Re: problem with lost connection while running long PL/R query - Mailing list pgsql-general

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On 05/16/2013 08:40 AM, Tom Lane wrote:
> "David M. Kaplan" <david.kaplan@ird.fr> writes:
>> Thanks for the help.  You have definitely identified the problem,
>> but I am still looking for a solution that works for me.  I tried
>> setting vm.overcommit_memory=2, but this just made the query
>> crash quicker than before, though without killing the entire
>> connection to the database.  I imagine that this means that I
>> really am trying to use more memory than the system can handle?
>
>> I am wondering if there is a way to tell postgresql to flush a
>> set of table lines out to disk so that the memory they are using
>> can be liberated.
>
> Assuming you don't have work_mem set to something unreasonably
> large, it seems likely that the excessive memory consumption is
> inside your PL/R function, and not the fault of Postgres per se.
> You might try asking in some R-related forums about how to reduce
> the code's memory usage.

The two "classic" approaches to this with PL/R are either create a
custom aggregate with the PL/R as the final function (i.e. work on one
group at a time) or use the SPI cursor functionality within the PL/R
function and page your data using a cursor. Not all forms of analysis
lend themselves to these approaches, but perhaps yours does.

Ultimately I would like to implement a form of R data.frame that does
the paging with a cursor transparently for you, but I have not been
able to find the time so far.

Joe


- --
Joe Conway
credativ LLC: http://www.credativ.us
Linux, PostgreSQL, and general Open Source
Training, Service, Consulting, & 24x7 Support
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