str, optional
            The output filename for the model. If not specified, then if the
            input file name contains ``.rtin``, then this is replaced with
            ``.rtout``, and otherwise ``.rtout`` is appended to the input
            filename.
        logfile : str, optional
            If specified, the standard output and errors will be output to
            this log file
        mpi : bool, optional
            Whether to run the model using the parallel (MPI) version of
            Hyperion.
        n_processes : int, optional
            If ``mpi`` is set to ``True``, this can be used to specify the
            number of processes to run Hyperion on.
        overwrite : bool, optional
            If set to ``True``, the output file is overwritten without
            warning.
        """
    
        if self.filename is None:
            raise ValueError("Input file does not exist - write() needs to be called before run()")
    
        if mpi:
            option = '-m {0}'.format(n_processes)
        else:
            option = ''
    
        input_file = self.filename
        if filename is None:
            if '.rtin' in self.filename:
                output_file = self.filename.replace('.rtin', '.rtout')
            else:
                output_file = self.filename + '.rtout'
        else:
            output_file = filename
    
        if overwrite and os.path.exists(output_file):
            os.remove(output_file)
    
        if logfile:
            flog = open(logfile, 'wb')
            returncode = subprocess.call('hyperion %s %s %s' % (option, input_file, output_file), stdout=flog, stderr=flog, shell=True)
        else:
            returncode = subprocess.call('hyperion %s %s %s' % (option, input_file, output_file), shell=True)
    
        if returncode != 0:
>           raise SystemExit("An error occurred, and the run did not complete")
E           SystemExit: An error occurred, and the run did not complete

hyperion/model/model.py:1066: SystemExit
---------------------------- Captured stderr setup -----------------------------
WARNING: Planck function for lowest temperature not completely covered by opacity function [hyperion.dust.mean_opacities]
WARNING: Planck function for lowest temperature not completely covered by opacity function [hyperion.dust.emissivities]
------------------------------ Captured log setup ------------------------------
mean_opacities.py           54 WARNING  Planck function for lowest temperature not completely covered by opacity function
emissivities.py             46 WARNING  Planck function for lowest temperature not completely covered by opacity function
----------------------------- Captured stdout call -----------------------------
 ------------------------------------------------------------
 Hyperion v1.0.0
 Started on 05 February 2019 at 15:00:53
 Input:  /tmp/tmp8ee8ggsh/test_ptsource_vertices_noclip1/0DuHZ9Ld56s8OYlTJ7ibFnhKcjzq41pV
 Output: /tmp/tmp8ee8ggsh/test_ptsource_vertices_noclip1/xd6RoNaWA3IUKe8lSFZ0jsM4zhLPQJHG
 ------------------------------------------------------------
 [main] using random seed = -124902
 [dust] reading dust_001
 [setup_grid_geometry] Reading cylindrical polar grid
 [grid_physics] reading density grid
 [grid_physics] reading minimum_specific_energy
 [grid_physics] checking energy_abs
 WARNING: specific_energy below minimum allowed in some cells - resetting [update_energy_abs]
 [grid_physics] updating energy_abs_tot
 [sources] setting up sources
 [main] starting Lucy iteration 1
 [grid_physics] pre-computing jnu_var

        # Photons    CPU time (sec)    Photons/sec  
      ----------------------------------------------
Run did not complete successfully: output file appears to be corrupt
----------------------------- Captured stderr call -----------------------------
At line 683 of file src/grid/grid_geometry_cylindrical_3d.f90
Fortran runtime error: Index '18' of dimension 1 of array 'geo%w2' above upper bound of 17

Error termination. Backtrace:
#0  0x7f69bc5062da in ???
#1  0x7f69bc506ec5 in ???
#2  0x7f69bc507297 in ???
#3  0x5586c8604831 in __grid_geometry_specific_MOD_find_wall
	at src/grid/grid_geometry_cylindrical_3d.f90:683
#4  0x5586c86420e9 in __grid_propagate_MOD_grid_integrate
	at src/grid/grid_propagate_3d.f90:103
#5  0x5586c8662131 in __iteration_lucy_MOD_do_lucy
	at src/main/iter_lucy.f90:156
#6  0x5586c866572c in MAIN__
	at src/main/main.f90:183
#7  0x5586c86662a0 in main
	at src/main/main.f90:3
``