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Debug params behavior with multiple input arguments #63

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merged 6 commits into from
May 20, 2024
Merged

Debug params behavior with multiple input arguments #63

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4c293c7
debug multiparams
CodyCBakerPhD May 19, 2024
2b359bf
some results
CodyCBakerPhD May 19, 2024
63c6133
Merge branch 'lindi_update' into debug_params
CodyCBakerPhD May 19, 2024
077a763
almost full results from slice timings
CodyCBakerPhD May 19, 2024
080575c
Merge branch 'debug_params' of https://github.com/neurodatawithoutbor…
CodyCBakerPhD May 19, 2024
6108e9e
Merge branch 'lindi_update' into debug_params
CodyCBakerPhD May 20, 2024
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57 changes: 57 additions & 0 deletions ...5-18-21-50-43_machine-Ackermann_environment-91bf3abc58d3f9487dc3b25977d808fc1536e53f.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
{
"version": 2,
"timestamp": "2024-05-18-21-50-43",
"commit_hash": "4c293c783a25f7e07880474d81b2b0873563e06a",
"environment_hash": "91bf3abc58d3f9487dc3b25977d808fc1536e53f",
"machine_hash": "Ackermann",
"results": {
"time_remote_slicing.FsspecNoCacheContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.577229900052771,
0.5970238998997957,
0.5664639000315219
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
1.0336655001156032,
1.2907407998573035,
0.9944616998545825
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
0.17991229984909296,
0.2016158001497388,
0.18414429994300008
]
},
"time_remote_slicing.Ros3ContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.0035342001356184483,
0.003450800199061632,
0.0036127998027950525
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
0.0007092999294400215,
0.0007117001805454493,
0.000698799965903163
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
6.3811555066292796e-06,
6.141684663765631e-06,
6.1631210492300295e-06
]
},
"time_remote_slicing.ZarrContinuousSliceBenchmark.time_slice": {
"(\"'s3://aind-open-data/ecephys_625749_2022-08-03_15-15-06_nwb_2023-05-16_16-34-55/ecephys_625749_2022-08-03_15-15-06_nwb/ecephys_625749_2022-08-03_15-15-06_experiment1_recording1.nwb.zarr/'\", \"'ElectricalSeriesProbe A-LFP'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
1.2064452001359314,
1.45879239984788,
1.137998699909076
]
},
"time_remote_slicing.ZarrForceNoConsolidatedContinuousSliceBenchmark.time_slice": {
"(\"'s3://aind-open-data/ecephys_625749_2022-08-03_15-15-06_nwb_2023-05-16_16-34-55/ecephys_625749_2022-08-03_15-15-06_nwb/ecephys_625749_2022-08-03_15-15-06_experiment1_recording1.nwb.zarr/'\", \"'ElectricalSeriesProbe A-LFP'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
1.0744982999749482,
1.1373234000056982,
1.347178699914366
]
}
}
}
108 changes: 108 additions & 0 deletions ...5-18-22-41-54_machine-Ackermann_environment-91bf3abc58d3f9487dc3b25977d808fc1536e53f.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,108 @@
{
"version": 2,
"timestamp": "2024-05-18-22-41-54",
"commit_hash": "2b359bffe2a1c2061d2ae13f0a85f3422b1d04ca",
"environment_hash": "91bf3abc58d3f9487dc3b25977d808fc1536e53f",
"machine_hash": "Ackermann",
"results": {
"time_remote_slicing.FsspecNoCacheContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.5770294000394642,
0.5558074999134988,
0.5851527999620885
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
1.0202222999650985,
1.0687915000598878,
1.1272402999456972
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
0.1669504998717457,
0.15758339990861714,
0.23897469998337328
]
},
"time_remote_slicing.FsspecWithCacheContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.46691940003074706,
0.434342100052163,
0.42370989988557994
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
0.29375869990326464,
0.26918979990296066,
0.286825800081715
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
6.63219959654271e-05,
5.873775452703179e-05,
6.128844388626707e-05
]
},
"time_remote_slicing.RemfileNoCacheContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.5421017999760807,
0.5975515998434275,
0.6133785999845713
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
0.5068071000277996,
0.5669373997952789,
0.5368534000590444
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
6.4188481480264605e-06,
6.4300173820972165e-06,
6.257184445771317e-06
]
},
"time_remote_slicing.RemfileWithCacheContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.7116888999007642,
0.7746200999245048,
0.7001597001217306
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
0.6674359999597073,
0.5512343000154942,
0.5494779001455754
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
6.591881237390126e-06,
6.737569993630903e-06,
6.343617024732397e-06
]
},
"time_remote_slicing.Ros3ContinuousSliceBenchmark.time_slice": {
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/fec/8a6/fec8a690-2ece-4437-8877-8a002ff8bd8a'\", \"'ElectricalSeriesAp'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
0.0033102999441325665,
0.0034116001334041357,
0.0033524997998028994
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/38c/c24/38cc240b-77c5-418a-9040-a7f582ff6541'\", \"'TwoPhotonSeries'\", '(slice(0, 3, None), slice(0, 796, None), slice(0, 512, None))')": [
0.0008107998874038458,
0.0007931999862194061,
0.0007380000315606594
],
"(\"'https://dandiarchive.s3.amazonaws.com/blobs/c98/3a4/c983a4e1-097a-402c-bda8-e6a41cb7e24a'\", \"'data_00002_AD0'\", '(slice(0, 30000, None),)')": [
6.302597341961204e-06,
5.955957081368722e-06,
6.150705781925674e-06
]
},
"time_remote_slicing.ZarrContinuousSliceBenchmark.time_slice": {
"(\"'s3://aind-open-data/ecephys_625749_2022-08-03_15-15-06_nwb_2023-05-16_16-34-55/ecephys_625749_2022-08-03_15-15-06_nwb/ecephys_625749_2022-08-03_15-15-06_experiment1_recording1.nwb.zarr/'\", \"'ElectricalSeriesProbe A-LFP'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
1.1419850999955088,
1.1669653998687863,
1.228188700042665
]
},
"time_remote_slicing.ZarrForceNoConsolidatedContinuousSliceBenchmark.time_slice": {
"(\"'s3://aind-open-data/ecephys_625749_2022-08-03_15-15-06_nwb_2023-05-16_16-34-55/ecephys_625749_2022-08-03_15-15-06_nwb/ecephys_625749_2022-08-03_15-15-06_experiment1_recording1.nwb.zarr/'\", \"'ElectricalSeriesProbe A-LFP'\", '(slice(0, 30000, None), slice(0, 384, None))')": [
1.0642591000068933,
1.097299600020051,
1.493450199952349
]
}
}
}
16 changes: 8 additions & 8 deletions src/nwb_benchmarks/benchmarks/time_remote_slicing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,14 +33,14 @@
object_name="TwoPhotonSeries",
slice_range=(slice(0, 3), slice(0, 796), slice(0, 512)),
),
# IcephysTestCase=dict(
# s3_url=get_s3_url(
# dandiset_id="000717",
# dandi_path="sub-1214579789_ses-1214621812_icephys/sub-1214579789_ses-1214621812_icephys.nwb",
# ),
# object_name="data_00002_AD0",
# slice_range=(slice(0, 30_000),),
# ),
IcephysTestCase=dict(
s3_url=get_s3_url(
dandiset_id="000717",
dandi_path="sub-1214579789_ses-1214621812_icephys/sub-1214579789_ses-1214621812_icephys.nwb",
),
object_name="data_00002_AD0",
slice_range=(slice(0, 30_000),),
),
)

zarr_parameter_cases = dict(
Expand Down
29 changes: 17 additions & 12 deletions src/nwb_benchmarks/setup/_reduce_results.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import shutil
import subprocess
import sys
import warnings
from typing import Dict, List


Expand Down Expand Up @@ -58,19 +59,23 @@ def reduce_results(raw_results_file_path: pathlib.Path, raw_environment_info_fil

# Skipped results in JSON are writen as `null` and read back into Python as `None`
non_skipped_results = [result for result in raw_results_list[11] if result is not None]
assert len(serialized_flattened_joint_params) == len(non_skipped_results), (
f"Length mismatch between flattened joint parameters ({serialized_flattened_joint_params} and result "
f"samples ({len(non_skipped_results)}) in test case '{test_case}'! "
"Please raise an issue and share your intermediate results file."
)
reduced_results.update(
{
test_case: {
joint_params: raw_result
for joint_params, raw_result in zip(serialized_flattened_joint_params, non_skipped_results)
if len(serialized_flattened_joint_params) != len(non_skipped_results):
message = (
f"In intermediate results for test case {test_case}: \n"
f"\tLength mismatch between flattened joint parameters ({len(serialized_flattened_joint_params)}) and "
f"result samples ({len(non_skipped_results)})!\n\n"
"Please raise an issue and share your intermediate results file."
)
warnings.warn(message=message)
else:
reduced_results.update(
{
test_case: {
joint_params: raw_result
for joint_params, raw_result in zip(serialized_flattened_joint_params, non_skipped_results)
}
}
}
)
)

if len(reduced_results) == 0:
raise ValueError(
Expand Down