[postgis-users] Performance problems with ST_Union on postgres 9.6, postgis 2.4.3 running on top of Red Hat 7.4

Regina Obe lr at pcorp.us
Thu Apr 26 00:42:31 PDT 2018


Jonas,

Follow up to this, I have ticketed this in GEOS and strk thinks he may have found the issue.

 

https://trac.osgeo.org/geos/ticket/867

 

so hopefully we can have this resolved in short-order and put out a GEOS 3.6.3 release soon.

 

Thanks,

Regina

 

 

From: postgis-users [mailto:postgis-users-bounces at lists.osgeo.org] On Behalf Of Jonas Nygaard Pedersen
Sent: Tuesday, April 24, 2018 7:58 AM
To: 'PostGIS Users Discussion' <postgis-users at lists.osgeo.org>
Subject: Re: [postgis-users] Performance problems with ST_Union on postgres 9.6, postgis 2.4.3 running on top of Red Hat 7.4

 

Hi Regina

 

I’ve enclosed a sample dataset of 31489 rows (enclosed in separate email to Regina) that I hope can serve as a basis for more tests. It’s definitely not top secret, just building polygons for an area in Western Jutland, Denmark (the total dataset would be for all of Denmark).

 

It should be noted that both the windows and redhat machine are specked with NVMe ssd disks that holds the postgres instance and data. 

The windows machine has 64 and the redhat has 128 GB of ram. Both have fairly recent workstation/server-grade cpus.

 

Windows:

'POSTGIS="2.3.2 r15302" GEOS="3.5.0-CAPI-1.9.0 r4084" PROJ="Rel. 4.9.2, 08 September 2015" GDAL="GDAL 1.11.5, released 2016/07/01" LIBXML="2.9.4" TOPOLOGY RASTER'

‘PostgreSQL 9.6.3 on x86_64-pc-mingw64, compiled by gcc.exe (Rev5, Built by MSYS2 project) 4.9.2, 64-bit’

 

Red Hat 7.4:

'POSTGIS="2.4.3 r16312" PGSQL="96" GEOS="3.6.2-CAPI-1.10.2 4d2925d6" SFCGAL="1.2.2" PROJ="Rel. 4.9.3, 15 August 2016" GDAL="GDAL 1.11.4, released 2016/01/25" LIBXML="2.9.1" LIBJSON="0.11" RASTER'

‘PostgreSQL 9.6.8 on x86_64-pc-linux-gnu, compiled by gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16), 64-bit’

 

On the windows version the statement:

 

select 

    st_multi((st_dump(geom)).geom)::geometry(multipolygon,25832) as geom

  from (

    select st_union(b.geom) as geom 

    from  temp_jonyp.st_union_test  b

    ) foo

;

Runs with a ‘Total query runtime: 19.5 secs 18423 rows retrieved.’ 

 

 

The same statement and data on the redhat machine runs with a ‘Total query runtime: 01:17 minutes  18423 rows retrieved.’

 

Both have almost identical execution plans:

 

Subquery Scan on foo  (cost=1428.62..1433.88 rows=1000 width=32)

  ->  Aggregate  (cost=1428.62..1428.62 rows=1 width=32)

        ->  Seq Scan on st_union_test b  (cost=0.00..1349.89 rows=31489 width=170)

 

Both have been vacuumed and analyzed beforehand. And max_parallel_workers have been set to 0 on the redhat machine.

 

I haven’t tried to do a postgis ticket, but let me know if you need that instead.

 

Kind regards Jonas

 

 

Fra: postgis-users [mailto:postgis-users-bounces at lists.osgeo.org] På vegne af Regina Obe
Sendt: 24. april 2018 09:07
Til: 'PostGIS Users Discussion' <postgis-users at lists.osgeo.org <mailto:postgis-users at lists.osgeo.org> >
Emne: Re: [postgis-users] Performance problems with ST_Union on postgres 9.6, postgis 2.4.3 running on top of Red Hat 7.4

 

 

Couple of things to try

 

1)      Can you reduce the dataset down a bit to the point you can run it in a reasonable amount of time and see differences?

2)      On the 2.4.3 plan I see it is running using parallel mode, can you turn off the parallel to rule that out as an issue. 

Set max_parallel_workers_per_gather = 0;

I don't know what your 2.4.2 was running, but for 2.3, it probably wouldn't run in parallel just because fewer functions were flagged as parallel safe

 

If you can reduce the set some something reasonable where we can test, I'd be happy to test on various OS/ PostGIS config.

I wouldn't rule out a regression issue on our end.

 

You can provide a sample on a postgis ticket, if it's not too top secret or just send directly to me.

 

http://postgis.net/support/

 

 

Thanks,

Regina

 

From: postgis-users [mailto:postgis-users-bounces at lists.osgeo.org] On Behalf Of Jonas Nygaard Pedersen
Sent: Monday, April 23, 2018 11:15 AM
To: 'postgis-users at lists.osgeo.org' <postgis-users at lists.osgeo.org <mailto:postgis-users at lists.osgeo.org> >
Subject: [postgis-users] Performance problems with ST_Union on postgres 9.6, postgis 2.4.3 running on top of Red Hat 7.4

 

Hi list

 

I'm facing some performance issues when trying to execute the following query on a Red Hat 7.4 machine with Postgres 9.6 (PostgreSQL 9.6.8 on x86_64-pc-linux-gnu, compiled by gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16), 64-bit) and postgis 2.4.3:

 

select st_multi((st_dump(geom)).geom)::geometry(multipolygon,25832) as geom

  from (

    select st_union(b.geom) as geom 

    from  b.gdk_bygning b

        ) foo;

 

Previously the statement above finished in about 3.5 hours but now it seems to go on forever, and I'll cancel it after 3 days.

 

The table contains 5310482 rows and the CREATE TABLE statement looks like this:

 

CREATE TABLE b.gdk_bygning

(

  id_lokalid bigint,

  objektstatus character varying(4000),

  registreringfra timestamp(6) without time zone,

  virkningfra timestamp(6) without time zone,

  plannoejagtighed double precision,

  vertikalnoejagtighed double precision,

  bygninguuid character varying(4000),

  bygningstype character varying(4000),

  underminimumbygning character varying(5),

  status character varying(4000),

  geom geometry(Polygon,25832)

)

 

Indexes:

CREATE INDEX gdk_bygning_id_lokalid_idx

  ON b.gdk_bygning

  USING btree

  (id_lokalid);

 

CREATE INDEX sidx_gdk_bygning_geom

  ON b.gdk_bygning

  USING gist

  (geom);

  

I'm not sure where the issue stems from, but from an approximation of when the issue started and near coincidental update from postgis 2.4.1 to 2.4.3, I suspect that the issue is rooted here, and probably combined with some clumsy settings in my postgresql.conf file.

 

Below I have compiled some documentation that I think will be relevant:

                             * the original Postgis install with 'yum', 

                             * the update with 'yum', 

                             * what I think are the relevant settings from my postgresql.conf, 

                             * the query plan for the statement on the current 2.4.3 postgis version, 

                             * and lastly the query plan on a windows machine running postgis 2.3.2 (I'm not able to roll back to 2.4.1 with GEOS 3.5).

                             

The only thing that stands out to me is that the GEOS version is upgraded from 3.5.0 to 3.6.2 but I'm definitely unsure about what's going on and I hope that someone on the list can give me some advice.

Regards Jonas  

 

OUTPUT OF 'yum history info' FOR ORIGINAL INSTALL OF POSTGIS:

 

Loaded plugins: langpacks, product-id, rhnplugin, search-disabled-repos, subscription-manager

This system is receiving updates from RHN Classic or Red Hat Satellite.

Transaction ID : 7

Begin time     : Mon Oct  9 17:56:25 2017

Begin rpmdb    : 1379:99b8afbfabf2cf72ff17087d17a2a1607e29a909

End time       :            17:56:35 2017 (10 seconds)

End rpmdb      : 1421:bd1fa883ae52216121f1a7c6a2eb06d2d6e36075

User           :  <b031513>

Return-Code    : Success

Command Line   : install postgis24_96.x86_64 postgis24_96-client.x86_64 postgis24_96-devel.x86_64 postgis24_96-utils.x86_64 SFCGAL.x86_64 pgrouting_96.x86_64

Transaction performed with:

    Installed     rpm-4.11.3-25.el7.x86_64                  @rhel-x86_64-server-7

    Updated       subscription-manager-1.19.21-1.el7.x86_64 @rhel-x86_64-server-7

    Installed     yum-3.4.3-154.el7.noarch                  @rhel-x86_64-server-7

    Installed     yum-metadata-parser-1.1.4-10.el7.x86_64   @anaconda/7.2

    Installed     yum-rhn-plugin-2.0.1-9.el7.noarch         @rhel-x86_64-server-7

Packages Altered:

    Dep-Install CGAL-4.7-1.rhel7.x86_64                     @pgdg96

    Dep-Install CharLS-1.0-5.el7.x86_64                     @rhel-x86_64-server-7-epel

    Install     SFCGAL-1.2.2-1.rhel7.x86_64                 @pgdg96

    Dep-Install SFCGAL-libs-1.2.2-1.rhel7.x86_64            @pgdg96

    Dep-Install armadillo-4.320.0-1.el7.x86_64              @rhel-x86_64-server-7-epel

    Dep-Install arpack-3.1.3-2.el7.x86_64                   @rhel-x86_64-server-7-epel

    Dep-Install atlas-3.10.1-12.el7.x86_64                  @rhel-x86_64-server-7

    Dep-Install blas-3.4.2-8.el7.x86_64                     @rhel-x86_64-server-7

    Dep-Install boost-atomic-1.53.0-27.el7.x86_64           @rhel-x86_64-server-7

    Dep-Install boost-chrono-1.53.0-27.el7.x86_64           @rhel-x86_64-server-7

    Dep-Install boost-serialization-1.53.0-27.el7.x86_64    @rhel-x86_64-server-7

    Dep-Install cfitsio-3.370-1.el7.x86_64                  @rhel-x86_64-server-7-epel

    Dep-Install freexl-1.0.0i-1.el7.x86_64                  @rhel-x86_64-server-7-epel

    Dep-Install gdal-libs-1.11.4-10.rhel7.x86_64            @pgdg96

    Dep-Install geos-3.5.0-1.rhel7.x86_64                   @pgdg96

    Dep-Install hdf5-1.8.12-8.el7.x86_64                    @rhel-x86_64-server-7-epel

    Dep-Install lapack-3.4.2-8.el7.x86_64                   @rhel-x86_64-server-7

    Dep-Install libdap-3.13.1-2.el7.x86_64                  @rhel-x86_64-server-7-epel

    Dep-Install libgeotiff-1.4.0-1.rhel7.x86_64             @pgdg96

    Dep-Install libgfortran-4.8.5-16.el7.x86_64             @rhel-x86_64-server-7

    Dep-Install libgta-1.0.4-1.el7.x86_64                   @rhel-x86_64-server-7-epel

    Dep-Install libquadmath-4.8.5-16.el7.x86_64             @rhel-x86_64-server-7

    Dep-Install netcdf-4.3.3.1-5.el7.x86_64                 @rhel-x86_64-server-7-epel

    Dep-Install ogdi-3.2.0-0.19.beta2.el7.x86_64            @rhel-x86_64-server-7-epel

    Dep-Install openjpeg2-2.1.0-7.el7.x86_64                @rhel-x86_64-server-7-epel

    Dep-Install perl-Compress-Raw-Bzip2-2.061-3.el7.x86_64  @rhel-x86_64-server-7

    Dep-Install perl-Compress-Raw-Zlib-1:2.061-4.el7.x86_64 @rhel-x86_64-server-7

    Dep-Install perl-DBD-Pg-2.19.3-4.el7.x86_64             @rhel-x86_64-server-7

    Dep-Install perl-DBI-1.627-4.el7.x86_64                 @rhel-x86_64-server-7

    Dep-Install perl-Data-Dumper-2.145-3.el7.x86_64         @rhel-x86_64-server-7

    Dep-Install perl-IO-Compress-2.061-2.el7.noarch         @rhel-x86_64-server-7

    Dep-Install perl-Net-Daemon-0.48-5.el7.noarch           @rhel-x86_64-server-7

    Dep-Install perl-PlRPC-0.2020-14.el7.noarch             @rhel-x86_64-server-7

    Dep-Install perl-version-3:0.99.07-2.el7.x86_64         @rhel-x86_64-server-7

    Install     pgrouting_96-2.5.0-1.rhel7.x86_64           @pgdg96

    Install     postgis24_96-2.4.0-1.rhel7.x86_64           @pgdg96

    Install     postgis24_96-client-2.4.0-1.rhel7.x86_64    @pgdg96

    Install     postgis24_96-devel-2.4.0-1.rhel7.x86_64     @pgdg96

    Install     postgis24_96-utils-2.4.0-1.rhel7.x86_64     @pgdg96

    Dep-Install proj-4.8.0-4.el7.x86_64                     @rhel-x86_64-server-7-epel

    Dep-Install unixODBC-2.3.1-11.el7.x86_64                @rhel-x86_64-server-7

    Dep-Install xerces-c-3.1.1-8.el7_2.x86_64               @rhel-x86_64-server-7

history info

 

OUTPUT OF 'yum history info' FOR THE UPDATE:

 

Loaded plugins: langpacks, product-id, rhnplugin, search-disabled-repos, subscription-manager

This system is receiving updates from RHN Classic or Red Hat Satellite.

Transaction ID : 35

Begin time     : Tue Apr  3 11:30:58 2018

Begin rpmdb    : 1748:db6ede4f0b0b9815a1f8704452181b47f0a32796

End time       :            11:31:04 2018 (6 seconds)

End rpmdb      : 1749:83a1f934015ebd6db6adc07214b1937477780af4

User           :  <b031513>

Return-Code    : Success

Command Line   : update postgis

Transaction performed with:

    Installed     rpm-4.11.3-25.el7.x86_64                    @rhel-x86_64-server-7

    Installed     subscription-manager-1.19.23-1.el7_4.x86_64 @rhel-x86_64-server-7

    Installed     yum-3.4.3-154.el7.noarch                    @rhel-x86_64-server-7

    Installed     yum-metadata-parser-1.1.4-10.el7.x86_64     @anaconda/7.2

    Installed     yum-rhn-plugin-2.0.1-9.el7.noarch           @rhel-x86_64-server-7

Packages Altered:

    Dep-Install geos36-3.6.2-3.1.rhel7.x86_64            @pgdg96

    Updated     postgis24_96-2.4.1-1.rhel7.x86_64        @pgdg96

    Update                   2.4.3-1.rhel7.x86_64        @pgdg96

    Updated     postgis24_96-client-2.4.1-1.rhel7.x86_64 @pgdg96

    Update                          2.4.3-1.rhel7.x86_64 @pgdg96

    Updated     postgis24_96-devel-2.4.1-1.rhel7.x86_64  @pgdg96

    Update                         2.4.3-1.rhel7.x86_64  @pgdg96

    Updated     postgis24_96-utils-2.4.1-1.rhel7.x86_64  @pgdg96

    Update                         2.4.3-1.rhel7.x86_64  @pgdg96

history info

 

 

WHAT I THINK ARE THE RELEVANT OPTIONS IN MY 'postgresql.conf' THAT ARE DIFFERENT FROM THE ONE THAT CAME WITH 9.6 FROM 'pgdg96' REPOSITORY:

shared_buffers = 50GB                   # min 128kB

                                        # (change requires restart)

#huge_pages = try                       # on, off, or try

                                        # (change requires restart)

#temp_buffers = 8MB                     # min 800kB

#max_prepared_transactions = 0          # zero disables the feature

                                        # (change requires restart)

 

work_mem = 5GB                          # min 64kB

maintenance_work_mem = 5GB

#replacement_sort_tuples = 150000       # limits use of replacement selection sort

#autovacuum_work_mem = -1               # min 1MB, or -1 to use maintenance_work_mem

#max_stack_depth = 2MB                  # min 100kB

dynamic_shared_memory_type = posix      # the default is the first option

 

 

effective_io_concurrency = 200          # 1-1000; 0 disables prefetching

max_worker_processes = 64       # (change requires restart)

max_parallel_workers_per_gather = 12    # taken from max_worker_processes

 

seq_page_cost = 1.0                     # measured on an arbitrary scale

random_page_cost = 2.0                  # same scale as above

#cpu_tuple_cost = 0.01                  # same scale as above

#cpu_index_tuple_cost = 0.005           # same scale as above

#cpu_operator_cost = 0.0025             # same scale as above

parallel_tuple_cost = 0.001             # same scale as above

parallel_setup_cost = 100.0                                                                 # same scale as above

#min_parallel_relation_size = 8MB

effective_cache_size = 90GB

 

QUERY PLAN AFTER UPDATE TO POSTGIS 2.4.3 ('POSTGIS="2.4.3 r16312" PGSQL="96" GEOS="3.6.2-CAPI-1.10.2 4d2925d6" SFCGAL="1.2.2" PROJ="Rel. 4.9.3, 15 August 2016" GDAL="GDAL 1.11.4, released 2016/01/25" LIBXML="2.9.1" LIBJSON="0.11" RASTER')

 

 

                                             QUERY PLAN

-----------------------------------------------------------------------------------------------------

Subquery Scan on foo  (cost=231732.65..231737.92 rows=1000 width=32)

   ->  Aggregate  (cost=231732.65..231732.66 rows=1 width=32)

         ->  Gather  (cost=100.00..218456.45 rows=5310482 width=169)

               Workers Planned: 5

               ->  Parallel Seq Scan on gdk_bygning b  (cost=0.00..213045.96 rows=1062096 width=169)

(5 rows)

 

QUERY PLAN ON WINDOWS MACHINE ('POSTGIS="2.3.2 r15302" GEOS="3.5.0-CAPI-1.9.0 r4084" PROJ="Rel. 4.9.2, 08 September 2015" GDAL="GDAL 1.11.5, released 2016/07/01" LIBXML="2.9.4" TOPOLOGY RASTER'):

 

                                             QUERY PLAN

-------------------------------------------------------------------------------------

Subquery Scan on foo  (cost=216558.28..216563.55 rows=1000 width=32)

  ->  Aggregate  (cost=216558.28..216558.29 rows=1 width=32)

        ->  Seq Scan on gdk_bygning b  (cost=0.00..204498.02 rows=4824102 width=175)

 

Jonas Nygaard Pedersen │Geodataanalytiker │Eff – Effektivisering│Tel. 7254 5510│jonyp at sdfe.dk

 

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