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* 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
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