R help - Dec 2017 - PSOCK cluster and renice

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

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.

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.