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| author | Munyoki Kilyungi | 2023-02-03 12:58:13 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2023-02-03 13:08:35 +0300 |
| commit | c7d242233403594d7a5422344a49a16c2c738222 (patch) | |
| tree | 216ce9923cc103e05790cf6d3ae4d304fb3a6018 /scripts/performance/README.org | |
| parent | ceaefbd3022044f13ba2d763598460b83bfa19ee (diff) | |
| download | genenetwork2-c7d242233403594d7a5422344a49a16c2c738222.tar.gz | |
Add perf scripts that compare fetching a trait using GN API vs LMDB
* scripts/performance/(README,org, timeit_gn2.py, timeit_lmdb.py): New
files.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'scripts/performance/README.org')
| -rw-r--r-- | scripts/performance/README.org | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/scripts/performance/README.org b/scripts/performance/README.org new file mode 100644 index 00000000..f7fb392f --- /dev/null +++ b/scripts/performance/README.org @@ -0,0 +1,41 @@ +* Introduction + +This directory contains scripts that are used to instrument the performance of fetching a trait using the GN2 API vs using LMDB. Assuming you have a script called ,runcmd: + +#+name: ,runcmd +#+begin_src sh +#!/bin/sh + +env GN2_PROFILE=$HOME/opt/genenetwork2 \ + TMPDIR=$HOME/tmp SERVER_PORT=5004 \ + WEBSERVER_MODE=DEV \ + GENENETWORK_FILES=$HOME/data/genotype_files/ \ + SPARQL_ENDPOINT=http://localhost:8892/sparql\ + SQL_URI="mysql://root:root@localhost:3306/db_webqtl_s"\ + GN_PROXY_URL=http://localhost:8080 \ + GN_SERVER_URL=http://localhost:8083/api \ + GN3_LOCAL_URL=http://localhost:8083 \ + GN_LOCAL_URL=http://localhost:8083 \ + $HOME/projects/oqo-genenetwork2/bin/genenetwork2 \ + $HOME/projects/oqo-genenetwork2/etc/default_settings.py\ + -cli $* +#+end_src + +To run the script 10 times, execute: + +: ,runcmd testing python $HOME/projects/oqo-genenetwork2/testing/scripts/performance/timeit_gn2.py 10 + +: ,runcmd testing python $HOME/projects/oqo-genenetwork2/testing/scripts/performance/timeit_lmdb.py 10 + +Here are some rudimentary results: + +Assuming you have already dumped "HLCPublish/10001" - which contains 476 strains - somewhere in LMDB, the time it takes to fetch "HLCPublish/10001" N times is: + +| Number | gn2 (seconds) | lmdb (seconds) | gn2/lmdb | +|--------+--------------------+---------------------+-----------| +| 10 | 0.5971280680023483 | 0.04270002100020065 | 13.984257 | +| 50 | 3.6268229950001114 | 0.15371317300014198 | 23.594744 | +| 100 | 5.885073402001581 | 0.3161755159999302 | 18.613312 | +| 1_000 | 60.6393681030022 | 3.107457533998968 | 19.514142 | +| 10_000 | 723.0237347940019 | 27.541215700002795 | 26.252426 | +#+TBLFM: $4=$2/$3 |