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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/bootstrap
parentc1391060cc4575365f81fc674e35d8c182ccde83 (diff)
downloadfatcat-186c03c2b9e1b08e4298383fc6593d1b2c3a5dd8.tar.gz
fatcat-186c03c2b9e1b08e4298383fc6593d1b2c3a5dd8.zip
start organizing notes into subdirectories
Diffstat (limited to 'notes/bootstrap')
-rw-r--r--notes/bootstrap/import_timing_20180815.txt292
-rw-r--r--notes/bootstrap/import_timing_20180908.txt249
-rw-r--r--notes/bootstrap/import_timing_20180910.txt319
-rw-r--r--notes/bootstrap/import_timing_20180920.txt96
-rw-r--r--notes/bootstrap/import_timing_20180923.txt91
-rw-r--r--notes/bootstrap/initial_sources.txt26
-rw-r--r--notes/bootstrap/old_imports.txt20
7 files changed, 1093 insertions, 0 deletions
diff --git a/notes/bootstrap/import_timing_20180815.txt b/notes/bootstrap/import_timing_20180815.txt
new file mode 100644
index 00000000..1206cc41
--- /dev/null
+++ b/notes/bootstrap/import_timing_20180815.txt
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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;
diff --git a/notes/bootstrap/import_timing_20180908.txt b/notes/bootstrap/import_timing_20180908.txt
new file mode 100644
index 00000000..3091e4fa
--- /dev/null
+++ b/notes/bootstrap/import_timing_20180908.txt
@@ -0,0 +1,249 @@
+
+Changes since last time:
+- auto-accept flag (potentially no need to UPDATE/vacuum database)
+- large CRUD code refactor (but not complete removal of api_server CRUD yet)
+- removed "single query insert per entity", but added row-based inserts
+
+## Laptop Rough Timing
+
+HTTP-VERB branch 7354899493f6448bed5698ad6ade1dbebcf39379:
+=> note: in this branch, importer is sitll creating editgroups in separate request
+
+ time ./fatcat_import.py import-issn /home/bnewbold/code/oa-journals-analysis/upload-2018-04-05/journal_extra_metadata.csv
+ real 0m28.779s
+ user 0m5.716s
+ sys 0m0.208s
+
+ cat /data/crossref/crossref-works.2018-01-21.badsample_100k.json | time parallel -j4 --round-robin --pipe ./fatcat_import.py import-crossref - /data/issn/20180216.ISSN-to-ISSN-L.txt
+
+ 89.83user 4.58system 1:46.67elapsed 88%CPU (0avgtext+0avgdata 386184maxresident)k
+ 78632inputs+385408outputs (1major+579693minor)pagefaults 0swaps
+ # 1:46.67 elapsed
+
+ # running again
+ time ./fatcat_import.py import-issn /home/bnewbold/code/oa-journals-analysis/upload-2018-04-05/journal_extra_metadata.csv
+ real 0m29.714s
+ user 0m6.048s
+ sys 0m0.212s
+
+ cat /data/crossref/crossref-works.2018-01-21.badsample_100k.json | time parallel -j4 --round-robin --pipe ./fatcat_import.py import-crossref - /data/issn/20180216.ISSN-to-ISSN-L.txt
+ 89.07user 4.52system 1:48.11elapsed 86%CPU (0avgtext+0avgdata 385940maxresident)k
+ 0inputs+377456outputs (0major+583532minor)pagefaults 0swaps
+ # 1:48.11 elapsed
+
+MASTER branch 0053d133f8ff96aa4dedc1ff7e2754812ddfc79a
+
+ time ./fatcat_import.py import-issn /home/bnewbold/code/oa-journals-analysis/upload-2018-04-05/journal_extra_metadata.csv
+ real 1m8.061s
+ user 0m7.384s
+ sys 0m0.280s
+
+ cat /data/crossref/crossref-works.2018-01-21.badsample_100k.json | time parallel -j4 --round-robin --pipe ./fatcat_import.py import-crossref - /data/issn/20180216.ISSN-to-ISSN-L.txt
+ 96.68user 5.25system 3:23.05elapsed 50%CPU (0avgtext+0avgdata 385516maxresident)k
+ 0inputs+389168outputs (0major+586810minor)pagefaults 0swaps
+ # 3:23.05 elapsed
+
+AUTO-ACCEPT branch 8cccbcdef11e7ddc761ec494cb894a8d49a0d510
+
+ time ./fatcat_import.py import-issn /home/bnewbold/code/oa-journals-analysis/upload-2018-04-05/journal_extra_metadata.csv
+ real 1m7.757s
+ user 0m6.240s
+ sys 0m0.228s
+
+ cat /data/crossref/crossref-works.2018-01-21.badsample_100k.json | time parallel -j4 --round-robin --pipe ./fatcat_import.py import-crossref - /data/issn/20180216.ISSN-to-ISSN-L.txt
+ 91.73user 4.65system 3:26.61elapsed 46%CPU (0avgtext+0avgdata 385512maxresident)k
+ 0inputs+384976outputs (0major+580544minor)pagefaults 0swaps
+
+So, annecdotally, seems like autoaccept didn't do much here (not
+vacuum-limited?), but the row inserts were more than a factor of 2x performance
+improvement. Great! Could try experimenting with even larger batch sizes...
+
+
+## Production Import
+
+http-verb branch 7354899493f6448bed5698ad6ade1dbebcf39379
+
+ time ./fatcat_import.py import-issn /srv/datasets/journal_extra_metadata.csv
+
+ real 0m30.845s
+ user 0m8.884s
+ sys 0m0.312s
+
+
+ time parallel --bar --pipepart -j8 -a /srv/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid -
+ # TPS: 1181
+ real 6m54.019s => down from 22m!
+ user 25m33.980s
+ sys 1m30.480s
+
+ 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
+ # fatcatd at 200% CPU (2 full cores); many PIDs/workers, but only one so busy (must be diesel/db driver?)
+ # parallel at ~80%
+ # postgres pretty busy; looks like doing PARSE on ever request? some idle in transaction
+ # postgres still does a vacuum to analyze; good!
+ # ~600-1000 TPS near start (large variance)
+ # left to run overnight...
+ # slowed down to ~50-80 TPS about 10 hours later
+ # lots of IOWAIT
+ # only at 40309165 rows in the morning; this could take a long time
+
+ # PostgreSQL 10.4 - wbgrp-svc500.us.archive.org - postgres@localhost:5432/postgres - Ref.: 2s
+ # Size: 153.71G - 1.90M/s | TPS: 77
+ # Mem.: 68.70% - 22.60G/49.14G | IO Max: 20448/s
+ # Swap: 3.80% - 1.88G/50.00G | Read : 10.17M/s - 2603/s
+ # Load: 11.71 11.80 12.01 | Write: 4.00M/s - 1024/s
+
+ 92530.17user 2891.76system 35:45:15elapsed 74%CPU (0avgtext+0avgdata 463520maxresident)k
+ 1093736inputs+302588448outputs (52568major+36405225minor)pagefaults 0swaps
+ # 35:45:15 elapsed
+
+ time ./fatcat_import.py import-manifest /srv/datasets/idents_files_urls.sqlite
+
+## Perf Tweaks
+
+
+
+ SELECT
+ relname,
+ seq_scan - idx_scan AS too_much_seq,
+ CASE
+ WHEN
+ seq_scan - coalesce(idx_scan, 0) > 0
+ THEN
+ 'Missing Index?'
+ ELSE
+ 'OK'
+ END,
+ pg_relation_size(relname::regclass) AS rel_size, seq_scan, idx_scan
+ FROM
+ pg_stat_all_tables
+ WHERE
+ schemaname = 'public'
+ AND pg_relation_size(relname::regclass) > 80000
+ ORDER BY
+ too_much_seq DESC;
+
+ relname | too_much_seq | case | rel_size | seq_scan | idx_scan
+----------------------+--------------+------+--------------+----------+-----------
+ file_rev_url | -1 | OK | 163323904 | 2 | 3
+ file_release | -3 | OK | 24461312 | 2 | 5
+ release_edit | -10265 | OK | 6080495616 | 2 | 10267
+ container_edit | -10265 | OK | 31170560 | 2 | 10267
+ work_edit | -10265 | OK | 6080364544 | 2 | 10267
+ file_edit | -10265 | OK | 49111040 | 2 | 10267
+ creator_edit | -10265 | OK | 330924032 | 2 | 10267
+ changelog | -11692 | OK | 106668032 | 2 | 11694
+ release_ref | -374197 | OK | 125437673472 | 3 | 374200
+ release_contrib | -374202 | OK | 16835354624 | 3 | 374205
+ release_rev_abstract | -374919 | OK | 162250752 | 3 | 374922
+ file_ident | -1047172 | OK | 41926656 | 2 | 1047174
+ container_rev | -1378943 | OK | 50356224 | 724612 | 2103555 <=
+ file_rev | -2407647 | OK | 68493312 | 4 | 2407651
+ abstracts | -2765610 | OK | 1450901504 | 1 | 2765611
+ creator_ident | -7127467 | OK | 242688000 | 2 | 7127469
+ creator_rev | -7943007 | OK | 353370112 | 839155 | 8782162 <=
+ container_ident | -57488245 | OK | 23060480 | 2 | 57488247
+ release_ident | -66085389 | OK | 4459159552 | 14 | 66085403
+ work_rev | -130613391 | OK | 2892775424 | 1 | 130613392
+ work_ident | -130633923 | OK | 4459192320 | 2 | 130633925
+ editgroup | -136775970 | OK | 120561664 | 1 | 136775971
+ release_rev | -718337215 | OK | 36850507776 | 8 | 718337223
+
+
+Slowest queries:
+
+ 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_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = $2 AND "creator_ident"."redirect_id" IS NULL LIMIT $3
+
+ 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" = $1 AND "container_rev"."issnl" IS NOT NULL AND "container_ident"."is_live" = $2 AND "container_ident"."redirect_id" IS NULL LIMIT $3
+
+ SELECT $2 FROM ONLY "public"."release_rev" x WHERE "id" OPERATOR(pg_catalog.=) $1 FOR KEY SHARE OF x:...skipping...
+
+ 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_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = $2 AND "creator_ident"."redirect_id" IS NULL LIMIT $3
+
+
+DEBUG: (while a file import is running)
+
+Creator lookup where row exists:
+
+ time curl localhost:9411/v0/creator/lookup?orcid=0000-0002-8867-1663
+ real 0m0.020s
+ user 0m0.004s
+ sys 0m0.004s
+
+ SELECT "creator_ident"."id", "creator_ident"."is_live", "creator_ident"."rev_id", "creator_ident"."redirect_id", "creator_rev"."id", "creator_rev"."extra_json", "creator_rev"."display_name", "creator_rev"."given_name", "creator_rev"."surname", "creator_rev"."orcid", "creator_rev"."wikidata_qid" FROM ("creator_ident" INNER JOIN "creator_rev" ON "creator_ident"."rev_id" = "creator_rev"."id") WHERE "creator_rev"."orcid" = '0000-0002-8867-1663' AND "creator_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = 't' AND "creator_ident"."redirect_id" IS NULL LIMIT 1;
+ => (1 row)
+ Time: 0.988 ms
+
+Creator lookup where row doesn't exist:
+
+ bnewbold@wbgrp-svc500$ time curl localhost:9411/v0/creator/lookup?orcid=0000-0002-8867-166X
+ {"message":"Not found: 0000-0002-8867-166X"}
+ real 0m1.282s
+ user 0m0.008s
+ sys 0m0.000s
+ Sep 10 21:50:49 wbgrp-svc500.us.archive.org fatcat-api[25327]: Sep 10 21:50:49.231 INFO GET http://localhost:9411/v0/creator/lookup?orcid=0000-0002-8867-166X 404 Not Found (1282 ms)
+
+ 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" = '0000-0002-8867-166X' AND "creator_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = 't' AND "creator_ident"."redirect_id" IS NULL LIMIT 1;
+ => (0 rows)
+ Time: 0.810 ms
+
+-------
+
+ 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;
+
+ 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_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = 't' AND "creator_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" = '0000-0002-8867-166X' AND "creator_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = 't' AND "creator_ident"."redirect_id" IS NULL LIMIT 1;
+
+from logs:
+
+ execute __diesel_stmt_5: 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_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = $2 AND "creator_ident"."redirect_id" IS NULL LIMIT $3
+
+NOTE: have been doing *full* postgres logs this whole time! probably a ton of disk churn. :(
+
+
+ exact logs:
+ SET TIME ZONE 'UTC'
+ SET CLIENT_ENCODING TO 'UTF8'
+ SELECT 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" = $1 AND "creator_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = $2 AND "creator_ident"."redirect_id" IS NULL LIMIT $3
+ parameters: $1 = '0000-0002-8867-166X', $2 = 't', $3 = '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" = '0000-0002-8867-166X' AND "creator_rev"."orcid" IS NOT NULL AND "creator_ident"."is_live" = 't' AND "creator_ident"."redirect_id" IS NULL LIMIT '1';
+
+CHANGES:
+- restart fatcat-api
+- restart postgresql
+- select pg_stat_reset();
+
+seems like the fetch involves a index scans on creator_rev and creator_ident, *and* a scan on creator_rev.
+
+
+ table_name | table_size | indexes_size | total_size
+--------------------------------------------------------------+------------+--------------+------------
+ "public"."release_ref" | 117 GB | 34 GB | 151 GB
+ "public"."release_rev" | 34 GB | 9202 MB | 43 GB
+ "public"."release_contrib" | 16 GB | 17 GB | 33 GB
+ "public"."work_edit" | 5800 MB | 4033 MB | 9833 MB
+ "public"."release_edit" | 5800 MB | 4032 MB | 9833 MB
+ "public"."work_ident" | 4254 MB | 5102 MB | 9356 MB
+ "public"."release_ident" | 4254 MB | 5095 MB | 9349 MB
+ "public"."work_rev" | 2759 MB | 2545 MB | 5304 MB
+ "public"."abstracts" | 1417 MB | 114 MB | 1530 MB
+ "public"."creator_rev" | 337 MB | 277 MB | 614 MB
+ "public"."creator_edit" | 316 MB | 221 MB | 536 MB
+ "public"."creator_ident" | 232 MB | 279 MB | 511 MB
+ "public"."file_rev_url" | 260 MB | 101 MB | 361 MB
+ "public"."release_rev_abstract" | 155 MB | 200 MB | 355 MB
+ "public"."file_rev" | 109 MB | 124 MB | 233 MB
+ "public"."changelog" | 102 MB | 106 MB | 208 MB
+ "public"."editgroup" | 116 MB | 69 MB | 184 MB
+ "public"."file_ident" | 66 MB | 70 MB | 136 MB
+ "public"."file_edit" | 78 MB | 53 MB | 131 MB
+ "public"."file_release" | 38 MB | 64 MB | 103 MB
+ "public"."container_rev" | 48 MB | 26 MB | 74 MB
+ "public"."container_edit" | 30 MB | 20 MB | 50 MB
+ "public"."container_ident" | 22 MB | 26 MB | 48 MB
+
+CHANGES:
+- remove "IS NOT NULL" from creator_rev, that seemed to be a significant speedup for the "row not found" case.
+
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.
+
diff --git a/notes/bootstrap/import_timing_20180920.txt b/notes/bootstrap/import_timing_20180920.txt
new file mode 100644
index 00000000..a57ffd77
--- /dev/null
+++ b/notes/bootstrap/import_timing_20180920.txt
@@ -0,0 +1,96 @@
+
+This was on fatcat-prod-vm (2TB disk).
+
+ time ./fatcat_import.py import-issn /srv/fatcat/datasets/journal_extra_metadata.csv
+
+ Processed 53300 lines, inserted 53283, updated 0.
+ real 0m32.463s
+ user 0m8.716s
+ sys 0m0.284s
+
+ time parallel --bar --pipepart -j8 -a /srv/fatcat/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid -
+
+ Processed 48900 lines, inserted 48731, updated 0. <= these numbers times 80x
+ 100% 80:0=0s
+
+ real 10m20.598s
+ user 26m16.544s
+ sys 1m40.284s
+
+ time xzcat /srv/fatcat/datasets/crossref-works.2018-01-21.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py import-crossref - /srv/fatcat/datasets/20180216.ISSN-to-ISSN-L.txt /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3
+
+ Processed 4679900 lines, inserted 3755867, updated 0.
+ 107730.08user 4110.22system 16:31:25elapsed 188%CPU (0avgtext+0avgdata 447496maxresident)k
+ 77644160inputs+361948352outputs (105major+49094767minor)pagefaults 0swaps
+
+ => 16.5 hours, faster!
+
+ select count(id) from release_ident; => 75106713
+
+ kernel/system crashed after first file import (!), so don't have numbers from that.
+
+Table sizes at this point:
+
+ select count(id) from file_ident; => 6334606
+
+ Size: 389.25G
+
+ table_name | table_size | indexes_size | total_size
+--------------------------------------------------------------+------------+--------------+------------
+ "public"."release_ref" | 170 GB | 47 GB | 217 GB
+ "public"."release_rev" | 44 GB | 21 GB | 65 GB
+ "public"."release_contrib" | 19 GB | 20 GB | 39 GB
+ "public"."release_edit" | 6671 MB | 6505 MB | 13 GB
+ "public"."work_edit" | 6671 MB | 6505 MB | 13 GB
+ "public"."release_ident" | 4892 MB | 5875 MB | 11 GB
+ "public"."work_ident" | 4892 MB | 5874 MB | 11 GB
+ "public"."work_rev" | 3174 MB | 2936 MB | 6109 MB
+ "public"."file_rev_url" | 3634 MB | 1456 MB | 5090 MB
+ "public"."file_rev" | 792 MB | 1281 MB | 2073 MB
+ "public"."abstracts" | 1665 MB | 135 MB | 1800 MB
+ "public"."file_edit" | 565 MB | 561 MB | 1126 MB
+ "public"."file_release" | 380 MB | 666 MB | 1045 MB
+ "public"."file_ident" | 415 MB | 496 MB | 911 MB
+ "public"."creator_rev" | 371 MB | 457 MB | 828 MB
+ "public"."creator_edit" | 347 MB | 353 MB | 700 MB
+ "public"."creator_ident" | 255 MB | 305 MB | 559 MB
+ "public"."release_rev_abstract" | 183 MB | 237 MB | 421 MB
+ "public"."changelog" | 122 MB | 126 MB | 247 MB
+ "public"."editgroup" | 138 MB | 81 MB | 219 MB
+ "public"."container_rev" | 52 MB | 38 MB | 89 MB
+ "public"."container_edit" | 32 MB | 30 MB | 62 MB
+ "public"."container_ident" | 24 MB | 28 MB | 52 MB
+
+
+ relname | too_much_seq | case | rel_size | seq_scan | idx_scan
+----------------------+--------------+------+--------------+----------+----------
+ release_edit | 0 | OK | 6993084416 | 0 | 0
+ container_rev | 0 | OK | 54124544 | 0 | 0
+ creator_ident | 0 | OK | 266919936 | 0 | 0
+ creator_edit | 0 | OK | 363921408 | 0 | 0
+ work_rev | 0 | OK | 3327262720 | 0 | 0
+ creator_rev | 0 | OK | 388726784 | 0 | 0
+ work_ident | 0 | OK | 5128560640 | 0 | 0
+ work_edit | 0 | OK | 6993108992 | 0 | 0
+ container_ident | 0 | OK | 25092096 | 0 | 0
+ file_edit | 0 | OK | 598278144 | 0 | 0
+ container_edit | 0 | OK | 33857536 | 0 | 0
+ changelog | 0 | OK | 127549440 | 0 | 0
+ abstracts | -4714 | OK | 1706713088 | 0 | 4714
+ file_release | -13583 | OK | 401752064 | 0 | 13583
+ file_rev_url | -13583 | OK | 3832389632 | 0 | 13583
+ editgroup | -74109 | OK | 144277504 | 0 | 74109
+ release_contrib | -76699 | OK | 20357849088 | 0 | 76699
+ release_ref | -76700 | OK | 183009157120 | 3 | 76703
+ release_rev_abstract | -76939 | OK | 192102400 | 0 | 76939
+ release_rev | -77965 | OK | 47602647040 | 0 | 77965
+ file_ident | -100089 | OK | 438255616 | 3 | 100092
+ release_ident | -152809 | OK | 5128617984 | 0 | 152809
+ file_rev | -440780 | OK | 837705728 | 0 | 440780
+(23 rows)
+
+Continuing imports:
+
+ zcat /srv/fatcat/datasets/2018-08-27-2352.17-matchcrossref.insertable.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched -
+ => HTTP response body: {"message":"duplicate key value violates unique constraint \"file_edit_editgroup_id_ident_id_key\""}
+
diff --git a/notes/bootstrap/import_timing_20180923.txt b/notes/bootstrap/import_timing_20180923.txt
new file mode 100644
index 00000000..c7161842
--- /dev/null
+++ b/notes/bootstrap/import_timing_20180923.txt
@@ -0,0 +1,91 @@
+
+ 105595.18user 3903.65system 15:59:39elapsed 190%CPU (0avgtext+0avgdata 458836maxresident)k
+ 71022792inputs+327828472outputs (176major+31149593minor)pagefaults 0swaps
+
+ real 959m39.521s
+ user 1845m10.392s
+ sys 70m33.780s
+
+Did I get the same error again? I'm confused:
+
+ HTTP response body: {"message":"number of parameters must be between 0 and 65535\n"}
+ (but not in all threads)
+
+Yes, ugh, because 50*2500 can be over (it's not just individual large releases,
+they come in big batches).
+
+But:
+
+ select count(id) from release_ident; => 70006121
+
+A lot, though not 72 million like last time, hrm. I'm... going to move ahead I
+guess.
+
+"Processed 4440850 lines, inserted 3509600, updated 0."
+ => implies 79029915 records
+
+ time zcat /srv/fatcat/datasets/ia_papers_manifest_2018-01-25.matched.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched --no-file-update -
+ Processed 530750 lines, inserted 435239, updated 0. (etc)
+ Command exited with non-zero status 1
+ 15121.47user 676.49system 2:23:52elapsed 183%CPU (0avgtext+0avgdata 70076maxresident)k
+ 127760inputs+3477184outputs (116major+475489minor)pagefaults 0swaps
+
+ real 143m52.681s
+ user 252m31.620s
+ sys 11m21.608s
+
+ zcat /srv/fatcat/datasets/2018-08-27-2352.17-matchcrossref.insertable.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched -
+
+ Processed 485200 lines, inserted 244101, updated 168344. (etc)
+ 22671.44user 1069.84system 3:27:47elapsed 190%CPU (0avgtext+0avgdata 39348maxresident)k
+ 99672inputs+2497848outputs (109major+422150minor)pagefaults 0swaps
+
+fatcat-export dump:
+
+ INFO 2018-09-25T10:01:06Z: fatcat_export: Done reading (70006121 lines), waiting for workers to exit...
+ 197GiB 4:56:17 [11.4MiB/s] [ <=> ]
+
+How big is everything?
+
+ select count(*) from file_release; => 10,485,964
+ select count (distinct target_release_ident_id) from file_release; => 6,486,934
+ select count(id) from release_ident; => 70,006,121
+ select count(*) from container_ident; => 354,793
+ select count(*) from creator_ident; => 3,906,990
+ Size: 324.24G
+ /dev/vda1 1.8T 511G 1.2T 31% /
+
+ table_name | table_size | indexes_size | total_size
+--------------------------------------------------------------+------------+--------------+------------
+ "public"."release_ref" | 121 GB | 42 GB | 163 GB
+ "public"."release_rev" | 33 GB | 19 GB | 52 GB
+ "public"."release_contrib" | 21 GB | 18 GB | 39 GB
+ "public"."release_edit" | 6218 MB | 6084 MB | 12 GB
+ "public"."work_edit" | 6218 MB | 6084 MB | 12 GB
+ "public"."release_ident" | 4560 MB | 5470 MB | 10030 MB
+ "public"."work_ident" | 4560 MB | 5466 MB | 10027 MB
+ "public"."file_rev_url" | 5543 MB | 2112 MB | 7655 MB
+ "public"."work_rev" | 2958 MB | 2733 MB | 5691 MB
+ "public"."file_rev" | 1201 MB | 1811 MB | 3012 MB
+ "public"."abstracts" | 2294 MB | 184 MB | 2478 MB
+ "public"."file_edit" | 931 MB | 864 MB | 1795 MB
+ "public"."file_release" | 605 MB | 1058 MB | 1663 MB
+ "public"."file_ident" | 529 MB | 633 MB | 1162 MB
+ "public"."creator_rev" | 371 MB | 456 MB | 826 MB
+ "public"."creator_edit" | 347 MB | 352 MB | 699 MB
+ "public"."release_rev_abstract" | 250 MB | 325 MB | 575 MB
+ "public"."creator_ident" | 255 MB | 304 MB | 559 MB
+ "public"."changelog" | 122 MB | 127 MB | 250 MB
+ "public"."editgroup" | 138 MB | 82 MB | 220 MB
+ "public"."container_rev" | 52 MB | 38 MB | 89 MB
+ "public"."container_edit" | 32 MB | 30 MB | 62 MB
+ "public"."container_ident" | 24 MB | 28 MB | 52 MB
+
+Hrm, bunch of not-accepted containers:
+
+ select count(*) from container_ident where is_live='f'; => 301507
+ select count(*) from release_ident where is_live='f'; => 0
+ select count(*) from work_ident where is_live='f'; => 0
+ select count(*) from creator_ident where is_live='f'; => 1 (there was a hang earlier)
+ select count(*) from file_ident where is_live='f'; => 0
+
diff --git a/notes/bootstrap/initial_sources.txt b/notes/bootstrap/initial_sources.txt
new file mode 100644
index 00000000..cc22019d
--- /dev/null
+++ b/notes/bootstrap/initial_sources.txt
@@ -0,0 +1,26 @@
+
+Probably start with:
+
+ crossref (including citations)
+ arxiv
+ medline
+
+then merge in:
+
+ dblp
+ CORE
+ MSAG dump
+ VIAF
+ archive.org paper/url manifest
+ semantic scholar
+ oaDOI
+
+and later:
+
+ wikidata
+ opencitations
+ openlibrary
+
+national libraries:
+
+ http://www.dnb.de/EN/Service/DigitaleDienste/LinkedData/linkeddata_node.html
diff --git a/notes/bootstrap/old_imports.txt b/notes/bootstrap/old_imports.txt
new file mode 100644
index 00000000..1233d4a8
--- /dev/null
+++ b/notes/bootstrap/old_imports.txt
@@ -0,0 +1,20 @@
+
+## ORCID
+
+Directly from compressed tarball; takes about 2 hours in production:
+
+ tar xf /srv/datasets/public_profiles_API-2.0_2017_10_json.tar.gz -O | jq -c . | grep '"person":' | time parallel -j12 --pipe --round-robin ./fatcat_import.py import-orcid -
+
+After tuning database, `jq` CPU seems to be bottleneck, so, from pre-extracted
+tarball:
+
+ tar xf /srv/datasets/public_profiles_API-2.0_2017_10_json.tar.gz -O | jq -c . | rg '"person":' > /srv/datasets/public_profiles_1_2_json.all.json
+ time parallel --bar --pipepart -j8 -a /srv/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid -
+
+Does not work:
+
+ ./fatcat_import.py import-orcid /data/orcid/partial/public_profiles_API-2.0_2017_10_json/3/0000-0001-5115-8623.json
+
+Instead:
+
+ cat /data/orcid/partial/public_profiles_API-2.0_2017_10_json/3/0000-0001-5115-8623.json | jq -c . | ./fatcat_import.py import-orcid -