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Diffstat (limited to 'notes/bootstrap/import_timing_20180910.txt')
| -rw-r--r-- | notes/bootstrap/import_timing_20180910.txt | 319 |
1 files changed, 319 insertions, 0 deletions
diff --git a/notes/bootstrap/import_timing_20180910.txt b/notes/bootstrap/import_timing_20180910.txt new file mode 100644 index 00000000..43c76e43 --- /dev/null +++ b/notes/bootstrap/import_timing_20180910.txt @@ -0,0 +1,319 @@ + +Changes since last time: +- removed "WHERE IS NOT NULL" from lookup indexes +- some cleanups +- JSONB + +## QA Timing + +master branch b15fa552e288bec5bbc2b07a3e11bab9235a1e7c + + time ./fatcat_import.py import-issn /srv/datasets/journal_extra_metadata.csv # --batch-size 100 + real 0m30.249s + user 0m9.364s + sys 0m0.268s + + time parallel --bar --pipepart -j8 -a /srv/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid - # --batch-size 100 + => something went sort of wrong? seemed to hang, with no activity. + => may have sent a signal or something accidentally? + + 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 --batch-size 100 + => ran for a few seconds before restarting with increased batch size + => increased batch size seems to be too much for releases? stick with 50 + => still lots of long autovacuum (ANALYZE) + + 67017.73user 2054.96system 25:59:38elapsed 73%CPU (0avgtext+0avgdata 424692maxresident)k + 2085872inputs+219678920outputs (100457major+30837042minor)pagefaults 0swaps + # 25:59:38 elapsed + + time ./fatcat_import.py import-manifest /srv/datasets/idents_files_urls.sqlite # --batch-size 100 + => taking longer to start than I remembered... + + Done! Inserted 6607075 + real 1521m37.856s + user 305m38.444s + sys 18m13.916s + => 25.5 hours + +Disk/table usage: + + Size: 233.95G + + table_name | table_size | indexes_size | total_size + --------------------------------------------------------------+------------+--------------+------------ + "public"."release_ref" | 92 GB | 26 GB | 118 GB + "public"."release_rev" | 30 GB | 14 GB | 45 GB + "public"."release_contrib" | 12 GB | 13 GB | 26 GB + "public"."release_edit" | 4710 MB | 3353 MB | 8062 MB + "public"."work_edit" | 4710 MB | 3352 MB | 8062 MB + "public"."work_ident" | 3454 MB | 4153 MB | 7608 MB + "public"."release_ident" | 3454 MB | 4152 MB | 7606 MB + "public"."work_rev" | 2241 MB | 2076 MB | 4317 MB + "public"."file_rev_url" | 1994 MB | 778 MB | 2772 MB + "public"."file_rev" | 827 MB | 1215 MB | 2042 MB + "public"."file_ident" | 501 MB | 533 MB | 1034 MB + "public"."file_edit" | 590 MB | 411 MB | 1001 MB + "public"."creator_rev" | 371 MB | 455 MB | 826 MB + "public"."abstracts" | 649 MB | 52 MB | 701 MB + "public"."file_release" | 251 MB | 435 MB | 686 MB + "public"."creator_edit" | 347 MB | 242 MB | 590 MB + "public"."creator_ident" | 255 MB | 305 MB | 560 MB + "public"."release_rev_abstract" | 70 MB | 90 MB | 160 MB + "public"."changelog" | 52 MB | 53 MB | 106 MB + "public"."editgroup" | 60 MB | 35 MB | 94 MB + "public"."container_rev" | 40 MB | 27 MB | 67 MB + "public"."container_edit" | 24 MB | 16 MB | 39 MB + "public"."container_ident" | 17 MB | 20 MB | 37 MB + +I think this is before the JSONB schema change, so won't reflect actual/final. + +Perf: + + relname | too_much_seq | case | rel_size | seq_scan | idx_scan + ----------------------+--------------+------+-------------+----------+----------- + file_rev_url | -18 | OK | 2089836544 | 2 | 20 + file_release | -4001 | OK | 263249920 | 2 | 4003 + container_edit | -132140 | OK | 24608768 | 2 | 132142 + release_edit | -132140 | OK | 4937408512 | 2 | 132142 + work_edit | -132140 | OK | 4937351168 | 2 | 132142 + file_edit | -132140 | OK | 618545152 | 2 | 132142 + creator_edit | -132140 | OK | 363954176 | 2 | 132142 + changelog | -134456 | OK | 54919168 | 5 | 134461 + container_rev | -1276670 | OK | 41680896 | 592993 | 1869663 + abstracts | -1353093 | OK | 669425664 | 3 | 1353096 + release_ref | -3429019 | OK | 99223470080 | 3 | 3429022 + release_contrib | -3429026 | OK | 13406437376 | 3 | 3429029 + release_rev_abstract | -3435251 | OK | 73359360 | 3 | 3435254 + creator_ident | -5360858 | OK | 266977280 | 11 | 5360869 + creator_rev | -8071846 | OK | 388734976 | 257781 | 8329627 + file_ident | -13478348 | OK | 524746752 | 7 | 13478355 + file_rev | -30368193 | OK | 867401728 | 4 | 30368197 + container_ident | -47140767 | OK | 18219008 | 9 | 47140776 + release_ident | -61021070 | OK | 3620864000 | 24 | 61021094 + work_rev | -106056502 | OK | 2349146112 | 1 | 106056503 + work_ident | -106320780 | OK | 3620954112 | 6 | 106320786 + editgroup | -117742455 | OK | 62398464 | 2 | 117742457 + release_rev | -563415274 | OK | 32455860224 | 8 | 563415282 + +Thought I had resoled those scans... hrm. Pretty sure (but not 100%) that I +cleared the counters. + +Dumps! + + time psql fatcat_prod < ../extra/quick_dump.sql + real 4m5.729s + user 0m0.056s + sys 0m0.016s + => while other stuff running + + time ./ident_table_snapshot.sh + => seems very dominated by tar/xz compression time; should switch back to gzip + + DATABASE_URL=$DATABASE_URL time ./ident_table_snapshot.sh /tmp + 614.80user 31.74system 13:23.51elapsed 80%CPU (0avgtext+0avgdata 10124maxresident)k + 8311456inputs+9761200outputs (2major+3792minor)pagefaults 0swaps + => 13.5 minutes + => fatcat_idents.2018-09-13.215147.r874951.tar.gz: 4.7GB + => uncompressed, 8.3GB total + + cat ../extra/sql_dumps/fatcat_ident_releases.tsv | time ./target/release/fatcat-export release -j8 -q | pv -l | gzip > fatcat_release_dump.json.gz + => can not run with more than -j8, it seems (postgres client limit) + => TPS: 12522 (!) + => 101k 0:00:34 [2.99k/s] + => estimate 6.5 hours + + # NOTE AFTER THE FACT: had "contaner" typo in the below, so wasn't expanding containers + cat ../extra/sql_dumps/fatcat_ident_releases.tsv | time ./target/release/fatcat-export release --expand files,contaner -j8 -q | pv -l | gzip > fatcat_release_dump_expanded.json.gz + => TPS: 29605 (!) + => 183k 0:00:35 [ 5.8k/s] (how is this faster than the above? other disk stuff finished?) + => 341k 0:01:07 [3.48k/s] (ah, must have been in disk cache) + => 4.12M 0:16:11 (averaging 4.2k/s; estimate 4 hours total) + => fatcat_release_dump_expanded.json.gz: 3.4G with 6.76M lines, so expecting 35GB or so + + ----total-cpu-usage---- -dsk/total- -net/total- ---paging-- ---system-- + usr sys idl wai hiq siq| read writ| recv send| in out | int csw + 14 3 73 8 0 2| 43M 21M| 143k 326B| 0 0 | 64k 113k + 18 4 72 5 0 2| 55M 4096k| 246k 326B| 0 0 | 84k 157k + 17 4 72 6 0 2| 53M 9964k| 428k 908B| 0 0 | 84k 155k + 14 3 73 8 0 1| 46M 20M| 143k 87k| 0 0 | 71k 132k + 18 3 72 5 0 2| 52M 8880k| 318k 95k| 0 0 | 82k 149k + + => fatcat-export using about 200% CPU in a single thread; other 8 threads at about 25% each + => might be interesting to profile... too many copies? switch to tsv library? + => seems like postgres only about 50% utilized + +Benchmarks! + + # stub entity + $ wrk -t8 -c100 -d30s http://localhost:9411/v0/work/aaaaaaaaaaaaavkvaaaaaaaaai + Running 30s test @ http://localhost:9411/v0/work/aaaaaaaaaaaaavkvaaaaaaaaai + 8 threads and 100 connections + Thread Stats Avg Stdev Max +/- Stdev + Latency 7.44ms 5.26ms 67.53ms 60.07% + Req/Sec 1.71k 113.55 2.07k 68.79% + 408986 requests in 30.01s, 117.01MB read + Requests/sec: 13627.62 + Transfer/sec: 3.90MB + => TPS: 39958 + => lots of "BEGIN" and "SELECT 1", implying new connections? hrm. + => should run longer for more stable results + + wrk -t12 -c400 -d2m --latency http://localhost:9411/v0/work/aaaaaaaaaaaaavkvaaaaaaaaai + + Running 2m test @ http://localhost:9411/v0/work/aaaaaaaaaaaaavkvaaaaaaaaai + 12 threads and 400 connections + Thread Stats Avg Stdev Max +/- Stdev + Latency 25.75ms 17.02ms 263.74ms 65.11% + Req/Sec 1.05k 377.38 1.82k 74.81% + Latency Distribution + 50% 25.40ms + 75% 26.56ms + 90% 49.57ms + 99% 76.47ms + 1128253 requests in 2.00m, 322.80MB read + Socket errors: connect 0, read 10, write 0, timeout 0 + Requests/sec: 9396.03 + Transfer/sec: 2.69MB + + => single 470% fatcatd thread; diesel? + => 50% systemd-journald + + # rich entity + $ wrk -t8 -c100 -d30s https://api.qa.fatcat.wiki/v0/release/aaaaaaaaaaaaarceaaaaaaaaam?expand=files,container + Running 30s test @ https://api.qa.fatcat.wiki/v0/release/aaaaaaaaaaaaarceaaaaaaaaam?expand=files,container + 8 threads and 100 connections + Thread Stats Avg Stdev Max +/- Stdev + Latency 33.35ms 14.01ms 152.05ms 79.98% + Req/Sec 363.14 30.36 464.00 76.48% + 86719 requests in 30.04s, 234.46MB read + Requests/sec: 2886.55 + Transfer/sec: 7.80MB + + wrk -t12 -c400 -d2m --latency https://api.qa.fatcat.wiki/v0/release/aaaaaaaaaaaaarceaaaaaaaaam?expand=files,container + + Running 2m test @ https://api.qa.fatcat.wiki/v0/release/aaaaaaaaaaaaarceaaaaaaaaam?expand=files,container + 12 threads and 400 connections + Thread Stats Avg Stdev Max +/- Stdev + Latency 149.19ms 125.30ms 1.93s 95.06% + Req/Sec 237.89 34.60 650.00 73.54% + Latency Distribution + 50% 129.86ms + 75% 134.14ms + 90% 210.42ms + 99% 904.26ms + 340625 requests in 2.00m, 0.90GB read + Socket errors: connect 0, read 0, write 0, timeout 303 + Requests/sec: 2836.17 + Transfer/sec: 7.67MB + + => TPS: 9090 + ----total-cpu-usage---- -dsk/total- -net/total- ---paging-- ---system-- + usr sys idl wai hiq siq| read writ| recv send| in out | int csw + 4 0 93 3 0 0|2401k 13M| 0 0 |2317B 4812B|4274 3824 + 22 6 68 0 0 3|4096B 0 | 57k 956B|4096B 0 | 135k 255k + 21 7 68 0 0 3|4096B 0 | 61k 66B|4096B 0 | 137k 259k + 21 7 68 0 0 3| 16k 8192B| 179k 636B| 16k 0 | 134k 252k + 21 7 68 0 0 3| 0 0 | 53k 66B| 0 0 | 135k 255k + 22 6 68 0 0 3| 0 17M| 51k 326B| 0 0 | 137k 261k + 22 6 68 0 0 3| 0 0 | 82k 903B| 0 0 | 136k 257k + + # static (404) + wrk -t12 -c400 -d2m --latency http://localhost:9411/v0/asdf + => full 2600+% CPU in a single fatcat process (?) + => lots of load in wrk also + => system at a whole basically 100% CPU on all cores, though mostly kernel + + ----total-cpu-usage---- -dsk/total- -net/total- ---paging-- ---system-- + usr sys idl wai hiq siq| read writ| recv send| in out | int csw + 4 0 93 3 0 0|2399k 13M| 0 0 |2315B 4808B|4359 3976 + 26 66 2 0 0 6| 0 0 |4191k 956B| 0 0 | 465k 536k + 26 67 1 0 0 6| 0 0 | 511k 66B| 0 0 | 466k 543k + 27 64 3 0 0 6| 0 0 |2648k 318B| 0 0 | 481k 555k + 25 67 2 0 0 6| 0 0 |1909k 768B| 0 0 | 481k 550k + + Running 2m test @ http://localhost:9411/v0/asdf + 12 threads and 400 connections + Thread Stats Avg Stdev Max +/- Stdev + Latency 1.40ms 1.65ms 219.48ms 93.33% + Req/Sec 17.71k 8.97k 65.69k 63.84% + Latency Distribution + 50% 1.13ms + 75% 1.89ms + 90% 2.71ms + 99% 4.76ms + 21145472 requests in 2.00m, 1.61GB read + Socket errors: connect 0, read 12, write 0, timeout 0 + Non-2xx or 3xx responses: 21145472 + Requests/sec: 176071.79 + Transfer/sec: 13.77MB + +Noting pretty non-trival traffic to 207.241.229.230 and +es-worker-02.us.archive.org (207.241.229.246)... probably because this is a +datanode? + +## Misc + +Postgres really wanted to log: <https://wiki.postgresql.org/wiki/Per-user_log_settings> + + ALTER DATABASE fatcat_prod SET log_statement = 'ddl'; + ALTER USER fatcat SET log_statement = 'ddl'; + + +## Later Imports + + zcat /srv/datasets/2018-08-27-2352.17-matchcrossref.insertable.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched - + => only ~40 TPS + => looks like almost all selects... probably skipping? huge postgres CPU churn, huh. missing index? + + relname | too_much_seq | case | rel_size | seq_scan | idx_scan + ----------------------+--------------+----------------+-------------+----------+---------- + file_rev | -5343173 | OK | 867483648 | 693 | 5343866 + + EXPLAIN SELECT "file_ident"."id", "file_ident"."is_live", "file_ident"."rev_id", "file_ident"."redirect_id", "file_rev"."id", "file_rev"."extra_json", "file_rev"."size", "file_rev"."sha1", "file_rev"."sha256", "file_rev"."md5", "file_rev"."mimetype" FROM ("file_ident" INNER JOIN "file_rev" ON "file_ident"."rev_id" = "file_rev"."id") WHERE "file_rev"."sha1" = '7d97e98f8af710c7e7fe703abc8f639e0ee507c4' AND "file_rev"."sha1" IS NOT NULL AND "file_ident"."is_live" = 't' AND "file_ident"."redirect_id" IS NULL LIMIT 1; + +Ugh, this whole cycle again. Query only takes 1ms for a no-hit, or 5ms for success. + + http get http://localhost:9411/v0/file/lookup?sha1=d77cb2a8b207507e0df27ba1393e8118eec9217f => not found + http get http://localhost:9411/v0/file/lookup?sha1=d6c3f6ca785ee63293da02615c8495c5cd25fa25 => found + => but no releases? + +SET auto_explain.log_min_duration = 0; +SET auto_explain.log_analyze = true; +ALTER USER fatcat SET log_statement = 'all'; +ALTER USER fatcat SET auto_explain.log_min_duration = 0; +ALTER USER fatcat SET auto_explain.log_analyze = true;; +sudo service fatcat-api restart + + +2018-09-16 00:42:29.883 UTC [13868] fatcat@fatcat_prod LOG: duration: 3028.143 ms plan: + Query Text: SELECT "file_ident"."id", "file_ident"."is_live", "file_ident"."rev_id", "file_ident"."redirect_id", "file_rev"."id", "file_rev"."extra_json", "file_rev"."size", "file_rev"."sha1", "file_rev"."sha256", "file_rev"."md5", "file_rev"."mimetype" FROM ("file_ident" INNER JOIN "file_rev" ON "file_ident"."rev_id" = "file_rev"."id") WHERE "file_rev"."sha1" = $1 AND "file_rev"."sha1" IS NOT NULL AND "file_ident"."is_live" = $2 AND "file_ident"."redirect_id" IS NULL LIMIT $3 + Limit (cost=0.43..8.56 rows=1 width=454) (actual time=3028.139..3028.139 rows=0 loops=1) + -> Nested Loop (cost=0.43..268756.48 rows=33056 width=454) (actual time=3028.138..3028.138 rows=0 loops=1) + -> Seq Scan on file_rev (cost=0.00..205023.16 rows=33042 width=405) (actual time=3028.137..3028.137 rows=0 loops=1) + Filter: ((sha1 IS NOT NULL) AND ((sha1)::text = 'd68d4e2cc420647109cdfe410efed86cd64465e5'::text)) + Rows Removed by Filter: 6607786 + -> Index Scan using file_ident_rev_idx on file_ident (cost=0.43..1.92 rows=1 width=49) (never executed) + Index Cond: (rev_id = file_rev.id) + Filter: (is_live AND (redirect_id IS NULL)) + + +fatcat_prod=# EXPLAIN SELECT "file_ident"."id", "file_ident"."is_live", "file_ident"."rev_id", "file_ident"."redirect_id", "file_rev"."id", "file_rev"."extra_json", "file_rev"."size", "file_rev"."sha1", "file_rev"."sha256", "file_rev"."md5", "file_rev"."mimetype" FROM ("file_ident" INNER JOIN "file_rev" ON "file_ident"."rev_id" = "file_rev"."id") WHERE "file_rev"."sha1" = '3f242a192acc258bdfdb15194341943222222222222440c313' AND "file_rev"."sha1" IS NOT NULL AND "file_ident"."is_live" = 't' AND "file_ident"."redirect_id" IS NULL LIMIT 1; + QUERY PLAN +-------------------------------------------------------------------------------------------------------------------------- + Limit (cost=0.99..5.04 rows=1 width=454) + -> Nested Loop (cost=0.99..5.04 rows=1 width=454) + -> Index Scan using file_rev_sha1_idx on file_rev (cost=0.56..2.58 rows=1 width=405) + Index Cond: ((sha1 IS NOT NULL) AND (sha1 = '3f242a192acc258bdfdb15194341943222222222222440c313'::bpchar)) + -> Index Scan using file_ident_rev_idx on file_ident (cost=0.43..2.45 rows=1 width=49) + Index Cond: (rev_id = file_rev.id) + Filter: (is_live AND (redirect_id IS NULL)) + +After all this debugging, asked on IRC and learned that I really shouldn't ever +use CHAR() (or even VARCHAR()). Will update the schema. + +## Investigating Missing Rows + + fatcat_prod=# select count(*) from release_ident; => 53028167 + +Thought I had more than that previously? Table sizes were also bigger. Hrm. + |