Inconsistencies between Tardis versions #455
Comments
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Tardis version aa7da17 produces compatible results: |
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Unfortunately, this discrepancy also affects the simpler LTE treatment:
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unoebauer
changed the title
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Lacking better ideas, I'll look through the commit history and will try to pin-point it to a specific change. Any other insights into the problem, @aoifeboyle, @wkerzendorf, @ssim, @orbitfold? |
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Status of commit-bisection (works implies no discrepancies between :
still bisecting... Note the following when reading through the above list:
Note 1:---------------------------------------------------------------------------
PlasmaMissingModule Traceback (most recent call last)
<ipython-input-2-6282305a6c09> in <module>()
----> 1 mdl = tardis.run_tardis(config)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/base.pyc in run_tardis(config, atom_data)
38 tardis_config = config_reader.Configuration.from_config_dict(
39 config_dict, atom_data=atom_data)
---> 40 radial1d_mdl = model.Radial1DModel(tardis_config)
41
42 simulation.run_radial1d(radial1d_mdl)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/model.pyc in __init__(self, tardis_config)
134 excitation_mode=tardis_config.plasma.excitation,
135 line_interaction_type=tardis_config.plasma.line_interaction_type,
--> 136 link_t_rad_t_electron=0.9)
137
138 self.spectrum = TARDISSpectrum(tardis_config.spectrum.frequency, tardis_config.supernova.distance)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/standard_plasmas.pyc in __init__(self, number_densities, atomic_data, time_explosion, t_rad, delta_treatment, nlte_config, ionization_mode, excitation_mode, line_interaction_type, link_t_rad_t_electron)
103 delta_input=delta_treatment, nlte_species=nlte_config.species,
104 previous_electron_densities=initial_electron_densities,
--> 105 previous_beta_sobolevs=initial_beta_sobolevs)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/base.pyc in __init__(self, plasma_properties, **kwargs)
18 self.plasma_properties = self._init_properties(plasma_properties,
19 **kwargs)
---> 20 self._build_graph()
21 # self.write_to_tex('Plasma_Graph', 'Plasma_Formulae')
22 self.update(**kwargs)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/base.pyc in _build_graph(self)
79 '{1} which has not been added'
80 ' to this plasma'.format(
---> 81 plasma_property.name, input))
82 try:
83 position = self.outputs_dict[input].outputs.index(input)
PlasmaMissingModule: Module PhiSahaNebular requires input t_electron which has not been added to this plasmaNote 2:ValueError Traceback (most recent call last)
<ipython-input-2-6282305a6c09> in <module>()
----> 1 mdl = tardis.run_tardis(config)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/base.pyc in run_tardis(config, atom_data)
40 radial1d_mdl = model.Radial1DModel(tardis_config)
41
---> 42 simulation.run_radial1d(radial1d_mdl)
43
44 return radial1d_mdl
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/simulation.pyc in run_radial1d(radial1d_model, history_fname)
25 logger.info('Remaining run %d', radial1d_model.iterations_remaining)
26 radial1d_model.simulate(update_radiation_field=update_radiation_field, enable_virtual=False, initialize_nlte=initialize_nlte,
---> 27 initialize_j_blues=initialize_j_blues)
28 initialize_j_blues=False
29 initialize_nlte=False
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/model.pyc in simulate(self, update_radiation_field, enable_virtual, initialize_j_blues, initialize_nlte)
333
334 self.calculate_j_blues(init_detailed_j_blues=initialize_j_blues)
--> 335 self.update_plasmas(initialize_nlte=initialize_nlte)
336
337
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/model.pyc in update_plasmas(self, initialize_nlte)
237
238 self.plasma_array.update_radiationfield(self.t_rads.value, self.ws, self.j_blues,
--> 239 self.tardis_config.plasma.nlte, initialize_nlte=initialize_nlte, n_e_convergence_threshold=0.05)
240
241 if self.tardis_config.plasma.line_interaction_type in ('downbranch', 'macroatom'):
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/standard_plasmas.pyc in update_radiationfield(self, t_rad, ws, j_blues, nlte_config, t_electrons, n_e_convergence_threshold, initialize_nlte)
50 if nlte_config.species:
51 self.store_previous_properties()
---> 52 self.update(t_rad=t_rad, w=ws, j_blues=j_blues)
53
54 def __init__(self, number_densities, atomic_data, time_explosion,
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/base.pyc in update(self, **kwargs)
141
142 for module_name in self._resolve_update_list(kwargs.keys()):
--> 143 self.plasma_properties_dict[module_name].update()
144
145 def _update_module_type_str(self):
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/properties/base.pyc in update(self)
84 if len(self.outputs) == 1:
85 setattr(self, self.outputs[0], self.calculate(
---> 86 *self._get_input_values()))
87 else:
88 new_values = self.calculate(*self._get_input_values())
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/properties/ion_population.pyc in calculate(self, general_phi, t_rad, w, zeta_data, t_electrons, delta)
65 '- requested {2}'.format(
66 zeta_data.columns.values.min(), zeta_data.columns.values.max(),
---> 67 t_rad))
68 phis = general_phi * delta * w * (zeta + w * (1 - zeta)) * \
69 (t_electrons/t_rad) ** .5
ValueError: t_rads outside of zeta factor interpolation zeta_min=2000.00 zeta_max=40000.00 - requested [ 24829.47853128 29255.41589326 33609.08295046 37345.62521055
40019.28004965 40953.81576507 38383.82271919 34434.31244872
32665.86581665 30041.40250129 27808.87307025 25354.81563128
23264.0689412 21349.97604201 20834.53491125 20280.93368913
20109.54322745 19707.24624127 19069.69093371 18789.89685196] |
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@unoebauer I have no idea. Pinpointing the commit that first created the problem is probably the best thing to do for now. I'm surprised Travis didn't catch this? |
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@aoifeboyle: no, unfortunately, Travis did never catch this. However, the problem considered here is much harder than our final spectral test... |
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@unoebauer Ah I see. We should try to create some kind of faster test to determine if the code is going wrong without having to run 20 iterations with 50k packets, I think? So we need to find the simplest possible case where the divergence is observed. |
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@aoifeboyle: I think that I've pinpointed the regime in the commit history during which the problem was introduced - see list above. It happens somewhere between PR #360 and PR #365:
Any thoughts, @aoifeboyle? I'll try to devise a less expensive test which triggers the same problem. |
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I've created a "low-resolution" version of the test problem:
It triggers the same problem as described above, but completes 10 times faster than the original one.
@aoifeboyle does this help? |
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Yes it should do! Was at a conference today but I have time to investigate now. I'll keep you updated. |
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this all sounds rather worrying! |
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@ssim: currently trying to isolate the problem. The tardis_example problem doesn't seem to be affected. |
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Ok - perhaps we can take a look in Wurzburg? In the meantime, good luck Sherlock! |
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Issue is not related to OMP: I get the same results when running the |
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Maybe some progress towards narrowing down the exact cause of the problem: Three more test setups, derived from tardis_test.yml (detailed setup files will be provided in next comment):
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@unoebauer That's interesting. I was working through the yaml file and changing parameters to see what eliminated the problem, but looks like you beat me to it. Can we safely say the issue is related to the structure file then? Or do you think there's something else involved? |
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@aoifeboyle: not completely sure that it's the structure file alone. I have the suspicion that it is related to high densities...but I need to confirm that. I'll update you as soon as I have the results. |
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Here are the yaml files for the different runs:
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@aoifeboyle, @ssim: From the comparison calculations I've performed, it looks like very high densities are triggering the problem. The branch85_w7 has lower densities in the innermost cells compared to what has been set up in This could also explain, why Travis didn't catch this problem and why it doesn't show up in the tardis_example setup: we typically use times since explosions around 15d. The resulting densities are comparable to the last test run. |
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@unoebauer I find that the differences are small when using the original yaml file, but with scatter instead of downbranch. This is a comparison for commit 45eca24 (blue) vs. the current version (green). |
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@aoifeboyle: Very interesting! - maybe that's an indication that something is wrong with the |
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The issue also occurs when macroatom is used. That narrows the issue down a lot. So something to do with high densities and downbranch/macroatom. |
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Very interesting, @aoifeboyle. It may not be so simple though...I've tried to trigger the issue with the tardis_example setup as well. I've changed a few parameters to mimic the tardis_test_unifab_branch setup, but so far the problem didn't show up (in all of the runs macroatom has been used):
Update No difference always refers to "above the noise level" when comparing the current version with commit 45eca24. The only test in which the differences might be slightly larger than the noise level is the second one... |
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I've narrowed the issue down to be something related to the |
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@aoifeboyle: Thanks - hopefully that's it. We will discuss this issue today during the workshop in Wuerzburg. |
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@unoebauer I've been trying to work this out all day today and I'm not getting very far. I think it might be something to do with the montecarlo stuff rather than the plasma. I fixed the zeta problem in d864eb3, since it's the first one that fails, and I've been comparing it with 45eca24, the last one that works. The two plasmas seem identical after they are first initialised and first updated, and then after the first montecarlo runs the returned packet nus average out to a different value. For some reason the montecarlo runner is included in 45eca24 but not in d864eb3. I'll try to make some more progress tomorrow. @wkerzendorf do you have any ideas? |
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@aoifeboyle Thanks for the detailed analysis. This seems to be consistent with some of my findings: as a test I looked at two different setups (always comparing current version with 45eca24):
I think that these two tests point into the same direction, namely that something goes wrong when updating the plasma. In my opinion there are two possibilities:
@wkerzendorf performed a git-bisect bug search and identified a commit in which only the C part was changed. I was sceptical at the beginning that we performed the correct search, but thinking about it in light of @aoifeboyle's findings and these tests, git-bisect may have been right. @wkerzendorf - can you elaborate on the git-bisect results? After X-mas of course ;) |
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FYI @aoifeboyle, @wkerzendorf, @ssim: I've had a closer look: UPDATE See my follow-up comment: discrepancies in tau_sobolevs are mostly likely not real. The virtual spectrum comparison plot and the printout of the nu_bar_estimators are still relevant, though ORIGINAL POST I reinvestigated the problem with the fixed plasma and boundary state, running only the spectral calculation (the yaml file is posted below). Comparing the results obtained with 45eca24 and the current branch revealed the following differences in the plasma state:
There are a number of line transitions (more accurately 13519), for which the relative difference in the tau Sobolevs is above 1e-10. Some of these lines are quite strong, as the following plot of the relative vs. the absolute difference in tau Sobolev shows:
These differences could also explain the (small but visible) discrepancies in the virtual spectrum:
It could be possible that these differences in the tau Sobolevs are the reason for the different nu_bar estimates after the Monte Carlo calculation. Having looked into the source code, I didn't spot any differences in the algorithm with which these estimates are calculated between the two Tardis versions. Moreover, the relative differences between the nubar_estimators are on the few per cent level: In [1]: config = yaml.safe_load(open("tardis_00173_2_fix.yml"))
In [2]: mdl_old = tardis.run_tardis(config)
tardis.io.config_reader - INFO - Reading Atomic Data from kurucz_cd23_chianti_H_He.h5
tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8
tardis.io.model_reader - WARNING - v_inner_boundary requested too small for readin file. Boundary shifted to match file.
tardis.io.model_reader - WARNING - v_outer_boundary requested too large for readin file. Boundary shifted to match file.
tardis.io.config_reader - WARNING - Abundances have not been normalized to 1. - normalizing
tardis.io.config_reader - WARNING - No "species" given - ignoring other NLTE options given:
{ 'classical_nebular': False, 'coronal_approximation': False}
tardis.io.config_reader - WARNING - No convergence criteria selected - just damping by 0.5 for w, t_rad and t_inner
tardis.simulation - INFO - Doing last run
tardis.model - INFO - Calculating J_blues for radiative_rates_type=dilute-blackbody
tardis.packet_source - INFO - Calculating 500000 packets for t_inner=10000.00
Running with OpenMP - 16 threadstardis.simulation - INFO - Finished in 1 iterations and took 498.82 s
In [3]: mdl_old.runner.nu_bar_estimator
Out[3]:
array([ 5.86773400e+28, 5.02563144e+28, 4.34765138e+28,
3.70558614e+28, 2.96558255e+28, 2.02856011e+28,
1.37465171e+28, 1.25736437e+28, 1.19699029e+28,
1.14731265e+28, 1.10559996e+28, 1.04484887e+28,
9.92324586e+27, 9.82713255e+27, 1.04365404e+28,
1.14142807e+28, 1.26513448e+28, 1.42094539e+28,
1.61340125e+28, 1.85833208e+28])
In [1]: config = yaml.safe_load(open("tardis_00173_2_fix.yml"))
In [2]: mdl_new = tardis.run_tardis(config)
tardis.io.config_reader - INFO - Reading Atomic Data from kurucz_cd23_chianti_H_He.h5
tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8
tardis.io.model_reader - WARNING - v_inner_boundary requested too small for readin file. Boundary shifted to match file.
tardis.io.model_reader - WARNING - v_outer_boundary requested too large for readin file. Boundary shifted to match file.
tardis.io.config_reader - WARNING - Abundances have not been normalized to 1. - normalizing
tardis.io.config_reader - WARNING - No "species" given - ignoring other NLTE options given:
{ 'classical_nebular': False, 'coronal_approximation': False}
tardis.io.config_reader - WARNING - No convergence criteria selected - just damping by 0.5 for w, t_rad and t_inner
tardis.plasma.properties.atomic - WARNING - Zeta_data missing - replaced with 1s. Missing ions: [(9, 10), (11, 12), (12, 13), (13, 14), (14, 15), (15, 16), (16, 17), (17, 18), (18, 19), (19, 20), (20, 21), (21, 22), (22, 23), (23, 24), (24, 25), (25, 26), (26, 27), (27, 28), (28, 29), (29, 1), (29, 2), (29, 3), (29, 4), (29, 5), (29, 6), (29, 7), (29, 8), (29, 9), (29, 10), (29, 11), (29, 12), (29, 13), (29, 14), (29, 15), (29, 16), (29, 17), (29, 18), (29, 19), (29, 20), (29, 21), (29, 22), (29, 23), (29, 24), (29, 25), (29, 26), (29, 27), (29, 28), (29, 29), (29, 30), (30, 1), (30, 2), (30, 3), (30, 4), (30, 5), (30, 6), (30, 7), (30, 8), (30, 9), (30, 10), (30, 11), (30, 12), (30, 13), (30, 14), (30, 15), (30, 16), (30, 17), (30, 18), (30, 19), (30, 20), (30, 21), (30, 22), (30, 23), (30, 24), (30, 25), (30, 26), (30, 27), (30, 28), (30, 29), (30, 30), (30, 31)]
tardis.model - INFO - Calculating J_blues for radiative_rates_type=dilute-blackbody
tardis.simulation.base - INFO - Doing last run
Running with OpenMP - 1 threads
tardis.simulation.base - INFO - Finished in 0 iterations and took 149.83 s
In [3]: mdl_new.runner.nu_bar_estimator
Out[3]:
array([ 6.01178210e+28, 5.13461157e+28, 4.43216973e+28,
3.77940227e+28, 3.04304078e+28, 2.10994277e+28,
1.43991981e+28, 1.31111096e+28, 1.22309477e+28,
1.16231763e+28, 1.11305261e+28, 1.05664707e+28,
1.00899515e+28, 1.00840642e+28, 1.07745764e+28,
1.17769597e+28, 1.30562338e+28, 1.46607607e+28,
1.66597070e+28, 1.91696842e+28])What we see in the original setup (posted at the beginning of this issue) is a runaway process during many (20) ionization iterations. Config file: |
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I did another bisect run and there seem to be several bugs indeed. bisect reports e9fb778 as first bad commit. gives commits e2eac6d - ec8fcda as possible first bad commits. Maybe one of the issues was fixed by @aoifeboyle I didn't look into the case with |
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@wkerzendorf I accidentally deleted my comment from last night, could you please paste it into this conversation somewhere? I think you should have it as an email? The bug that I found in the plasma/restructure commit is something that I had already corrected at a later time, but it was not corrected at the time of the merge of the plasma/restructure. So I think that explains what you found @yeganer. My aim for now is to get consistent results for our test between the last working version (45eca24) and the plasma restructure commit (41d8fcd). There are too many differences between 45eca24 and the current version to easily debug it. But once I get this right, it should either solve all the problems or at least considerably reduce the number of problems. |
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@aoifeboyle in my opinion it is better to compare 30d1cb9 with ec8fcda because that's the smalles difference in code where the bug appears. I added your comment at the bottom of my comment, if that's okay |
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I am re-posting @aoifeboyle's originial comment: The bug that I found in the plasma/restructure commit is something that I had already corrected at a later time, but it was not corrected at the time of the merge of the plasma/restructure. So I think that explains what you found. My aim for now is to get consistent results for our test between the last working version (45eca24) and the plasma restructure commit (41d8fcd). There are too many differences between 45eca24 and the current version to easily debug it. But once I get this right, it should either solve all the problems or at least considerably reduce the number of problems. |
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Also @yeganer, what I'm comparing is basically the same thing that you're suggesting. 30d1cb9 is effectively 45eca24 because the model was still calling the old plasma structure. And ec8fcda is when the nebular ionisation was added to the new plasma, but this was on the old plasma/restructure branch rather than on the main Tardis branch, so it's less confusing for me to work with 41d8fcd. I think I'm making good progress anyway. The only discrepancy I can find in the plasma now is j_blues being an array in one version and a dataframe in the other, so I'm going to correct that. |
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@unoebauer @yeganer |
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@aoifeboyle: I just looked at your PR #462. Unfortunately, it crashes when running the In [2]: config = yaml.safe_load(open("plasma_fail_test.yml"))
In [3]: mdl = tardis.run_tardis(config)
tardis.io.config_reader - INFO - Reading Atomic Data from kurucz_cd23_chianti_H_He.h5
tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8
tardis.io.model_reader - WARNING - v_inner_boundary requested too small for readin file. Boundary shifted to match file.
tardis.io.model_reader - WARNING - v_outer_boundary requested too large for readin file. Boundary shifted to match file.
tardis.io.config_reader - WARNING - Abundances have not been normalized to 1. - normalizing
tardis.io.config_reader - WARNING - No "species" given - ignoring other NLTE options given:
{ 'classical_nebular': False, 'coronal_approximation': False}
tardis.io.config_reader - WARNING - No convergence criteria selected - just damping by 0.5 for w, t_rad and t_inner
tardis.plasma.properties.atomic - WARNING - Zeta_data missing - replaced with 1s
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-3-6282305a6c09> in <module>()
----> 1 mdl = tardis.run_tardis(config)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/base.pyc in run_tardis(config, atom_data)
38 tardis_config = config_reader.Configuration.from_config_dict(
39 config_dict, atom_data=atom_data)
---> 40 radial1d_mdl = model.Radial1DModel(tardis_config)
41
42 simulation.run_radial1d(radial1d_mdl)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/model.pyc in __init__(self, tardis_config)
130 excitation_mode=tardis_config.plasma.excitation,
131 line_interaction_type=tardis_config.plasma.line_interaction_type,
--> 132 link_t_rad_t_electron=0.9)
133
134 self.spectrum = TARDISSpectrum(tardis_config.spectrum.frequency, tardis_config.supernova.distance)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/standard_plasmas.pyc in __init__(self, number_densities, atomic_data, time_explosion, t_rad, delta_treatment, nlte_config, ionization_mode, excitation_mode, line_interaction_type, link_t_rad_t_electron)
103 delta_input=delta_treatment, nlte_species=nlte_config.species,
104 previous_electron_densities=initial_electron_densities,
--> 105 previous_beta_sobolevs=initial_beta_sobolevs)
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/base.pyc in __init__(self, plasma_properties, **kwargs)
20 self._build_graph()
21 # self.write_to_tex('Plasma_Graph', 'Plasma_Formulae')
---> 22 self.update(**kwargs)
23
24 def __getattr__(self, item):
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/base.pyc in update(self, **kwargs)
141
142 for module_name in self._resolve_update_list(kwargs.keys()):
--> 143 self.plasma_properties_dict[module_name].update()
144
145 def _update_module_type_str(self):
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/properties/base.pyc in update(self)
84 if len(self.outputs) == 1:
85 setattr(self, self.outputs[0], self.calculate(
---> 86 *self._get_input_values()))
87 else:
88 new_values = self.calculate(*self._get_input_values())
/afs/mpa/home/ulnoe/local/lib/python2.7/site-packages/tardis_sn-1.0.1-py2.7-linux-x86_64.egg/tardis/plasma/properties/radiative_properties.pyc in calculate(lines, j_blues_array, beta_rad)
159 @staticmethod
160 def calculate(lines, j_blues_array, beta_rad):
--> 161 return pd.DataFrame(j_blues_array, index=lines.index)
162
163 class LTEJBlues(ProcessingPlasmaProperty):
/opt/python-2.7.9/lib/python2.7/site-packages/pandas/core/frame.pyc in __init__(self, data, index, columns, dtype, copy)
237 else:
238 mgr = self._init_ndarray(data, index, columns, dtype=dtype,
--> 239 copy=copy)
240 elif isinstance(data, (list, types.GeneratorType)):
241 if isinstance(data, types.GeneratorType):
/opt/python-2.7.9/lib/python2.7/site-packages/pandas/core/frame.pyc in _init_ndarray(self, values, index, columns, dtype, copy)
405 values = _possibly_infer_to_datetimelike(values)
406
--> 407 return create_block_manager_from_blocks([values], [columns, index])
408
409 @property
/opt/python-2.7.9/lib/python2.7/site-packages/pandas/core/internals.pyc in create_block_manager_from_blocks(blocks, axes)
3526 blocks = [getattr(b, 'values', b) for b in blocks]
3527 tot_items = sum(b.shape[0] for b in blocks)
-> 3528 construction_error(tot_items, blocks[0].shape[1:], axes, e)
3529
3530
/opt/python-2.7.9/lib/python2.7/site-packages/pandas/core/internals.pyc in construction_error(tot_items, block_shape, axes, e)
3507 raise e
3508 raise ValueError("Shape of passed values is {0}, indices imply {1}".format(
-> 3509 passed,implied))
3510
3511
ValueError: Shape of passed values is (0, 0), indices imply (0, 270394)
In [4]: |
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@unoebauer Strange - it worked fine for me. Let me look and see where I went wrong. |
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@unoebauer I tried checking it out directly from the PR rather than using my own branch and it still works for me. Is this the test you're talking about? atom_data: kurucz_cd23_chianti_H_He.h5 |
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In case anyone's following this, the problem is apparently just our different pandas versions. I'm going to tweak it a bit so it works with both versions now. |
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@unoebauer I've fixed it for pandas-0.16.0. Could you please check that it's working for you now? |
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@aoifeboyle: Looks good now - thanks. The |
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The discussion is getting out of hand. Too many loose and dead ends have accumulated here (and I am as much to blame for this as anybody) and are muddying the picture. I think it's time to take a step back, review the current status and take a fresh, re-focused start. For this purpose, I am closing this issue and will open a new one in the hope of simplifying the problem solving process. Please don't post anything here any more but use the new issue, #464. |
* added config files for the original setup triggering tardis-sn#455 * renamed it from tardis_00173_2 to abn_tom_test (for abundance tomography test)
Deleted atom_data._lines and atom_data._levels This change ensures that the BasePlasma always gets prepared data. A proper fix will take more time and will be done later.
The old files contained wrong values (see issue tardis-sn#455) With this change the following tests will run again: * test_packet_output * test_plasma_estimates * TestPlasma.test_lte_plasma One should consider updating tardis/simulation/tests/test_simulation.py since it creates a new model which essentially tests the whole codebase. These tests will always fail if something in the codebase changes ( see comment in the file ).
Changed behavior to raise a custom exception instead of a generic one. This is done to better reflect the error. Related Issues: tardis-sn#455 tardis-sn#464 Pull Request tardis-sn#471
Main description:
TARDIS produces different output between 45eca24 and master with this YML file. Why? and what commit introduced this change.
The following YML files provide a minimum "working" example": issue_455.zip
The diagnosis of the problem at hand is still work in progress, but it seems the most recent Tardis version, c9e1b17, is inconsistent with a previous state of Tardis.
All this has been triggered by re-examining some detailed runs performed during the Abundance Tomography Project of Talytha. For that, we mainly used a Tardis version similar to aa7da17 (a working Open-MP implementation has just been incorporated, PR #338). Comparing the virtual spectra obtained with the recent Tardis version for the same setup, reveals huge discrepancies:
The new Tardis version finds a much higher inner temperature. This goes hand in hand with a much higher radiation temperature in the ejecta and a higher ionisation state (and in turn electron density).
Setup:
tardis_00173_2.ymldensities_00173_2.databundances_00173_2.datThe text was updated successfully, but these errors were encountered: