From murdoch at stats.uwo.ca  Thu Jan 25 15:21:41 2007
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Thu, 25 Jan 2007 09:21:41 -0500
Subject: [Rd] serialize() takes too long when serializing to a raw vector
In-Reply-To: <2AB7346A3227A74BB97F9A0D79E3E65A090DB1@kalyptomail.dnsalias.com>
References: <2AB7346A3227A74BB97F9A0D79E3E65A090DB1@kalyptomail.dnsalias.com>
Message-ID: <45B8BCF5.6050509@stats.uwo.ca>

On 1/25/2007 6:32 AM, Ashish Kulkarni wrote:
> Hello,
> 
> R version 2.4.1 (2006-12-18) 
> i386-pc-mingw32
> 
> Calling serialize() with a NULL connection serializes it to a raw vector. However, when the object to be serialized is large, it takes a very long time:
> 
>> system.time( serialize(matrix(0, 1000, 1000), NULL) )
> [1] 38.25 40.73 81.54    NA    NA
> 
>> system.time( serialize(matrix(0, 2000, 2000), NULL) )
> [1]  609.72  664.75 1318.57      NA      NA
> 
> I was using this in Rmpi, where a clustered call returned a large matrix. However, serializing to a file or sockets is very fast for the very same matrix -- hence I wrote this function which runs much faster:
> 
> .mpi.quick.serialize <- function (object)
> {
>     fname <- tempfile("Rmpi")
>     stream <- file(fname, "wb")
>     on.exit({
>         close(stream)
>         file.remove(fname)
>     })
>     serialize(object, stream)
>     close(stream)
>     size <- file.info(fname)$size
>     stream <- file(fname, "rb")
>     return(readBin(stream, "raw", n = size))
> }
> 
>> system.time( .mpi.quick.serialize(matrix(0, 1000, 1000) ) )
> [1] 0.2500000000000000 0.0499999999999545 0.3000000000001819
> [4]                 NA                 NA
> 
>> system.time( .mpi.quick.serialize(matrix(0, 2000, 2000) ) )
> [1] 1.059999999999945 0.220000000000027 1.289999999999964
> [4]                NA                NA
> 
> Does anyone have an idea why the performance difference is so 
> large? Also, I was wondering if there is a better way -- the 
> above solution feels like a quick fix rather than a correct
> approach.

It looks like a bug in the serialize code:  it's reallocating the output 
buffer far too often, and that's slowing things down.  I'll confirm 
that's what's going on and fix it.

Duncan Murdoch



[Rd] serialize() takes too long when serializing to a raw vector
Duncan Murdoch