IO:DataFileRead - Amazon Aurora

IO:DataFileRead

The IO:DataFileRead event occurs when a connection waits on a backend process to read a required page from storage because the page isn't available in shared memory.

Supported engine versions

This wait event information is supported for all versions of Aurora PostgreSQL.

Context

All queries and data manipulation (DML) operations access pages in the buffer pool. Statements that can induce reads include SELECT, UPDATE, and DELETE. For example, an UPDATE can read pages from tables or indexes. If the page being requested or updated isn't in the shared buffer pool, this read can lead to the IO:DataFileRead event.

Because the shared buffer pool is finite, it can fill up. In this case, requests for pages that aren't in memory force the database to read blocks from disk. If the IO:DataFileRead event occurs frequently, your shared buffer pool might be too small to accommodate your workload. This problem is acute for SELECT queries that read a large number of rows that don't fit in the buffer pool. For more information about the buffer pool, see Buffer pool.

Likely causes of increased waits

Common causes for the IO:DataFileRead event include the following:

Connection spikes

You might find multiple connections generating the same number of IO:DataFileRead wait events. In this case, a spike (sudden and large increase) in IO:DataFileRead events can occur.

SELECT and DML statements performing sequential scans

Your application might be performing a new operation. Or an existing operation might change because of a new execution plan. In such cases, look for tables (particularly large tables) that have a greater seq_scan value. Find them by querying pg_stat_user_tables. To track queries that are generating more read operations, use the extension pg_stat_statements.

CTAS and CREATE INDEX for large data sets

A CTAS is a CREATE TABLE AS SELECT statement. If you run a CTAS using a large data set as a source, or create an index on a large table, the IO:DataFileRead event can occur. When you create an index, the database might need to read the entire object using a sequential scan. A CTAS generates IO:DataFile reads when pages aren't in memory.

Multiple vacuum workers running at the same time

Vacuum workers can be triggered manually or automatically. We recommend adopting an aggressive vacuum strategy. However, when a table has many updated or deleted rows, the IO:DataFileRead waits increase. After space is reclaimed, the vacuum time spent on IO:DataFileRead decreases.

Ingesting large amounts of data

When your application ingests large amounts of data, ANALYZE operations might occur more often. The ANALYZE process can be triggered by an autovacuum launcher or invoked manually.

The ANALYZE operation reads a subset of the table. The number of pages that must be scanned is calculated by multiplying 30 by the default_statistics_target value. For more information, see the PostgreSQL documentation. The default_statistics_target parameter accepts values between 1 and 10,000, where the default is 100.

Resource starvation

If instance network bandwidth or CPU are consumed, the IO:DataFileRead event might occur more frequently.

Actions

We recommend different actions depending on the causes of your wait event.

Check predicate filters for queries that generate waits

Assume that you identify specific queries that are generating IO:DataFileRead wait events. You might identify them using the following techniques:

  • Performance Insights

  • Catalog views such as the one provided by the extension pg_stat_statements

  • The catalog view pg_stat_all_tables, if it periodically shows an increased number of physical reads

  • The pg_statio_all_tables view, if it shows that _read counters are increasing

We recommend that you determine which filters are used in the predicate (WHERE clause) of these queries. Follow these guidelines:

  • Run the EXPLAIN command. In the output, identify which types of scans are used. A sequential scan doesn't necessarily indicate a problem. Queries that use sequential scans naturally produce more IO:DataFileRead events when compared to queries that use filters.

    Find out whether the column listed in the WHERE clause is indexed. If not, consider creating an index for this column. This approach avoids the sequential scans and reduces the IO:DataFileRead events. If a query has restrictive filters and still produces sequential scans, evaluate whether the proper indexes are being used.

  • Find out whether the query is accessing a very large table. In some cases, partitioning a table can improve performance, allowing the query to only read necessary partitions.

  • Examine the cardinality (total number of rows) from your join operations. Note how restrictive the values are that you're passing in the filters for your WHERE clause. If possible, tune your query to reduce the number of rows that are passed in each step of the plan.

Minimize the effect of maintenance operations

Maintenance operations such as VACUUM and ANALYZE are important. We recommend that you don't turn them off because you find IO:DataFileRead wait events related to these maintenance operations. The following approaches can minimize the effect of these operations:

  • Run maintenance operations manually during off-peak hours. This technique prevents the database from reaching the threshold for automatic operations.

  • For very large tables, consider partitioning the table. This technique reduces the overhead of maintenance operations. The database only accesses the partitions that require maintenance.

  • When you ingest large amounts of data, consider disabling the autoanalyze feature.

The autovacuum feature is automatically triggered for a table when the following formula is true.

pg_stat_user_tables.n_dead_tup > (pg_class.reltuples x autovacuum_vacuum_scale_factor) + autovacuum_vacuum_threshold

The view pg_stat_user_tables and catalog pg_class have multiple rows. One row can correspond to one row in your table. This formula assumes that the reltuples are for a specific table. The parameters autovacuum_vacuum_scale_factor (0.20 by default) and autovacuum_vacuum_threshold (50 tuples by default) are usually set globally for the whole instance. However, you can set different values for a specific table.

Find tables consuming unnecessary space

To find tables consuming unnecessary space, run the following query.

/* WARNING: Run with a nonsuperuser role, the query inspects only tables * that you have the permission to read. * This query is compatible with PostgreSQL 9.0 and later. */ SELECT current_database(), schemaname, tblname, bs*tblpages AS real_size, (tblpages-est_tblpages)*bs AS extra_size, CASE WHEN tblpages - est_tblpages > 0 THEN 100 * (tblpages - est_tblpages)/tblpages::float ELSE 0 END AS extra_ratio, fillfactor, (tblpages-est_tblpages_ff)*bs AS bloat_size, CASE WHEN tblpages - est_tblpages_ff > 0 THEN 100 * (tblpages - est_tblpages_ff)/tblpages::float ELSE 0 END AS bloat_ratio, is_na -- , (pst).free_percent + (pst).dead_tuple_percent AS real_frag FROM ( SELECT ceil( reltuples / ( (bs-page_hdr)/tpl_size ) ) + ceil( toasttuples / 4 ) AS est_tblpages, ceil( reltuples / ( (bs-page_hdr)*fillfactor/(tpl_size*100) ) ) + ceil( toasttuples / 4 ) AS est_tblpages_ff, tblpages, fillfactor, bs, tblid, schemaname, tblname, heappages, toastpages, is_na -- , stattuple.pgstattuple(tblid) AS pst FROM ( SELECT ( 4 + tpl_hdr_size + tpl_data_size + (2*ma) - CASE WHEN tpl_hdr_size%ma = 0 THEN ma ELSE tpl_hdr_size%ma END - CASE WHEN ceil(tpl_data_size)::int%ma = 0 THEN ma ELSE ceil(tpl_data_size)::int%ma END ) AS tpl_size, bs - page_hdr AS size_per_block, (heappages + toastpages) AS tblpages, heappages, toastpages, reltuples, toasttuples, bs, page_hdr, tblid, schemaname, tblname, fillfactor, is_na FROM ( SELECT tbl.oid AS tblid, ns.nspname AS schemaname, tbl.relname AS tblname, tbl.reltuples, tbl.relpages AS heappages, coalesce(toast.relpages, 0) AS toastpages, coalesce(toast.reltuples, 0) AS toasttuples, coalesce(substring( array_to_string(tbl.reloptions, ' ') FROM 'fillfactor=([0-9]+)')::smallint, 100) AS fillfactor, current_setting('block_size')::numeric AS bs, CASE WHEN version()~'mingw32' OR version()~'64-bit|x86_64|ppc64|ia64|amd64' THEN 8 ELSE 4 END AS ma, 24 AS page_hdr, 23 + CASE WHEN MAX(coalesce(null_frac,0)) > 0 THEN ( 7 + count(*) ) / 8 ELSE 0::int END + CASE WHEN tbl.relhasoids THEN 4 ELSE 0 END AS tpl_hdr_size, sum( (1-coalesce(s.null_frac, 0)) * coalesce(s.avg_width, 1024) ) AS tpl_data_size, bool_or(att.atttypid = 'pg_catalog.name'::regtype) OR count(att.attname) <> count(s.attname) AS is_na FROM pg_attribute AS att JOIN pg_class AS tbl ON att.attrelid = tbl.oid JOIN pg_namespace AS ns ON ns.oid = tbl.relnamespace LEFT JOIN pg_stats AS s ON s.schemaname=ns.nspname AND s.tablename = tbl.relname AND s.inherited=false AND s.attname=att.attname LEFT JOIN pg_class AS toast ON tbl.reltoastrelid = toast.oid WHERE att.attnum > 0 AND NOT att.attisdropped AND tbl.relkind = 'r' GROUP BY 1,2,3,4,5,6,7,8,9,10, tbl.relhasoids ORDER BY 2,3 ) AS s ) AS s2 ) AS s3 ; -- WHERE NOT is_na -- AND tblpages*((pst).free_percent + (pst).dead_tuple_percent)::float4/100 >= 1

Find indexes consuming unnecessary space

To find indexes consuming unnecessary space, run the following query.

-- WARNING: run with a nonsuperuser role, the query inspects -- only indexes on tables you have permissions to read. -- WARNING: rows with is_na = 't' are known to have bad statistics ("name" type is not supported). -- This query is compatible with PostgreSQL 8.2 and later. SELECT current_database(), nspname AS schemaname, tblname, idxname, bs*(relpages)::bigint AS real_size, bs*(relpages-est_pages)::bigint AS extra_size, 100 * (relpages-est_pages)::float / relpages AS extra_ratio, fillfactor, bs*(relpages-est_pages_ff) AS bloat_size, 100 * (relpages-est_pages_ff)::float / relpages AS bloat_ratio, is_na -- , 100-(sub.pst).avg_leaf_density, est_pages, index_tuple_hdr_bm, -- maxalign, pagehdr, nulldatawidth, nulldatahdrwidth, sub.reltuples, sub.relpages -- (DEBUG INFO) FROM ( SELECT coalesce(1 + ceil(reltuples/floor((bs-pageopqdata-pagehdr)/(4+nulldatahdrwidth)::float)), 0 -- ItemIdData size + computed avg size of a tuple (nulldatahdrwidth) ) AS est_pages, coalesce(1 + ceil(reltuples/floor((bs-pageopqdata-pagehdr)*fillfactor/(100*(4+nulldatahdrwidth)::float))), 0 ) AS est_pages_ff, bs, nspname, table_oid, tblname, idxname, relpages, fillfactor, is_na -- , stattuple.pgstatindex(quote_ident(nspname)||'.'||quote_ident(idxname)) AS pst, -- index_tuple_hdr_bm, maxalign, pagehdr, nulldatawidth, nulldatahdrwidth, reltuples -- (DEBUG INFO) FROM ( SELECT maxalign, bs, nspname, tblname, idxname, reltuples, relpages, relam, table_oid, fillfactor, ( index_tuple_hdr_bm + maxalign - CASE -- Add padding to the index tuple header to align on MAXALIGN WHEN index_tuple_hdr_bm%maxalign = 0 THEN maxalign ELSE index_tuple_hdr_bm%maxalign END + nulldatawidth + maxalign - CASE -- Add padding to the data to align on MAXALIGN WHEN nulldatawidth = 0 THEN 0 WHEN nulldatawidth::integer%maxalign = 0 THEN maxalign ELSE nulldatawidth::integer%maxalign END )::numeric AS nulldatahdrwidth, pagehdr, pageopqdata, is_na -- , index_tuple_hdr_bm, nulldatawidth -- (DEBUG INFO) FROM ( SELECT i.nspname, i.tblname, i.idxname, i.reltuples, i.relpages, i.relam, a.attrelid AS table_oid, current_setting('block_size')::numeric AS bs, fillfactor, CASE -- MAXALIGN: 4 on 32bits, 8 on 64bits (and mingw32 ?) WHEN version() ~ 'mingw32' OR version() ~ '64-bit|x86_64|ppc64|ia64|amd64' THEN 8 ELSE 4 END AS maxalign, /* per page header, fixed size: 20 for 7.X, 24 for others */ 24 AS pagehdr, /* per page btree opaque data */ 16 AS pageopqdata, /* per tuple header: add IndexAttributeBitMapData if some cols are null-able */ CASE WHEN max(coalesce(s.null_frac,0)) = 0 THEN 2 -- IndexTupleData size ELSE 2 + (( 32 + 8 - 1 ) / 8) -- IndexTupleData size + IndexAttributeBitMapData size ( max num filed per index + 8 - 1 /8) END AS index_tuple_hdr_bm, /* data len: we remove null values save space using it fractionnal part from stats */ sum( (1-coalesce(s.null_frac, 0)) * coalesce(s.avg_width, 1024)) AS nulldatawidth, max( CASE WHEN a.atttypid = 'pg_catalog.name'::regtype THEN 1 ELSE 0 END ) > 0 AS is_na FROM pg_attribute AS a JOIN ( SELECT nspname, tbl.relname AS tblname, idx.relname AS idxname, idx.reltuples, idx.relpages, idx.relam, indrelid, indexrelid, indkey::smallint[] AS attnum, coalesce(substring( array_to_string(idx.reloptions, ' ') from 'fillfactor=([0-9]+)')::smallint, 90) AS fillfactor FROM pg_index JOIN pg_class idx ON idx.oid=pg_index.indexrelid JOIN pg_class tbl ON tbl.oid=pg_index.indrelid JOIN pg_namespace ON pg_namespace.oid = idx.relnamespace WHERE pg_index.indisvalid AND tbl.relkind = 'r' AND idx.relpages > 0 ) AS i ON a.attrelid = i.indexrelid JOIN pg_stats AS s ON s.schemaname = i.nspname AND ((s.tablename = i.tblname AND s.attname = pg_catalog.pg_get_indexdef(a.attrelid, a.attnum, TRUE)) -- stats from tbl OR (s.tablename = i.idxname AND s.attname = a.attname)) -- stats from functionnal cols JOIN pg_type AS t ON a.atttypid = t.oid WHERE a.attnum > 0 GROUP BY 1, 2, 3, 4, 5, 6, 7, 8, 9 ) AS s1 ) AS s2 JOIN pg_am am ON s2.relam = am.oid WHERE am.amname = 'btree' ) AS sub -- WHERE NOT is_na ORDER BY 2,3,4;

Find tables that are eligible to be autovacuumed

To find tables that are eligible to be autovacuumed, run the following query.

--This query shows tables that need vacuuming and are eligible candidates. --The following query lists all tables that are due to be processed by autovacuum. -- During normal operation, this query should return very little. WITH vbt AS (SELECT setting AS autovacuum_vacuum_threshold FROM pg_settings WHERE name = 'autovacuum_vacuum_threshold') , vsf AS (SELECT setting AS autovacuum_vacuum_scale_factor FROM pg_settings WHERE name = 'autovacuum_vacuum_scale_factor') , fma AS (SELECT setting AS autovacuum_freeze_max_age FROM pg_settings WHERE name = 'autovacuum_freeze_max_age') , sto AS (SELECT opt_oid, split_part(setting, '=', 1) as param, split_part(setting, '=', 2) as value FROM (SELECT oid opt_oid, unnest(reloptions) setting FROM pg_class) opt) SELECT '"'||ns.nspname||'"."'||c.relname||'"' as relation , pg_size_pretty(pg_table_size(c.oid)) as table_size , age(relfrozenxid) as xid_age , coalesce(cfma.value::float, autovacuum_freeze_max_age::float) autovacuum_freeze_max_age , (coalesce(cvbt.value::float, autovacuum_vacuum_threshold::float) + coalesce(cvsf.value::float,autovacuum_vacuum_scale_factor::float) * c.reltuples) as autovacuum_vacuum_tuples , n_dead_tup as dead_tuples FROM pg_class c JOIN pg_namespace ns ON ns.oid = c.relnamespace JOIN pg_stat_all_tables stat ON stat.relid = c.oid JOIN vbt on (1=1) JOIN vsf ON (1=1) JOIN fma on (1=1) LEFT JOIN sto cvbt ON cvbt.param = 'autovacuum_vacuum_threshold' AND c.oid = cvbt.opt_oid LEFT JOIN sto cvsf ON cvsf.param = 'autovacuum_vacuum_scale_factor' AND c.oid = cvsf.opt_oid LEFT JOIN sto cfma ON cfma.param = 'autovacuum_freeze_max_age' AND c.oid = cfma.opt_oid WHERE c.relkind = 'r' AND nspname <> 'pg_catalog' AND ( age(relfrozenxid) >= coalesce(cfma.value::float, autovacuum_freeze_max_age::float) or coalesce(cvbt.value::float, autovacuum_vacuum_threshold::float) + coalesce(cvsf.value::float,autovacuum_vacuum_scale_factor::float) * c.reltuples <= n_dead_tup -- or 1 = 1 ) ORDER BY age(relfrozenxid) DES;

Respond to high numbers of connections

When you monitor Amazon CloudWatch, you might find that the DatabaseConnections metric spikes. This increase indicates an increased number of connections to your database. We recommend the following approach:

  • Limit the number of connections that the application can open with each instance. If your application has an embedded connection pool feature, set a reasonable number of connections. Base the number on what the vCPUs in your instance can parallelize effectively.

    If your application doesn't use a connection pool feature, considering using Amazon RDS Proxy or an alternative. This approach lets your application open multiple connections with the load balancer. The balancer can then open a restricted number of connections with the database. As fewer connections are running in parallel, your DB instance performs less context switching in the kernel. Queries should progress faster, leading to fewer wait events. For more information, see Using Amazon RDS Proxy.

  • Whenever possible, take advantage of reader nodes for Aurora PostgreSQL and read replicas for RDS for PostgreSQL. When your application runs a read-only operation, send these requests to the reader-only endpoint. This technique spreads application requests across all reader nodes, reducing the I/O pressure on the writer node.

  • Consider scaling up your DB instance. A higher-capacity instance class gives more memory, which gives Aurora PostgreSQL a larger shared buffer pool to hold pages. The larger size also gives the DB instance more vCPUs to handle connections. More vCPUs are particularly helpful when the operations that are generating IO:DataFileRead wait events are writes.