[Bioc-devel] BiocParallel on Windows Never Ends
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
bpstart(SnowParam(2))
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
127.0.0.1, you could add the argument 'manager.hostname = "127.0.0.1"`.
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 = "127.0.0.1",
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")
parallel::makeCluster
snow::makeSOCKcluster
snow::newSOCKnode
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).
Martin
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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}