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Question: bplapply breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
0
19 months ago by
schweringmarc010 wrote:

Hi,

when I use bplapply the process basically stalls. I have to cancel it, when called from RStudio I also have to kill the process.

It happens with:

bplapply(1:10, paste)

I've seen a similar issue with someone on a Windows (https://support.bioconductor.org/p/70435/).

I am working on a openSUSE Leap 42.1 (x86_64)

R version 3.3.1 (2016-06-21)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 42.1 (x86_64)

locale:
[1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocParallel_1.6.6

loaded via a namespace (and not attached):
[1] parallel_3.3.1 tools_3.3.1
modified 19 months ago by jan.winter0 • written 19 months ago by schweringmarc010

Ok, I think BiocParallel is not the problem. It seems Rmpi is messed up on Suse.

ADD REPLYlink modified 19 months ago by Martin Morgan ♦♦ 22k • written 19 months ago by schweringmarc010

I fixed my mpi and Rmpi installation, however I still have the bplapply problem.

0
19 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

It could be ports are blocked, and that, in BiocParallel 1.8.1 (the current version of Bioconductor for R 3.3.1) you could options(port=...) to a port that you know to be open.

Unfortunately, this did not help.

..or options(bphost="localhost") ? This must be on BiocParallel version 1.8.1 or later.

Hi Martin,

actually this was the "workaround" you mentioned during the CSAMA2016 course - and for me it works now.

cheers
Jan

On my system (suse) this doesn't change anything.

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19 months ago by
jan.winter0 wrote:

Hi Martin,

I also observe this issue on my Mac (Yosemite) on sporadic cases.

Sometimes it works without any issue, sometimes it just starts creating zombie processes, sometimes it doesn't do anything.
I tried setting ports, setting the Multicoreparam manually, nothing helps.

I can remember that we encountered a similar issue during the CSAMA2016 course in Brixen back in July and you had a solution for that (that also worked on Windows machines). Unfortunately I can't remember what it was, all I know is that it was a trivial thing :(

Best

Jan