Hi Nathaniel,
Thanks for the suggestion.
Im actually not really using R to do any real work.
Im 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 havent configured hardly anything.
Im just loading a few plain packages.
Thanks,
Tom
On Aug 6, 2014, at 2:20 PM, Nathaniel Smith <n...@pobox.com> wrote:
> On Wed, Aug 6, 2014 at 6:01 AM, Tom Kraljevic <t...@0xdata.com> wrote:
>>
>> Hi,
>>
>>
>> (Using R 3.1.1 on Ubuntu 12.04.4 LTS)
>>
>>
>> What is the recommended way for R to fork a (non-R) process that is not CPU
>> limited?
>> Currently I am using R's system2() call, and this is inheriting the
>> environment of the R process.
>>
>>
>> I notice that (at least on Linux) when I am poking around /proc that the R
>> process itself is setting up cpu limitations for itself (max 1 core).
>>
>>
>> Using strace, I see the following:
>>
>> (strace output)
>> out.20612:sched_setaffinity(0, 128, {100, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>> 0, 0, 0, 0}) = 0
>>
>>
>> And proc shows:
>>
>> (cat /proc/nnn/status)
>> Cpus_allowed: 00000001
>> Cpus_allowed_list: 0
>>
>>
>> See that the Cpus_allowed bitmask is a single core. Normally it's fff...f.
>
> When I run R I see:
>
> Cpus_allowed: ff
> Cpus_allowed_list: 0-7
>
> It's possible (likely?) that the culprit here isn't R but rather some
> other library that R is loading. Are you using OpenBLAS? By default
> OpenBLAS will set an obnoxious cpu mask, unless you override this
> using some obscure build system settings. (There might be a runtime
> option for disabling it too, I don't remember. Note also that this is
> just one of several obnoxious things OpenBLAS does unless you override
> a bunch of obscure build system defaults -- building OpenBLAS
> correctly is highly non-trivial.)
>
> -n
>
> --
> Nathaniel J. Smith
> Postdoctoral researcher - Informatics - University of Edinburgh
> http://vorpus.org
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