R help - Mar 2014 - R Running slow on Ubuntu

Hi All,

I've run across an odd phenomenon and I am wondering if someone might be
able to provide insight as to what is going on. I'm running some R code
that was provided by a collaborator, who is not a very experienced R
programmer (e.g., the code is functional but not very efficient). When I
run it from the terminal or command line everything executes, albeit very
slowly- the logfile suggests that the program is about 5% done after
running over last weekend. Top indicates that it is maxing out one of my
CPUs and chewing up a lot of memory, which I expect.

 The strange thing is that my collaborator insists that the code executes
on the order of minutes on his 2012 macbook pro with 8G of memory. I am
running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow as
molasses. That suggests a configuration issue of some kind with R that I
might not be aware of (I am more experienced in R and usually don't write
code that requires resources like that). I have played with my swappiness
and the effect seems to be minimal. Can anyone suggest something else that
could be going on? I have considered trying to run it directly on a unix
server, but the code has a lot of third-party dependencies that would be a
bit of work to set up for simple troubleshooting. And naturally I'd prefer
that R be configured correctly in the event that I need to locally run
something more intense in the future.

 Thanks in advance for any advice you can give. This message has been
cross-posted omn the ubuntu forums.

-R

	[[alternative HTML version deleted]]

My guess is that maybe the default Ubuntu binaries aren't compiled
with MKL (Math Kernel Library) support and thus with no
multithreading.

I would suggest doing a quick research on how to re-compile R with MKL
support and maybe you'll be good to go.

On Fri, Mar 14, 2014 at 9:45 PM, Russell Bainer <russ.bainer at gmail.com>
wrote:
> Hi All,
>
> I've run across an odd phenomenon and I am wondering if someone might
be
> able to provide insight as to what is going on. I'm running some R code
> that was provided by a collaborator, who is not a very experienced R
> programmer (e.g., the code is functional but not very efficient). When I
> run it from the terminal or command line everything executes, albeit very
> slowly- the logfile suggests that the program is about 5% done after
> running over last weekend. Top indicates that it is maxing out one of my
> CPUs and chewing up a lot of memory, which I expect.
>
>  The strange thing is that my collaborator insists that the code executes
> on the order of minutes on his 2012 macbook pro with 8G of memory. I am
> running it with ubuntu 12.04 on a dual-core i7 with 32G, and it's slow
as
> molasses. That suggests a configuration issue of some kind with R that I
> might not be aware of (I am more experienced in R and usually don't
write
> code that requires resources like that). I have played with my swappiness
> and the effect seems to be minimal. Can anyone suggest something else that
> could be going on? I have considered trying to run it directly on a unix
> server, but the code has a lot of third-party dependencies that would be a
> bit of work to set up for simple troubleshooting. And naturally I'd
prefer
> that R be configured correctly in the event that I need to locally run
> something more intense in the future.
>
>  Thanks in advance for any advice you can give. This message has been
> cross-posted omn the ubuntu forums.
>
> -R
>
>         [[alternative HTML version deleted]]
>
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-- 
Augusto