Improve performance for Trip Segmentation Stage

[humbleOldSage]

Aim : To improve the performance of the trip segmentation stage of the pipeline by reducing the number of DB calls and performing more in-memory operations (potentially using pandas).

[humbleOldSage]

Spent week and a half to figure out the pipeline flow (including the trip segmentation flow) from

a. Dr. Shankari's thesis

b. discussion with @mukuFlash03 where he gave Issue https://github.com/e-mission/e-mission-docs/issues/950 as a good way to understand the flow of prediction pipeline.

pipeline begins from intake_stage.py file run_intake_pipeline_for_user function which shows the various stage calls as well.

We'll currently focus on the eaist.segment_current_trips stage ( at emission/analysis/intake/segmentation/trip_segmentation.py ).

[humbleOldSage]

The very first point of improvement I could find is related to the negation of out of order data :

out_of_order_points = loc_df[loc_df.ts.diff() < 0]
if len(out_of_order_points) > 0:
      .
      .
      .
      .
    out_of_order_id_list = out_of_order_points["_id"].tolist()
    logging.debug("out_of_order_id_list = %s" % out_of_order_id_list)
    for ooid in out_of_order_id_list:
        ts.invalidate_raw_entry(ooid)

where invalidate_raw_entry is as below :

    def invalidate_raw_entry(self, obj_id):
        self.timeseries_db.update_one({"_id": obj_id, "user_id": self.user_id}, {"$set": {"invalid": True}})

This is done one ID at a time, which can be inefficient, especially with large list. We can improve this as below :

1. Create list of update operations . somethign like below

   update_operations = [
     UpdateOne({"_id": obj_id, "user_id": self.user_id}, {"$set": {"invalid": True}})
     for obj_id in out_of_order_id_list
   ]

   and then use bulk_write method to execute all updates at once.

   
   if update_operations:
     self.timeseries_db.bulk_write(update_operations)
   

[humbleOldSage]

To handle too big of a list, we can make batches and then create bulk operations on those batches.

[humbleOldSage]

To test the above, I flipped the loc_df dataframe as

 loc_df=loc_df[::-1]

thus allowing us to test the out_of_order part of the code.

Another thing I tried was experimenting with the scale of data by appending the same dataframe to the end of itself as :

 for _ in range(n_fold):
    loc_df=pd.concat([loc_df,loc_df],ignore_index=True)

where n_fold means the no_of_times you want to upscale the dataframe. After this I reversed the dataframe as above.

Results were as below :

Trips considered as out_of_order ->	327	327*5
Time taken by Old implementation	0.363	12.101
Time taken by New Implementation	0.037	0.777

[humbleOldSage]

I did try the batch method( with bulk_write ) as well, using different batch sizes ( 500,1000,2000) but there no improvement as compared to bulk_write.

[humbleOldSage]

PR : https://github.com/e-mission/e-mission-server/pull/953

[humbleOldSage]

there's two other dependency for invalidate_raw_entry that we'll have to handle after this update:

1. from dwell_segmentaion_dist_filter
2. from abstract_timeseries.py

 grep -rl invalidate_raw_entry | grep -v __pycache__
./emission/analysis/intake/segmentation/trip_segmentation.py
./emission/analysis/intake/segmentation/trip_segmentation_methods/dwell_segmentation_dist_filter.py
./emission/storage/timeseries/abstract_timeseries.py
./emission/storage/timeseries/builtin_timeseries.py

[shankari]

1. For the invalid entries improvement, I don't disagree but I am not sure that it is the biggest bang for the buck. Invalid entries are very rare, and this is a corner case that we handle to avoid errors. Before working on that any further, can you estimate how many invalid entries we actually have in our datasets to determine whether to prioritize this.
2. To clarify again, you tested the improvement with this, but you did it on fake data. There is no evidence that this will actually improve real-world performance.
3. For performance improvements on existing/running systems, you don't start with looking through the code to find something that you can understand and optimize. Instead, you start with looking at the system logs to understand where the time is being spent, and then you look at the code related to that and then you optimize it.

For example, in the issue here: https://github.com/e-mission/e-mission-docs/issues/950 we did not start by looking at the code and determining what incremental improvement we should do. Instead, we looked at the logs and determined, through timestamps, where the time was being spent, and then determined why and then determined how to fix it.

[humbleOldSage]

Looking into the Android run time for now. It took ~6.8s to run the entire segment_current_trips from testSegmentationWrapperAndroid from TestTripSegmentation.py, out of which ~6.775s is to run the segment_into_trips from dwell_segmentation_filter.py.

Out of this, almost all the time ( ~ 6.774) is to run the for loop (335 iterations)

.
.
 for idx, row in filtered_points_df.iterrows():
.
.

Inside the loop, for each iteration run it took

~0.0043s to run from beginning of the loop :

currPoint = ad.AttrDict(row)
 .
 .
 .

till

.
.
last5MinTimes = last5MinsPoints_df.apply(timeToLast, axis=1)

AND another ~ 0.011 from

.
.
.
if self.has_trip_ended(prevPoint, currPoint, timeseries, last10PointsDistances, last5MinsDistances, last5MinTimes,transition_df):

till rest of the loops,i.e., till

            else:
                prevPoint = currPoint

Meaning that the second part of the loop is currently taking the most time.

[humbleOldSage]

In this part, the has_trip_ended is the almost the major contributor, inside which is_tracking_restarted_in_range took ~0.005s and get_ongoing_m option_in_range took ~0.004s ( This is still inside the for look).

To improve is_tracking_restarted_in_range :

There was this db call

tq = estt.TimeQuery(timeType="data.ts", startTs=start_ts,
                    endTs=end_ts)
transition_df = timeseries.get_data_df("statemachine/transition", tq)

which was run in every iteration. Instead , we can place this upstream outside the for loop in segment_into_trips ( dwell_segmentation_time_filter.py) and get all the trips for user in a df beforerhand. However, there's call to is_tracking_restarted_in_range from further upstream in segment_current_trips ->create_places_and_trips -> found_untracked_period ->_is_tracking_restarted (trip_Segmentation.py ) and so, we'll make db calls from segment_current_trips

Once we have the df, since all the rows are sorted by ts, we can do a log(n) search on start index and end index in every iteration as below .

    transition_df_start_idx=transition_df.ts.searchsorted(start_ts,side='left')    
    transition_df_end_idx=transition_df.ts.searchsorted(end_ts,side='right')
    transition_df_for_current=transition_df.iloc[transition_df_start_idx:transition_df_end_idx]

Similar changes in get_ongoing_motion_in_range where I moved

    tq = estt.TimeQuery(timeType = "data.ts", startTs = start_ts,
                        endTs = end_ts)
    motion_list = list(timeseries.find_entries(["background/motion_activity"], tq))

upstream to extract in a df and replace by :

    motion_df_start_idx=motion_df.ts.searchsorted(start_ts,side='left')    
    motion_df_end_idx=motion_df.ts.searchsorted(end_ts,side='right')
    motion_list=motion_df.iloc[motion_df_start_idx:motion_df_end_idx]

[humbleOldSage]

With these changes the runtime can down to ~0.0001 (from .005) for is_tracking_restarted_in_range and ~0.0001 (from ~0.004) for get_ongoing_motion_in_range.

So all in all the second part of the for loop that took ~.011s came down to ~0.0006 s.

In total , the segment_current_trips runtime reduced to ~2.12.

[humbleOldSage]

https://github.com/e-mission/e-mission-server/pull/953/commits/1d1b31f1f4160af775479b8646a0c9726ca98771 handles these changes. This was bound to fail.

[humbleOldSage]

And with these changes inside for loop, the first part now takes longer to run ( 0.0043 per iteration as mentioned above as well ).

I tried some pandas improvements which might be overkill ( in which case we can roll this back) which reduced overall runtime from ~2.12 to ~1.5.

For this , started by adding Vectorised implementation in calDistance (emission\core\common.py) :

def calDistance(point1, point2, coordinates=False):
    .
    .
    rest of the code
     .
     .
     .

    if isinstance(point1,np.ndarray) and isinstance(point2,np.ndarray):
        dLat = np.radians(point1[:,1]-point2[:,1])
        dLon = np.radians(point1[:,0]-point2[:,0])
        lat1 = np.radians(point1[:,1])
        lat2 = np.radians(point2[:,1]) 

        a = (np.sin(dLat/2) ** 2) + ((np.sin(dLon/2) ** 2) * np.cos(lat1) * np.cos(lat2))
        c = 2 * np.arctan2(np.sqrt(a), np.sqrt(1-a))
        d = earthRadius * c

        return d
     .
     .
     .
     rest of the implementation

and in segment_into_trips, the calculations for last5MinTimesand others are vectorized.

[humbleOldSage]

For the iOS wrapper, the necessary changes to support the generalized flow of trip and that brought the iOS runtime to 0.3s.

However, when running the combinedWrapper (iOS+Android), the loc_df db call

    loc_df = ts.get_data_df("background/filtered_location", time_query)

isn't work not when placed upstream in trip_segmentation.py and passed to dwell_segmentation_dist_filter.py and dwell_segmentation_dist_filter.py. It only seems to work correctly when placed separately from dwell_segmentation_dist_filter.py and dwell_segmentation_dist_filter.py.

For now, on dummy data, this additional call is increasing android runtime from 1.5 to ~1.6 and iOS from 0.3 to 0.4.

Lets try to figure out why upstream call isn't working

[humbleOldSage]

Also, current CombinedWrapper runtime is 2.1s

[humbleOldSage]

On the side, after yesterday's PR, I was expecting all the tests to pass.

Figured from the logs that testJackUntrackedTimeMar12 test from /Users/ssaini/Documents/GitHub/e-mission-server/emission/tests/analysisTests/intakeTests/TestPipelineRealData.py was failing after get_ongoing_motion_in_range was shifted from list-based to df-based in restart_checking.py. The dataframe implementation was unable to handle an empty df case. This was fixed accordingly.

[humbleOldSage]

Indwell_segmentation_time_filter.py, for evaluating last10PointsDistance and last5MinsDistances, the calculations are now vectored . To support vectorised calculations , calDistance in common.py now has numpy related changes.

This brought the runtime for this entire loop

 for idx, row in filtered_points_df.iterrows():

from ~ 2s to 1.2s over 327 iterations.

[shankari]

I think we should revisit this from first principles and then validate that what Satyam came up aligns with what you find. I would like to handle this in a principled fashion, by:

• instrumenting to see the bottlenecks
• fix the bottlenecks
• show the improvement

we can instrument in two ways:

• add additional logs
• we can insert additional entries as server stats (as in emission/pipeline/intake_stage.py)

Pro of the logs: it is quick and easy to see as you are making changes Pro of the stats: you can see the behavior in production without having to pull logs from cloudwatch

I would suggest additional logs initially so you can fix it and potentially generate some stats around improvements on pulled data and do lots of analysis

and then we deploy to production and then we can run analyses (before and after) on multiple deployments of various sizes