From ripley at stats.ox.ac.uk  Mon Sep 28 12:01:42 2009
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 28 Sep 2009 11:01:42 +0100 (BST)
Subject: [Rd] Windows Laptop specification query
In-Reply-To: <200909281044.06278.ct529@york.ac.uk>
References: <4AC03013.1030402@wehi.edu.au>
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	<alpine.LFD.2.00.0909280903260.22690@gannet.stats.ox.ac.uk>
	<200909281044.06278.ct529@york.ac.uk>
Message-ID: <alpine.LFD.2.00.0909281100040.31119@toucan.stats.ox.ac.uk>

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 <keith at 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
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> -- 
> 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: ct529 at york.ac.uk
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Windows Laptop specification query
Prof Brian Ripley