From osklyar at ebi.ac.uk  Sat May 26 13:41:47 2007
From: osklyar at ebi.ac.uk (Oleg Sklyar)
Date: Sat, 26 May 2007 12:41:47 +0100
Subject: [Rd] R scripts slowing down after repeated called to compiled
 code
In-Reply-To: <18007.36866.90420.541219@basebud.nulle.part>
References: <1180134776.6736.15.camel@braunm1>
	<18007.36866.90420.541219@basebud.nulle.part>
Message-ID: <46581CFB.5050401@ebi.ac.uk>

I work with images with a lot of processing done in C code. Quite often 
I allocate memory there up to several gigs in chunks of 10-15 Mb each 
plus hundreds of protected dims, names etc. I had a similar problem only 
once when due to some erroneous use of an external library, internally 
created objects were not freed correctly. Otherwise, after correcting 
this, I never have seen any slow down on large number of objects created 
and manipulated. And then, it was so difficult to track the memory leak 
that I would really suggest to double and triple check all the memory 
allocations. Your code does not use any temp files? This could be a real 
pain. Oleg

Dirk Eddelbuettel wrote:
> On 25 May 2007 at 19:12, Michael Braun wrote:
> | So I'm stuck.  Can anyone help?
> 
> It sounds like a memory issue. Your memory may just get fragmented. One tool
> that may help you find leaks is valgrind -- see the 'R Extensions' manual. I
> can also recommend the visualisers like kcachegrind (part of KDE).
> 
> But it may not be a leak. I found that R just doesn't cope well with many
> large memory allocations and releases -- I often loop over data request that
> I subset and process. This drives my 'peak' memory use to 1.5 or 1.7gb on
> 32bit/multicore machine with 4gb, 6gb or 8gb (but 32bit leading to the hard
> 3gb per process limit) .  And I just can't loop over many such task.  So I
> now use the littler frontend to script this, dump the processed chunks as
> Rdata files and later re-read the pieces. That works reliably.
> 
> So one think you could try is to dump your data in 'gsl ready' format from R,
> quit R, leave it out of the equation and then see if what happens if you do
> the iterations in only GSL and your code.
> 
> Hth, Dirk
> 

-- 
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466



[Rd] R scripts slowing down after repeated called to compiled code
Oleg Sklyar