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authorBryan Newbold <bnewbold@robocracy.org>2018-09-25 15:44:39 -0700
committerBryan Newbold <bnewbold@robocracy.org>2018-09-25 15:44:39 -0700
commit186c03c2b9e1b08e4298383fc6593d1b2c3a5dd8 (patch)
treeb116678710d9a69df023f7dc90525d7563506891 /notes/performance
parentc1391060cc4575365f81fc674e35d8c182ccde83 (diff)
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-rw-r--r--notes/performance/postgres_performance.txt203
-rw-r--r--notes/performance/speed.txt82
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diff --git a/notes/performance/postgres_performance.txt b/notes/performance/postgres_performance.txt
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+
+## Setup
+
+Add to postgres.conf:
+
+ shared_preload_libraries = 'auto_explain,pg_stat_statements'
+
+ # Increase the max size of the query strings Postgres records
+ track_activity_query_size = 2048
+
+ # Track statements generated by stored procedures as well
+ pg_stat_statements.track = all
+
+Also:
+
+ track_counts (already default)
+ autovacuum (already default?)
+ log_min_error = warning
+ log_min_duration_statement = 5000
+
+Then from shell:
+
+ create extension pg_stat_statements;
+
+Regularly want to run:
+
+ VACUUM ANALYZE
+
+## Tuning Values
+
+postgres config:
+
+ max_connections = 100 (default)
+ shared_buffers = 128MB -> 10GB (while elastic on same machine; later 16 or more)
+ effective_cache_size = 4GB -> 24GB (while elastic on same machine)
+ work_mem = 4MB -> 128MB # relatively few connections/box
+ fsync = on
+ commit_delay = ??? (and siblings)
+ random_page_cost = 1 (for SSD)
+ default_statistics_target = 100 -> 200
+ maintenance_work_mem = 64MB -> 8GB
+ synchronous_commit = off (during dev only! switch to on for production!)
+ wal_sync_method (keep default)
+ max_wal_size = 64 -> 128 (based on above HINT message)
+ # didn't mess with commit_delay/commit_siblings
+
+system:
+
+ sysctl -w vm.overcommit_memory=2
+ TODO: ulimit -n 65536
+ TODO: ulimit -p 800
+ LimitNOFILE
+ /lib/systemd/system/postgresql.service
+
+## Resources
+
+https://www.geekytidbits.com/performance-tuning-postgres/
+
+Could try pgbadger to handle auto_explain type output.
+
+https://www.postgresql.org/docs/10/static/runtime-config-wal.html
+
+IA-specific resources:
+ https://git.archive.org/ia/mint/blob/master/postgres/postgres_9_2.yml
+ https://git.archive.org/ia/mint/blob/master/postgres/put_datadir_on_ssd.sh
+ https://git.archive.org/ia/mint/blob/master/postgres/templates/postgresql.conf.j2
+
+For bulk inserts:
+- make write-ahead-log larger (eg, 16MB. done.)
+- transactions of ~1000+ inserts
+- https://www.postgresql.org/docs/current/static/populate.html
+- https://www.depesz.com/2007/07/05/how-to-insert-data-to-database-as-fast-as-possible/
+- https://stackoverflow.com/questions/12206600/how-to-speed-up-insertion-performance-in-postgresql
+
+## 2018-06-27 Measurements (pre-tuning)
+
+fatcat_prod=# select count(*) from release_ident; 20983019
+fatcat_prod=# select count(*) from work_ident; 20988140
+fatcat_prod=# select count(*) from file_ident; 1482335
+fatcat_prod=# select count(*) from creator_ident; 4167419
+fatcat_prod=# select count(*) from container_ident; 61793
+
+select count(*) from release_contrib; 59798133
+
+bnewbold@wbgrp-svc500$ sudo du -sh /var/lib/postgresql/
+43G
+
+running import-crossref with 20 threads, and manifest importer with one (at 33%
+complete). had already imported ~7million works+releases previously.
+
+
+ PostgreSQL 10.4 - wbgrp-svc500.us.archive.org - postgres@localhost:5432/postgre
+ Size: 41.38G - 323.40K/s | TPS: 885
+ Mem.: 50.80% - 23.86G/49.14G | IO Max: 79539/s
+ Swap: 0.80% - 408.89M/50.00G | Read : 67.04K/s - 16/s
+ Load: 6.69 7.41 7.69 | Write: 1.93M/s - 493/s
+
+
+----total-cpu-usage---- -dsk/total- -net/total- ---paging-- ---system--
+usr sys idl wai hiq siq| read writ| recv send| in out | int csw
+ 32 6 62 0 0 0| 296k 3880k| 334k 3144B| 0 0 | 21k 65k
+ 31 6 62 0 0 0| 0 3072k| 391k 318B| 0 0 | 51k 141k
+ 31 6 63 0 0 0| 16k 1080k| 344k 1988B| 0 0 | 35k 104k
+ 29 6 65 0 0 0| 136k 2608k| 175k 332B| 0 0 |9835 15k
+ 28 5 67 0 0 0| 408k 4368k| 285k 832B| 0 0 | 14k 17k
+ 33 5 62 0 0 0| 56k 3256k| 219k 99B| 0 0 | 22k 49k
+ 31 6 63 0 0 0| 188k 5120k| 158k 318B| 0 0 | 17k 29k
+ 30 6 64 0 0 0| 200k 6984k| 239k 988B| 0 0 | 16k 24k
+ 30 6 64 0 0 0| 168k 5504k| 159k 152B| 0 0 | 14k 20k
+ 28 7 65 0 0 0| 440k 12M| 236k 420B| 0 0 | 15k 18k
+ 29 6 65 0 0 0| 428k 6968k| 352k 310B| 0 0 | 19k 31k
+ 32 6 62 0 0 0| 64k 3480k| 288k 318B| 0 0 | 18k 55k
+ 32 6 62 0 0 0| 32k 2080k| 155k 318B| 0 0 | 20k 52k
+
+
+bnewbold@wbgrp-svc500$ uptime
+ 22:00:42 up 28 days, 22:31, 6 users, load average: 7.94, 7.56, 7.72
+
+
+2018-06-27 21:57:36.102 UTC [401] LOG: checkpoints are occurring too frequently (13 seconds apart)
+2018-06-27 21:57:36.102 UTC [401] HINT: Consider increasing the configuration parameter "max_wal_size".
+
+
+ relname | too_much_seq | case | rel_size | seq_scan | idx_scan
+-----------------+--------------+----------------+-------------+----------+-----------
+ changelog | 1274670 | Missing Index? | 39411712 | 1274670 | 0
+ file_edit | 612386 | Missing Index? | 108298240 | 612386 | 0
+ creator_edit | 612386 | Missing Index? | 285540352 | 612386 | 0
+ container_edit | 612386 | Missing Index? | 4784128 | 612386 | 0
+ release_edit | 612386 | Missing Index? | 1454489600 | 612386 | 0
+ work_edit | 612386 | Missing Index? | 1454415872 | 612386 | 0
+ release_contrib | 296675 | Missing Index? | 4725645312 | 296675 | 0
+ release_ref | 296663 | Missing Index? | 8999837696 | 296663 | 0
+ file_release | -113 | OK | 13918208 | 110 | 223
+ container_rev | -979326 | OK | 16285696 | 63 | 979389
+ file_ident | -3671516 | OK | 109002752 | 362 | 3671878
+ file_rev | -3944155 | OK | 302940160 | 95 | 3944250
+ creator_rev | -8420205 | OK | 318283776 | 1226 | 8421431
+ creator_ident | -9525338 | OK | 309141504 | 52330 | 9577668
+ container_ident | -20581876 | OK | 4833280 | 272457 | 20854333
+ release_ident | -40548858 | OK | 1440948224 | 4160919 | 44709777
+ work_rev | -42534913 | OK | 1124671488 | 1161 | 42536074
+ editgroup | -48864662 | OK | 34136064 | 1 | 48864663
+ work_ident | -65008911 | OK | 1503313920 | 1239 | 65010150
+ release_rev | -185735794 | OK | 13649428480 | 128 | 185735922
+
+## 2018-06-28 (after basic tuning + indexes)
+
+Early loading (manifest and 20x release):
+
+ PostgreSQL 10.4 - wbgrp-svc500.us.archive.org - postgres@localhost:5432/postgres - Ref.: 2s
+ Size: 4.57G - 6.45M/s | TPS: 18812
+ Mem.: 59.70% - 23.62G/49.14G | IO Max: 3601/s
+ Swap: 1.30% - 675.05M/50.00G | Read : 0.00B/s - 0/s
+ Load: 12.98 10.58 5.25 | Write: 2.65M/s - 677/s
+
+
+ PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
+ 24045 webcrawl 20 0 908872 204948 11756 S 153.3 0.4 16:13.03 fatcatd
+ 24328 webcrawl 20 0 78148 45220 4324 R 87.1 0.1 8:44.16 perl
+ 24056 postgres 20 0 10.441g 3.906g 3.886g R 69.9 7.9 6:57.47 postgres
+ 24063 postgres 20 0 10.447g 3.899g 3.873g S 67.9 7.9 6:55.89 postgres
+ 24059 postgres 20 0 10.426g 3.888g 3.883g R 67.5 7.9 6:59.15 postgres
+ 24057 postgres 20 0 10.430g 3.883g 3.874g S 67.2 7.9 6:58.68 postgres
+ 24061 postgres 20 0 10.448g 3.909g 3.881g R 66.2 8.0 6:54.30 postgres
+ 24058 postgres 20 0 10.428g 3.883g 3.876g R 65.9 7.9 6:59.35 postgres
+ 24062 postgres 20 0 10.426g 5.516g 5.511g R 64.9 11.2 6:58.29 postgres
+ 24055 postgres 20 0 10.426g 3.878g 3.873g R 64.2 7.9 6:59.38 postgres
+ 24054 postgres 20 0 10.430g 5.499g 5.491g R 63.6 11.2 6:57.27 postgres
+ 24060 postgres 20 0 10.448g 3.900g 3.873g R 61.9 7.9 6:55.45 postgres
+ 21711 postgres 20 0 10.419g 5.762g 5.760g D 16.6 11.7 3:00.67 postgres
+ 21713 postgres 20 0 10.419g 21432 19512 S 11.3 0.0 3:25.11 postgres
+ 24392 webcrawl 20 0 5309636 400912 8696 S 7.9 0.8 0:53.18 python3
+ 24383 webcrawl 20 0 5309436 400628 8648 S 7.6 0.8 0:52.29 python3
+ 24387 webcrawl 20 0 5309776 402968 8620 S 7.3 0.8 0:52.81 python3
+ 24394 webcrawl 20 0 5309624 400732 8644 S 7.3 0.8 0:53.30 python3
+ 24384 webcrawl 20 0 5309916 400948 8600 S 7.0 0.8 0:53.18 python3
+
+Still get a *lot* of:
+
+ 2018-06-29 00:14:05.948 UTC [21711] LOG: checkpoints are occurring too frequently (1 second apart)
+ 2018-06-29 00:14:05.948 UTC [21711] HINT: Consider increasing the configuration parameter "max_wal_size".
+
+VACUUM is running basically continuously; should prevent that? 6 hours or
+longer on release_rev and release_ref tables. An auto-approve batch method
+would resovle this, I think (no update after insert).
+
+max_wal_size wasn't getting set correctly.
+
+The statements taking the most time are the complex inserts (multi-table
+inserts); they take a fraction of a second though (mean less than a
+milisecond).
+
+Manifest import runs really slow if release import is concurrent; much faster
+to wait until release import is done first (like a factor of 10x or more).
+
+With some 60 million releases:
+
+ bnewbold@wbgrp-svc500$ sudo du -sh /var/lib/postgresql/
+ 184G /var/lib/postgresql/
+
+TODO: slow query log doesn't seem to be working (let alone auto_explain)
+
diff --git a/notes/performance/speed.txt b/notes/performance/speed.txt
new file mode 100644
index 00000000..f885aea7
--- /dev/null
+++ b/notes/performance/speed.txt
@@ -0,0 +1,82 @@
+
+## Early Prototyping
+
+### 2018-04-23
+
+- fatcat as marshmallow+sqlalchemy+flask, with API client
+- no refs, contibs, files, release contribs, containers, etc
+- no extra_json
+- sqlite
+- laptop
+- editgroup every 250 edits
+
+
+ /data/crossref/crossref-works.2018-01-21.badsample_5k.json
+
+ real 3m42.912s
+ user 0m20.448s
+ sys 0m2.852s
+
+ ~22 lines per second
+ 12.5 hours per million
+ ~52 days for crossref (100 million)
+
+target:
+ crossref (100 million) loaded in 48 hours
+ 579 lines per second
+ this test in under 10 seconds
+ ... but could be in parallel
+
+same except postgres, via:
+
+ docker run -p 5432:5432 postgres:latest
+ ./run.py --init-db --database-uri postgres://postgres@localhost:5432
+ ./run.py --database-uri postgres://postgres@localhost:5432
+
+ API processing using 60-100% of a core. postgres 12% of a core;
+ docker-proxy similar (!). overall 70 of system CPU idle.
+
+ real 2m27.771s
+ user 0m22.860s
+ sys 0m2.852s
+
+no profiling yet; need to look at database ops. probably don't even have any
+indices!
+
+## Rust Updates (2018-05-23)
+
+Re-running with tweaked python code, 5k sample file, postgres 9.6 running locally (not in docker):
+
+ real 2m27.598s
+ user 0m24.892s
+ sys 0m2.836s
+
+Using postgres and fatcat rust:
+
+ real 0m44.443s
+ user 0m25.288s
+ sys 0m0.880s
+
+api_client about half a core; fatcatd 3x processes, about 10% each; postgres
+very small.
+
+a bit faster, basically maxing out CPU:
+
+ time cat /data/crossref/crossref-works.2018-01-21.badsample_5k.json | parallel -j4 --pipe ./fatcat_client.py --host-url http://localhost:9411 ic -
+
+ real 0m28.998s
+ user 1m5.304s
+ sys 0m3.420s
+
+ 200 lines per second; within a factor of 3; can perhaps hit target with
+ non-python client?
+
+python processes (clients) seem to be CPU limit in this case; all 4 cores
+effectively maxed out.
+
+running python again in parallel mode:
+
+ real 2m29.532s
+ user 0m47.692s
+ sys 0m4.840s
+