My current set-up in a variety of packages is that every parallelizable
function has a BPPARAM= argument. This makes it explicit about which steps are
being parallelized. Requiring users to respecify BPPARAM= in each function
isn’t as annoying as you’d think, because not many steps are actually heavy
enough to warrant parallelization.
Ideally, I'd have BPPARAM=bpparam() by default, allowing me to both respond to
the register()'d bpparam() as well as any custom argument that might be
supplied by the user, e.g., if they don't want to change bpparam(). However,
for various reasons (discussed in the other SerialParam() thread), the current
default is BPPARAM=SerialParam().
To be honest, I've never thought it necessary to have a global package-specific
parameter for parallelization as you've done (for scPipe, presumably). The
current options - global across all packages with register(), or local to
individual functions with BPPARAM= - seem to be satisfactory in the vast
majority of cases. At least to me.
And at least for RNGs, if a function from another package is giving greatly
different results upon parallelization (excepting some numerical error with
changed order of summation), I'd say that's a bug of some sort. That should be
fixed on their end, rather than requiring other packages and users to tiptoe
around them.
-A
> On 10 Jan 2019, at 23:59, Shian Su <s...@wehi.edu.au> wrote:
>
> Hello Developers,
>
> I’m using BiocParallel for parallelism, and I understand that register() is
> the recommended method for setting threads. But I am reluctant to ask people
> to run code for my package which changes how other packages operate, so I
> figured I’d use local bp params. Recent discussions of RNG has made me
> worried there may be hidden state gotcha’s I’ve not considered. The current
> implementation is
>
> set_mypkg_threads <- function(n) {
> if (n == 1) {
> options(“mypkg.bpparam” = SerialParam())
> } else if (n > 1) {
> if (.Platform$OS.type == "windows") {
> options(“mypkg.bpparam" = SnowParam(nthreads))
> } else {
> options(“mypkg.bpparam" = MulticoreParam(nthreads))
> }
> }
> }
>
> Then elsewhere in my package I make use of parallelism as follows
>
> bplapply(
> BPPARAM = getOption(“mypkg.bpparam”, bpparam()),
> …
> )
>
> Where getOption() either retrieves my set option or the default value given
> by bpparam(). So the behaviour is that if users have not registered params
> for my package specifically then it will take the BiocParallel default, but
> otherwise it will use my package’s local bpparam.
>
> Also I know that as currently implemented, I preclude cluster parallelism on
> non-Windows machines. But it’s easy to fix. Just looking for feedback on the
> approach.
>
> Kind regards,
> Shian Su
>
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