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Daylily-Informatics / bloom

Templated Abstract Polymorphic (and opinionated) LIMS
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Accessioning WF load test findings #14

Open adamtracy opened 10 months ago

adamtracy commented 10 months ago

Summary

Assess performance of Bloom Db as number of rows scales

Approach

I'm running repeated invocations of test_create_acceessioning_wf() and monitoring the size of the generic_instance table in a script. Evaluation to follow

Environment

Database

Application

adamtracy commented 10 months ago

Evaluation

I wrote a script to repeatedly call test_create_accessioning_wf() and followed the total number of rows accumulating in the generic_instance relation. The objective was to get to 1M rows, however the script began to get progressively slower over time. I ruled out some cumulative memory/resource leak in the app code as restarting the python shell did not ameliorate the slowness. At this point I reinitiated the test with a profiler to see what parts of the application code were taking longest.

Profile Output


   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
       10    0.005    0.000 1983.815  198.381 <ipython-input-3-03a06f60031b>:13(test_create_accessioning_wf)
       90    0.012    0.000 1958.471   21.761 /home/ubuntu/bloom/bloom_lims/bdb.py:1676(do_action)
    95613    0.392    0.000 1820.401    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:1372(execute)
    95613    0.419    0.000 1820.009    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/elements.py:507(_execute_on_connection)
    95613    2.116    0.000 1819.590    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:1589(_execute_clauseelement)
    95619    1.177    0.000 1790.707    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:1790(_execute_context)
   282398    0.609    0.000 1785.628    0.006 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/attributes.py:552(__get__)
242356/97416    0.725    0.000 1785.182    0.018 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/attributes.py:1063(get)
81047/80636    0.299    0.000 1783.116    0.022 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/attributes.py:1108(_fire_loader_callables)
    95619    1.540    0.000 1781.311    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:1852(_exec_single_context)
    95623 1769.883    0.019 1775.501    0.019 {method 'execute' of 'psycopg2.extensions.cursor' objects}
    95619    0.289    0.000 1774.573    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/default.py:921(do_execute)
       10    0.376    0.038 1768.347  176.835 /home/ubuntu/bloom/bloom_lims/bdb.py:2010(do_action_add_container_to_assay_q)
    72875    1.187    0.000 1765.852    0.024 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/strategies.py:867(_load_for_state)
    72875    3.777    0.000 1764.119    0.024 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/strategies.py:994(_emit_lazyload)
    91229    0.350    0.000 1727.504    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:2247(execute)
    91229    2.006    0.000 1727.154    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:2077(_execute_internal)
    91227    0.639    0.000 1714.511    0.019 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/context.py:283(orm_execute_statement)
    95777    0.332    0.000  130.381    0.001 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:4282(flush)
     4360    0.189    0.000  129.615    0.030 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:4331(_flush)
     4360    0.070    0.000  127.917    0.029 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py:441(execute)
     4370    0.026    0.000  123.396    0.028 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py:640(execute)
     4370    0.151    0.000  123.370    0.028 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py:40(save_obj)
      150    0.007    0.000  113.897    0.759 /home/ubuntu/bloom/bloom_lims/bdb.py:674(create_instances)
       20    0.021    0.001  103.910    5.195 /home/ubuntu/bloom/bloom_lims/bdb.py:1781(do_action_stamp_copy_plate)
      150    0.053    0.000  103.310    0.689 /home/ubuntu/bloom/bloom_lims/bdb.py:755(_process_instantiation_layouts)
     1000    0.044    0.000   89.805    0.090 /home/ubuntu/bloom/bloom_lims/bdb.py:823(_create_child_instance)
     4370    0.155    0.000   75.946    0.017 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py:957(_emit_insert_statements)
       40    0.001    0.000   71.235    1.781 /home/ubuntu/bloom/bloom_lims/bdb.py:670(create_instances_from_uuid)
    85849    0.230    0.000   53.738    0.001 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/result.py:1778(all)
    88801    1.160    0.000   53.709    0.001 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/result.py:549(_allrows)
    85849    0.195    0.000   50.895    0.001 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/result.py:1692(_fetchall_impl)
    85845    0.766    0.000   50.700    0.001 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/result.py:2289(_fetchall_impl)
   182454    0.701    0.000   49.090    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:203(chunks)
      960    0.053    0.000   48.838    0.051 /home/ubuntu/bloom/bloom_lims/bdb.py:792(create_generic_instance_lineage_by_euids)
     1150    0.082    0.000   48.701    0.042 /home/ubuntu/bloom/bloom_lims/bdb.py:607(create_instance)
     4370    0.077    0.000   46.588    0.011 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py:725(_emit_update_statements)
146449/111379    0.730    0.000   41.701    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py:95(_go)
8210/7920    0.025    0.000   38.126    0.005 <string>:1(commit)
8210/7920    0.192    0.000   38.066    0.005 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:1249(commit)
       10    0.002    0.000   37.981    3.798 /home/ubuntu/bloom/bloom_lims/bdb.py:1940(do_action_fill_plate_undirected)
     3850    0.013    0.000   37.766    0.010 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:1933(commit)
    12970    0.223    0.000   28.028    0.002 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/query.py:2671(all)
    95613    0.715    0.000   26.291    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/elements.py:669(_compile_w_cache)
     3470    0.036    0.000   25.382    0.007 /home/ubuntu/bloom/bloom_lims/bdb.py:931(get_by_euid)
    12970    0.220    0.000   24.814    0.002 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/query.py:2842(_iter)
   150470    0.699    0.000   24.530    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:1463(polymorphic_instance)
     3470    0.248    0.000   24.490    0.007 /home/ubuntu/bloom/bloom_lims/bdb.py:1020(query_all_tables_by_euid)
    91227    0.483    0.000   23.548    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/result.py:543(_raw_all_rows)
    94183    0.227    0.000   23.244    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/cursor.py:2101(_fetchall_impl)
      160    0.002    0.000   23.061    0.144 /home/ubuntu/bloom/bloom_lims/bdb.py:818(create_instance_by_code)
    94183    0.411    0.000   23.017    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/cursor.py:1129(fetchall)
    94203    0.714    0.000   22.979    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/util/langhelpers.py:1272(oneshot)
    94203    0.318    0.000   22.265    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/cache_key.py:396(_generate_cache_key)
    94203    0.735    0.000   21.947    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/cache_key.py:332(_generate_cache_key)
    94183    2.161    0.000   21.582    0.000 {method 'fetchall' of 'psycopg2.extensions.cursor' objects}
   169252    6.741    0.000   21.043    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:807(_instance_processor)
     3670    0.012    0.000   20.736    0.006 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:2602(commit)
     3670    0.031    0.000   20.725    0.006 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:2719(_do_commit)
     3670    0.015    0.000   20.687    0.006 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:2694(_connection_commit_impl)
     3670    0.027    0.000   20.672    0.006 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/base.py:1123(_commit_impl)
     3670    0.028    0.000   20.641    0.006 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/default.py:694(do_commit)
     3670   20.598    0.006   20.598    0.006 {method 'commit' of 'psycopg2.extensions.connection' objects}
783163/94203   10.226    0.000   20.500    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/cache_key.py:208(_gen_cache_key)
    91227    0.987    0.000   19.784    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/context.py:555(orm_setup_cursor_result)
     5222    0.074    0.000   18.717    0.004 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/state.py:779(_load_expired)
     5222    0.126    0.000   18.535    0.004 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:1576(load_scalar_attributes)
    91227    2.583    0.000   17.446    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:78(instances)
     5382    0.187    0.000   16.809    0.003 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:522(load_on_pk_identity)
     5222    0.117    0.000   16.359    0.003 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:483(load_on_ident)
    72875    0.691    0.000   15.376    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/strategies.py:830(_generate_lazy_clause)
   144940    1.396    0.000   14.685    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/mapper.py:3569(_get_state_attr_by_column)
       10    0.001    0.000   13.937    1.394 /home/ubuntu/bloom/bloom_lims/bdb.py:1828(do_action_cfdna_quant)
   165930    0.796    0.000   13.818    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/annotation.py:376(__eq__)
374068/166044    0.941    0.000   13.508    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/operators.py:583(__eq__)
   155692    1.771    0.000   13.448    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:1046(_instance)
       10    0.000    0.000   13.184    1.318 /home/ubuntu/bloom/bloom_lims/bdb.py:1561(do_action)
352964/310984    0.640    0.000   12.692    0.000 {built-in method _operator.eq}
       10    0.001    0.000   12.667    1.267 /home/ubuntu/bloom/bloom_lims/bdb.py:1613(do_action_create_package_and_first_workflow_step)
   166108    0.488    0.000   12.583    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/elements.py:1610(operate)
    91227    0.686    0.000   12.145    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/context.py:2680(row_processor)
   166108    0.907    0.000   11.327    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/type_api.py:186(operate)
   191189    0.492    0.000   11.286    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/util/_collections.py:345(__missing__)
       20    0.002    0.000   10.955    0.548 /home/ubuntu/bloom/bloom_lims/bdb.py:2086(do_action_create_child_container_and_link_child_workflow_step)
       10    0.012    0.001   10.620    1.062 /home/ubuntu/bloom/bloom_lims/bdb.py:1724(_add_random_values_to_plate)
   160128    0.448    0.000   10.614    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/psycopg2/_json.py:159(typecast_json)
    78455    0.564    0.000   10.433    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/loading.py:1436(configure_subclass_mapper)
   166098    1.348    0.000   10.418    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/sql/default_comparator.py:51(_boolean_compare)
   155694    0.828    0.000   10.166    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/json/__init__.py:299(loads)
      100    0.020    0.000    9.658    0.097 /home/ubuntu/bloom/bloom_lims/bdb.py:1319(_do_action_base)
     3850    2.080    0.001    9.169    0.002 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:1082(_remove_snapshot)
   155694    3.497    0.000    9.003    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/json/decoder.py:332(decode)
   382390    1.089    0.000    8.808    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/psycopg2/extras.py:669(<lambda>)
      3/2    0.004    0.001    8.488    4.244 /home/ubuntu/bloom/bloom_lims/bdb.py:461(__init__)
    95613    2.093    0.000    8.028    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/engine/default.py:1274(_init_compiled)
   382390    5.444    0.000    7.719    0.000 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/uuid.py:139(__init__)
       10    0.002    0.000    7.594    0.759 /home/ubuntu/bloom/bloom_lims/bdb.py:1858(do_action_link_tubes_auto)
       60    0.001    0.000    7.353    0.123 /home/ubuntu/bloom/bloom_lims/bdb.py:1121(create_instance_by_template_components)
8210/7920    0.020    0.000    7.136    0.001 <string>:1(_prepare_impl)
8210/7920    0.039    0.000    7.089    0.001 /home/ubuntu/anaconda3/envs/BLOOM/lib/python3.12/site-packages/sqlalchemy/orm/session.py:1214(_prepare_impl)
adamtracy commented 10 months ago

The profiling output clearly brackets do_action_add_container_to_assay_q() where most of the time is spent waiting on postgres.

In the "real world", I would imagine the assay queue would have batches moving forward in the progression as opposed to this test where we're just accumulating more and more items into the queue. Why does it matter, though?