[Bioc-devel] Using SerialParam() as the registered back-end for all platforms

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Mon Jan 7 13:09:31 CET 2019

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())) {


On 1/6/19, 11:16 PM, "Bioc-devel on behalf of Aaron Lun" <bioc-devel-bounces using r-project.org on behalf of infinite.monkeys.with.keyboards using 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
    invisible(bplapply(1:5, identity))
    rnorm(1) # 0.1315312
    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. 
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