start organizing notes into subdirectories

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diff --git a/notes/import_timing_20180908.txt b/notes/import_timing_20180908.txt
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--- a/notes/import_timing_20180908.txt
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@@ -1,249 +0,0 @@
-
-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.
-