Why Loading ZINC Is So Slow

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the problem is with the "resolution" and "loading" steps of the catalog script. these steps ensure the uniqueness of molecules in the substance and catalog_substance table respectively

a. sorting & queries

in order to be sure that each molecule is unique, the database must effectively sort molecules as they come in- this is equivalent to a btree select+insert for each new molecule

THEORETICALLY this is fine, but practically it is not

when relatively few molecules are being added to the database this is fine, but for large inserts on a large database this becomes inefficient

there is a significant amount of overhead involved in each select, at least compared to the insert operation when done in bulk

the solution is to ensure the uniqueness of each molecule *before* they are inserted into the database. this can be done by a sorting program like `sort -u`

it is better to load the entire dataset in memory and sort it manually beforehand than to let the database software figure it out as we gradually feed it the data

dropping the select operations allows us to make a further optimization... (see b)

b. indexes

there are a lot of indexes on the substance and catalog data

indexes tend to slow down insert operations significantly (https://use-the-index-luke.com/sql/dml/insert), for large operations this becomes intolerable

the solution is to "shut off" the indexes for the duration of the insert operation and rebuild them once it has completed

again, it is better to build the indexes when the entire table is loaded rather than piece-by-piece

c. improvement

after disabling the loading and resolution steps, turning off indices, and manually sorting, the time it took to load 2.34m molecules into ZINC went from

12+ hours (maybe more, i never let it finish)

down to

1 hour

and the uniqueness of the molecules is still preserved


at it's core this is a balance issue- having to both insert and select for a query means making sacrifices. let me explain: in order to make select fast (sub O(n) time), you need to create indexes for the table. in order to make insert fast (O(1)- constant time) you need to disable indexes for the table. if you need to perform both operations in the same query, you must sacrifice one's performance for the other. by removing the select operation from this query, we can utilize the full speed-up for an insert.