From ashish.kulkarni at kalyptorisk.com  Thu Jan 25 14:26:22 2007
From: ashish.kulkarni at kalyptorisk.com (Ashish Kulkarni)
Date: Thu, 25 Jan 2007 18:56:22 +0530
Subject: [Rd] serialize() takes too long when serializing to a raw vector
In-Reply-To: <45B8AA93.2000801@cimr.cam.ac.uk>
Message-ID: <2AB7346A3227A74BB97F9A0D79E3E65A090DC9@kalyptomail.dnsalias.com>

Hin-Tak Leung wrote:
> 
> It might be interesting to know get some details on your hardware.
> 

It's a P4 2.66GHz with a standard Intel motherboard having 1GB RAM.

> On my box, linux native seems to be a little slower than
> your quick.serialize times:
> 
>  > system.time( serialize(matrix(0, 1000, 1000), NULL) )
> [1] 0.372 0.288 0.692 0.000 0.000
>  > system.time( serialize(matrix(0, 2000, 2000), NULL) )
> [1] 1.237 1.195 2.501 0.000 0.000
> 
> running R 2.4.1 windows under wine (same box) is a good deal s
> lower, but is not anywhere nearly as slow as yours.
> 
>  > system.time( serialize(matrix(0, 1000, 1000), NULL) )
> [1] 0.00 0.00 6.08   NA   NA
>  > system.time( serialize(matrix(0, 2000, 2000), NULL) )
> [1]  0.01  0.01 78.00    NA    NA
>  >
> 

Well, the timings certainly differ quite a bit. What kind of
hardware do you have? I suspect that most of the delay may be
caused by memory reallocation since the size of the output 
raw array is not known up front. I would imagine that WINE 
would use the system memory allocator, not the one used by 
the windows kernel.

> Since you mentioned that you are using Rmpi, there is a possibility
> that you might be calling a different serialize() than base::serialize
> all together???

Nope, I hit this problem while using Rmpi and tracked it down
to .mpi.serialize, which in turn calls base::serialize. From Rmpi:

.mpi.serialize <- function (obj) 
{
    trans_obj = serialize(obj, NULL)
    if (getRversion() >= "2.4.0") 
        return(trans_obj)
    else return(charToRaw(trans_obj))
}

Regards,
ashish



[Rd] serialize() takes too long when serializing to a raw vector
Ashish Kulkarni