Re: Update statement results in Out of memory

On 07/06/2016 02:13 AM, Ivan Bianchi wrote:
> Hello,
>
> I am trying to update a column using a PostGIS ST_Buffer
> <http://postgis.net/docs/ST_Buffer.html> function into a table
> of 4.257.769 rows, but after 6 hours, an /Out of memory/ error appears
> and the kernel starts killing processes until a /Kernel Panic/ shows up.
>
> I have simplified the buffer target geometry and also added a gist index
> to that column.
>
> The statement is the following:
>
> psql -h host -U user -W -d database -c "UPDATE table SET buffer =
> ST_Buffer(simplified_geometry, 0.005);"

I would say the issue is the above, you are running in a single
transaction. Given that an UPDATE in Postgres is a DELETE/INSERT and
that both the new and old rows have to be kept around until the
transaction completes I see only problems with doing it this way.

>
>
> After reading and tunning the configuration, I still have the same result.
>
> Here's the initial memory stats:
>
> total used freeshared buff/cache
> available
> Mem: 15G 1.5G 12G 503M 1.4G
> 13G
> Swap: 7.8G 0B 7.8G
>
>
>
> I'm running out of ideas, as I think the postgresql.conf memory
> parameters are quite low for the machine specs. I understand I can split
> the process and paginate the rows, but I can't see why I can't deal with
> this full statement right now.

See above.

>
> Do you think this issue is related with the postgres memory parameters
> configuration? Why is not respecting the shared_buffers or
> effective_cache_size parameters and keeps growing?
>
>
> Here's some info:
> *
> *
> _Machine specs_
>
> * Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz (8 cores)
> * 16 GB of memory
> * Fedora release 23 (Twenty Three)
> * Kernel - 4.5.7-202.fc23.x86_64
>
> _postgresql.conf_
>
> * effective_cache_size = 5GB
> * shared_buffers = 3GB
> * work_mem = 10MB
>
> * maintenance_work_mem = 800MB
> * wal_buffers = 16MB
>
> _Kernel parameters_
>
> * vm.overcommit_memory=2
>
> * kernel.shmmax = 8340893696
> * kernel.shmall = 2036351
>
> _Versions:_
>
> * PostgreSQL 9.5.3 on x86_64-pc-linux-gnu, compiled by gcc (GCC) 5.3.1
> 20160406 (Red Hat 5.3.1-6), 64-bit
> * POSTGIS="2.2.2 r14797" GEOS="3.5.0-CAPI-1.9.0 r4084" PROJ="Rel.
> 4.9.1, 04 March 2015" GDAL="GDAL 2.0.2, released 2016/01/26"
> LIBXML="2.9.3" LIBJSON="0.12" RASTER
>
>
> Many thanks,
>
> --
> Ivan

--
Adrian Klaver
adrian(dot)klaver(at)aklaver(dot)com