`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
2
0
Entering edit mode
@schweringmarc01-11945
Last seen 7.9 years ago

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
biocparallel bplapply Suse error process • 2.0k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
@martin-morgan-1513
Last seen 3 months ago
United States

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 COMMENT
0
Entering edit mode

Unfortunately, this did not help.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi Martin,

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

cheers
Jan

 

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
jan.winter • 0
@janwinter-11947
Last seen 7.6 years ago

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 COMMENT

Login before adding your answer.

Traffic: 663 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6