From keith at wehi.EDU.AU  Fri Oct  2 08:32:02 2009
From: keith at wehi.EDU.AU (Keith Satterley)
Date: Fri, 02 Oct 2009 16:32:02 +1000
Subject: [Rd] Windows Laptop specification query
In-Reply-To: <alpine.LFD.2.00.0909281100040.31119@toucan.stats.ox.ac.uk>
References: <4AC03013.1030402@wehi.edu.au>
	<8ed68eed0909272330k744b89f4m1add09313c5728fb@mail.gmail.com>
	<alpine.LFD.2.00.0909280903260.22690@gannet.stats.ox.ac.uk>
	<200909281044.06278.ct529@york.ac.uk>
	<alpine.LFD.2.00.0909281100040.31119@toucan.stats.ox.ac.uk>
Message-ID: <4AC59E62.7030808@wehi.edu.au>

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 <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
>>
>



[Rd] Windows Laptop specification query
Keith Satterley