tour_mode_choice throws runtime error for some tours

[toliwaga]

Runtime error in tour_mode_choice_simulate running the full zone dataset with 12000 HH sample and random seed of 0

settings.yaml:

preload_3d_skims: True
households_sample_size: 12000

simulation.py:

def set_random_seed():
    np.random.seed(0)

orca.add_injectable("set_random_seed", set_random_seed)

Stack trace on error:

Traceback (most recent call last):
  File "/Applications/PyCharm.app/Contents/helpers/pydev/pydevd.py", line 2411, in <module>
    globals = debugger.run(setup['file'], None, None, is_module)
  File "/Applications/PyCharm.app/Contents/helpers/pydev/pydevd.py", line 1802, in run
    launch(file, globals, locals)  # execute the script
  File "/Users/jeff.doyle/work/activitysim/sandbox/simulation.py", line 104, in <module>
    orca.run(['tour_mode_choice_simulate'])
  File "/Users/jeff.doyle/anaconda/envs/asim/lib/python2.7/site-packages/orca/orca.py", line 1876, in run
    step()
  File "/Users/jeff.doyle/anaconda/envs/asim/lib/python2.7/site-packages/orca/orca.py", line 780, in __call__
    return self._func(**kwargs)
  File "/Users/jeff.doyle/work/activitysim/activitysim/defaults/models/mode.py", line 195, in tour_mode_choice_simulate
    cache_skim_key_values=cache_skim_key_values)
  File "/Users/jeff.doyle/work/activitysim/activitysim/defaults/models/mode.py", line 130, in _mode_choice_simulate
    locals_d=locals_d)
  File "/Users/jeff.doyle/work/activitysim/activitysim/activitysim.py", line 216, in simple_simulate
    choices = make_choices(probs)
  File "/Users/jeff.doyle/work/activitysim/activitysim/mnl.py", line 67, in make_choices
    return pd.Series(choices, index=probs.index)
  File "/Users/jeff.doyle/anaconda/envs/asim/lib/python2.7/site-packages/pandas/core/series.py", line 228, in __init__
    data = SingleBlockManager(data, index, fastpath=True)
  File "/Users/jeff.doyle/anaconda/envs/asim/lib/python2.7/site-packages/pandas/core/internals.py", line 3752, in __init__
    fastpath=True)
  File "/Users/jeff.doyle/anaconda/envs/asim/lib/python2.7/site-packages/pandas/core/internals.py", line 2461, in make_block
    return klass(values, ndim=ndim, fastpath=fastpath, placement=placement)
  File "/Users/jeff.doyle/anaconda/envs/asim/lib/python2.7/site-packages/pandas/core/internals.py", line 84, in __init__
    len(self.mgr_locs)))
ValueError: Wrong number of items passed 1277, placement implies 1278

[toliwaga]

This is caused because one tour ((19970) has zero probabilities for all modes because all NaN utilities

probs.loc[19970,].sum(axis=0) = 1.8e-299

Alternative
BIKE              1.000000e-300
DRIVEALONEFREE    1.000000e-300
DRIVEALONEPAY     1.000000e-300
DRIVE_COM         1.000000e-300
DRIVE_EXP         1.000000e-300
DRIVE_HVY         1.000000e-300
DRIVE_LOC         1.000000e-300
DRIVE_LRF         1.000000e-300
SHARED2FREE       1.000000e-300
SHARED2PAY        1.000000e-300
SHARED3FREE       1.000000e-300
SHARED3PAY        1.000000e-300
WALK              1.000000e-300
WALK_COM          1.000000e-300
WALK_EXP          1.000000e-300
WALK_HVY          1.000000e-300
WALK_LOC          1.000000e-300
WALK_LRF          1.000000e-300
Name: 19970, dtype: float64

utilities.loc[19970,]

Alternative
BIKE              NaN
DRIVEALONEFREE    NaN
DRIVEALONEPAY     NaN
DRIVE_COM         NaN
DRIVE_EXP         NaN
DRIVE_HVY         NaN
DRIVE_LOC         NaN
DRIVE_LRF         NaN
SHARED2FREE       NaN
SHARED2PAY        NaN
SHARED3FREE       NaN
SHARED3PAY        NaN
WALK              NaN
WALK_COM          NaN
WALK_EXP          NaN
WALK_HVY          NaN
WALK_LOC          NaN
WALK_LRF          NaN
Name: 19970, dtype: object

choosers.loc[19970,]

destination                       1439
destination_in_cbd                 NaN
person_id                       820171
tour_departure_and_duration         36
tour_num                             1
tour_type                       school
start                                6
end                                 23
duration                            17

[toliwaga]

make_choices in mnl.py probably should check for probs not summing to 1 or being NaNs?

def make_choices(probs):
    """
    Make choices for each chooser from among a set of alternatives.

    Parameters
    ----------
    probs : pandas.DataFrame
        Rows for choosers and columns for the alternatives from which they
        are choosing. Values are expected to be valid probabilities across
        each row, e.g. they should sum to 1.

    """

[toliwaga]

Tour 19970 was assigned destination TAZ 1439 which has a dest_density_index Nan because land_use.household_density and land_use.employment_density in that TAZ are both 0 so density_index is undefined.

@orca.column("land_use")
def density_index(land_use):
    return (land_use.household_density * land_use.employment_density) / \
        (land_use.household_density + land_use.employment_density)

Thus the 10 rows in tour_mode_choice.csv that use dest_density_index eval to NaN for this tour

Thus the Utilities computed by the cross product with spec are likewise Nan when

utilities = model_design.dot(spec)

utilities.loc[19970,]

Alternative
BIKE              NaN
DRIVEALONEFREE    NaN
DRIVEALONEPAY     NaN
DRIVE_COM         NaN
DRIVE_EXP         NaN
DRIVE_HVY         NaN
DRIVE_LOC         NaN
DRIVE_LRF         NaN
SHARED2FREE       NaN
SHARED2PAY        NaN
SHARED3FREE       NaN
SHARED3PAY        NaN
WALK              NaN
WALK_COM          NaN
WALK_EXP          NaN
WALK_HVY          NaN
WALK_LOC          NaN
WALK_LRF          NaN
Name: 19970, dtype: object

Which makes the probabilities for tour 19970 all NaN

Which causes the groupby at line 66 of make_choices in mnl.py to come up one row short:

choices = (s.iat[0] for _, s in pd.Series(cols).groupby(rows))

And so the choices array has one less row than probs.index so the attempr to create a series fails:

return pd.Series(choices, index=probs.index)

ValueError: Wrong number of items passed 1277, placement implies 1278

[toliwaga]

Tour model shouldn't choose destination TAZ where employment_density is 0?

But this is a school tour, so maybe it is a legitimate destination?

Here is the dest TAZ 1439 land use:

DISTRICT                  34
SD                        34
COUNTY                     9
TOTHH                      0
HHPOP                      0
TOTPOP                  4855
EMPRES                     0
SFDU                       0
MFDU                       0
HHINCQ1                    0
HHINCQ2                    0
HHINCQ3                    0
HHINCQ4                    0
TOTACRE                   26
RESACRE                    0
CIACRE                    13
SHPOP62P                0.05
TOTEMP                     0
AGE0004                    5
AGE0519                   98
AGE2044                 3598
AGE4564                 1050
AGE65P                   104
RETEMPN                    0
FPSEMPN                    0
HEREMPN                    0
OTHEMPN                    0
AGREMPN                    0
MWTEMPN                    0
PRKCST                     0
OPRKCST                    0
area_type                  4
HSENROLL                   0
COLLFTE                    0
COLLPTE                    0
TOPOLOGY                   3
TERMINAL              7.3102
ZERO                       0
hhlds                      0
sftaz                   1439
gqpop                   4855
employment_density         0
total_acres               26
total_households           0
density_index            NaN
county_name            Marin
household_density          0
county_id                  9
total_employment           0
Name: 1439, dtype: object

0 households, population 4855, high school and college population is 0, but group quarters population GQPOP is 4855 - I'm guessing this is either a barracks, a monastery, or a prison?

So probably shouldn't be the destination of a school tour?

[toliwaga]

San Quentin State Prison?

[wusun2]

This is a very good catch. There are a few issues/observations here:

1. This is a destination with no school enrollment, why it was picked as a school tour destination? Probably due to the shadow pricing mechanism, used to enforce consistency between school location choices and enrollment inputs, is not in place in the school location choice model yet?

2. Employment density (population and dwelling unit densities too in the SANDAG case) is used as a proxy to represent urban forms which affect the likelihood of choosing non-motorized modes (bike and walk). Employment density not only affects tour/trip mode choice for work purpose, but also affects trip/tour mode choices for other purposes, including school trips.

3. More importantly, the all NaN probability situation could also happen in other places, such as stop location choices per the SANDAG experience. We put temporary fixes to default choices to an alternative we think is relatively reasonable to get by. However, it would be great to have a more sounding solution to the no alternative is available cases like this.

4. @toliwaga suggestion of checking the sum of probability equal to 1 is a good way to detect (not solve) problems like this.

[toliwaga]

Crash fixed in #82 but leaving open to remind us to add check for probs not summing to 1 or being NaNs

[toliwaga]

props currently end up not summing to 1 rather frequently. Specifically, when all the utilities are large negative numbers.

this happens for instance in non_mandatory_scheduling call to vectorize_tour_scheduling when all utilities are between -990 and -999

When this happens, all the exp(utils) are zero and so the conversion to probabilities zero-divides when it does this:

    prob_min = 1e-300
    prob_max = np.inf

    utils_arr = np.exp(utils.as_matrix().astype('float'))
    arr_sum = utils_arr.sum(axis=1)

    if np.isinf(arr_sum).any():
        raise RuntimeError('utilities have infinite values')

    np.clip(utils_arr, prob_min, prob_max, out=utils_arr)
    np.divide(
        utils_arr, arr_sum.reshape(len(utils_arr), 1),
        out=utils_arr)
    utils_arr[np.isnan(utils_arr)] = prob_min

    np.clip(utils_arr, prob_min, prob_max, out=utils_arr)

Moving the computation of arr_sum to after the clip makes mathematical sense and appears to solve the problem.

Anyone see any obvious reason not to make this change?

Note: this wasn't getting caught because numpy.divide() wasn't throwing a zero-divide error. This is apparently a pandas feature.

Running this:

import numpy as np
print "np.geterr()", np.geterr()

import pandas as pd
print "np.geterr()", np.geterr()

Yields this:

np.geterr() without pandas: {'over': 'warn', 'divide': 'warn', 'invalid': 'warn', 'under': 'ignore'}
np.geterr() with pandas: {'over': 'ignore', 'divide': 'ignore', 'invalid': 'ignore', 'under': 'ignore'}

[wusun2]

Why probabilities are not summing up to 1 frequently? If this happens only when the util has large negative values like -999, it is kind of understandable. If this also happens to util with values not 'too' negative (such as -200), then it is a significant issue, because it is likely the -200 is a legit choice util, but then the math engine can't get the probabilities computed right. Is this a precision issue in Python when it come to mathematic computation?

[wusun2]

For the clipping, what if we have a case like this:
Two alternatives available. Alternative 2 is meant to be blocked, so the utility is assigned a value -999.

before clipping: util1=-100, util2=-999
after clipping: util1=-100, util2=-300 (if I understand the clipping correctly)

Now, both choices will have a valid probability computed for them. But then the Monte Carlo could well pick alternative 2, which was really meant to be a non-valid choice.

[wusun2]

The existing CT-RAMP has the same issue of probabilities not summing up to 1. One odd case we had was something like this:
Choice 1 is assigned with a probability 0.95, choice 2, 3, and 4 are blocked with -999 utils. In Monte Carlo, if the generated random number <0.95, then it is ok and alternative 1 is chosen. But, there are times the random number is >0.95 and no alternative can be chosen and caused model bombing.

[toliwaga]

The large negative values are like -998, -997 not -200

[bstabler]

In general, every choice should have at least one alternative available. If not, then the problem is usually due to a data issue (often in the skims) in combination with an error in expression definitions. Ultimately we need to log when a choice cannot be made and exit the simulation.

Also, it looks like we need to review/audit the expressions to ensure we don't get any -998, -997s since these are probably the result of errors in the expression definitions. In CT-RAMP, once a -999 was encountered, the rest of the expressions in the UEC were skipped and the alternative was turned off. We need to think some more about how best to incorporate the treatment of NAs in the system.

[wusun2]

It seems to me there are two different issues:

1. probabilities not summing up to 1
2. all choice alternatives are blocked with larger negative utils

For issue 2, as @bstabler mentioned, it is caused by data, we need to log the error with informative info so the users know where to check data.

For issue 1, a lot of times it happens when one or more of the alternative is blocked with large negative utils. We might be able remove the blocked alternatives from the alternative set, only leave valid alternatives in the set, and it might help to resolve sum not 1 issues.

[guyrousseau]

Regarding mode choice nesting coefficients, we also have to be careful about how they are applied

alogit style:

Unest = ln(sum(exp(U))

or

utility style (McFadden)

Unest = 1/lambda * sum (exp(lambda * U))

and whether there are any "dummy" nodes to correct for the problems of alogit style