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Question: `bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
0
gravatar for schweringmarc01
11 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                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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
ADD COMMENTlink modified 11 months ago by jan.winter0 • written 11 months ago by schweringmarc010

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

ADD REPLYlink modified 11 months ago by Martin Morgan ♦♦ 20k • written 11 months ago by schweringmarc010

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

ADD REPLYlink modified 11 months ago • written 11 months ago by schweringmarc010
0
gravatar for Martin Morgan
11 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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.

ADD COMMENTlink written 11 months ago by Martin Morgan ♦♦ 20k

Unfortunately, this did not help.

ADD REPLYlink written 11 months ago by schweringmarc010

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

ADD REPLYlink written 11 months ago by Martin Morgan ♦♦ 20k

Hi Martin,

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

cheers
Jan

 

ADD REPLYlink written 11 months ago by jan.winter0

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

ADD REPLYlink written 11 months ago by schweringmarc010
0
gravatar for jan.winter
11 months ago by
jan.winter0
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

ADD COMMENTlink written 11 months ago by jan.winter0
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