bug fixed in r14074

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 bug¹, because it also occurs on Mac OS X

¹ other than perhaps the shared BSD code between Linux and Mac, but this is unlikely unless they cross-pollinate system updates
.

test case¶

see the following pg_stat_activity snapshots (note the JOIN columns in the EXPLAIN output below each query):

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
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/) # or NY
#declare -ax inputs; inputs=(inputs/{ARIZ,SALVIAS}/) # SALVIAS was part of the original test case
. bin/import_all
# once problem occurs, clean up:
kill % # cancel after_import()
. bin/stop_imports
sudo pkill -f postgres
sudo pkill -f postgres # sometimes the first pkill doesn't kill everything

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))
        -> 
*/

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))
        -
*/

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)
*/

fix¶

1. check if r13361 fixed this (see explanation in r13392) no, problem still occurs
2. see proposed steps in #905