Thanks everyone for advice on this matter.
I've been asked to report our conclusion.
We have decide to order a duo processor(3.06GHz) Dell Precision 4400
laptop with 8GB memory and 500GB disk.
It will be running Vista 64 bit to begin with, moving over to Windows 7
once a little experience is gained with it elsewhere.
We will leave the multi CPU use of R to our larger unix servers.
cheers,
Keith
Prof Brian Ripley wrote:
The answer to (1) is in the rw-FAQ, so see
library(fortunes)
fortune('WTFM')
On Mon, 28 Sep 2009, Corrado wrote:
1) Would a package compiled for Windows 32bit run on Windows 64 bit
and use
the extended memory or not?
2) As for buying a performant laptop for R, I bought a Dell M6300 mobile
workstation which is actually portable, and installed Kubuntu 904 64 bit
alongside the standard windows installation. When I run R I only use
it in
Linux and access the data in Windows through the file system. If I
need to run
Office because some one else is sending me document to correct, I
have installed
Windows XP Pro SP3 in a virtual machine using Virtual Box, which runs
very
fairly on the M6300, and can switch it on and off whenever I need
(booting on
the virtual machine is matter of few seconds). This setup allows for
running
64 bit R on Linux (eventually compiled with -O3 -march=native by the
way, if
you feel like experimenting) which is more performant and used the
memory more
efficiently, without loosing the interacting with your windows based
colleagues.
The virtual machine can go full screen at the click of a mouse :D and
it looks
as if you were using a native Windows machine. You can install all
software
and network clients on the virtual machine. I have not booted Windows
for ages
.... I have been using this machine fort he last 18 months. The dual
core
works great (I chose the top processor to run simulations when I am
not in the
office), and in Linux you can control the CPU frequency. The new one
which
substitutes the M6300 is the M6400 and I would go for that possibly
(Linux
supported):
http://www1.euro.dell.com/uk/en/business/Laptops/workstation-precision-m6400-
cov/pd.aspx?refid=workstation-precision-m6400-cov&s=bsd&cs=ukbsdt1
PS: I apologise for the question on memory management but I have
never used R
on Windows but some free spirit decided to release a package only for
Windows
and only pre compiled (no sources) and I need to use it to compare
.... (Sorry
for the harsh comment and the rant , but I am not sure it is really
fair to
use an open source packages and programming languages for you daily
work and
make money out of it, and the first time you release something you
release it
crappy and closed source .... even if it is legal and allowed of
course .... :
( ....)
On Monday 28 September 2009 09:16:23 Prof Brian Ripley wrote:
On Mon, 28 Sep 2009, Sean O'Riordain wrote:
Good morning Keith,
Have a look at
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-
a-limit-on-the-memory-it-uses_0021
The short answer is that "it depends"...
a) memory is limited under windows
Yes, but 64-bit builds can be used on Windows -- that needs commercial
compilers and there are commercial vendors of such builds.
Even with the CRAN binary, a 64-bit version of Windows offers double
the memory over a (vanilla) 32-bit version.
b) R is essentially a serial program - HOWEVER it depends what you're
actually doing - if you're working with large matrices then there are
parallel versions of BLAS that can be used... On a multi-core windows
machine with lots of memory you can of course run up multiple
copies of R
and run each independently
There are several packages that parallelize their computations with
MPI etc, and others that help with parallelization (papply, foreach,
gputools, ....). And apart from Rmpi/rpvm/snow there is also
'multicore', but not on Windows. See the R-sig-hpc list for follow up
on such issues.
As for Vista vs Windows 7, this is not the right list but Windows 7
behaves just like a version of Vista as far as we have explored it
(and the current rw-FAQ includes it and Server 2008 in the Vista
section).
Many of us have bought dual quad-core servers in the last year or so:
that includes Uwe Ligges' winbuilder machine. I suspect most of the
usage is separate R jobs running simultaneously: certainly that is the
case in my dept (where there are at least 6 8-core servers running R
jobs).
Kind regards,
Sean
On Mon, Sep 28, 2009 at 4:40 AM, Keith Satterley <ke...@wehi.edu.au>
wrote:
I've read some postings back in 2002/2006 about running R on multiple
core CPUs. The answer was basically separate processes work fine, but
parallelization needs to be implemented using snow/rmpi. Are the
answers
still the same?
I ask because we are about to order a laptop running Windows for a
new
staff member. Some advice on the following would be helpful.
It will be ordered with Vista, with a free upgrade to Windows 7.
It will
have 8GB of memory
A quad core CPU costs about AUD$1100 more than the fastest (Intel
T9900-6M Cache, 3.06 GHz) dual core CPU.
I'm wondering if there is value in ordering the quad core. We are
looking at a time frame of 3-4 years.
Is anyone aware of near future plans to implement some form or
parallelization that would more or less be hidden from the normal
user?
It is anticipated that analysis of Next Gen sequence data will be
important.
I've read the Windows FAQ about running R under Vista. We will
probably
start with Vista. I've read some posts in R-devel indicating
people are
running R under Windows 7. Is it safe to assume that R will run under
Windows 7 after it is released?
We are hoping to make use the 8GB of memory. Am I right in
assuming that
when the 64 bit version of Windows 7 is available, it will allow R
users
to make good use of the 8GB of memory. Does this happen under the
current higher end versions of 64 bit Vista?
cheers,
Keith
========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
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--
Corrado Topi
Global Climate Change & Biodiversity Indicators
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk
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