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 within 5 min into the import ("00:34:57" - "00:29:50"; see @ARIZ.omoccurrences@ in snapshot below)
* see the following @pg_stat_activity@ snapshots (note the @JOIN@ columns in the @EXPLAIN@ output below each query):
<pre><code class="SQL">
config: Ubuntu 12.04 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><pre><code class="SQL">
config: Ubuntu 14.04 with official Ubuntu version of Postgres
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: Mac OS X 10.8 with the installer version of Postgres 9.3.1 (not the standalone .app)
import command:
$0 # nested shell, don't use screen yet
unset TMOUT # TMOUT causes screen to exit even with background processes
set -o ignoreeof #prevent Ctrl+D from exiting `screen` to keep attached jobs
unset n
unset log
export version=test_import
declare -ax inputs; inputs=(inputs/{ARIZ,SALVIAS}/) # or NY; this problem does not occur in SALVIAS because it's part of the test case
. bin/import_all
kill % # cancel after_import()
/*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>
* 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/Ubuntu bug, it may be the same bug that caused the disk space leak (#887)
* it is more likely caused by a Postgres/Ubuntu 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
h3. fix
# -check if r13361 fixed this (see explanation in r13392)- _no, problem still occurs_
# see proposed steps in #905