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

Hi,

Of course today after a reboot to update to the newest kernel,
everything works without crashing...

I imagine that yesterday the problem was that I had forgotten that I had
a Windows virtual machine running on the server that was eating a good
piece of memory. Still, using a cursor to page through the data should
have avoided major memory difficulties...

As a footnote, I can confirm that PL/R was not eating up memory little
by little (see results of memory.profile() at beginning and end of each
function invokation below).

Thanks,
David

Run 1:

NOTICE: Starting predict_classification_model
NOTICE: NULL symbol pairlist closure environment
promise
NOTICE: 1 7847 173768 4308 1129 6273
NOTICE: language special builtin char logical
integer
NOTICE: 46996 189 1839 9387 7351 17229
NOTICE: double complex character ... any list
NOTICE: 2190 1 42810 1 0 13456
NOTICE: expression bytecode externalptr weakref raw S4
NOTICE: 3 10246 823 198 199 1061

NOTICE: Ending predict_classification_model
NOTICE: NULL symbol pairlist closure environment
promise
NOTICE: 1 8062 181354 4360 1129 6273
NOTICE: language special builtin char logical
integer
NOTICE: 50616 189 1839 2085318 7496 17972
NOTICE: double complex character ... any list
NOTICE: 2393 1 43459 1 0 13929
NOTICE: expression bytecode externalptr weakref raw S4
NOTICE: 3 10683 814 187 188 1061

Run 2:

NOTICE: Starting predict_classification_model
NOTICE: NULL symbol pairlist closure environment
promise
NOTICE: 1 8062 180936 4360 1128 6271
NOTICE: language special builtin char logical
integer
NOTICE: 50536 189 1839 9684 7496 17878
NOTICE: double complex character ... any list
NOTICE: 2258 1 43312 1 0 13899
NOTICE: expression bytecode externalptr weakref raw S4
NOTICE: 3 10683 813 188 189 1061

NOTICE: Ending predict_classification_model
NOTICE: NULL symbol pairlist closure environment
promise
NOTICE: 1 8062 181356 4360 1129 6273
NOTICE: language special builtin char logical
integer
NOTICE: 50617 189 1839 2085317 7496 17972
NOTICE: double complex character ... any list
NOTICE: 2393 1 43459 1 0 13929
NOTICE: expression bytecode externalptr weakref raw S4
NOTICE: 3 10683 814 187 188 1061

Run 3:

NOTICE: Starting predict_classification_model
NOTICE: NULL symbol pairlist closure environment
promise
NOTICE: 1 8062 180936 4360 1128 6271
NOTICE: language special builtin char logical
integer
NOTICE: 50536 189 1839 9684 7496 17878
NOTICE: double complex character ... any list
NOTICE: 2258 1 43312 1 0 13899
NOTICE: expression bytecode externalptr weakref raw S4
NOTICE: 3 10683 813 188 189 1061

NOTICE: Ending predict_classification_model
NOTICE: NULL symbol pairlist closure environment
promise
NOTICE: 1 8062 181356 4360 1129 6273
NOTICE: language special builtin char logical
integer
NOTICE: 50617 189 1839 2085319 7496 17972
NOTICE: double complex character ... any list
NOTICE: 2393 1 43459 1 0 13929
NOTICE: expression bytecode externalptr weakref raw S4
NOTICE: 3 10683 814 187 188 1061

On 05/16/2013 11:40 PM, Joe Conway wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> 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
Charge de Recherche 1

Institut de Recherche pour le Developpement
Centre de Recherche Halieutique Mediterraneenne et Tropicale
av. Jean Monnet
B.P. 171
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France

Phone: +33 (0)4 99 57 32 27
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http://www.umr-eme.org/team/dkaplan/
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