On 23.08.2023 15:58, Jeff Newmiller wrote:
To whom are you addressing this question? The OpenMP developers who define the
missing-OMP_THREAD_LIMIT behaviour and-or supply default config files? The CRAN
server administrators who set the variable in their site-wide configuration
intentionally or unintentionally? Or the package authors expected to kludge in
settings to override those defaults for CRAN testing while not overriding them
in normal use?
Of course , the CRAN teams controls the env vars on the CRAN servers,
but not on a server a user might use. And a user is typically unaware
that a package uses multithreading.
R users are typically not developers with a lot of insight in computer
science. Most R users I know would not even know how to set an env var.
So why do you ecxpect your users to set an appropriate OMP_THREAD_LIMIT?
Particularly when they aim at parallelization, they have to set it to 1.
I advocate not only to limit the number of cores for CRAN but also (and
inparticular) the default! Something we cannot check easily.
An alternative would be to teach R to set OMP_THREAD_LIMIT=1 locally by
default and a mechanism to change that for users.
Best,
Uwe Ligges
I would vote for explicitly addressing this (rhetorical?) question to the CRAN
server administrators...
On August 23, 2023 6:31:01 AM PDT, Uwe Ligges <lig...@statistik.tu-dortmund.de>
wrote:
I (any many collegues here) have been caught several times by the following
example:
1. did something in parallel on a cluster, set up via parallel::makeCluster().
2. e.g. allocated 20 cores and got them on one single machine
3. ran some code in parallel via parLapply()
Bang! 400 threads;
So I have started 20 parallel processes, each of which is using the
automatically set max. 20 threads as OMP_THREAD_LIMIT was also adjusted by the
cluster to 20 (rather than 1).
Hence, I really believe a default should always be small, not only in examples
and tests, but generally. And people who aim for more should be able to
increase the defaults.
Do you believe a software that auto-occupies a 96 core machines with 96 threads
by default is sensible?
Best,
Uwe Ligges
On 21.08.2023 21:59, Berry Boessenkool wrote:
If you add that to each exported function, isn't that a lot of code to read +
maintain?
Also, it seems like unnecessary computational overhead.
From a software design point of view, it might be nicer to set that in the
examples + tests.
Regards,
Berry
________________________________
From: R-package-devel <r-package-devel-boun...@r-project.org> on behalf of Scott
Ritchie <sritchi...@gmail.com>
Sent: Monday, August 21, 2023 19:23
To: Dirk Eddelbuettel <e...@debian.org>
Cc: r-package-devel@r-project.org <r-package-devel@r-project.org>
Subject: Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server
Thanks Dirk and Ivan,
I took a slightly different work-around of forcing the number of threads to
1 when running functions of the test dataset in the package, by adding the
following to each user facing function:
```
# Check if running on package test_data, and if so, force data.table to
be
# single threaded so that we can avoid a NOTE on CRAN submission
if (isTRUE(all.equal(x, ukbnmr::test_data))) {
registered_threads <- getDTthreads()
setDTthreads(1)
on.exit({ setDTthreads(registered_threads) }) # re-register so no
unintended side effects for users
}
```
(i.e. here x is the input argument to the function)
It took some trial and error to get to pass the CRAN tests; the number of
columns in the input data was also contributing to the problem.
Best,
Scott
On Mon, 21 Aug 2023 at 14:38, Dirk Eddelbuettel <e...@debian.org> wrote:
On 21 August 2023 at 16:05, Ivan Krylov wrote:
| Dirk is probably right that it's a good idea to have OMP_THREAD_LIMIT=2
| set on the CRAN check machine. Either that, or place the responsibility
| on data.table for setting the right number of threads by default. But
| that's a policy question: should a CRAN package start no more than two
| threads/child processes even if it doesn't know it's running in an
| environment where the CPU time / elapsed time limit is two?
Methinks that given this language in the CRAN Repository Policy
If running a package uses multiple threads/cores it must never use more
than two simultaneously: the check farm is a shared resource and will
typically be running many checks simultaneously.
it would indeed be nice if this variable, and/or equivalent ones, were set.
As I mentioned before, I had long added a similar throttle (not for
data.table) in a package I look after (for work, even). So a similar
throttler with optionality is below. I'll add this to my `dang` package
collecting various functions.
A usage example follows. It does nothing by default, ensuring 'full power'
but reflects the minimum of two possible options, or an explicit count:
> dang::limitDataTableCores(verbose=TRUE)
Limiting data.table to '12'.
> Sys.setenv("OMP_THREAD_LIMIT"=3);
dang::limitDataTableCores(verbose=TRUE)
Limiting data.table to '3'.
> options(Ncpus=2); dang::limitDataTableCores(verbose=TRUE)
Limiting data.table to '2'.
> dang::limitDataTableCores(1, verbose=TRUE)
Limiting data.table to '1'.
>
That makes it, in my eyes, preferable to any unconditional 'always pick 1
thread'.
Dirk
##' Set threads for data.table respecting possible local settings
##'
##' This function set the number of threads \pkg{data.table} will use
##' while reflecting two possible machine-specific settings from the
##' environment variable \sQuote{OMP_THREAD_LIMIT} as well as the R
##' option \sQuote{Ncpus} (uses e.g. for parallel builds).
##' @title Set data.table threads respecting default settingss
##' @param ncores A numeric or character variable with the desired
##' count of threads to use
##' @param verbose A logical value with a default of \sQuote{FALSE} to
##' operate more verbosely
##' @return The return value of the \pkg{data.table} function
##' \code{setDTthreads} which is called as a side-effect.
##' @author Dirk Eddelbuettel
##' @export
limitDataTableCores <- function(ncores, verbose = FALSE) {
if (missing(ncores)) {
## start with a simple fallback: 'Ncpus' (if set) or else 2
ncores <- getOption("Ncpus", 2L)
## also consider OMP_THREAD_LIMIT (cf Writing R Extensions), gets
NA if envvar unset
ompcores <- as.integer(Sys.getenv("OMP_THREAD_LIMIT"))
## and then keep the smaller
ncores <- min(na.omit(c(ncores, ompcores)))
}
stopifnot("Package 'data.table' must be installed." =
requireNamespace("data.table", quietly=TRUE))
stopifnot("Argument 'ncores' must be numeric or character" =
is.numeric(ncores) || is.character(ncores))
if (verbose) message("Limiting data.table to '", ncores, "'.")
data.table::setDTthreads(ncores)
}
|
| --
| Best regards,
| Ivan
|
| ______________________________________________
| R-package-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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