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diff --git a/notes/es-indexing.md b/notes/es-indexing.md new file mode 100644 index 0000000..04fca2e --- /dev/null +++ b/notes/es-indexing.md @@ -0,0 +1,103 @@ + +Going to do some initial indexing of refs ("BiblioRefs" schema) into +elasticsearch 7 cluster. + +## 2021-04-12 + +Reduced `number_of_shards` from 12 to 6. + +Create index from schema: + + # note, *not* include_type_name=true in the URL + http put :9200/fatcat_ref_v01 < ref_schema.json + +Force all shards to a single machine (wbgrp-svc500): + + http put ":9200/fatcat_ref_v01/_settings" index.routing.allocation.include._name=wbgrp-svc500 + + # would run this later, after adding more nodes to list, for production deployment + #http put ":9200/fatcat_ref_v01/_settings" index.number_of_replicas=1 + +Confirm shard locations: + + http get :9200/_cat/shards/fatcat_ref_v01 + + fatcat_ref_v01 3 p STARTED 0 208b 207.241.225.228 wbgrp-svc500 + fatcat_ref_v01 1 p STARTED 0 208b 207.241.225.228 wbgrp-svc500 + fatcat_ref_v01 2 p STARTED 0 208b 207.241.225.228 wbgrp-svc500 + fatcat_ref_v01 4 p STARTED 0 208b 207.241.225.228 wbgrp-svc500 + fatcat_ref_v01 5 p STARTED 0 208b 207.241.225.228 wbgrp-svc500 + fatcat_ref_v01 0 p STARTED 0 208b 207.241.225.228 wbgrp-svc500 + +Copied over `aitio:/magna/refcat/BiblioRefV2/date-2021-02-20.json.zst`, which +seems to have been output on 2021-03-24 (the date in the filename refers to the +date of the source raw reference dump, I believe). + + du -sh /srv/fatcat/datasets/date-2021-02-20.json.zst + 39G /srv/fatcat/datasets/date-2021-02-20.json.zst + +Check that esbulk is updated: + + esbulk -v + 0.7.3 + +Expecting on the order of: + + 785,569,011 edges (~103% of 12/2020 OCI/crossref release), ~39G compressed, ~288G uncompressed + +Start with 1 million documents to index: + + zstdcat /srv/fatcat/datasets/date-2021-02-20.json.zst | head -n1000000 | esbulk -verbose -size 2000 -id _id -w 8 -index fatcat_ref_v01 + + => 2021/04/13 02:55:17 1000000 docs in 19.89s at 50265.935 docs/s with 8 workers + + => green open fatcat_ref_v01 tpHidEK_RSSrY0YDYgTH2Q 6 0 983111 16889 305.5mb 305.5mb + +Very fast! + +Not 1 million documents; presumably some duplication due to duplicate checks? +If we thought we could extrapolate from 1mil ~= 0.3 GB, then 1bil ~= 300 GByte, +which seems pretty reasonable. + +Bump to 20 million: + + zstdcat /srv/fatcat/datasets/date-2021-02-20.json.zst | head -n20000000 | esbulk -verbose -size 2000 -id _id -w 8 -index fatcat_ref_v01 + + => 2021/04/13 03:05:17 20000000 docs in 396.53s at 50437.434 docs/s with 8 workers + + => green open fatcat_ref_v01 tpHidEK_RSSrY0YDYgTH2Q 6 0 19731816 171926 5.4gb 5.4gb + +Configured es-public-proxy to enable public access to `fatcat_ref`, and added an alias: + + http put :9200/fatcat_ref_v01/_alias/fatcat_ref + +Crude queries are like: + + http https://search.fatcat.wiki/fatcat_ref/_search q==target_work_ident:o547luzdqragbd66ejlm4pughi + +Seems like these were all join/exact matches. Would like some others, so do an additional `shuf` instead of head: + + zstdcat /srv/fatcat/datasets/date-2021-02-20.json.zst | shuf -n20000000 | esbulk -verbose -size 2000 -id _id -w 8 -index fatcat_ref_v01 + +Interestingly, `shuf` takes more CPU than `zstdcat`, presumably because it is +doing a lot of random number generation. Note that `shuf` uses reservoir +sampling, so is usually pretty efficient. + +Back over on `aitio`, trying: + + zstdcat /magna/tmp/date-2021-02-20.json.zst | jq ._id -c | sort -u | wc -l + +Ok, just run the whole thing: + + zstdcat /srv/fatcat/datasets/date-2021-02-20.json.zst | esbulk -verbose -size 2000 -id _id -w 8 -index fatcat_ref_v01 + + => 2021/04/13 10:10:12 785569011 docs in 22309.29s at 35212.641 docs/s with 8 workers + => green open fatcat_ref_v01 tpHidEK_RSSrY0YDYgTH2Q 6 0 734856532 38611510 184.2gb 184.2gb + +Took a bit over 6 hours, and ~180 GByte total index size. Nice! + +## Notes and Thoughts + +- many of the `ref_key` are pretty large, like `bibr4-0036933016674866`. Maybe these can be parsed down. +- might want aggregations on `source_release_stage`, `source_year`, etc? +- `update_ts` may not have come through correctly? it is an integer, not a datetime |