[Bioc-devel] BiocParallel on Windows Never Ends

Martin Morgan m@rtin@morg@n @ending from ro@wellp@rk@org
Wed Jun 13 11:11:18 CEST 2018

It's more likely that it never starts, probably because it tries to 
create socket connections on ports that are not available, or perhaps 
because the file path to the installed location of the BiocParallel 
package is on a network share, or the 'master' node needs to be 
specified with an IP address.

Can you investigate? A starting point is


which I guess never returns. If you're able to discover the IP address 
or host name of your computer or use the local 'loopback' ip address, you could add the argument 'manager.hostname = ""`. 
Likewise if you are able to determine ports that are available for 
communication you can add `manager.port = 12345` to SnowParam

   param = bpstart(SnowParam(2, manager.hostname = "", 
manager.port = 12345))

Once past this stage you could use bplapply(..., BPPARAM = param) and 
bpstop(param) for further debugging.

The basic calling sequence for bpstart() is

   selectMethod("bpstart", "SnowParam")

and you could try to debug() each of these to step through the code to 
see where exactly things go wrong (I'd start at the bottom).


On 06/12/2018 11:00 PM, Dario Strbenac wrote:
> Good day,
> I was interested how the performance of my package is on a 32-bit Windows computer because I'm going to give a workshop about it soon and some people might bring old laptops. I found that using SnowParam with workers set to more than 1 never finishes. The minimal code to cause the issue is:
> bplapply(1:10, function(i) LETTERS[i], BPPARAM = SnowParam(workers = 1)) # Immediately returns a result.
> bplapply(1:10, function(i) LETTERS[i], BPPARAM = SnowParam(workers = 2)) # Never completes.
>> sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: i386-w64-mingw32/i386 (32-bit)
> Running under: Windows 7 (build 7601) Service Pack 1
> Matrix products: default
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] BiocParallel_1.14.1
> loaded via a namespace (and not attached):
> [1] compiler_3.5.0 snow_0.4-2     parallel_3.5.0
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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