Task #902
Updated by Aaron Marcuse-Kubitza over 10 years ago
h3. issue * in some queries, the columns being joined on are completely the wrong set (columns that are not even used in any unique index) * this creates unusual (and perhaps unstable) query plans (#884), which in turn trigger a disk space leak in Postgres/Ubuntu (#887) and make the query hang indefinitely * the problem occurs 8 min into the import ("03:00:28" - "02:52:30"; see snapshot below > Mac > @ARIZ.omoccurrences@) * was not an issue in the last successful import * this is definitely the cause of the incorrect query plans (#884), but is _not_ the cause of the disk space leak (#887), as that is a Postgres bug _triggered by_ the unusual query plans (no query plan should ever cause a disk space leak or make the query hang indefinitely). * if this is caused by a Postgres bug, it may be the same bug that caused the disk space leak (#887) * it is more likely caused by a Postgres bug than our import code, because the changes we made since the last successful import (2014-2-2) do not look like they would cause radical changes in the joins * it is almost certainly not an Ubuntu bug[1], because it also occurs on Mac OS X fn1. other than perhaps the shared BSD code between Linux and Mac, but this is unlikely unless they cross-pollinate system updates . h3. test case p(. see the following @pg_stat_activity@ snapshots (note the @JOIN@ columns in the @EXPLAIN@ output below each query): <pre><code class="SQL"> config: Mac OS X 10.8 (on starscream) with the installer version of Postgres 9.3.1 (not the standalone .app) import command: $0 # nested shell to contain the env changes unset TMOUT # TMOUT causes shell to exit even with background processes set -o ignoreeof # prevent Ctrl+D from exiting shell to keep attached jobs unset n # clear any limit set in .profile (unless desired) unset log # allow logging output to go to log files export version=test_import declare -ax inputs; inputs=(inputs/ARIZ/) inputs=(inputs/{ARIZ,SALVIAS}/) # or NY #declare -ax inputs; inputs=(inputs/{ARIZ,SALVIAS}/) # NY; SALVIAS was because it's part of the original test case . bin/import_all kill % # cancel after_import() backend_start 2014-05-09 02:52:29.987578-07 query_start 2014-05-09 03:00:28.378299-07 /*ARIZ.omoccurrences*/ CREATE TEMP TABLE "location_pkeys" AS SELECT "in#6"."occurrenceID" , "location"."location_id" AS "out.location_id" FROM "in#6" JOIN "location" ON COALESCE("location"."elevation_m", CAST('NaN' AS double precision)) = COALESCE("in#6"."_alt(1=verbatimElevation, 2=_avg(1=minimumElevat.result::double", CAST('NaN' AS double precision)) /* EXPLAIN: Merge Join (cost=86617.89..9234073.27 rows=609750474 width=8) Merge Cond: ((COALESCE("in#6"."_alt(1=verbatimElevation, 2=_avg(1=minimumElevat.result::double", 'NaN'::double precision)) = (COALESCE(location.elevation_m, 'NaN'::double precision))) -> Sort (cost=28258.34..28857.47 rows=239654 width=12) Sort Key: (COALESCE("in#6"."_alt(1=verbatimElevation, 2=_avg(1=minimumElevat.result::double", 'NaN'::double precision)) -> Seq Scan on "in#6" (cost=0.00..6844.54 rows=239654 width=12) -> Sort (cost=58359.55..59631.70 rows=508859 width=12) Sort Key: (COALESCE(location.elevation_m, 'NaN'::double precision)) -> */ </code></pre><pre><code class="SQL"> config: Ubuntu 14.04 (on vegbiendev) with official Ubuntu version of Postgres 9.3 import command: declare -ax inputs=(inputs/{ARIZ,SALVIAS}/) # SALVIAS because it's part of the test case export version=test_import . bin/import_all /*ARIZ.omoccurrences*/ CREATE TEMP TABLE "location_pkeys" AS SELECT "in#6"."occurrenceID" , "location"."location_id" AS "out.location_id" FROM "in#6" JOIN "location" ON COALESCE("location"."elevation_m", CAST('NaN' AS double precision)) = COALESCE("in#6"."_alt(1=verbatimElevation, 2=_avg(1=minimumElevat.result::double", CAST('NaN' AS double precision)) /* EXPLAIN: Merge Join (cost=52039.20..3508151.98 rows=230343442 width=8) Merge Cond: ((COALESCE(location.elevation_m, 'NaN'::double precision)) = (COALESCE("in#6"."_alt(1=verbatimElevation, 2=_avg(1=minimumElevat.result::double", 'NaN'::double precision))) -> Sort (cost=23780.86..24261.44 rows=192230 width=12) Sort Key: (COALESCE(location.elevation_m, 'NaN'::double precision)) -> Seq Scan on location (cost=0.00..6910.30 rows=192230 width=12) -> Sort (cost=28258.34..28857.47 rows=239654 width=12) Sort Key: (COALESCE("in#6"."_alt(1=verbatimElevation, 2=_avg(1=minimumElevat.result::double", 'NaN'::double precision)) - */ </code></pre><pre><code class="SQL"> config: Ubuntu 12.04 (on vegbiendev) with compatibility version of Postgres 9.3 import command: . bin/import_all # all datasources /*NVS.StemObservation*/ CREATE TEMP TABLE "stemobservation_pkeys" AS SELECT "in#11"."row_num" , "stemobservation"."stemobservation_id" AS "out.stemobservation_id" FROM "in#11" JOIN "stemobservation" ON COALESCE("stemobservation"."height_m", CAST('NaN' AS double precision)) = COALESCE("in#11"."NVS.StemObservation.Height::double", CAST('NaN' AS double precision)) /* EXPLAIN: Merge Join (cost=1045217.21..95909185.15 rows=6323041431 width=8) Merge Cond: ((COALESCE(stemobservation.height_m, 'NaN'::double precision)) = (COALESCE("in#11"."NVS.StemObservation.Height::double", 'NaN'::double precision))) -> Sort (cost=30039.56..30492.76 rows=181279 width=12) Sort Key: (COALESCE(stemobservation.height_m, 'NaN'::double precision)) -> Seq Scan on stemobservation (cost=0.00..14206.79 rows=181279 width=12) -> Materialize (cost=1015177.64..1050057.81 rows=6976033 width=12) -> Sort (cost=1015177.64..1032617.73 rows=6976033 width=12) Sort Key: (COALESCE("in#11"."NVS.StemObs /*CVS.taxon_observation.***/ CREATE TEMP TABLE "location_pkeys" AS SELECT "in#5"."row_num" , "location"."location_id" AS "out.location_id" FROM "in#5" JOIN "location" ON ("location"."accesslevel" = "in#5"."CVS.taxon_observation.**.accessRights::accesslevel" OR ("location"."accesslevel" IS NULL AND "in#5"."CVS.taxon_observation.**.accessRights::accesslevel" IS NULL)) /* EXPLAIN: Nested Loop (cost=0.00..83049883712.45 rows=27683225000 width=8) Join Filter: ((location.accesslevel = "in#5"."CVS.taxon_observation.**.accessRights::accesslevel") OR ((location.accesslevel IS NULL) AND ("in#5"."CVS.taxon_observation.**.accessRights::accesslevel" IS NULL))) -> Seq Scan on location (cost=0.00..175778.45 rows=5536645 width=8) -> Materialize (cost=0.00..35434.00 rows=1000000 width=8) -> Seq Scan on "in#5" (cost=0.00..30434.00 rows=1000000 width=8) */ </code></pre> h3. fix # -check if r13361 fixed this (see explanation in r13392)- _no, problem still occurs_ # see proposed steps in #905