[R] PSOCK cluster and renice

[Andreas Leha]

Hi Henrik,

Thanks for the detailed in fast reply!

My guess would be that the confusion comes from the different use of nice and renice.

The workraund you provided work fine!  Thanks a lot.

Best,
Andreas



Henrik Bengtsson <henrik.bengtsson at gmail.com> writes:

> Looks like a bug to me due to wrong assumptions about 'nice'
> arguments, but could be because a "non-standard" 'nice' is used.  If
> we do:
>
>> trace(system, tracer = quote(print(command)))
> Tracing function "system" in package "base"
>
> we see that the system call used is:
>
>> cl <- parallel::makePSOCKcluster(2L, renice = 19)
> Tracing system(cmd, wait = FALSE) on entry
> [1] "nice +19 '/usr/lib/R/bin/Rscript'
> --default-packages=datasets,utils,grDevices,graphics,stats,methods -e
> 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11146 OUT=/dev/null
> TIMEOUT=2592000 XDR=TRUE"
> nice: ‘+19’: No such file or directory
> ^C
>
> The code that prepends that 'nice +19' is in parallel:::newPSOCKnode:
>
>     if (!is.na(renice) && renice)
>         cmd <- sprintf("nice +%d %s", as.integer(renice), cmd)
>
> I don't know where that originates from and on what platform it was
> tests/validated.  On Ubuntu 16.04, CentOS 6.6, and CentOS 7.4, I have
> 'nice' from "GNU coreutils" and they all complain about using '+',
> e.g.
>
> $ nice +19 date
> nice: +19: No such file or directory
>
> but '-' works:
>
> $ nice -19 date
> Sun Dec  3 20:01:31 PST 2017
>
> Neither 'nice --help' nor 'man help' mention the use of a +n option.
>
>
> WORKAROUND:  As a workaround, you can use:
>
> cl <- future::makeClusterPSOCK(2L, rscript = c("nice",
> "--adjustment=10", file.path(R.home("bin"), "Rscript")))
>
> which is backward compatible with parallel::makePSOCKcluster() but
> provides you with more detailed control.  Try adding verbose = TRUE to
> see what the exact call looks like.
>
> /Henrik
>
>
> On Sun, Dec 3, 2017 at 7:35 PM, Andreas Leha
> <andreas.leha at med.uni-goettingen.de> wrote:
>> Hi all,
>>
>> Is it possible to use the 'renice' option together with parallel
>> clusters of type 'PSOCK'?  The help page for parallel::makeCluster is
>> not specific about which options are supported on which types and I am
>> getting the following message when passing renice = 19 :
>>
>>> cl <- parallel::makeCluster(2, renice = 19)
>> nice: ‘+19’: No such file or directory
>>
>> Kind regards,
>> Andreas
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.