Very slow PSQL query with several JOINs

Question

I've been having problems with super slow query in PostgreSQL.

DB ER diagram part focused in this problem:

Table culture has 6 records, table microclimate_value has roughly 190k records, table location has 3 records and table crop_yield has roughly 40k records.

Query:

SELECT max(cy.value) AS yield, EXTRACT(YEAR FROM cy.date) AS year
FROM microclimate_value AS mv
JOIN culture AS c ON mv.id_culture = c.id
JOIN location AS l ON mv.id_location = l.id
JOIN crop_yield AS cy ON l.id = cy.id_location
WHERE c.id = :cultureId AND l.id = :locationId
GROUP BY year
ORDER BY year

This query should result with max value from (crop_yield table) for every year for given :cultureId (primary key from culture table) and :locationId (primary key from location table). It would look something like this (yield == value column from crop_yield table):

[
    {
        "year": 2014,
        "yield": 0.0
    },
    {
        "year": 2015,
        "yield": 1972.6590590838807
    },
    {
        "year": 2016,
        "yield": 3254.6370785040726
    },
    {
        "year": 2017,
        "yield": 2335.5804000689095
    },
    {
        "year": 2018,
        "yield": 3345.2244602819046
    },
    {
        "year": 2019,
        "yield": 3004.7096788680583
    },
    {
        "year": 2020,
        "yield": 2920.8721807693764
    },
    {
        "year": 2021,
        "yield": 0.0
    }
]

Enhancement attempt:

Initially, this query took around 10 minutes, so there is some big problem with optimization or with the query itself. The first thing I did was indexing foreign keys in microclimate_value and crop_yield table, which resulted in far better performance, but the query still takes 2-3 minutes to execute.

Does anyone have any tip on how to improve this? I am open for any tips, including changing the whole schema if needed, considering the fact I'm still learning SQL.

Thanks in advance!

Edit:

Adding EXPLAIN PSQL

Adding second EXPLAIN ANALYZE PSQL after adding indexes:

user_271959 · Answer

Make some combinations of columns in a single index. I would start with this, to get rid of all the filtering after searching for the data:

CREATE INDEX idx_crop_yield_id_location_year_value ON crop_yield(id_location, (EXTRACT ( YEAR FROM DATE )), value);

CREATE INDEX idx_microclimate_value_id_location_id_culture ON microclimate_value(id_location, id_culture);

Maybe a different order in the columns works better, that's something you have to find out.

I would also leave the unused table "culture" out:

SELECT MAX( cy.VALUE ) AS yield,
    EXTRACT ( YEAR FROM cy.DATE ) AS YEAR 
FROM
    microclimate_value AS mv
        JOIN LOCATION AS l ON mv.id_location = l.ID 
        JOIN crop_yield AS cy ON l.ID = cy.id_location 
WHERE
    mv.id_culture = : cultureId 
AND l.ID = : locationId 
GROUP BY    YEAR 
ORDER BY    YEAR;

And after every change in the query or the indexes, run EXPLAIN(ANALYZE, VERBOSE, BUFFERS) again.

Tometzky_15862 · Answer

Based on your explain analyze there are 10,970 rows of microclimate_value for location=2 and id_culture=1. Also there are 12,316 rows for location=2 in crop_yield.

As there is no other condition for join of those 2 tables, the database has to create in memory a table with 10,970*12,316=135,106,520 rows and then group its results. It might take some time…

I think you are missing some condition in your query. Are you sure there should not be the same date on microclimate_value.date and crop_yield.date? Because, IMHO, without it, the query does not make much sense.

If there's no connection with those dates, then the only information that might be useful in microclimate_value is whether matching location_id=? and culture_id=? exists there:

select
  max(value) as max_value,
  extract(year from date) as year,
from crop_yield
where location_id=?
  and exists(
    select 1
    from microclimate_value
    where location_id=? and culture_id=?
  )
group by year

You'll either get results, if they match somewhere, or won't get any. The design of this schema seems questionable.

Very slow PSQL query with several JOINs

2 Answers