[META] Protobuf for Search API

VachaShah commented 10 months ago

Proposal

With the experiment done for using protobuf in _cat/nodes API (see https://github.com/opensearch-project/OpenSearch/issues/6844#issuecomment-1742250229) and a 15-30% improvement depending on the size of the cluster, we can assess the benefits of protobuf for Search API in terms of serialization and de-serialization of the requests and responses in between nodes and at the REST level.

Next Steps

Do a similar experiment for the Search API to understand the performance improvements using protobuf. (This is a work in progress)

Details

In order to experiment and see incremental benefits, some of the classes I am targeting to convert to protobuf: SearchRequest, SearchResponse, SearchPhaseResult, FetchSearchResult, ShardFetchRequest, ShardSearchRequest, QueryFetchSearchResult, QuerySearchRequest, QuerySearchResult. Also, classes related to TransportSearchAction are required to support protobuf requests and responses.

Code changes

The code changes for the experiment are being added in a branch on my fork: https://github.com/VachaShah/OpenSearch/compare/poc-cat-nodes-protobuf...VachaShah:OpenSearch:poc-search-protobuf?expand=1

Sub tasks/Milestones

Next steps as discussed with @msfroh and @getsaurabh02. Let me know if I missed something here.

[ ] Convert QuerySearchResult, FetchSearchResult and QueryFetchSearchResult into a proto message and add support to communicate this response between nodes using protobuf bytes. This includes adding support for protobuf in OutboundHandler and InboundHandler. Deliver this as an experimental feature. There will be a feature flag which if enabled will allow node-to-node communication using protobuf.
[ ] Add support for aggregations (in QuerySearchResult), NestedIdentity (in SearchHit) and other optional fields in SearchHit as protobuf messages.
[ ] Repeat the same for other search results and requests.

Note: All of the above changes go behind an experimental feature flag. Once the incremental changes are in for the Search API:

[ ] Add backwards compatibility for the node-to-node communication protocols with version checks during node-to-node communication and remove the experimental feature flag.

Yeah what we'd like to know is serialization/de-serialization causing performance latency, and is that during query phase or fetch phase etc. This will help us narrow down which area to work on first. The idea so far (theoretically) is we will work on fetch phase where the responses are serialized on data nodes and de-serialized on co-ordinator which will have the best benefits for protobuf.

navneet1v commented 10 months ago

For vector search it will be fetch phase only, because that is where a vector having like lets say 100 dimension is getting serialized and de-serialized per document. Consider like every float is represented as 4bytes it becomes like 400 bytes just alone for vectors.

and the same gets transported over the wire to customers too. Hence once we start to make the change it will help a lot.

The idea so far (theoretically) is we will work on fetch phase where the responses are serialized on data nodes and de-serialized on co-ordinator which will have the best benefits for protobuf.

+1 on this.

From benchmarks I will see what I can provide, but I can surely help setup the benchmark code so that you guys can run of different custom OpenSearch to get more numbers if you want.

VachaShah commented 10 months ago

That would be super helpful @navneet1v!

navneet1v commented 10 months ago

@saratvemulapalli , @VachaShah Here is one of the benchmarking notebook which you can use, to test k-NN with any OpenSearch cluster with Security Enabled.

https://github.com/navneet1v/OpenSearchVectorDB/blob/main/benchmarking/sift-128/sift-128-benchmarking.ipynb

This is something I was working on. This replicates the behavior on how we do perf testing in K-NN. Good thing about this is its is easy to run.

import numpy as np
from tqdm.notebook import tqdm

# search in the index
def searchQueryGen(input_array=X_TEST):
    for i, vec in enumerate(input_array):
        yield {
            "_source": False, # Don't get the source as this impacts latency
            "size": 100,
            "query": {
                "knn": {
                    "vec": {
                        "vector": vec.tolist(),
                        "k": 100
                    }
                }
            }
        }

neighbors_lists = []
search_latency = []
took_time = []
for query in tqdm(searchQueryGen(), total=len(X_TEST)):
    start = time.time()
    search_response = client.search(body=query, index=vector_index_name, _source=False, docvalue_fields=["_id"], stored_fields="_none_")
    end = time.time()
    search_latency.append(end - start)
    took_time.append(search_response["took"])
    search_hits = search_response['hits']['hits']
    search_neighbors = [int(hit["fields"]["_id"][0]) for hit in search_hits]
    neighbors_lists.append(search_neighbors)

You can remove all the optimization that we have added:

not getting _source for documents.
not getting stored fields.
Getting _id as doc value rather than from stored field.

Please let me know if you need any more details happy to help.

getsaurabh02 commented 10 months ago

This is super exciting @VachaShah!! Would you like to share insights on what Transport classes are good candidates for trying out and experimenting the improvements first. Do you think instrumenting the node-to-node interaction for Query and Fetch phases, especially targeting implementations for SearchPhaseResult could be a good idea?

This could include heavily exercised code paths during query executions such as QuerySearchResult, FetchSearchResult, ScrollQuerySearchResult and more.

VachaShah commented 10 months ago

Thank you @getsaurabh02! I have added the classes that I am targeting first in the issue description. They include the Query and Fetch phase implementations of SearchPhaseResult and other related request, response and transport action classes.

VachaShah commented 9 months ago

The code for end-to-end working POC with _search_protobuf API which is a version of _search API with requests, responses and node-to-node communication using protobuf is built on top of _cat/nodes API POC. The code can be found in this diff: https://github.com/VachaShah/OpenSearch/compare/poc-cat-nodes-protobuf...VachaShah:OpenSearch:poc-search-protobuf?expand=1.

The current POC is for QUERY_THEN_FETCH search types with some embedded objects in the Response as bytes. The next step is to convert those embedded objects into proto messages as well.

I am going to micro benchmarking the protobuf integrated API to compare with the original search API.

Next steps

Convert the embedded objects in responses to proto messages.
Micro benchmarking for numbers.

hdhalter commented 9 months ago

@VachaShah - Will this require documentation? If so, can you please create a doc issue, let me know who will be submitting the doc PR, and add it to the unified tracker project? Thank you!

VachaShah commented 8 months ago

@VachaShah - Will this require documentation? If so, can you please create a doc issue, let me know who will be submitting the doc PR, and add it to the unified tracker project? Thank you!

@hdhalter This does not require documentation as of now since it is a performance improvement. I am going to divide this meta issue into sub tasks and if any of them have a need for documentation, I will make sure to create a doc issue for those.

VachaShah commented 8 months ago

In order to divide this issue into deliverables, converting this issue into a meta issue. Sub tasks will be listed in the issue description.

saratvemulapalli commented 8 months ago

Thanks @VachaShah for breaking it down. Tagging @dbwiddis who is interested in contributing.

VachaShah commented 8 months ago

Benchmarks

The benchmarks are taken using opensearch-benchmark for both the original search API and protobuf version of the API for default searches in benchmarks. The workload used is nyc_taxis.

5 nodes cluster

Seeing a 19.1% decrease in latency for default search with protobuf integration.

Original API

Metric	Task	Value	Unit
Cumulative indexing time of primary shards		0.00248333	min
Min cumulative indexing time across primary shards		0.00248333	min
Median cumulative indexing time across primary shards		0.00248333	min
Max cumulative indexing time across primary shards		0.00248333	min
Cumulative indexing throttle time of primary shards		0	min
Min cumulative indexing throttle time across primary shards		0	min
Median cumulative indexing throttle time across primary shards		0	min
Max cumulative indexing throttle time across primary shards		0	min
Cumulative merge time of primary shards		0	min
Cumulative merge count of primary shards		0
Min cumulative merge time across primary shards		0	min
Median cumulative merge time across primary shards		0	min
Max cumulative merge time across primary shards		0	min
Cumulative merge throttle time of primary shards		0	min
Min cumulative merge throttle time across primary shards		0	min
Median cumulative merge throttle time across primary shards		0	min
Max cumulative merge throttle time across primary shards		0	min
Cumulative refresh time of primary shards		0.00153333	min
Cumulative refresh count of primary shards		5
Min cumulative refresh time across primary shards		0.00153333	min
Median cumulative refresh time across primary shards		0.00153333	min
Max cumulative refresh time across primary shards		0.00153333	min
Cumulative flush time of primary shards		0	min
Cumulative flush count of primary shards		0
Min cumulative flush time across primary shards		0	min
Median cumulative flush time across primary shards		0	min
Max cumulative flush time across primary shards		0	min
Total Young Gen GC time		0.008	s
Total Young Gen GC count		1
Total Old Gen GC time		0	s
Total Old Gen GC count		0
Store size		0.000252848	GB
Translog size		5.12227e-08	GB
Heap used for segments		0	MB
Heap used for doc values		0	MB
Heap used for terms		0	MB
Heap used for norms		0	MB
Heap used for points		0	MB
Heap used for stored fields		0	MB
Segment count		8
Min Throughput	index	26349.6	docs/s
Mean Throughput	index	26349.6	docs/s
Median Throughput	index	26349.6	docs/s
Max Throughput	index	26349.6	docs/s
50th percentile latency	index	31.8154	ms
100th percentile latency	index	38.6998	ms
50th percentile service time	index	31.8154	ms
100th percentile service time	index	38.6998	ms
error rate	index	0	%
Min Throughput	wait-until-merges-finish	163.69	ops/s
Mean Throughput	wait-until-merges-finish	163.69	ops/s
Median Throughput	wait-until-merges-finish	163.69	ops/s
Max Throughput	wait-until-merges-finish	163.69	ops/s
100th percentile latency	wait-until-merges-finish	5.62406	ms
100th percentile service time	wait-until-merges-finish	5.62406	ms
error rate	wait-until-merges-finish	0	%
Min Throughput	default	83.27	ops/s
Mean Throughput	default	83.27	ops/s
Median Throughput	default	83.27	ops/s
Max Throughput	default	83.27	ops/s
100th percentile latency	default	17.6042	ms
100th percentile service time	default	5.37617	ms
error rate	default	0	%
Min Throughput	range	112.38	ops/s
Mean Throughput	range	112.38	ops/s
Median Throughput	range	112.38	ops/s
Max Throughput	range	112.38	ops/s
100th percentile latency	range	14.9054	ms
100th percentile service time	range	5.7996	ms
error rate	range	0	%

API with Protobuf

Metric	Task	Value	Unit
Cumulative indexing time of primary shards		0.00171667	min
Min cumulative indexing time across primary shards		0.00171667	min
Median cumulative indexing time across primary shards		0.00171667	min
Max cumulative indexing time across primary shards		0.00171667	min
Cumulative indexing throttle time of primary shards		0	min
Min cumulative indexing throttle time across primary shards		0	min
Median cumulative indexing throttle time across primary shards		0	min
Max cumulative indexing throttle time across primary shards		0	min
Cumulative merge time of primary shards		0	min
Cumulative merge count of primary shards		0
Min cumulative merge time across primary shards		0	min
Median cumulative merge time across primary shards		0	min
Max cumulative merge time across primary shards		0	min
Cumulative merge throttle time of primary shards		0	min
Min cumulative merge throttle time across primary shards		0	min
Median cumulative merge throttle time across primary shards		0	min
Max cumulative merge throttle time across primary shards		0	min
Cumulative refresh time of primary shards		0.001	min
Cumulative refresh count of primary shards		5
Min cumulative refresh time across primary shards		0.001	min
Median cumulative refresh time across primary shards		0.001	min
Max cumulative refresh time across primary shards		0.001	min
Cumulative flush time of primary shards		0	min
Cumulative flush count of primary shards		0
Min cumulative flush time across primary shards		0	min
Median cumulative flush time across primary shards		0	min
Max cumulative flush time across primary shards		0	min
Total Young Gen GC time		0.004	s
Total Young Gen GC count		1
Total Old Gen GC time		0	s
Total Old Gen GC count		0
Store size		0.000253422	GB
Translog size		5.12227e-08	GB
Heap used for segments		0	MB
Heap used for doc values		0	MB
Heap used for terms		0	MB
Heap used for norms		0	MB
Heap used for points		0	MB
Heap used for stored fields		0	MB
Segment count		8
Min Throughput	index	31452.4	docs/s
Mean Throughput	index	31452.4	docs/s
Median Throughput	index	31452.4	docs/s
Max Throughput	index	31452.4	docs/s
50th percentile latency	index	25.6299	ms
100th percentile latency	index	26.2214	ms
50th percentile service time	index	25.6299	ms
100th percentile service time	index	26.2214	ms
error rate	index	0	%
Min Throughput	wait-until-merges-finish	292.51	ops/s
Mean Throughput	wait-until-merges-finish	292.51	ops/s
Median Throughput	wait-until-merges-finish	292.51	ops/s
Max Throughput	wait-until-merges-finish	292.51	ops/s
100th percentile latency	wait-until-merges-finish	3.01014	ms
100th percentile service time	wait-until-merges-finish	3.01014	ms
error rate	wait-until-merges-finish	0	%
Min Throughput	default	110.58	ops/s
Mean Throughput	default	110.58	ops/s
Median Throughput	default	110.58	ops/s
Max Throughput	default	110.58	ops/s
100th percentile latency	default	14.2405	ms
100th percentile service time	default	3.97145	ms
error rate	default	0	%
Min Throughput	range	142.97	ops/s
Mean Throughput	range	142.97	ops/s
Median Throughput	range	142.97	ops/s
Max Throughput	range	142.97	ops/s
100th percentile latency	range	11.715	ms
100th percentile service time	range	4.50792	ms
error rate	range	0	%

10 nodes cluster

Seeing a 23.03% decrease in latency for default search with protobuf integration.

Original API

Metric	Task	Value	Unit
Cumulative indexing time of primary shards		0.00198333	min
Min cumulative indexing time across primary shards		0.00198333	min
Median cumulative indexing time across primary shards		0.00198333	min
Max cumulative indexing time across primary shards		0.00198333	min
Cumulative indexing throttle time of primary shards		0	min
Min cumulative indexing throttle time across primary shards		0	min
Median cumulative indexing throttle time across primary shards		0	min
Max cumulative indexing throttle time across primary shards		0	min
Cumulative merge time of primary shards		0	min
Cumulative merge count of primary shards		0
Min cumulative merge time across primary shards		0	min
Median cumulative merge time across primary shards		0	min
Max cumulative merge time across primary shards		0	min
Cumulative merge throttle time of primary shards		0	min
Min cumulative merge throttle time across primary shards		0	min
Median cumulative merge throttle time across primary shards		0	min
Max cumulative merge throttle time across primary shards		0	min
Cumulative refresh time of primary shards		0.00126667	min
Cumulative refresh count of primary shards		5
Min cumulative refresh time across primary shards		0.00126667	min
Median cumulative refresh time across primary shards		0.00126667	min
Max cumulative refresh time across primary shards		0.00126667	min
Cumulative flush time of primary shards		0	min
Cumulative flush count of primary shards		0
Min cumulative flush time across primary shards		0	min
Median cumulative flush time across primary shards		0	min
Max cumulative flush time across primary shards		0	min
Total Young Gen GC time		0.007	s
Total Young Gen GC count		1
Total Old Gen GC time		0	s
Total Old Gen GC count		0
Store size		0.000223138	GB
Translog size		5.12227e-08	GB
Heap used for segments		0	MB
Heap used for doc values		0	MB
Heap used for terms		0	MB
Heap used for norms		0	MB
Heap used for points		0	MB
Heap used for stored fields		0	MB
Segment count		5
Min Throughput	index	24834.7	docs/s
Mean Throughput	index	24834.7	docs/s
Median Throughput	index	24834.7	docs/s
Max Throughput	index	24834.7	docs/s
50th percentile latency	index	41.3685	ms
100th percentile latency	index	45.1308	ms
50th percentile service time	index	41.3685	ms
100th percentile service time	index	45.1308	ms
error rate	index	0	%
Min Throughput	wait-until-merges-finish	167.27	ops/s
Mean Throughput	wait-until-merges-finish	167.27	ops/s
Median Throughput	wait-until-merges-finish	167.27	ops/s
Max Throughput	wait-until-merges-finish	167.27	ops/s
100th percentile latency	wait-until-merges-finish	5.51836	ms
100th percentile service time	wait-until-merges-finish	5.51836	ms
error rate	wait-until-merges-finish	0	%
Min Throughput	default	90.29	ops/s
Mean Throughput	default	90.29	ops/s
Median Throughput	default	90.29	ops/s
Max Throughput	default	90.29	ops/s
100th percentile latency	default	18.8456	ms
100th percentile service time	default	6.55805	ms
error rate	default	0	%
Min Throughput	range	100.27	ops/s
Mean Throughput	range	100.27	ops/s
Median Throughput	range	100.27	ops/s
Max Throughput	range	100.27	ops/s
100th percentile latency	range	19.1147	ms
100th percentile service time	range	8.94176	ms
error rate	range	0	%

API with protobuf

Metric	Task	Value	Unit
Cumulative indexing time of primary shards		0.00223333	min
Min cumulative indexing time across primary shards		0.00223333	min
Median cumulative indexing time across primary shards		0.00223333	min
Max cumulative indexing time across primary shards		0.00223333	min
Cumulative indexing throttle time of primary shards		0	min
Min cumulative indexing throttle time across primary shards		0	min
Median cumulative indexing throttle time across primary shards		0	min
Max cumulative indexing throttle time across primary shards		0	min
Cumulative merge time of primary shards		0	min
Cumulative merge count of primary shards		0
Min cumulative merge time across primary shards		0	min
Median cumulative merge time across primary shards		0	min
Max cumulative merge time across primary shards		0	min
Cumulative merge throttle time of primary shards		0	min
Min cumulative merge throttle time across primary shards		0	min
Median cumulative merge throttle time across primary shards		0	min
Max cumulative merge throttle time across primary shards		0	min
Cumulative refresh time of primary shards		0.00111667	min
Cumulative refresh count of primary shards		5
Min cumulative refresh time across primary shards		0.00111667	min
Median cumulative refresh time across primary shards		0.00111667	min
Max cumulative refresh time across primary shards		0.00111667	min
Cumulative flush time of primary shards		0	min
Cumulative flush count of primary shards		0
Min cumulative flush time across primary shards		0	min
Median cumulative flush time across primary shards		0	min
Max cumulative flush time across primary shards		0	min
Total Young Gen GC time		0	s
Total Young Gen GC count		0
Total Old Gen GC time		0	s
Total Old Gen GC count		0
Store size		0.000251911	GB
Translog size		5.12227e-08	GB
Heap used for segments		0	MB
Heap used for doc values		0	MB
Heap used for terms		0	MB
Heap used for norms		0	MB
Heap used for points		0	MB
Heap used for stored fields		0	MB
Segment count		8
Min Throughput	index	27541	docs/s
Mean Throughput	index	27541	docs/s
Median Throughput	index	27541	docs/s
Max Throughput	index	27541	docs/s
50th percentile latency	index	30.1443	ms
100th percentile latency	index	31.1228	ms
50th percentile service time	index	30.1443	ms
100th percentile service time	index	31.1228	ms
error rate	index	0	%
Min Throughput	wait-until-merges-finish	221.57	ops/s
Mean Throughput	wait-until-merges-finish	221.57	ops/s
Median Throughput	wait-until-merges-finish	221.57	ops/s
Max Throughput	wait-until-merges-finish	221.57	ops/s
100th percentile latency	wait-until-merges-finish	3.96129	ms
100th percentile service time	wait-until-merges-finish	3.96129	ms
error rate	wait-until-merges-finish	0	%
Min Throughput	default	138.62	ops/s
Mean Throughput	default	138.62	ops/s
Median Throughput	default	138.62	ops/s
Max Throughput	default	138.62	ops/s
100th percentile latency	default	15.7351	ms
100th percentile service time	default	5.31692	ms
error rate	default	0	%
Min Throughput	range	117.22	ops/s
Mean Throughput	range	117.22	ops/s
Median Throughput	range	117.22	ops/s
Max Throughput	range	117.22	ops/s
100th percentile latency	range	15.5039	ms
100th percentile service time	range	6.77485	ms
error rate	range	0	%

Bukhtawar commented 8 months ago

Just a quick note, please also benchmark/profile for CPU and JVM overhead reduction with the change during ser/de.

backslasht commented 8 months ago

@VachaShah - 100th percentile is generally skewed, 90th percentile is more reliable, can you please share the numbers for 90th and 99th percentile. Also, are these single runs or average of 'N' runs?

VachaShah commented 8 months ago

@VachaShah - 100th percentile is generally skewed, 90th percentile is more reliable, can you please share the numbers for 90th and 99th percentile. Also, are these single runs or average of 'N' runs?

OSB runs 100 iterations for search, so this is average for those 100 runs. OSB publishes the 100th percentile for the operations, I think the OSB code needs to be modified to get the other percentiles. @gkamat Is there a way to customize this from command line?

VachaShah commented 8 months ago

CPU Utilization

I analyzed the CPU used when running benchmarks and with async-profiler.

CPU used during search

CPU spike during original search API runs with OSB: 15.8%
CPU spike during protobuf search API runs with OSB: 12.7%

async-profiler CPU profile

executeFetchPhase for original search API - CPU 67.05%
executeFetchPhase for search API with protobuf - CPU 29.77%

Default Search

Protobuf Search

kiranprakash154 commented 7 months ago

Hi, are we on track for this to be released in 2.12 ?

getsaurabh02 commented 7 months ago

Given we are trying to build some cleaner abstractions around detecting the protocol and making it pluggable through some refactoring, this will need some more time and I believe the code will be in a good state by 2.13

VachaShah commented 3 months ago

Update

With the discussion on using protobuf for API request/response and node-to-node communication in the transport layer, we have first taken up making the transport layer abstract to support multiple protocols for serialization and deserialization. This will decouple the node-to-node communication in the transport layer from the current serialization mechanism (which is now referred to as native protocol in the codebase).

After these changes, we will take up adding protobuf into the codebase for search API in a way that the API request/response layer is not tightly coupled with the serialization mechanisms (which is the case currently for example how Writeable is implemented by model classes and request/response classes).

Transport layer abstractions and decoupling

Abstracting the inbound side of transport to support multiple serialization protocols - https://github.com/opensearch-project/OpenSearch/pull/12967, https://github.com/opensearch-project/OpenSearch/pull/13126
Abstracting the outbound side of transport to support multiple serialization protocols - https://github.com/opensearch-project/OpenSearch/pull/13293

Introduction of protobuf for search API (WIP - might be divided into more PRs)

Separating out native serialization from Search classes - https://github.com/opensearch-project/OpenSearch/pull/13697 (this came up from the discussion in #13178 since the current serialization is tightly tied to request/response classes not allowing protobuf to be added in an extensible manner)
Adding proto models for basic search related classes - https://github.com/opensearch-project/OpenSearch/pull/13178
Integrating protobuf structures into search along with node-to-node communication at the transport layer using protobuf - https://github.com/opensearch-project/OpenSearch/pull/11910

opensearch-project / OpenSearch