I hope for 1. to have a 'local socket' (i.e., not using ports) implementation
shortly.
I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have
> library(BiocParallel)
> set.seed(1); p = bpparam(); rnorm(1)
[1] -0.6264538
> set.seed(1); p = bpparam(); rnorm(1)
[1] -0.6264538
at the expensive of using the generator when the package is loaded.
> set.seed(1); rnorm(1)
[1] -0.6264538
> set.seed(1); library(BiocParallel); rnorm(1)
[1] 0.1836433
Is that bad? It will be consistent across platforms.
This behavior
> set.seed(1); unlist(bplapply(1:2, function(i) rnorm(1)))
[1] 0.9624337 0.8925947
> set.seed(1); unlist(bplapply(1:2, function(i) rnorm(1)))
[1] -0.5703597 0.1102093
seems wrong, but is consistent with mclapply
> set.seed(1); unlist(mclapply(1:2, function(i) rnorm(1)))
[1] -0.02704527 0.40721777
> set.seed(1); unlist(mclapply(1:2, function(i) rnorm(1)))
[1] -0.8239765 1.2957928
The documented behavior is to us the RNGseed= argument to *Param, but I think
it could be made consistent (by default, obey the global random number seed on
workers) at least on a single machine (where the default number of cores is
constant).
I have not (yet?) changed the default behavior to SerialParam. I guess the cost
of SerialParam is from the dependent packages that need to be loaded
> system.time(suppressPackageStartupMessages(library(DelayedArray)))
user system elapsed
3.068 0.082 3.150
If fastMNN() makes several calls to bplapply(), it might make sense to start
the default cluster at the top of the function once
if (!isup(bpparam())) {
bpstart(bpparam())
on.exit(bpstop(bpparam()))
}
Martin
On 1/6/19, 11:16 PM, "Bioc-devel on behalf of Aaron Lun"
<bioc-devel-boun...@r-project.org on behalf of
infinite.monkeys.with.keyboa...@gmail.com> wrote:
As we know, the default BiocParallel backends are currently set to
MulticoreParam (Linux/Mac) or SnowParam (Windows). I can understand this to
some extent because a new user running, say, bplapply() without additional
arguments or set-up would expect some kind of parallelization. However, from a
developer’s perspective, I would argue that it makes more sense to use
SerialParam() by default.
1. It avoids problems with MulticoreParam stalling (especially on Macs)
when the randomly chosen port is in already use. This used to be a major
problem, to the point that all my BiocParallel-using functions in scran passed
BPPARAM=SerialParam() by default. Setting SerialParam() as package default
would ensure BiocParallel functions run properly in the first place; if the
code stalls due to switching to MulticoreParam, then it’s obvious where the
problem lies (and how to fix it).
2. It avoids the alteration of the random seed when the MulticoreParam
instance is constructed for the first time.
library(BiocParallel) # new R session
set.seed(100)
invisible(bplapply(1:5, identity))
rnorm(1) # 0.1315312
set.seed(100)
invisible(bplapply(1:5, identity))
rnorm(1) # -0.5021924
This is because the first bplapply() call calls bpparam(), which constructs
a MulticoreParam() for the first time; this calls the PRNG to choose a random
port number. Ensuing random numbers are altered, as seen above. To avoid this,
I need to define the MulticoreParam() object prior to set.seed(), which
undermines the utility of a default-defined bpparam().
3. Job dispatch via SnowParam() is quite slow, which potentially makes
Windows package builds run slower by default. A particularly bad example is
that of scran::fastMNN(), which has a few matrix multiplications that use
DelayedArray:%*%. The %*% is parallelized with the default bpparam(), resulting
in SNOW parallelization on Windows. This slowed down fastMNN()’s examples from
4 seconds (unix) to ~100 seconds (windows). Clearly, serial execution is the
faster option here. A related problem is MulticoreParam()’s tendency to copy
the environment, which may result in problems from inflated memory consumption.
So, can we default to SerialParam() on all platforms? And by this I mean
the BiocParallel in-built default - I don’t want to have to instruct all my
users to put a “register(SerialParam())” at the start of their analysis
scripts. I feel that BiocParallel’s job is to provide downstream code with the
potential for parallelization. If end-users want actual parallelization, they
had better be prepared to specify an appropriate scheme via *Param() objects.
-A
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