Which Linux OS on Athlon amd64, to comfortably run R?

Dear R-users.
I eventually bought myself a new computer with the following 
characteristics:

Processor AMD ATHLON 64 DUAL CORE 4000+ (socket AM2)
Mother board ASR SK-AM2 2
Ram Corsair Value 1 GB DDR2 800 Mhz
Hard Disk WESTERN DIGITAL 160 GB SATA2 8MB

I'm a newcomer to the Linux world.
I started using it (Ubuntu 7.10 at work and FC4 on laptop) on a regular 
basis on May.
I must say I'm quite comfortable with it, even if I have to re-learn a 
lot of things.  But this is not a problem, I will improve my knowledge 
with time.

My main problem now, is that I installed Ubuntu 7.10 Gutsy Gibbon on the 
new one amd64.

To install R on it i followed the directions found here
http://help.nceas.ucsb.edu/index.php/Installing_R_on_Ubuntu

but unfortunately it did not work.

After reading some posts on the R-SIG-debian list, such as

https://stat.ethz.ch/pipermail/r-sig-debian/2007-October/000253.html

I immediately realize that an amd64 is not the right processor to make 
life easy.

Therefore I would like to know from you, how can I solve this problem:
Should I install the i386 version of R ?
Should I install another flavour of Linux ?
Which one ?
Fedora Core 7 ?
Debian ?

Thanks a lot, for any suggestion

 

Hi,

I've got an Athlon 64bits 3000+ processor and Ubuntu LTS (dapper) 
installed (64 bits version) on my laptop. I do not have any problem to 
install R from the sources, as long as the correct 
libraries/compilers/etc. are installed. But it is no pain if you just 
follow what the configure script tells you (and use apt-get to install 
missing packages). I guess a common mistake is to forget to install 
"-dev" versions of packages, which sometimes contain required headers. 
However, you should not have troubles installing R on different R 
distributions, 64bits or not.

Hope this help.

Thibaut, 64bit-linux-Ruser and still alive.

######################################
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biom?trie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
T?l. : 04.72.43.29.35
Fax : 04.72.43.13.88
jombart at biomserv.univ-lyon1.fr
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://pbil.univ-lyon1.fr/software/adegenet/

but unfortunately it did not work.

What did not work? Provide some information more...
By the way, isn't 'gfortran' the new GNU fortran compiler which
replaced 'g77'? Or not on Ubuntu?

I immediately realize that an amd64 is not the right processor to make
life easy.

??? Example of bad extrapolation ;)

Should I install the i386 version of R ?

I assume you are talking about installing from source. You installed
the i386 version of Ubuntu? Then yes. Else no.

But rather let apt-get do it for you. Just install the binary provided
by the Ubuntu community. It is the best way to get things working and
avoid problems.

Should I install another flavour of Linux ?

It depends. Ubuntu is good to start, and has the widest users base;
Archlinux my best choice (but you need to be already somewhat
advanced).

ScionForbai

Hi Ottorino,

I have been using R on 64-bit Ubuntu for about a year without
problems, both Intel and AMD CPUs. Installing and using several
packages (e1071, svmpath, survival) also works. However, I had to
install R from source:

$ gunzip -c R-2.6.1.tar.gz | tar xvf -
$ cd R-2.6.1
$ ./configure --enable-R-shlib; make; make pdf
# make install; make install-pdf

Notice that `make install' has to be run as root.

I am using Feisty Fawn (Ubuntu 7.04), although I doubt that makes a
difference.

Hope this helps,

Ljubomir

8rino-Luca Pantani writes:
 > Dear R-users.
 > I eventually bought myself a new computer with the following 
 > characteristics:
 > 
 > Processor AMD ATHLON 64 DUAL CORE 4000+ (socket AM2)
 > Mother board ASR SK-AM2 2
 > Ram Corsair Value 1 GB DDR2 800 Mhz
 > Hard Disk WESTERN DIGITAL 160 GB SATA2 8MB
 > 
 > I'm a newcomer to the Linux world.
 > I started using it (Ubuntu 7.10 at work and FC4 on laptop) on a regular 
 > basis on May.
 > I must say I'm quite comfortable with it, even if I have to re-learn a 
 > lot of things.  But this is not a problem, I will improve my knowledge 
 > with time.
 > 
 > My main problem now, is that I installed Ubuntu 7.10 Gutsy Gibbon on the 
 > new one amd64.
 > 
 > To install R on it i followed the directions found here
 > http://help.nceas.ucsb.edu/index.php/Installing_R_on_Ubuntu
 > 
 > but unfortunately it did not work.
 > 
 > After reading some posts on the R-SIG-debian list, such as
 > 
 > https://stat.ethz.ch/pipermail/r-sig-debian/2007-October/000253.html
 > 
 > I immediately realize that an amd64 is not the right processor to make 
 > life easy.
 > 
 > Therefore I would like to know from you, how can I solve this problem:
 > Should I install the i386 version of R ?
 > Should I install another flavour of Linux ?
 > Which one ?
 > Fedora Core 7 ?
 > Debian ?
 > 
 > Thanks a lot, for any suggestion
 > 
 > -- 
 > Ottorino-Luca Pantani, Universit? di Firenze
 > Dip. Scienza del Suolo e Nutrizione della Pianta
 > P.zle Cascine 28 50144 Firenze Italia
 > Tel 39 055 3288 202 (348 lab) Fax 39 055 333 273 
 > OLPantani at unifi.it  http://www4.unifi.it/dssnp/
 > 
 > ______________________________________________
 > R-help at r-project.org mailing list
 > https://stat.ethz.ch/mailman/listinfo/r-help
 > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 > and provide commented, minimal, self-contained, reproducible code.

Dear R-users.
I eventually bought myself a new computer with the following 
characteristics:

Processor AMD ATHLON 64 DUAL CORE 4000+ (socket AM2)
Mother board ASR SK-AM2 2
Ram Corsair Value 1 GB DDR2 800 Mhz
Hard Disk WESTERN DIGITAL 160 GB SATA2 8MB

I'm a newcomer to the Linux world.
I started using it (Ubuntu 7.10 at work and FC4 on laptop) on a regular 
basis on May.
I must say I'm quite comfortable with it, even if I have to re-learn a 
lot of things.  But this is not a problem, I will improve my knowledge 
with time.

My main problem now, is that I installed Ubuntu 7.10 Gutsy Gibbon on the 
new one amd64.

To install R on it i followed the directions found here
http://help.nceas.ucsb.edu/index.php/Installing_R_on_Ubuntu

but unfortunately it did not work.

After reading some posts on the R-SIG-debian list, such as

https://stat.ethz.ch/pipermail/r-sig-debian/2007-October/000253.html

I immediately realize that an amd64 is not the right processor to make 
life easy.

Therefore I would like to know from you, how can I solve this problem:
Should I install the i386 version of R ?
Should I install another flavour of Linux ?
Which one ?
Fedora Core 7 ?
Debian ?

Thanks a lot, for any suggestion

  

Amd64 architecture should not be a major issue for R on any of the major
platforms, as far as I know. I have Fedora 7 (soon-ish F8) on the "big"
machine back home (dual Opteron) and that one never had any major issues
with either of source builds or the "official" RPMs. The main (only?)
thing that still tends to bite people on 64 bit is browser plugins,
notably Java.

In general, I've been happy with Fedora, although its desire to update
itself constantly does require a good 'Net connection.

My SUSE desktop at work is also 64 bit and happy to deal with R (in fact
the official release builds are made on it). The KDE desktop has a few
annoying misfeatures (to me), though, and you need a little special
setup to include Detlefs repository as an install source.

One oddity about Ubuntu is that there are no CRAN builds for 64bit.
Presumably, the Debian packages work, or you can get the build script
and make your own build. This is not really within my domain, though.

O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

Note that Ottorino has only 1GB of RAM installed, which makes a 64-bit 
version of R somewhat moot.  See chapter 8 of

http://cran.r-project.org/doc/manuals/R-admin.html

I would install a i386 version of R on x86_64 Linux unless I had 2Gb or 
more of RAM.  I don't know how easily that works on Ubuntu these days, but 
I would try it.

Hi Ottorino,

I have been using R on 64-bit Ubuntu for about a year without
problems, both Intel and AMD CPUs. Installing and using several
packages (e1071, svmpath, survival) also works. However, I had to
install R from source:

$ gunzip -c R-2.6.1.tar.gz | tar xvf -
$ cd R-2.6.1
$ ./configure --enable-R-shlib; make; make pdf
# make install; make install-pdf

Notice that `make install' has to be run as root.

I am using Feisty Fawn (Ubuntu 7.04), although I doubt that makes a
difference.

Hope this helps,

Ljubomir

8rino-Luca Pantani writes:

Dear R-users.
I eventually bought myself a new computer with the following
characteristics:

Processor AMD ATHLON 64 DUAL CORE 4000+ (socket AM2)
Mother board ASR SK-AM2 2
Ram Corsair Value 1 GB DDR2 800 Mhz
Hard Disk WESTERN DIGITAL 160 GB SATA2 8MB

I'm a newcomer to the Linux world.
I started using it (Ubuntu 7.10 at work and FC4 on laptop) on a regular
basis on May.
I must say I'm quite comfortable with it, even if I have to re-learn a
lot of things.  But this is not a problem, I will improve my knowledge
with time.

My main problem now, is that I installed Ubuntu 7.10 Gutsy Gibbon on the
new one amd64.

To install R on it i followed the directions found here
http://help.nceas.ucsb.edu/index.php/Installing_R_on_Ubuntu

but unfortunately it did not work.

After reading some posts on the R-SIG-debian list, such as

https://stat.ethz.ch/pipermail/r-sig-debian/2007-October/000253.html

I immediately realize that an amd64 is not the right processor to make
life easy.

Therefore I would like to know from you, how can I solve this problem:
Should I install the i386 version of R ?
Should I install another flavour of Linux ?
Which one ?
Fedora Core 7 ?
Debian ?

Thanks a lot, for any suggestion

--
Ottorino-Luca Pantani, Universit? di Firenze
Dip. Scienza del Suolo e Nutrizione della Pianta
P.zle Cascine 28 50144 Firenze Italia
Tel 39 055 3288 202 (348 lab) Fax 39 055 333 273
OLPantani at unifi.it  http://www4.unifi.it/dssnp/

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

Note that Ottorino has only 1GB of RAM installed, which makes a 64-bit
version of R somewhat moot.  See chapter 8 of

http://cran.r-project.org/doc/manuals/R-admin.html

Only somewhat. The Opteron actually has 1GB too (Hey, it was bought in
2004!  And the main point was to see whether 64 bit builds would work at
all) but 16GB of swap. So large data sets will fit but be processed slowly.

I would install a i386 version of R on x86_64 Linux unless I had 2Gb
or more of RAM.  I don't know how easily that works on Ubuntu these
days, but I would try it.

It's not like the 64 bit build feels slow for basic usage, though. I
don't think you need to bother with mixing architectures unless you have
applications where it really matters (CPU intensive, but below 32-bit
addressing limitations). Buying more RAM is much to be preferred.

Now what kind of RAM does my Opteron board take... ?

O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

One oddity about Ubuntu is that there are no CRAN builds for 64bit.

Volunteers would be welcomed with open arms.

Dirk,

Three out of two people have difficulties with fractions.

[....]

|> One oddity about Ubuntu is that there are no CRAN builds for 64bit.
|> Presumably, the Debian packages work, or you can get the build
|> script and make your own build. This is not really within my
|> domain, though.

I've always used rpms (or debs for Debian-type OSes) but I install R
from source which is very easy to do.  Adding R packages with
install.packages() is also extremely easy.  If you have the 64bit OS,
it will compile R as 64 bit (enless you make some modifications to the
standard configuration).

One downside of that is that you'd be unable to use packages that have
only 32 bit versions.  One such is ASReml-R but if you never intend to
use such things, the only other consideration I can think of is the
relatively small amount of memory.  No great benefits of 64 bit
without lots of memory, but a few downsides.

HTH

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}          		 Great minds discuss ideas    
 _( Y )_  	  	        Middle minds discuss events 
(:_~*~_:) 	       		 Small minds discuss people  
 (_)-(_)  	                           ..... Anon
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

One oddity about Ubuntu is that there are no CRAN builds for 64bit.

Volunteers would be welcomed with open arms.

I don't think I know enough to volunteer (but I am open to suggestion  
off list), but I had no difficulty installing R from source on a 64  
bit Ubuntu machine (7.10, with, I believe, 1 GB of RAM) following the  
instructions in R-admin. I just kept installing necessary libraries  
until ./configure completed without errors. Then make, make check,  
and make install ran without a hitch.

Kevin

-------------------------------------------------
Kevin M. Middleton
Department of Biology
California State University San Bernardino
5500 University Parkway
San Bernardino CA 92507

Prof Brian Ripley a ?crit :

Note that Ottorino has only 1GB of RAM installed, which makes a 64-bit
version of R somewhat moot.  See chapter 8 of

http://cran.r-project.org/doc/manuals/R-admin.html

Thank you for this reminder|tip ! I didn't re-read this document since
... oh, my  ... very early (1.x ?) versions. At which time my favorite
peeve against R was the fixed memory allocation scheme.

I would have thought that 64 bits machines could take advantage of a
wider bus and (marginally ?) faster instructions to balance larger
pointers. Am I mistaken ?

Thank again !

					Emmanuel Charpentier

Prof Brian Ripley a ?crit :

Note that Ottorino has only 1GB of RAM installed, which makes a 64-bit
version of R somewhat moot.  See chapter 8 of

http://cran.r-project.org/doc/manuals/R-admin.html

Thank you for this reminder|tip ! I didn't re-read this document since
... oh, my  ... very early (1.x ?) versions. At which time my favorite
peeve against R was the fixed memory allocation scheme.

I would have thought that 64 bits machines could take advantage of a
wider bus and (marginally ?) faster instructions to balance larger
pointers. Am I mistaken ?

Yes, it is more complex than that.  If you run 32-bit instructions on a 
x86_64, the physical bus is the same as when you run 64-bit instructions. 
The larger code usually means the CPU caches spill more often, and some 
64-bit chips have more 32-bit than 64-bit registers which allows better 
scheduling.

The R-admin manual reports on some empirical testing.  But when you have 
limited RAM the larger code and data for a 64-bit build will cause more 
swapping and that is likely to dominate performance issues on large 
problems.

Note that the comparisons depend on both the chip and the OS: it seems 
that on Mac OS 10.5 on a Core 2 Duo the 64-bit version is faster (on small 
examples).  The original enquiry was about 'amd64 linux', but I've checked 
Intel Core 2 Duo as well: on my box 64-bit builds are faster than 32-bit 
ones, whereas the reverse is true for Opterons.  So it seems that the 
architectural differences of Core 2 Duo vs AMD64 do affect the issue.

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