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authorBryan Newbold <bnewbold@robocracy.org>2018-08-20 14:49:06 -0700
committerBryan Newbold <bnewbold@robocracy.org>2018-08-24 13:31:40 -0700
commit74ee26468cb0e48121d9f65e255401d34d6118c0 (patch)
tree89c65335d9176f456a7226574518c60b2b9c1877 /notes
parentf997c5bcbcc800a8780a62dc56a4b7f4e5b68c3c (diff)
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notes on recent bulk import
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+
+Schema changes since previous imports:
+- more fields (identifiers+indexes)
+- timestamps
+- UUIDs more places
+- fixed some crossref import bugs?
+- abstracts
+- file_urls as table (not single value)
+- timestamps
+- TEXT -> CHAR in a few places
+- removed many work fields
+
+## Containers
+
+(python)webcrawl@wbgrp-svc500:/srv/fatcat/src/python$ time ./fatcat_import.py import-issn /srv/datasets/journal_extra_metadata.csv
+
+real 1m25.292s
+user 0m12.640s
+sys 0m0.412s
+
+## Creators
+
+time parallel --bar --pipepart -j8 -a /srv/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid -
+
+(times very invalid due to hangs; got 3537837 creators, which is most of the way, so *shrug*)
+real 22m2.465s
+user 26m41.924s
+sys 1m33.844s
+
+## Releases
+
+xzcat /srv/datasets/crossref-works.2018-01-21.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py import-crossref - /srv/datasets/20180216.ISSN-to-ISSN-L.txt
+
+ 128516.30 user
+ 3905.14 system
+ 44:17:05 elapsed
+ 83% CPU
+
+Almost 44 hours... I think I remember more like 36 hours last time? Things
+slowed down a lot towards the end, many more ORCID cross-references?
+
+looking in htop, postgres seems to be primary bottleneck. At something like 12
+hours in, had 44 million release_ident rows, which is 1000/second.
+
+Note: seems like the more frequently `count(*)` is run, the more performant.
+Because in-memory?
+
+ 2018-08-16 16:54:16.977 UTC [17996] postgres@fatcat_prod LOG: duration: 42949.549 ms statement: select count(id) from release_ident;
+
+ fatcat_prod=# select count(*) from release_ident;
+ count
+ ----------
+ 44185608
+ (1 row)
+
+ Time: 2753.916 ms (00:02.754)
+ fatcat_prod=# select count(*) from release_ident;
+ count
+ ----------
+ 44187937
+ (1 row)
+
+ Time: 2711.670 ms (00:02.712)
+
+As expected, autovacuum very busy. Only ~150 TPS; but that includes batch
+writes? 75061172 rows.
+
+## Files
+
+ time ./fatcat_import.py import-manifest /srv/datasets/idents_files_urls.sqlite
+
+ Done! Inserted 6607075
+
+ real 2152m28.822s => 36 hours (!)
+ user 401m46.464s
+ sys 21m45.724s
+
+
+Going pretty slow, < 100 transactions/sec. Lots of SELECTs, which seem slow, on the abstract table?
+
+ SELECT "release_rev_abstract"."id", "release_rev_abstract"."release_rev", "release_rev_abstract"."abstract_sha1", "release_rev_abstract"."mimetype", "release_rev_abstract"."lang", "abstracts"."sha1", "abstracts"."content" FROM ("release_rev_abstract" INNER JOIN "abstracts" ON "release_rev_abstract"."abstract_sha1" = "abstracts"."sha1") WHERE "release_rev_abstract"."release_rev" = 'ffffffc0-4dd2-47ce-a51d-44051f3699ce';
+
+Created index:
+
+ CREATE INDEX release_rev_abstract_rev_idx ON release_rev_abstract(release_rev);
+
+... and things sped way up. Re-ran some crossref imports to EXPLAIN and didn't
+see non-indexed queries. Maybe an ANALYZE does need to happen?
+
+This being single-threaded is going to be a problem in the future. ~50 million
+files would be ~2 weeks.
+
+## Post-Import Status
+
+ Size: 358.89G (postgres self-reported)
+ Mem.: 57.10% - 16.85G/49.14G
+
+Was 184G last time in late June; doubled in size (!).
+
+ bnewbold@wbgrp-svc500$ df -h /
+ Filesystem Size Used Avail Use% Mounted on
+ /dev/vda1 858G 529G 286G 65% /
+
+ bnewbold@wbgrp-svc500$ sudo du -sh /var/lib/postgresql/ /srv/datasets/ /srv/elastic-blah/
+ 361G /var/lib/postgresql/
+ 83G /srv/datasets/
+ 77G /srv/elastic-blah/
+
+ fatcat_prod=# select count(*) from changelog; => 2,085,067
+
+ SELECT
+ table_name,
+ pg_size_pretty(table_size) AS table_size,
+ pg_size_pretty(indexes_size) AS indexes_size,
+ pg_size_pretty(total_size) AS total_size
+ FROM (
+ SELECT
+ table_name,
+ pg_table_size(table_name) AS table_size,
+ pg_indexes_size(table_name) AS indexes_size,
+ pg_total_relation_size(table_name) AS total_size
+ FROM (
+ SELECT ('"' || table_schema || '"."' || table_name || '"') AS table_name
+ FROM information_schema.tables
+ ) AS all_tables
+ ORDER BY total_size DESC
+ ) AS pretty_sizes;
+
+ table_name | table_size | indexes_size | total_size
+--------------------------------------------------------------+------------+--------------+------------
+ "public"."release_ref" | 159 GB | 47 GB | 206 GB
+ "public"."release_rev" | 40 GB | 10 GB | 51 GB
+ "public"."release_contrib" | 19 GB | 20 GB | 39 GB
+ "public"."release_ident" | 5797 MB | 6597 MB | 12 GB
+ "public"."work_ident" | 5787 MB | 6394 MB | 12 GB
+ "public"."release_edit" | 6674 MB | 4646 MB | 11 GB
+ "public"."work_edit" | 6674 MB | 4646 MB | 11 GB
+ "public"."work_rev" | 3175 MB | 2939 MB | 6114 MB
+ "public"."file_rev_url" | 1995 MB | 275 MB | 2270 MB
+ "public"."abstracts" | 1665 MB | 135 MB | 1800 MB
+ "public"."file_rev" | 829 MB | 954 MB | 1783 MB
+ "public"."file_ident" | 498 MB | 532 MB | 1030 MB
+ "public"."file_release" | 369 MB | 642 MB | 1011 MB
+ "public"."file_edit" | 591 MB | 410 MB | 1002 MB
+ "public"."creator_rev" | 337 MB | 318 MB | 655 MB
+ "public"."creator_ident" | 280 MB | 297 MB | 577 MB
+ "public"."creator_edit" | 316 MB | 220 MB | 536 MB
+ "public"."release_rev_abstract" | 183 MB | 84 MB | 267 MB
+ "public"."changelog" | 123 MB | 125 MB | 249 MB
+ "public"."editgroup" | 139 MB | 81 MB | 220 MB
+ "public"."container_rev" | 19 MB | 6912 kB | 26 MB
+ "public"."container_ident" | 6896 kB | 7016 kB | 14 MB
+ "public"."container_edit" | 8056 kB | 5240 kB | 13 MB
+
+In context, the full uncompressed crossref 2018-01-21 dump is about 285 GB.
+
+For many of these indexes, and the _ident tables, switching from UUID to
+BIGSERIAL would half the size.
+
+## Exports
+
+ time ./fatcat_export.py changelog - | pv -l | wc
+
+ As of:
+
+ 159k 1:17:35 [34.3 /s]
+ 159,740 lines
+ 2,427,277,881 chars (bytes; 2.4GB)
+
+ real 77m35.183s
+ user 15m36.208s
+ sys 0m31.484s
+
+Running at about 100/sec; estimate 6 hours for completion. Could shard using
+start/end flags, but am not here.
+
+Running `quick_dump.sql` (identifier tables, in a transaction):
+
+ 251M Aug 19 23:08 fatcat_ident_creators.tsv
+ 5.9M Aug 19 23:08 fatcat_ident_containers.tsv
+ 467M Aug 19 23:08 fatcat_ident_files.tsv
+ 5.2G Aug 19 23:10 fatcat_ident_releases.tsv
+ 5.2G Aug 19 23:11 fatcat_ident_works.tsv
+ 12K Aug 19 23:11 .
+ 1.8G Aug 19 23:12 fatcat_abstracts.json
+
+Work and Release tables in under 2 minutes each; say 5 minutes total.
+
+ time ./fatcat_export.py releases /tmp/fatcat_ident_releases.tsv - | pv -l | wc
+
+ 172k 1:07:08 [42.7 /s]
+ 172181 lines
+ 1,118,166,293 chars (bytes; 1.1 GB)
+
+ real 67m8.340s
+ user 10m21.988s
+ sys 0m34.612s
+
+Running at only 10/sec or so, this would take forever even if sharded. :(
+
+Both exports/dumps are running in parallel. "Expand" queries might help with speed?
+
+## Postgres Analysis
+
+SELECT *
+FROM
+ pg_stat_statements
+ORDER BY
+ total_time DESC LIMIT 5;
+
+Summary:
+
+ SELECT "creator_ident" by ORCID
+ 1,295,864 calls
+ 930,305,208 total time
+ 717.9 mean time <= this should be less than a ms!
+
+ INSERT INTO release_rev
+ 75144055 calls
+ 111470961 total time
+ 1.483 mean time
+
+ INSERT INTO work_rev
+ 75,144,055 calls
+ 82693994 total time
+ 1.1 mean time
+
+ INSERT INTO release_contrib (creator_ident_id = DEFAULT) RETURNING *
+ 26,008,280 calls <= why so few? different query depending on number
+ of rows inserted
+ 18955782 total time
+ 0.728 mean time
+
+ SELECT container_ident
+ 78,4143 calls
+ 17683156 total time
+ 22.55 mean time <= why so slow?
+
+ INSERT INTO release_contrib
+ 15,072,820 calls
+
+ INSERT INTO "release_contrib
+
+
+ relname | too_much_seq | case | rel_size | seq_scan | idx_scan
+----------------------+--------------+----------------+--------------+----------+-----------
+ file_rev_url | 2391 | Missing Index? | 2091147264 | 2391 | 0
+ file_release | -30670 | OK | 386899968 | 2 | 30672
+ container_rev | -979948 | OK | 20242432 | 784146 | 1764094
+ file_edit | -2206807 | OK | 619896832 | 6 | 2206813
+ creator_edit | -2206810 | OK | 331079680 | 11 | 2206821
+ work_edit | -2206811 | OK | 6996566016 | 14 | 2206825
+ release_edit | -2206811 | OK | 6996582400 | 14 | 2206825
+ container_edit | -2206816 | OK | 8216576 | 5 | 2206821
+ changelog | -2209659 | OK | 129286144 | 10 | 2209669
+ abstracts | -3486466 | OK | 1706237952 | 8 | 3486474
+ release_rev_abstract | -4975493 | OK | 191602688 | 42919 | 5018412
+ release_ref | -5032717 | OK | 170494861312 | 3 | 5032720
+ release_contrib | -5032744 | OK | 20370251776 | 3 | 5032747
+ creator_rev | -8400410 | OK | 353583104 | 1296507 | 9696917
+ file_ident | -13483224 | OK | 522190848 | 7 | 13483231
+ creator_ident | -16686744 | OK | 293625856 | 3 | 16686747
+ file_rev | -32405557 | OK | 868515840 | 4 | 32405561
+ container_ident | -69162337 | OK | 7028736 | 3 | 69162340
+ work_rev | -150288161 | OK | 3328589824 | 1 | 150288162
+ editgroup | -162783807 | OK | 146112512 | 9 | 162783816
+ release_ident | -165676917 | OK | 6076841984 | 52 | 165676969
+ work_ident | -229439828 | OK | 6066814976 | 3 | 229439831
+ release_rev | -930140217 | OK | 43360542720 | 9 | 930140226
+
+TODO changes:
+- don't return all as often; in particular, inserting release_contrib, release_ref
+x missing an index somewhere on file_rev_url, release_rev_abstract
+x why so many seq_scan on container_rev, creator_rev
+ => running/EXPLAIN same query on psql hits index, not seq_scan
+ => seemed to be an issue with VALUE params getting sent separately; query
+ planner only looked at query and wasn't using index on ORCID/ISSN-L because
+ it didn't know those values were not-NULL?
+ => adding NOT NULL to query seems to have sped up case of there being a
+ "hit", but no hit still slow. might need to change indices or something for
+ the (perhaps common in future) case of DOI lookups with invalid DOIs (eg,
+ CORE import)
+
+random DEBUG queries:
+
+ EXPLAIN ANALYSE SELECT "creator_ident"."id", "creator_ident"."is_live", "creator_ident"."rev_id", "creator_ident"."redirect_id", "creator_rev"."id", "creator_rev"."extra_json", "creator_rev"."display_name", "creator_rev"."given_name", "creator_rev"."surname", "creator_rev"."orcid", "creator_rev"."wikidata_qid" FROM ("creator_ident" INNER JOIN "creator_rev" ON "creator_ident"."rev_id" = "creator_rev"."id") WHERE "creator_rev"."orcid" = '0000-0002-8867-1663' AND "creator_ident"."is_live" = true AND "creator_ident"."redirect_id" IS NULL LIMIT 1;
+
+ EXPLAIN VERBOSE SELECT "creator_ident"."id", "creator_ident"."is_live", "creator_ident"."rev_id", "creator_ident"."redirect_id", "creator_rev"."id", "creator_rev"."extra_json", "creator_rev"."display_name", "creator_rev"."given_name", "creator_rev"."surname", "creator_rev"."orcid", "creator_rev"."wikidata_qid" FROM ("creator_ident" INNER JOIN "creator_rev" ON "creator_ident"."rev_id" = "creator_rev"."id") WHERE "creator_rev"."orcid" = $1 AND "creator_ident"."is_live" = true AND "creator_ident"."redirect_id" IS NULL VALUES ('0000-0002-8867-1669') LIMIT 1;
+
+ EXPLAIN SELECT "container_ident"."id", "container_ident"."is_live", "container_ident"."rev_id", "container_ident"."redirect_id", "container_rev"."id", "container_rev"."extra_json", "container_rev"."name", "container_rev"."publisher", "container_rev"."issnl", "container_rev"."wikidata_qid", "container_rev"."abbrev", "container_rev"."coden" FROM ("container_ident" INNER JOIN "container_rev" ON "container_ident"."rev_id" = "container_rev"."id") WHERE "container_rev"."issnl" = '0001-0782' AND "container_ident"."is_live" = true AND "container_ident"."redirect_id" IS NULL LIMIT 1;
+
+ SELECT "creator_ident"."id", "creator_ident"."is_live", "creator_ident"."rev_id", "creator_ident"."redirect_id", "creator_rev"."id", "creator_rev"."extra_json", "creator_rev"."display_name", "creator_rev"."given_name", "creator_rev"."surname", "creator_rev"."orcid", "creator_rev"."wikidata_qid" FROM ("creator_ident" INNER JOIN "creator_rev" ON "creator_ident"."rev_id" = "creator_rev"."id") WHERE "creator_rev"."orcid" = '0000-0002-8867-1663' AND "creator_ident"."is_live" = 't' AND "creator_ident"."redirect_id" IS NULL LIMIT 1;