Feb
21
2019
--

Parallel queries in PostgreSQL

parallel queries in postgresql

PostgreSQL logoModern CPU models have a huge number of cores. For many years, applications have been sending queries in parallel to databases. Where there are reporting queries that deal with many table rows, the ability for a query to use multiple CPUs helps us with a faster execution. Parallel queries in PostgreSQL allow us to utilize many CPUs to finish report queries faster. The parallel queries feature was implemented in 9.6 and helps. Starting from PostgreSQL 9.6 a report query is able to use many CPUs and finish faster.

The initial implementation of the parallel queries execution took three years. Parallel support requires code changes in many query execution stages. PostgreSQL 9.6 created an infrastructure for further code improvements. Later versions extended parallel execution support for other query types.

Limitations

  • Do not enable parallel executions if all CPU cores are already saturated. Parallel execution steals CPU time from other queries, and increases response time.
  • Most importantly, parallel processing significantly increases memory usage with high WORK_MEM values, as each hash join or sort operation takes a work_mem amount of memory.
  • Next, low latency OLTP queries can’t be made any faster with parallel execution. In particular, queries that returns a single row can perform badly when parallel execution is enabled.
  • The Pierian spring for developers is a TPC-H benchmark. Check if you have similar queries for the best parallel execution.
  • Parallel execution supports only SELECT queries without lock predicates.
  • Proper indexing might be a better alternative to a parallel sequential table scan.
  • There is no support for cursors or suspended queries.
  • Windowed functions and ordered-set aggregate functions are non-parallel.
  • There is no benefit for an IO-bound workload.
  • There are no parallel sort algorithms. However, queries with sorts still can be parallel in some aspects.
  • Replace CTE (WITH …) with a sub-select to support parallel execution.
  • Foreign data wrappers do not currently support parallel execution (but they could!)
  • There is no support for FULL OUTER JOIN.
  • Clients setting max_rows disable parallel execution.
  • If a query uses a function that is not marked as PARALLEL SAFE, it will be single-threaded.
  • SERIALIZABLE transaction isolation level disables parallel execution.

Test environment

The PostgreSQL development team have tried to improve TPC-H benchmark queries’ response time. You can download the benchmark and adapt it to PostgreSQL by using these instructions. It’s not an official way to use the TPC-H benchmark, so you shouldn’t use it to compare different databases or hardware.

  1. Download TPC-H_Tools_v2.17.3.zip (or newer version) from official TPC site.
  2. Rename makefile.suite to Makefile and modify it as requested at https://github.com/tvondra/pg_tpch . Compile the code with make command
  3. Generate data: ./dbgen -s 10 generates 23GB database which is enough to see the difference in performance for parallel and non-parallel queries.
  4. Convert tbl files to csv with for + sed
  5. Clone pg_tpch repository and copy csv files to pg_tpch/dss/data
  6. Generate queries with qgen command
  7. Load data to the database with ./tpch.sh command.

Parallel sequential scan

This might be faster not because of parallel reads, but due to scattering of data across many CPU cores. Modern OS provides good caching for PostgreSQL data files. Read-ahead allows getting a block from storage more than just the block requested by PG daemon. As a result, query performance is not limited due to disk IO. It consumes CPU cycles for:

  • reading rows one by one from table data pages
  • comparing row values and WHERE conditions

Let’s try to execute simple select query:

tpch=# explain analyze select l_quantity as sum_qty from lineitem where l_shipdate <= date '1998-12-01' - interval '105' day;
QUERY PLAN
--------------------------------------------------------------------------------------------------------------------------
Seq Scan on lineitem (cost=0.00..1964772.00 rows=58856235 width=5) (actual time=0.014..16951.669 rows=58839715 loops=1)
Filter: (l_shipdate <= '1998-08-18 00:00:00'::timestamp without time zone)
Rows Removed by Filter: 1146337
Planning Time: 0.203 ms
Execution Time: 19035.100 ms

A sequential scan produces too many rows without aggregation. So, the query is executed by a single CPU core.

After adding SUM(), it’s clear to see that two workers will help us to make the query faster:

explain analyze select sum(l_quantity) as sum_qty from lineitem where l_shipdate <= date '1998-12-01' - interval '105' day;
QUERY PLAN
----------------------------------------------------------------------------------------------------------------------------------------------------
Finalize Aggregate (cost=1589702.14..1589702.15 rows=1 width=32) (actual time=8553.365..8553.365 rows=1 loops=1)
-> Gather (cost=1589701.91..1589702.12 rows=2 width=32) (actual time=8553.241..8555.067 rows=3 loops=1)
Workers Planned: 2
Workers Launched: 2
-> Partial Aggregate (cost=1588701.91..1588701.92 rows=1 width=32) (actual time=8547.546..8547.546 rows=1 loops=3)
-> Parallel Seq Scan on lineitem (cost=0.00..1527393.33 rows=24523431 width=5) (actual time=0.038..5998.417 rows=19613238 loops=3)
Filter: (l_shipdate <= '1998-08-18 00:00:00'::timestamp without time zone)
Rows Removed by Filter: 382112
Planning Time: 0.241 ms
Execution Time: 8555.131 ms

The more complex query is 2.2X faster compared to the plain, single-threaded select.

Parallel Aggregation

A “Parallel Seq Scan” node produces rows for partial aggregation. A “Partial Aggregate” node reduces these rows with SUM(). At the end, the SUM counter from each worker collected by “Gather” node.

The final result is calculated by the “Finalize Aggregate” node. If you have your own aggregation functions, do not forget to mark them as “parallel safe”.

Number of workers

We can increase the number of workers without server restart:

alter system set max_parallel_workers_per_gather=4;
select * from pg_reload_conf();
Now, there are 4 workers in explain output:
tpch=# explain analyze select sum(l_quantity) as sum_qty from lineitem where l_shipdate <= date '1998-12-01' - interval '105' day;
QUERY PLAN
----------------------------------------------------------------------------------------------------------------------------------------------------
Finalize Aggregate (cost=1440213.58..1440213.59 rows=1 width=32) (actual time=5152.072..5152.072 rows=1 loops=1)
-> Gather (cost=1440213.15..1440213.56 rows=4 width=32) (actual time=5151.807..5153.900 rows=5 loops=1)
Workers Planned: 4
Workers Launched: 4
-> Partial Aggregate (cost=1439213.15..1439213.16 rows=1 width=32) (actual time=5147.238..5147.239 rows=1 loops=5)
-> Parallel Seq Scan on lineitem (cost=0.00..1402428.00 rows=14714059 width=5) (actual time=0.037..3601.882 rows=11767943 loops=5)
Filter: (l_shipdate <= '1998-08-18 00:00:00'::timestamp without time zone)
Rows Removed by Filter: 229267
Planning Time: 0.218 ms
Execution Time: 5153.967 ms

What’s happening here? We have changed the number of workers from 2 to 4, but the query became only 1.6599 times faster. Actually, scaling is amazing. We had two workers plus one leader. After a configuration change, it becomes 4+1.

The biggest improvement from parallel execution that we can achieve is: 5/3 = 1.66(6)X faster.

How does it work?

Processes

Query execution always starts in the “leader” process. A leader executes all non-parallel activity and its own contribution to parallel processing. Other processes executing the same queries are called “worker” processes. Parallel execution utilizes the Dynamic Background Workers infrastructure (added in 9.4). As other parts of PostgreSQL uses processes, but not threads, the query creating three worker processes could be 4X faster than the traditional execution.

Communication

Workers communicate with the leader using a message queue (based on shared memory). Each process has two queues: one for errors and the second one for tuples.

How many workers to use?

Firstly, the max_parallel_workers_per_gather parameter is the smallest limit on the number of workers. Secondly, the query executor takes workers from the pool limited by max_parallel_workers size. Finally, the top-level limit is max_worker_processes: the total number of background processes.

Failed worker allocation leads to single-process execution.

The query planner could consider decreasing the number of workers based on a table or index size. min_parallel_table_scan_size and min_parallel_index_scan_size control this behavior.

set min_parallel_table_scan_size='8MB'
8MB table => 1 worker
24MB table => 2 workers
72MB table => 3 workers
x => log(x / min_parallel_table_scan_size) / log(3) + 1 worker

Each time the table is 3X bigger than min_parallel_(index|table)_scan_size, postgres adds a worker. The number of workers is not cost-based! A circular dependency makes a complex implementation hard. Instead, the planner uses simple rules.

In practice, these rules are not always acceptable in production and you can override the number of workers for the specific table with ALTER TABLE … SET (parallel_workers = N).

Why parallel execution is not used?

Besides to the long list of parallel execution limitations, PostgreSQL checks costs:

parallel_setup_cost to avoid parallel execution for short queries. It models the time spent for memory setup, process start, and initial communication

parallel_tuple_cost : The communication between leader and workers could take a long time. The time is proportional to the number of tuples sent by workers. The parameter models the communication cost.

Nested loop joins

PostgreSQL 9.6+ could execute a “Nested loop” in parallel due to the simplicity of the operation.

explain (costs off) select c_custkey, count(o_orderkey)
                from    customer left outer join orders on
                                c_custkey = o_custkey and o_comment not like '%special%deposits%'
                group by c_custkey;
                                      QUERY PLAN
--------------------------------------------------------------------------------------
 Finalize GroupAggregate
   Group Key: customer.c_custkey
   ->  Gather Merge
         Workers Planned: 4
         ->  Partial GroupAggregate
               Group Key: customer.c_custkey
               ->  Nested Loop Left Join
                     ->  Parallel Index Only Scan using customer_pkey on customer
                     ->  Index Scan using idx_orders_custkey on orders
                           Index Cond: (customer.c_custkey = o_custkey)
                           Filter: ((o_comment)::text !~~ '%special%deposits%'::text)

Gather happens in the last stage, so “Nested Loop Left Join” is a parallel operation. “Parallel Index Only Scan” is available from version 10. It acts in a similar way to a parallel sequential scan. The

c_custkey = o_custkey

condition reads a single order for each customer row. Thus it’s not parallel.

Hash Join

Each worker builds its own hash table until PostgreSQL 11. As a result, 4+ workers weren’t able to improve performance. The new implementation uses a shared hash table. Each worker can utilize WORK_MEM to build the hash table.

select
        l_shipmode,
        sum(case
                when o_orderpriority = '1-URGENT'
                        or o_orderpriority = '2-HIGH'
                        then 1
                else 0
        end) as high_line_count,
        sum(case
                when o_orderpriority <> '1-URGENT'
                        and o_orderpriority <> '2-HIGH'
                        then 1
                else 0
        end) as low_line_count
from
        orders,
        lineitem
where
        o_orderkey = l_orderkey
        and l_shipmode in ('MAIL', 'AIR')
        and l_commitdate < l_receiptdate
        and l_shipdate < l_commitdate
        and l_receiptdate >= date '1996-01-01'
        and l_receiptdate < date '1996-01-01' + interval '1' year
group by
        l_shipmode
order by
        l_shipmode
LIMIT 1;
                                                                                                                                    QUERY PLAN
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 Limit  (cost=1964755.66..1964961.44 rows=1 width=27) (actual time=7579.592..7922.997 rows=1 loops=1)
   ->  Finalize GroupAggregate  (cost=1964755.66..1966196.11 rows=7 width=27) (actual time=7579.590..7579.591 rows=1 loops=1)
         Group Key: lineitem.l_shipmode
         ->  Gather Merge  (cost=1964755.66..1966195.83 rows=28 width=27) (actual time=7559.593..7922.319 rows=6 loops=1)
               Workers Planned: 4
               Workers Launched: 4
               ->  Partial GroupAggregate  (cost=1963755.61..1965192.44 rows=7 width=27) (actual time=7548.103..7564.592 rows=2 loops=5)
                     Group Key: lineitem.l_shipmode
                     ->  Sort  (cost=1963755.61..1963935.20 rows=71838 width=27) (actual time=7530.280..7539.688 rows=62519 loops=5)
                           Sort Key: lineitem.l_shipmode
                           Sort Method: external merge  Disk: 2304kB
                           Worker 0:  Sort Method: external merge  Disk: 2064kB
                           Worker 1:  Sort Method: external merge  Disk: 2384kB
                           Worker 2:  Sort Method: external merge  Disk: 2264kB
                           Worker 3:  Sort Method: external merge  Disk: 2336kB
                           ->  Parallel Hash Join  (cost=382571.01..1957960.99 rows=71838 width=27) (actual time=7036.917..7499.692 rows=62519 loops=5)
                                 Hash Cond: (lineitem.l_orderkey = orders.o_orderkey)
                                 ->  Parallel Seq Scan on lineitem  (cost=0.00..1552386.40 rows=71838 width=19) (actual time=0.583..4901.063 rows=62519 loops=5)
                                       Filter: ((l_shipmode = ANY ('{MAIL,AIR}'::bpchar[])) AND (l_commitdate < l_receiptdate) AND (l_shipdate < l_commitdate) AND (l_receiptdate >= '1996-01-01'::date) AND (l_receiptdate < '1997-01-01 00:00:00'::timestamp without time zone))
                                       Rows Removed by Filter: 11934691
                                 ->  Parallel Hash  (cost=313722.45..313722.45 rows=3750045 width=20) (actual time=2011.518..2011.518 rows=3000000 loops=5)
                                       Buckets: 65536  Batches: 256  Memory Usage: 3840kB
                                       ->  Parallel Seq Scan on orders  (cost=0.00..313722.45 rows=3750045 width=20) (actual time=0.029..995.948 rows=3000000 loops=5)
 Planning Time: 0.977 ms
 Execution Time: 7923.770 ms

Query 12 from TPC-H is a good illustration for a parallel hash join. Each worker helps to build a shared hash table.

Merge Join

Due to the nature of merge join it’s not possible to make it parallel. Don’t worry if it’s the last stage of the query execution—you can still can see parallel execution for queries with a merge join.

-- Query 2 from TPC-H
explain (costs off) select s_acctbal, s_name, n_name, p_partkey, p_mfgr, s_address, s_phone, s_comment
from    part, supplier, partsupp, nation, region
where
        p_partkey = ps_partkey
        and s_suppkey = ps_suppkey
        and p_size = 36
        and p_type like '%BRASS'
        and s_nationkey = n_nationkey
        and n_regionkey = r_regionkey
        and r_name = 'AMERICA'
        and ps_supplycost = (
                select
                        min(ps_supplycost)
                from    partsupp, supplier, nation, region
                where
                        p_partkey = ps_partkey
                        and s_suppkey = ps_suppkey
                        and s_nationkey = n_nationkey
                        and n_regionkey = r_regionkey
                        and r_name = 'AMERICA'
        )
order by s_acctbal desc, n_name, s_name, p_partkey
LIMIT 100;
                                                QUERY PLAN
----------------------------------------------------------------------------------------------------------
 Limit
   ->  Sort
         Sort Key: supplier.s_acctbal DESC, nation.n_name, supplier.s_name, part.p_partkey
         ->  Merge Join
               Merge Cond: (part.p_partkey = partsupp.ps_partkey)
               Join Filter: (partsupp.ps_supplycost = (SubPlan 1))
               ->  Gather Merge
                     Workers Planned: 4
                     ->  Parallel Index Scan using part_pkey on part
                           Filter: (((p_type)::text ~~ '%BRASS'::text) AND (p_size = 36))
               ->  Materialize
                     ->  Sort
                           Sort Key: partsupp.ps_partkey
                           ->  Nested Loop
                                 ->  Nested Loop
                                       Join Filter: (nation.n_regionkey = region.r_regionkey)
                                       ->  Seq Scan on region
                                             Filter: (r_name = 'AMERICA'::bpchar)
                                       ->  Hash Join
                                             Hash Cond: (supplier.s_nationkey = nation.n_nationkey)
                                             ->  Seq Scan on supplier
                                             ->  Hash
                                                   ->  Seq Scan on nation
                                 ->  Index Scan using idx_partsupp_suppkey on partsupp
                                       Index Cond: (ps_suppkey = supplier.s_suppkey)
               SubPlan 1
                 ->  Aggregate
                       ->  Nested Loop
                             Join Filter: (nation_1.n_regionkey = region_1.r_regionkey)
                             ->  Seq Scan on region region_1
                                   Filter: (r_name = 'AMERICA'::bpchar)
                             ->  Nested Loop
                                   ->  Nested Loop
                                         ->  Index Scan using idx_partsupp_partkey on partsupp partsupp_1
                                               Index Cond: (part.p_partkey = ps_partkey)
                                         ->  Index Scan using supplier_pkey on supplier supplier_1
                                               Index Cond: (s_suppkey = partsupp_1.ps_suppkey)
                                   ->  Index Scan using nation_pkey on nation nation_1
                                         Index Cond: (n_nationkey = supplier_1.s_nationkey)

The “Merge Join” node is above “Gather Merge”. Thus merge is not using parallel execution. But the “Parallel Index Scan” node still helps with the part_pkey segment.

Partition-wise join

PostgreSQL 11 disables the partition-wise join feature by default. Partition-wise join has a high planning cost. Joins for similarly partitioned tables could be done partition-by-partition. This allows postgres to use smaller hash tables. Each per-partition join operation could be executed in parallel.

tpch=# set enable_partitionwise_join=t;
tpch=# explain (costs off) select * from prt1 t1, prt2 t2
where t1.a = t2.b and t1.b = 0 and t2.b between 0 and 10000;
                    QUERY PLAN
---------------------------------------------------
 Append
   ->  Hash Join
         Hash Cond: (t2.b = t1.a)
         ->  Seq Scan on prt2_p1 t2
               Filter: ((b >= 0) AND (b <= 10000))
         ->  Hash
               ->  Seq Scan on prt1_p1 t1
                     Filter: (b = 0)
   ->  Hash Join
         Hash Cond: (t2_1.b = t1_1.a)
         ->  Seq Scan on prt2_p2 t2_1
               Filter: ((b >= 0) AND (b <= 10000))
         ->  Hash
               ->  Seq Scan on prt1_p2 t1_1
                     Filter: (b = 0)
tpch=# set parallel_setup_cost = 1;
tpch=# set parallel_tuple_cost = 0.01;
tpch=# explain (costs off) select * from prt1 t1, prt2 t2
where t1.a = t2.b and t1.b = 0 and t2.b between 0 and 10000;
                        QUERY PLAN
-----------------------------------------------------------
 Gather
   Workers Planned: 4
   ->  Parallel Append
         ->  Parallel Hash Join
               Hash Cond: (t2_1.b = t1_1.a)
               ->  Parallel Seq Scan on prt2_p2 t2_1
                     Filter: ((b >= 0) AND (b <= 10000))
               ->  Parallel Hash
                     ->  Parallel Seq Scan on prt1_p2 t1_1
                           Filter: (b = 0)
         ->  Parallel Hash Join
               Hash Cond: (t2.b = t1.a)
               ->  Parallel Seq Scan on prt2_p1 t2
                     Filter: ((b >= 0) AND (b <= 10000))
               ->  Parallel Hash
                     ->  Parallel Seq Scan on prt1_p1 t1
                           Filter: (b = 0)

Above all, a partition-wise join can use parallel execution only if partitions are big enough.

Parallel Append

Parallel Append partitions work instead of using different blocks in different workers. Usually, you can see this with UNION ALL queries. The drawback – less parallelism, because every worker could ultimately work for a single query.

There are just two workers launched even with four workers enabled.

tpch=# explain (costs off) select sum(l_quantity) as sum_qty from lineitem where l_shipdate <= date '1998-12-01' - interval '105' day union all select sum(l_quantity) as sum_qty from lineitem where l_shipdate <= date '2000-12-01' - interval '105' day;
                                           QUERY PLAN
------------------------------------------------------------------------------------------------
 Gather
   Workers Planned: 2
   ->  Parallel Append
         ->  Aggregate
               ->  Seq Scan on lineitem
                     Filter: (l_shipdate <= '2000-08-18 00:00:00'::timestamp without time zone)
         ->  Aggregate
               ->  Seq Scan on lineitem lineitem_1
                     Filter: (l_shipdate <= '1998-08-18 00:00:00'::timestamp without time zone)

Most important variables

  • WORK_MEM limits the memory usage of each process! Not just for queries: work_mem * processes * joins => could lead to significant memory usage.
  • max_parallel_workers_per_gather  – how many workers an executor will use for the parallel execution of a planner node
  • max_worker_processes – adapt the total number of workers to the number of CPU cores installed on a server
  • max_parallel_workers – same for the number of parallel workers

Summary

Starting from 9.6 parallel queries execution could significantly improve performance for complex queries scanning many rows or index records. In PostgreSQL 10, parallel execution was enabled by default. Do not forget to disable parallel execution on servers with a heavy OLTP workload. Sequential scans or index scans still consume a significant amount of resources. If you are not running a report against the whole dataset, you may improve query performance just by adding missing indexes or by using proper partitioning.

References


Image compiled from photos by Nathan Gonthier and Pavel Nekoranec on Unsplash

Feb
13
2019
--

plprofiler – Getting a Handy Tool for Profiling Your PL/pgSQL Code

plprofiler postgres performance tool

PostgreSQL is emerging as the standard destination for database migrations from proprietary databases. As a consequence, there is an increase in demand for database side code migration and associated performance troubleshooting. One might be able to trace the latency to a plsql function, but explaining what happens within a function could be a difficult question. Things get messier when you know the function call is taking time, but within that function there are calls to other functions as part of its body. It is a very challenging question to identify which line inside a function—or block of code—is causing the slowness. In order to answer such questions, we need to know how much time an execution spends on each line or block of code. The plprofiler project provides great tooling and extensions to address such questions.

Demonstration of plprofiler using an example

The plprofiler source contains a sample for testing plprofiler. This sample serves two purposes. It can be used for testing the configuration of plprofiler, and it is great place to see how to do the profiling of a nested function call. Files related to this can be located inside the “examples” directory. Don’t worry—I’ll be running through the installation of plprofiler later in this article.

$ cd examples/

The example expects you to create a database with name “pgbench_plprofiler”

postgres=# CREATE DATABASE pgbench_plprofiler;
CREATE DATABASE

The project provides a shell script along with a source tree to test plprofiler functionality. So testing is just a matter of running the shell script.

$ ./prepdb.sh
dropping old tables...
....

Running session level profiling

This profiling uses session level local-data. By default the plprofiler extension collects runtime data in per-backend hashtables (in-memory). This data is only accessible in the current session, and is lost when the session ends or the hash tables are explicitly reset. plprofiler’s run command will execute the plsql code and capture the profile information.

This is illustrated by below example,

$ plprofiler run --command "SELECT tpcb(1, 2, 3, -42)" -d pgbench_plprofiler --output tpcb-test1.html
SELECT tpcb(1, 2, 3, -42)
-- row1:
tpcb: -42
----
(1 rows)
SELECT 1 (0.073 seconds)

What happens during above plprofiler command run can be summarised in 3 steps:

  1. A function call with four parameters “SELECT tpcb(1, 2, 3, -42)” is presented to the plprofiler tool for execution.
  2. plprofiler establishes a connection to PostgreSQL and executes the function
  3. The tool collects the profile information captured in the local-data hash tables and generates an HTML report “tpcb-test1.html”

Global profiling

As mentioned previously, this method is useful if we want to profile the function executions in other sessions or on the entire database. During global profiling, data is captured into a shared-data hash table which is accessible for all sessions in the database. The plprofiler extension periodically copies the local-data from the individual sessions into shared hash tables, to make the statistics available to other sessions. See the

plprofiler monitor

  command, below, for details. This data still relies on the local database system catalog to resolve Oid values into object definitions.

In this example, the plprofiler tool will be running in monitor mode for a duration of 60 seconds. Every 10 seconds, the tool copies data from local-data to shared-data.

$ plprofiler monitor --interval=10 --duration=60 -d pgbench_plprofiler
monitoring for 60 seconds ...
done.

For testing purposes you can start executing a few functions at the same time.

Once the data is captured into shared-data, we can generate a report. For example:

$ plprofiler report --from-shared --title=MultipgMax --output=MultipgMax.html -d pgbench_plprofiler

The data in shared-data will be retained until it’s explicitly cleared using the

plprofiler reset

  command

$ plprofiler reset

If there is no profile data present in the shared hash tables, execution of the report will result in error message.

$ plprofiler report --from-shared --title=MultipgMax --output=MultipgMax.html
Traceback (most recent call last):
File "/usr/bin/plprofiler", line 11, in <module>
load_entry_point('plprofiler==4.dev0', 'console_scripts', 'plprofiler')()
File "/usr/lib/python2.7/site-packages/plprofiler-4.dev0-py2.7.egg/plprofiler/plprofiler_tool.py", line 67, in main
return report_command(sys.argv[2:])
File "/usr/lib/python2.7/site-packages/plprofiler-4.dev0-py2.7.egg/plprofiler/plprofiler_tool.py", line 493, in report_command
report_data = plp.get_shared_report_data(opt_name, opt_top, args)
File "/usr/lib/python2.7/site-packages/plprofiler-4.dev0-py2.7.egg/plprofiler/plprofiler.py", line 555, in get_shared_report_data
raise Exception("No profiling data found")
Exception: No profiling data found

Report on profile information

The HTML report generated by plprofiler is a self-contained HTML document and it gives detailed information about the PL/pgSQL function execution. There will be a clickable FlameGraph at the top of the report with details about functions in the profile. The plprofiler FlameGraph is based on the actual Wall-Clock time spent in the PL/pgSQL functions. By default, plprofiler provides details on the top ten functions, based on their self_time (total_time – children_time).

This section of the report is followed by tabular representation of function calls. For example:

This gives a lot of detailed information such as execution counts and time spend against each line of code.

Binary Packages

Binary distributions of plprofiler are not common. However the BigSQL project provides plprofiler packages as an easy to use bundle. Such ready-to-use packages are one of the reasons for BigSQL to remain as one of the most developer friendly PostgreSQL distributions. The first screen of Package manager installation of BigSQL provided me with the information I am looking for:


Appears that there was a recent release of BigSQL packages and plprofiler is an updated package within that.

Installation and configuration is made simple:

$ ./pgc install plprofiler-pg11
['plprofiler-pg11']
File is already downloaded.
Unpacking plprofiler-pg11-3.3-1-linux64.tar.bz2
install-plprofiler-pg11...
Updating postgresql.conf file:
old: #shared_preload_libraries = '' # (change requires restart)
new: shared_preload_libraries = 'plprofiler'

As we can see, even PostgreSQL parameters are updated to have plprofiler as a

shared_preload_library

 .  If need to use plprofiler for investigating code, these binary packages from the BigSQL project are my first preference because everything is ready to use. Definitely, this is developer-friendly.

Creation of extension and configuring the plprofiler tool

At the database level, we should create the plprofiler extension to profile the function execution. This step needs to be performed in both cases, whether we want global profiling where share_preload_libraries are set, or at session level where that is not required

postgres=# create extension plprofiler;
CREATE EXTENSION

plprofiler is not just an extension, but comes with tooling to invoke profiling or to generate reports. These scripts are primarily coded in Python and uses psycopg2 to connect to PostgreSQL. The python code is located inside the “python-plprofiler” directory of the source tree. There are a few perl dependencies too which will be resolved as part of installation

sudo yum install python-setuptools.noarch
sudo yum install python-psycopg2
cd python-plprofiler/
sudo python ./setup.py install

Building from source

If you already have a PostgreSQL instance running using binaries from PGDG repository OR you want to wet your hands by building everything from source, then installation needs a different approach. I have PostgreSQL 11 already running on the system. The first step is to get the corresponding development packages which have all the header files and libraries to support a build from source. Obviously this is the thorough way of getting plprofiler working.

$ sudo yum install postgresql11-devel

We need to have build tools, and since the core of plprofiler is C code, we have to install a C compiler and make utility.

$ sudo yum install gcc make

Preferably, we should build plprofiler using the same OS user that runs PostgreSQL server, which is “postgres” in most environments. Please make sure that all PostgreSQL binaries are available in the path and that you are able to execute the pg_config, which lists out build related information:

$ pg_config
BINDIR = /usr/pgsql-11/bin
..
INCLUDEDIR = /usr/pgsql-11/include
PKGINCLUDEDIR = /usr/pgsql-11/include
INCLUDEDIR-SERVER = /usr/pgsql-11/include/server
LIBDIR = /usr/pgsql-11/lib
PKGLIBDIR = /usr/pgsql-11/lib
LOCALEDIR = /usr/pgsql-11/share/locale
MANDIR = /usr/pgsql-11/share/man
SHAREDIR = /usr/pgsql-11/share
SYSCONFDIR = /etc/sysconfig/pgsql
PGXS = /usr/pgsql-11/lib/pgxs/src/makefiles/pgxs.mk
CONFIGURE = '--enable-rpath' '--prefix=/usr/pgsql-11' '--includedir=/usr/pgsql-11/include' '--mandir=/usr/pgsql-11/share/man' '--datadir=/usr/pgsql-11/share' '--with-icu' 'CLANG=/opt/rh/llvm-toolset-7/root/usr/bin/clang' 'LLVM_CONFIG=/usr/lib64/llvm5.0/bin/llvm-config' '--with-llvm' '--with-perl' '--with-python' '--with-tcl' '--with-tclconfig=/usr/lib64' '--with-openssl' '--with-pam' '--with-gssapi' '--with-includes=/usr/include' '--with-libraries=/usr/lib64' '--enable-nls' '--enable-dtrace' '--with-uuid=e2fs' '--with-libxml' '--with-libxslt' '--with-ldap' '--with-selinux' '--with-systemd' '--with-system-tzdata=/usr/share/zoneinfo' '--sysconfdir=/etc/sysconfig/pgsql' '--docdir=/usr/pgsql-11/doc' '--htmldir=/usr/pgsql-11/doc/html' 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' 'LDFLAGS=-Wl,--as-needed' 'PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig'
CC = gcc
...
VERSION = PostgreSQL 11.1

Now we’re ready to get the source code and build it. You should be able to checkout the git repository for plprofiler.

$ git clone https://github.com/pgcentral/plprofiler.git
Cloning into 'plprofiler'...
...

Building against PostgreSQL 11 binaries from PGDG can be a bit complicated because of th JIT feature. Configuration flag

--with-llvm

  will be enabled. So we may have to have LLVM present in the system as detailed in my previous blog about JIT in PostgreSQL11

Once we’re ready, we can move to the plprofiler directory and build it:

$ cd plprofiler
$ make USE_PGXS=1
--- Output ----
gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -fPIC -I. -I./ -I/usr/pgsql-11/include/server -I/usr/pgsql-11/include/internal -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include -c -o plprofiler.o plprofiler.c
gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -fPIC -shared -o plprofiler.so plprofiler.o -L/usr/pgsql-11/lib -Wl,--as-needed -L/usr/lib64/llvm5.0/lib -L/usr/lib64 -Wl,--as-needed -Wl,-rpath,'/usr/pgsql-11/lib',--enable-new-dtags
/opt/rh/llvm-toolset-7/root/usr/bin/clang -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I. -I./ -I/usr/pgsql-11/include/server -I/usr/pgsql-11/include/internal -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include -flto=thin -emit-llvm -c -o plprofiler.bc plprofiler.c

Now we should be able to install this extension:

$ sudo make USE_PGXS=1 install
--- Output ----
/usr/bin/mkdir -p '/usr/pgsql-11/lib'
/usr/bin/mkdir -p '/usr/pgsql-11/share/extension'
/usr/bin/mkdir -p '/usr/pgsql-11/share/extension'
/usr/bin/install -c -m 755 plprofiler.so '/usr/pgsql-11/lib/plprofiler.so'
/usr/bin/install -c -m 644 .//plprofiler.control '/usr/pgsql-11/share/extension/'
/usr/bin/install -c -m 644 .//plprofiler--1.0--2.0.sql .//plprofiler--2.0--3.0.sql .//plprofiler--3.0.sql '/usr/pgsql-11/share/extension/'
/usr/bin/mkdir -p '/usr/pgsql-11/lib/bitcode/plprofiler'
/usr/bin/mkdir -p '/usr/pgsql-11/lib/bitcode'/plprofiler/
/usr/bin/install -c -m 644 plprofiler.bc '/usr/pgsql-11/lib/bitcode'/plprofiler/./

The above command expects all build tools to be in the proper path even with sudo.

Profiling external sessions

To profile a function executed by another session, or all other sessions, we should load the libraries at global level. In production environments, that will be the case. This can be done by adding the extension library to the

shared_preload_libraries

  specification. You won’t need this if you only want to profile functions executed within your session. Session level profiling is generally possible only in Dev/Test environments.

To enable global profiling, verify the current value of

shared_preload_libraries

  and add plprofiler to the list.

postgres=# show shared_preload_libraries ;
shared_preload_libraries
--------------------------
(1 row)
postgres=# alter system set shared_preload_libraries = 'plprofiler';
ALTER SYSTEM
postgres=#

This change requires us to restart the PostgreSQL server

$ sudo systemctl restart postgresql-11

After the restart, it’s a good idea to verify the parameter change

postgres=# show shared_preload_libraries ;
shared_preload_libraries
--------------------------
plprofiler
(1 row)

From this point onwards, the steps are same as those for the binary package setup discussed above.

Summary

plprofiler is a wonderful tool for developers. I keep seeing many users who are in real need of it. Hopefully this blog post will help those who never tried it.

Aug
31
2018
--

PostgreSQL Performance Tuning: Optimizing Database Parameters for Maximum Efficiency

postgresql performance tuning

This blog was originally published in August 2018 and was updated in May 2023.

Out of the box, the default PostgreSQL configuration is not tuned for any particular workload. Default values are set to ensure that PostgreSQL runs everywhere, with the least resources it can consume, and so that it doesn’t cause any vulnerabilities. It has default settings for all of the database parameters. It is primarily the responsibility of the database administrator or developer to tune PostgreSQL according to their system’s workload. In this blog post, we will delve into the world of PostgreSQL performance tuning and establish some basic guidelines for setting database parameters to enhance the performance of your PostgreSQL database, based on the workload.

What is PostgreSQL performance tuning?

PostgreSQL performance optimization aims to improve the efficiency of a PostgreSQL database system by adjusting configurations and implementing best practices to identify and resolve bottlenecks, improve query speed, and maximize database throughput and responsiveness.

Key areas include:

  1. Configuration parameter tuning: This tuning involves altering variables such as memory allocation, disk I/O settings, and concurrent connections based on specific hardware and requirements.
  2. Query optimization: Analyzing query execution plans, identifying slow queries, and optimizing them through appropriate indexing techniques, query rewriting, or utilizing advanced features like partial indexes or materialized views.
  3. Hardware optimization: You need to ensure that the CPU, memory, and storage components meet the performance requirements of the database workload.
  4. Statistics and monitoring: By enabling and analyzing performance statistics and utilizing monitoring tools such as Percona Monitoring and Management you can identify bottlenecks and track query performance over time.
  5. Index tuning: PostgreSQL offers various types of indexes, including B-tree, hash, and generalized inverted indexes (GIN/GiST). Selecting the appropriate index type, creating composite indexes, and regularly analyzing and reindexing the database can substantially improve query speed.
  6. Schema design: Evaluating the database schema design and making adjustments such as partitioning large tables, eliminating redundant data, and denormalizing tables for frequently accessed information can improve performance.
  7. Connection pooling: Minimizing connection overhead and improving response times for frequently accessed data by implementing mechanisms for connection pooling and caching strategies.
  8. Load balancing and replication: Scaling the database system horizontally by distributing the workload across multiple servers using techniques like connection pooling, read replicas, or implementing a primary-replica replication setup.
  9. Memory management: Since PostgreSQL’s performance relies heavily on efficient memory usage, monitoring and adjusting key memory-related configuration parameters like shared_buffers, work_mem, and effective_cache_size can have a significant impact on performance.

PostgreSQL performance optimization is an ongoing process involving monitoring, benchmarking, and adjustments to maintain high-performing PostgreSQL databases. In addition, staying up-to-date on PostgreSQL releases and improvements can also help.

Why is PostgreSQL performance tuning important?

The performance of a PostgreSQL database has a significant impact on the overall effectiveness of an application. Here’s why it’s crucial for businesses to possess a high-performing database:

Responsiveness: Imagine waiting forever for the data you need immediately to show up. Nobody has time for that! Slow queries and data retrieval can lead to frustrating delays that impact the user experience. To ensure seamless interactions, a well-performing database is essential, delivering quick response times and satisfying user expectations.

Throughput: The throughput of an application is directly influenced by the speed at which the database can process and serve queries. A high-performance database significantly decreases query execution time, empowering the application to handle more concurrent requests and deliver data faster.

Scalability: As an application expands and needs to handle more data and user loads, the database must scale accordingly. A well-performing PostgreSQL database can effectively manage increased workloads, ensuring the application remains responsive and performs well even when under heavy usage.

Efficient Resource Utilization: Enabling the effective utilization of system resources like CPU, memory, and disk I/O can optimize your PostgreSQL database while maintaining functionality. This not only results in cost savings by minimizing hardware requirements but also has the potential to decrease cloud expenses.

Data Integrity: This is crucial for ensuring a reliable and efficient database. By incorporating features like ACID compliance, transaction management, and strong error handling, the database can safeguard against data corruption or loss. This is particularly important for businesses that rely on precise and consistent data for their decision-making and operational needs.

Competitive Advantage: User retention rates and customer satisfaction can make or break any business. A high-performing database that consistently ensures excellent application performance can give businesses a competitive advantage. 

 

Watch the PostgreSQL high-performance tuning and optimization webinar sessions

 

Understanding the impact of queries on PostgreSQL performance

Bear in mind that while optimizing PostgreSQL server configuration improves performance, a database developer must also be diligent when writing queries for the application. If queries perform full table scans where an index could be used or perform heavy joins or expensive aggregate operations, then the system can still perform poorly even if the database parameters are tuned. It is important to pay attention to performance when writing database queries.

Nevertheless, database parameters are very important, too, so let’s take a look at the eight that have the greatest potential to improve performance

Check out this blog to learn how to improve PostgreSQL query performance insights with pg_stat_monitor.

Tuneable PostgreSQL parameters

Below are some PostgreSQL parameters that can be adjusted for improved performance based on your system and specific workload.

shared_buffer

PostgreSQL uses its own buffer and also uses kernel-buffered IO. That means data is stored in memory twice, first in PostgreSQL buffer and then kernel buffer. Unlike other databases, PostgreSQL does not provide direct IO. This is called double buffering. The PostgreSQL buffer is called shared_buffer, which is the most effective tunable parameter for most operating systems. This parameter sets how much dedicated memory will be used by PostgreSQL for the cache.

The default value of shared_buffer is set very low and you will not benefit much from that. It’s low because certain machines and operating systems do not support higher values. But in most modern machines, you need to increase this value for optimal performance.

The recommended value is 25% of your total machine RAM. You should try some lower and higher values because in some cases we achieve good performance with a setting over 25%. The configuration really depends on your machine and the working data set. If your working set of data can easily fit into your RAM, then you might want to increase the shared_buffer value to contain your entire database so that the whole working set of data can reside in cache. That said, you obviously do not want to reserve all RAM for PostgreSQL.

In production environments, it is observed that a large value for shared_buffer gives really good performance, though you should always benchmark to find the right balance.

testdb=# SHOW shared_buffers;
shared_buffers
----------------
128MB
(1 row)

Note: Be careful as some kernels do not allow a bigger value, specifically in Windows, there is no use of a higher value.

wal_buffers

PostgreSQL writes its WAL (write ahead log) record into the buffers and then these buffers are flushed to disk. The default size of the buffer, defined by wal_buffers, is 16MB, but if you have a lot of concurrent connections, then a higher value can give better performance.

effective_cache_size

The effective_cache_size provides an estimate of the memory available for disk caching. It is just a guideline, not the exact allocated memory or cache size. It does not allocate actual memory but tells the optimizer the amount of cache available in the kernel. If the value of this is set too low the query planner can decide not to use some indexes, even if they’d be helpful. Therefore, setting a large value is always beneficial.

work_mem

This configuration is used for complex sorting. If you have to do complex sorting, then increase the value of work_mem for good results. In-memory sorts are much faster than sorts spilling to disk. Setting a very high value can cause a memory bottleneck for your deployment environment because this parameter is per-user sort operation. Therefore, if you have many users trying to execute sort operations, then the system will allocate

work_mem * total sort operations

  for all users. Setting this parameter globally can cause very high memory usage. So it is highly recommended to modify this at the session level.

testdb=# SET work_mem TO "2MB";
testdb=# EXPLAIN SELECT * FROM bar ORDER BY bar.b;
                                    QUERY PLAN                                     
-----------------------------------------------------------------------------------
Gather Merge  (cost=509181.84..1706542.14 rows=10000116 width=24)
   Workers Planned: 4
   ->  Sort  (cost=508181.79..514431.86 rows=2500029 width=24)
         Sort Key: b
         ->  Parallel Seq Scan on bar  (cost=0.00..88695.29 rows=2500029 width=24)
(5 rows)

The initial query’s sort node has an estimated cost of 514431.86. A cost is an arbitrary unit of computation. For the above query, we have a work_mem of only 2MB. For testing purposes, let’s increase this to 256MB and see if there is any impact on cost.

testdb=# SET work_mem TO "256MB";
testdb=# EXPLAIN SELECT * FROM bar ORDER BY bar.b;
                                    QUERY PLAN                                     
-----------------------------------------------------------------------------------
Gather Merge  (cost=355367.34..1552727.64 rows=10000116 width=24)
   Workers Planned: 4
   ->  Sort  (cost=354367.29..360617.36 rows=2500029 width=24)
         Sort Key: b
         ->  Parallel Seq Scan on bar  (cost=0.00..88695.29 rows=2500029 width=24)

The query cost is reduced to 360617.36 from 514431.86 — a 30% reduction.

maintenance_work_mem

maintenance_work_mem is a memory setting used for maintenance tasks. The default value is 64MB. Setting a large value helps in tasks like VACUUM, RESTORE, CREATE INDEX, ADD FOREIGN KEY, and ALTER TABLE.

postgres=# CHECKPOINT;
postgres=# SET maintenance_work_mem to '10MB';

postgres=# CREATE INDEX foo_idx ON foo (c);
CREATE INDEX
Time: 170091.371 ms (02:50.091)

postgres=# CHECKPOINT;
postgres=# set maintenance_work_mem to '256MB';

postgres=# CREATE INDEX foo_idx ON foo (c);
CREATE INDEX
Time: 111274.903 ms (01:51.275)

The index creation time is 170091.371ms when maintenance_work_mem is set to only 10MB, but that is reduced to 111274.903 ms when we increase maintenance_work_mem setting to 256MB.

synchronous_commit

This is used to enforce that commit will wait for WAL to be written on disk before returning a success status to the client. This is a trade-off between performance and reliability. If your application is designed such that performance is more important than reliability, then turn off synchronous_commit. This means that there will be a time gap between the success status and a guaranteed write-to-disk. In the case of a server crash, data might be lost even though the client received a success message on commit. In this case, a transaction commits very quickly because it will not wait for a WAL file to be flushed, but reliability is compromised.

checkpoint_timeout, checkpoint_completion_target

PostgreSQL writes changes into WAL. The checkpoint process flushes the data into the data files. This activity is done when CHECKPOINT occurs. This is an expensive operation and can cause a huge amount of IO. This whole process involves expensive disk read/write operations. Users can always issue CHECKPOINT whenever it seems necessary or automate the system by PostgreSQL’s parameters checkpoint_timeout and checkpoint_completion_target.

The checkpoint_timeout parameter is used to set the time between WAL checkpoints. Setting this too low decreases crash recovery time, as more data is written to disk, but it hurts performance, too, since every checkpoint ends up consuming valuable system resources. The checkpoint_completion_target is the fraction of time between checkpoints for checkpoint completion. A high frequency of checkpoints can impact performance. For smooth checkpointing, checkpoint_timeout must be a low value. Otherwise, the OS will accumulate all the dirty pages until the ratio is met and then go for a big flush.

Improve PostgreSQL performance tuning with Percona

There are more parameters that can be tuned to gain better performance but those have less impact than the ones highlighted here. In the end, we must always keep in mind that not all parameters are relevant for all application types. Some applications perform better by tuning a parameter and some don’t. Tuning PostgreSQL parameters must be done for the specific needs of an application and the OS it runs on.

Get Percona Distribution for PostgreSQL

 

Resources for PostgreSQL performance tuning

If your PostgreSQL database is running on a Linux OS, be sure to read my post about tuning Linux parameters to optimize PostgreSQL database performance.

After tuning your PostgreSQL database to improve its performance, the next step is to put your optimized database to the test. With sysbench, you can quickly evaluate your database’s performance. This process is especially important if you plan to run your database under an intensive workload. Our blog article, Tuning PostgreSQL for sysbench-tpcc, can guide you through the benchmarking process.

Optimizing your database is one way to course-correct poor database performance. However, the problem is not always the database itself! Several causes can contribute to your database’s lackluster performance. Our solution brief details the Top 5 Causes of Poor Database Performance. With this crucial information, you can better implement a quick and efficient resolution.

 

Discover why Percona and PostgreSQL work better together

Aug
29
2018
--

Tune Linux Kernel Parameters For PostgreSQL Optimization

Linux parameters for PostgreSQL performance tuning

For optimum performance, a PostgreSQL database depends on the operating system parameters being defined correctly. Poorly configured OS kernel parameters can cause degradation in database server performance. Therefore, it is imperative that these parameters are configured according to the database server and its workload. In this post, we will discuss some important kernel parameters that can affect database server performance and how these should be tuned.

SHMMAX / SHMALL

SHMMAX is a kernel parameter used to define the maximum size of a single shared memory segment a Linux process can allocate. Until version 9.2, PostgreSQL uses System V (SysV) that requires SHMMAX setting. After 9.2, PostgreSQL switched to POSIX shared memory. So now it requires fewer bytes of System V shared memory.

Prior to version 9.3 SHMMAX was the most important kernel parameter. The value of SHMMAX is in bytes.

Similarly SHMALL is another kernel parameter used to define system wide total amount of shared memory pages. To view the current values for SHMMAX, SHMALL or SHMMIN, use the ipcs command.

$ ipcs -lm
------ Shared Memory Limits --------
max number of segments = 4096
max seg size (kbytes) = 1073741824
max total shared memory (kbytes) = 17179869184
min seg size (bytes) = 1

$ ipcs -M
IPC status from  as of Thu Aug 16 22:20:35 PKT 2018
shminfo:
	shmmax: 16777216	(max shared memory segment size)
	shmmin:       1	(min shared memory segment size)
	shmmni:      32	(max number of shared memory identifiers)
	shmseg:       8	(max shared memory segments per process)
	shmall:    1024	(max amount of shared memory in pages)

PostgreSQL uses System V IPC to allocate the shared memory. This parameter is one of the most important kernel parameters. Whenever you get following error messages, it means that you have an older version PostgreSQL and you have a very low SHMMAX value. Users are expected to adjust and increase the value according to the shared memory they are going to use.

Possible misconfiguration errors

If SHMMAX is misconfigured, you can get an error when trying to initialize a PostgreSQL cluster using the initdb command.

DETAIL: Failed system call was shmget(key=1, size=2072576, 03600).
HINT: This error usually means that PostgreSQL's request for a shared memory segment exceeded your kernel's SHMMAX parameter.&nbsp;
You can either reduce the request size or reconfigure the kernel with larger SHMMAX. To reduce the request size (currently 2072576 bytes),
reduce PostgreSQL's shared memory usage, perhaps by reducing shared_buffers or max_connections.
If the request size is already small, it's possible that it is less than your kernel's SHMMIN parameter,
in which case raising the request size or reconfiguring SHMMIN is called for.
The PostgreSQL documentation contains more information about shared memory configuration. child process exited with exit code 1

Similarly, you can get an error when starting the PostgreSQL server using the pg_ctl command.

DETAIL: Failed system call was shmget(key=5432001, size=14385152, 03600).
HINT: This error usually means that PostgreSQL's request for a shared memory segment exceeded your kernel's SHMMAX parameter.
You can either reduce the request size or reconfigure the kernel with larger SHMMAX.; To reduce the request size (currently 14385152 bytes),
reduce PostgreSQL's shared memory usage, perhaps by reducing shared_buffers or max_connections.
If the request size is already small, it's possible that it is less than your kernel's SHMMIN parameter,
in which case raising the request size or reconfiguring SHMMIN is called for.
The PostgreSQL documentation contains more information about shared memory configuration.

Be aware of differing definitions

The definition of the SHMMAX/SHMALL parameters is slightly different between Linux and MacOS X. These are the definitions:

  • Linux: kernel.shmmax, kernel.shmall
  • MacOS X: kern.sysv.shmmax, kern.sysv.shmall

The sysctl command can be used to change the value temporarily. To permanently set the value, add an entry into /etc/sysctl.conf. The details are given below.

# Get the value of SHMMAX
sudo sysctl kern.sysv.shmmax
kern.sysv.shmmax: 4096
# Get the value of SHMALL
sudo sysctl kern.sysv.shmall
kern.sysv.shmall: 4096
# Set the value of SHMMAX
sudo sysctl -w kern.sysv.shmmax=16777216
kern.sysv.shmmax: 4096 -> 16777216<br>
# Set the value of SHMALL
sudo sysctl -w kern.sysv.shmall=16777216
kern.sysv.shmall: 4096 -> 16777216

# Get the value of SHMMAX
sudo sysctl kernel.shmmax
kernel.shmmax: 4096
# Get the value of SHMALL
sudo sysctl kernel.shmall
kernel.shmall: 4096
# Set the value of SHMMAX
sudo sysctl -w kernel.shmmax=16777216
kernel.shmmax: 4096 -> 16777216<br>
# Set the value of SHMALL
sudo sysctl -w kernel.shmall=16777216
kernel.shmall: 4096 -> 16777216

Remember: to make the change permanent add these values in

/etc/sysctl.conf

 

Huge Pages

Linux, by default uses 4K memory pages, BSD has Super Pages, whereas Windows has Large Pages. A page is a chunk of RAM that is allocated to a process. A process may own more than one page depending on its memory requirements. The more memory a process needs, the more pages that are allocated to it. The OS maintains a table of page allocation to processes. The smaller the page size, the bigger the table, the more time required to lookup a page in that page table. Therefore, huge pages make it possible to use large amount of memory with reduced overheads; fewer page look ups, fewer page faults, faster read/write operations through larger buffers. This results in improved performance.

PostgreSQL has support for bigger pages on Linux only. By default, Linux uses 4K of memory pages, so in cases where there are too many memory operations, there is a need to set bigger pages. Performance gains have been observed by using huge pages with sizes 2 MB and up to 1 GB. The size of Huge Page can be set boot time. You can easily check the huge page settings and utilization on your Linux box using cat /proc/meminfo | grep -i huge command.

Note: This is only for Linux, for other OS this operation is ignored$ cat /proc/meminfo | grep -i huge
AnonHugePages:         0 kB
ShmemHugePages:        0 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB

In this example, although huge page size is set at 2,048 (2 MB), the total number of huge pages has a value of 0. which signifies that huge pages are disabled.

Script to quantify Huge Pages

This is a simple script which returns the number of Huge Pages required. Execute the script on your Linux box while your PostgreSQL is running. Ensure that $PGDATA environment variable is set to PostgreSQL’s data directory.

#!/bin/bash
pid=`head -1 $PGDATA/postmaster.pid`
echo "Pid:            $pid"
peak=`grep ^VmPeak /proc/$pid/status | awk '{ print $2 }'`
echo "VmPeak:            $peak kB"
hps=`grep ^Hugepagesize /proc/meminfo | awk '{ print $2 }'`
echo "Hugepagesize:   $hps kB"
hp=$((peak/hps))
echo Set Huge Pages:     $hp

The output of the script looks like this:

Pid:            12737
VmPeak:         180932 kB
Hugepagesize:   2048 kB
Set Huge Pages: 88

The recommended huge pages are 88, therefore you should set the value to 88.

sysctl -w vm.nr_hugepages= 88

Check the huge pages now, you will see no huge page is in use (HugePages_Free = HugePages_Total).

$ cat /proc/meminfo | grep -i huge
AnonHugePages:         0 kB
ShmemHugePages:        0 kB
HugePages_Total:      88
HugePages_Free:       88
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB

Now set the parameter huge_pages “on” in $PGDATA/postgresql.conf and restart the server.

$ cat /proc/meminfo | grep -i huge
AnonHugePages:         0 kB
ShmemHugePages:        0 kB
HugePages_Total:      88
HugePages_Free:       81
HugePages_Rsvd:       64
HugePages_Surp:        0
Hugepagesize:       2048 kB

Now you can see that a very few of the huge pages are used. Let’s now try to add some data into the database.

postgres=# CREATE TABLE foo(a INTEGER);
CREATE TABLE
postgres=# INSERT INTO foo VALUES(generate_Series(1,10000000));
INSERT 0 10000000

Let’s see if we are now using more huge pages than before.

$ cat /proc/meminfo | grep -i huge
AnonHugePages:         0 kB
ShmemHugePages:        0 kB
HugePages_Total:      88
HugePages_Free:       18
HugePages_Rsvd:        1
HugePages_Surp:        0
Hugepagesize:       2048 kB

Now you can see that most of the huge pages are in use.

Note: The sample value for HugePages used here is very low, which is not a normal value for a big production machine. Please assess the required number of pages for your system and set those accordingly depending on your systems workload and resources.

vm.swappiness

vm.swappiness is another kernel parameter that can affect the performance of the database. This parameter is used to control the swappiness (swapping pages to and from swap memory into RAM) behaviour on a Linux system. The value ranges from 0 to 100. It controls how much memory will be swapped or paged out. Zero means disable swap and 100 means aggressive swapping.

You may get good performance by setting lower values.

Setting a value of 0 in newer kernels may cause the OOM Killer (out of memory killer process in Linux) to kill the process. Therefore, you can be on safe side and set the value to 1 if you want to minimize swapping. The default value on a Linux system is 60. A higher value causes the MMU (memory management unit) to utilize more swap space than RAM, whereas a lower value preserves more data/code in memory.

A smaller value is a good bet to improve performance in PostgreSQL.

vm.overcommit_memory / vm.overcommit_ratio

Applications acquire memory and free that memory when it is no longer needed. But in some cases an application acquires too much memory and does not release it.  This can invoke the OOM killer. Here are the possible values for vm.overcommit_memory parameter with a description for each:

    1. Heuristic overcommit, Do it intelligently (default); based kernel heuristics
    2. Allow overcommit anyway
    3. Don’t over commit beyond the overcommit ratio.

Reference: https://www.kernel.org/doc/Documentation/vm/overcommit-accounting

vm.overcommit_ratio is the percentage of RAM that is available for overcommitment. A value of 50% on a system with 2 GB of RAM may commit up to 3 GB of RAM.

A value of 2 for vm.overcommit_memory yields better performance for PostgreSQL. This value maximises RAM utilization by the server process without any significant risk of getting killed by the OOM killer process. An application will be able to overcommit, but only within the overcommit ratio, thus reducing the risk of having OOM killer kill the process. Hence a value to 2 gives better performance than the default 0 value. However, reliability can be improved by ensuring that memory beyond an allowable range is not overcommitted. It avoid the risk of the process being killed by OOM-killer.

On systems without swap, one may experience problem when vm.overcommit_memory is 2.

https://www.postgresql.org/docs/current/static/kernel-resources.html#LINUX-MEMORY-OVERCOMMIT

vm.dirty_background_ratio / vm.dirty_background_bytes

The vm.dirty_background_ratio is the percentage of memory filled with dirty pages that need to be flushed to disk. Flushing is done in the background. The value of this parameter ranges from 0 to 100; however a value lower than 5 may not be effective and some kernels do not internally support it. The default value is 10 on most Linux systems. You can gain performance for write intensive operations with a lower ratio, which means that Linux flushes dirty pages in the background.

You need to set a value of vm.dirty_background_bytes depending on your disk speed.

There are no “good” values for these two parameters since both depend on the hardware. However, setting vm.dirty_background_ratio to 5 and vm.dirty_background_bytes to 25% of your disk speed improves performance by up to ~25% in most cases.

vm.dirty_ratio / dirty_bytes

This is same as vm.dirty_background_ratio / dirty_background_bytes except that the flushing is done in the foreground, blocking the application. So vm.dirty_ratio should be higher than vm.dirty_background_ratio. This will ensure that background processes kick in before the foreground processes to avoid blocking the application, as much as possible. You can tune the difference between the two ratios depending on your disk IO load.

Summing up

You can tune other parameters for performance, but the improvement gains are likely to be minimal. We must keep in mind that not all parameters are relevant for all applications types. Some applications perform better by tuning some parameters and some applications don’t. You need to find a good balance between these parameter configurations for the expected application workload and type, and OS behaviour must also be kept in mind when making adjustments. Tuning kernel parameters is not as easy as tuning database parameters: it’s harder to be prescriptive.

In my next post, I’ll take a look at tuning PostgreSQL’s database parameters. You might also enjoy this post:

Tuning PostgreSQL for sysbench-tpcc

 

The post Tune Linux Kernel Parameters For PostgreSQL Optimization appeared first on Percona Database Performance Blog.

Aug
10
2018
--

Tuning Autovacuum in PostgreSQL and Autovacuum Internals

Tuning Autovacuum in PostgreSQL

The performance of a PostgreSQL database can be compromised by dead tuples, since they continue to occupy space and can lead to bloat. We provided an introduction to VACUUM and bloat in an earlier blog post. Now, though, it’s time to look at autovacuum for postgres, and the internals you to know to maintain a high performance PostgreSQL database needed by demanding applications.

What is autovacuum ?

Autovacuum is one of the background utility processes that starts automatically when you start PostgreSQL. As you see in the following log, the postmaster (parent PostgreSQL process) with pid 2862 has started the autovacuum launcher process with pid 2868. To start autovacuum, you must have the parameter autovacuum set to ON. In fact, you should not set it to OFF in a production system unless you are 100% sure about what you are doing and its implications.

avi@percona:~$ps -eaf | egrep "/post|autovacuum"
postgres  2862     1  0 Jun17 pts/0    00:00:11 /usr/pgsql-10/bin/postgres -D /var/lib/pgsql/10/data
postgres  2868  2862  0 Jun17 ?        00:00:10 postgres: autovacuum launcher process
postgres 15427  4398  0 18:35 pts/1    00:00:00 grep -E --color=auto /post|autovacuum

Why is autovacuum needed ? 

We need VACUUM to remove dead tuples, so that the space occupied by dead tuples can be re-used by the table for future inserts/updates. To know more about dead tuples and bloat, please read our previous blog post. We also need ANALYZE on the table that updates the table statistics, so that the optimizer can choose optimal execution plans for an SQL statement. It is the autovacuum in postgres that is responsible for performing both vacuum and analyze on tables.

There exists another background process in postgres called Stats Collector that tracks the usage and activity information. The information collected by this process is used by autovacuum launcher to identify the list of candidate tables for autovacuum. PostgreSQL identifies the tables needing vacuum or analyze automatically, but only when autovacuum is enabled. This ensures that postgres heals itself and stops the database from developing more bloat/fragmentation.

Parameters needed to enable autovacuum in PostgreSQL are :

autovacuum = on  # ( ON by default )
track_counts = on # ( ON by default )

track_counts

  is used by the stats collector. Without that in place, autovacuum cannot access the candidate tables.

Logging autovacuum

Eventually, you may want to log the tables on which autovacuum spends more time. In that case, set the parameter log_autovacuum_min_duration to a value (defaults to milliseconds), so that any autovacuum that runs for more than this value is logged to the PostgreSQL log file. This may help tune your table level autovacuum settings appropriately.

# Setting this parameter to 0 logs every autovacuum to the log file.
log_autovacuum_min_duration = '250ms' # Or 1s, 1min, 1h, 1d

Here is an example log of autovacuum vacuum and analyze

< 2018-08-06 07:22:35.040 EDT > LOG: automatic vacuum of table "vactest.scott.employee": index scans: 0
pages: 0 removed, 1190 remain, 0 skipped due to pins, 0 skipped frozen
tuples: 110008 removed, 110008 remain, 0 are dead but not yet removable
buffer usage: 2402 hits, 2 misses, 0 dirtied
avg read rate: 0.057 MB/s, avg write rate: 0.000 MB/s
system usage: CPU 0.00s/0.02u sec elapsed 0.27 sec
< 2018-08-06 07:22:35.199 EDT > LOG: automatic analyze of table "vactest.scott.employee" system usage: CPU 0.00s/0.02u sec elapsed 0.15 sec

When does PostgreSQL run autovacuum on a table ? 

As discussed earlier, autovacuum in postgres refers to both automatic VACUUM and ANALYZE and not just VACUUM. An automatic vacuum or analyze runs on a table depending on the following mathematic equations.

The formula for calculating the effective table level autovacuum threshold is :

Autovacuum VACUUM thresold for a table = autovacuum_vacuum_scale_factor * number of tuples + autovacuum_vacuum_threshold

With the equation above, it is clear that if the actual number of dead tuples in a table exceeds this effective threshold, due to updates and deletes, that table becomes a candidate for autovacuum vacuum.

Autovacuum ANALYZE threshold for a table = autovacuum_analyze_scale_factor * number of tuples + autovacuum_analyze_threshold

The above equation says that any table with a total number of inserts/deletes/updates exceeding this threshold—since last analyze—is eligible for an autovacuum analyze.

Let’s understand these parameters in detail.

  • autovacuum_vacuum_scale_factor Or autovacuum_analyze_scale_factor : Fraction of the table records that will be added to the formula. For example, a value of 0.2 equals to 20% of the table records.
  • autovacuum_vacuum_threshold Or autovacuum_analyze_threshold : Minimum number of obsolete records or dml’s needed to trigger an autovacuum.

Let’s consider a table: percona.employee with 1000 records and the following autovacuum parameters.

autovacuum_vacuum_scale_factor = 0.2
autovacuum_vacuum_threshold = 50
autovacuum_analyze_scale_factor = 0.1
autovacuum_analyze_threshold = 50

Using the above mentioned mathematical formulae as reference,

Table : percona.employee becomes a candidate for autovacuum Vacuum when,
Total number of Obsolete records = (0.2 * 1000) + 50 = 250

Table : percona.employee becomes a candidate for autovacuum ANALYZE when,
Total number of Inserts/Deletes/Updates = (0.1 * 1000) + 50 = 150

Tuning Autovacuum in PostgreSQL

We need to understand that these are global settings. These settings are applicable to all the databases in the instance. This means, regardless of the table size, if the above formula is reached, a table is eligible for autovacuum vacuum or analyze.

Is this a problem ?

Consider a table with ten records versus a table with a million records. Even though the table with a million records may be involved in transactions far more often, the frequency at which a vacuum or an analyze runs automatically could be greater for the table with just ten records.

Consequently, PostgreSQL allows you to configure individual table level autovacuum settings that bypass global settings.

ALTER TABLE scott.employee SET (autovacuum_vacuum_scale_factor = 0, autovacuum_vacuum_threshold = 100);

Output Log
----------
avi@percona:~$psql -d percona
psql (10.4)
Type "help" for help.
percona=# ALTER TABLE scott.employee SET (autovacuum_vacuum_scale_factor = 0, autovacuum_vacuum_threshold = 100);
ALTER TABLE

The above setting runs autovacuum vacuum on the table scott.employee only once there is more than 100 obsolete records.

How do we identify the tables that need their autovacuum settings tuned ? 

In order to tune autovacuum for tables individually, you must know the number of inserts/deletes/updates on a table for an interval. You can also view the postgres catalog view : pg_stat_user_tables to get that information.

percona=# SELECT n_tup_ins as "inserts",n_tup_upd as "updates",n_tup_del as "deletes", n_live_tup as "live_tuples", n_dead_tup as "dead_tuples"
FROM pg_stat_user_tables
WHERE schemaname = 'scott' and relname = 'employee';
 inserts | updates | deletes | live_tuples | dead_tuples
---------+---------+---------+-------------+-------------
      30 |      40 |       9 |          21 |          39
(1 row)

As observed in the above log, taking a snapshot of this data for a certain interval should help you understand the frequency of DMLs on each table. In turn, this should help you with tuning your autovacuum settings for individual tables.

How many autovacuum processes can run at a time ? 

There cannot be more than autovacuum_max_workers number of autovacuum processes running at a time, across the instance/cluster that may contain more than one database. Autovacuum launcher background process starts a worker process for a table that needs a vacuum or an analyze. If there are four databases with autovacuum_max_workers set to 3, then, the 4th database has to wait until one of the existing worker process gets free.

Before starting the next autovacuum, it waits for autovacuum_naptime, the default is 1 min on most of the versions. If you have three databases, the next autovacuum waits for 60/3 seconds. So, the wait time before starting next autovacuum is always (autovacuum_naptime/N) where N is the total number of databases in the instance.

Does increasing autovacuum_max_workers alone increase the number of autovacuum processes that can run in parallel ?
NO. This is explained better in next few lines.

Is VACUUM IO intensive? 

Autovacuum can be considered as a cleanup. As discussed earlier, we have 1 worker process per table. Autovacuum reads 8KB (default block_size) pages of a table from disk and modifies/writes to the pages containing dead tuples. This involves both read and write IO. Thus, this could be an IO intensive operation, when there is an autovacuum running on a huge table with many dead tuples, during a peak transaction time. To avoid this issue, we have a few parameters that are set to minimize the impact on IO due to vacuum.

The following are the parameters used to tune autovacuum IO

  • autovacuum_vacuum_cost_limit : total cost limit autovacuum could reach (combined by all autovacuum jobs).
  • autovacuum_vacuum_cost_delay : autovacuum will sleep for these many milliseconds when a cleanup reaching autovacuum_vacuum_cost_limit cost is done.
  • vacuum_cost_page_hit : Cost of reading a page that is already in shared buffers and doesn’t need a disk read.
  • vacuum_cost_page_miss : Cost of fetching a page that is not in shared buffers.
  • vacuum_cost_page_dirty : Cost of writing to each page when dead tuples are found in it.
Default Values for the parameters discussed above.
------------------------------------------------------
autovacuum_vacuum_cost_limit = -1 (So, it defaults to vacuum_cost_limit) = 200
autovacuum_vacuum_cost_delay = 20ms
vacuum_cost_page_hit = 1
vacuum_cost_page_miss = 10
vacuum_cost_page_dirty = 20

Consider autovacuum VACUUM running on the table percona.employee.

Let’s imagine what can happen in 1 second. (1 second = 1000 milliseconds)

In a best case scenario where read latency is 0 milliseconds, autovacuum can wake up and go for sleep 50 times (1000 milliseconds / 20 ms) because the delay between wake-ups needs to be 20 milliseconds.

1 second = 1000 milliseconds = 50 * autovacuum_vacuum_cost_delay

Since the cost associated per reading a page in shared_buffers is 1, in every wake up 200 pages can be read, and in 50 wake-ups 50*200 pages can be read.

If all the pages with dead tuples are found in shared buffers, with an autovacuum_vacuum_cost_delay of 20ms, then it can read: ((200 / vacuum_cost_page_hit) * 8) KB in each round that needs to wait forautovacuum_vacuum_cost_delay amount of time.

Thus, at the most, an autovacuum can read : 50 * 200 * 8 KB = 78.13 MB per second (if blocks are already found in shared_buffers), considering the block_size as 8192 bytes.

If the blocks are not in shared buffers and need to fetched from disk, an autovacuum can read : 50 * ((200 / vacuum_cost_page_miss) * 8) KB = 7.81 MB per second.

All the information we have seen above is for read IO.

Now, in order to delete dead tuples from a page/block, the cost of a write operation is : vacuum_cost_page_dirty, set to 20 by default.

At the most, an autovacuum can write/dirty : 50 * ((200 / vacuum_cost_page_dirty) * 8) KB = 3.9 MB per second.

Generally, this cost is equally divided to all the autovacuum_max_workers number of autovacuum processes running in the Instance. So, increasing the autovacuum_max_workers may delay the autovacuum execution for the currently running autovacuum workers. And increasing the autovacuum_vacuum_cost_limit may cause IO bottlenecks. An important point to note is that this behaviour can be overridden by setting the storage parameters of individual tables, which would subsequently ignore the global settings.

postgres=# alter table percona.employee set (autovacuum_vacuum_cost_limit = 500);
ALTER TABLE
postgres=# alter table percona.employee set (autovacuum_vacuum_cost_delay = 10);
ALTER TABLE
postgres=#
postgres=# \d+ percona.employee
Table "percona.employee"
Column | Type | Collation | Nullable | Default | Storage | Stats target | Description
--------+---------+-----------+----------+---------+---------+--------------+-------------
id | integer | | | | plain | |
Options: autovacuum_vacuum_threshold=10000, autovacuum_vacuum_cost_limit=500, autovacuum_vacuum_cost_delay=10

Thus, on a busy OLTP database, always have a strategy to implement manual VACUUM on tables that are frequently hit with DMLs, during a low peak window. You may have as many parallel vacuum jobs as possible when you run it manually after setting relevant autovacuum_* settings. For this reason, a scheduled manual Vacuum Job is always recommended alongside finely tuned autovacuum settings.

The post Tuning Autovacuum in PostgreSQL and Autovacuum Internals appeared first on Percona Database Performance Blog.

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