
Nathaniel, that did the trick.
Thanks so much for your help.

Tom


$ export OPENBLAS_MAIN_FREE=1
$ R

$ cat /proc/1538/status | grep Cpus_allowed
Cpus_allowed:   ffffffff
Cpus_allowed_list:      0-31




On Aug 6, 2014, at 2:41 PM, Nathaniel Smith <njs@pobox.com> wrote:

> On Wed, Aug 6, 2014 at 10:31 PM, Tom Kraljevic <tomk@0xdata.com> wrote:
>> 
>> Hi Nathaniel,
>> 
>> 
>> 
>> Thanks for the suggestion.
>> 
>> I’m actually not really using R to do any real work.
>> I’m starting the R H2O package (a Java machine learning package) and
>> forwarding all the work to H2O.
>> 
>> 
>> 
>> This is the list of packages I have in R:
>> 
>> 
>>> search()
>> [1] ".GlobalEnv"        "package:h2o"       "package:tools"
>> [4] "package:statmod"   "package:rjson"     "package:RCurl"
>> [7] "package:bitops"    "package:stats"     "package:graphics"
>> [10] "package:grDevices" "package:utils"     "package:datasets"
>> [13] "package:methods"   "Autoloads"         "package:base"
>> 
>> 
>> And here is the /proc info
>> 
>> tomk@mr-0xb4:~$ ps -efww | grep R | grep tomk
>> tomk      8366 13845  1 14:25 pts/0    00:00:01 /usr/lib/R/bin/exec/R
>> tomk     12960 27363  0 14:27 pts/3    00:00:00 grep --color=auto R
>> tomk@mr-0xb4:~$ grep Cpus /proc/8366/status
>> Cpus_allowed:   00000001
>> Cpus_allowed_list:      0
>> 
>> 
>> 
>> As you can see, my R is super vanilla.  I haven’t configured hardly
>> anything.  I’m just loading a few plain packages.
> 
> My suggestion is just a guess, really, but: R always uses (and thus
> loads by default) some underlying C library to implement its core
> linear algebra routines. OpenBLAS is one of the libraries that it
> might possibly be using, depending on how your R was set up.
> 
> Anyway, it looks like the quick way to check for this particular
> possible culprit is to run
> 
> env OPENBLAS_MAIN_FREE=1 R
> 
> and see if that helps.
> 
> -n
> 
> -- 
> Nathaniel J. Smith
> Postdoctoral researcher - Informatics - University of Edinburgh
> http://vorpus.org


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