Re: problem with lost connection while running long PL/R query

Hi Joe,

Thanks for responding as you would clearly be the expert on this sort of
problem. My current function does page through data using a cursor
precisely to avoid out of memory problems, which is why I am somewhat
surprised and stumped as to how this can be happening. It does return
all the data at once, but one call to the function would seem to work,
so I can't see why 4 wouldn't. I am currently planning to do some test
runs using memory.profile() to see if each successive call to the PL/R
function is somehow accumulating memory usage somewhere. Perhaps I am
not properly closing a query or something like that?

I am attaching my code. Perhaps you will have some insight. To give
you a basic idea of what I am trying to do, I have separately developed
a classification model for the state of a "system" based on the data in
the postgresql table. I want to apply that model to each line of the
table. I loop over the cursor and predict the state for batches of
10,000 lines at a time.

Thanks again for the help.

Cheers,
David

On 05/16/2013 11:40 PM, Joe Conway wrote:
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> On 05/16/2013 08:40 AM, Tom Lane wrote:
>> "David M. Kaplan" <david(dot)kaplan(at)ird(dot)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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David M. Kaplan
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