Question: bplapply doesn't work in the multicore mode on mac os x
1
gravatar for gmerino
2.8 years ago by
gmerino20
Argentina
gmerino20 wrote:

Dear list,

I'm trying to use the bplapply function in a multicore way but it doesn't work. The OS is Mac OS X (Sierra) and the macbook has 4 threads. 

To test the method, I have simply run the example code

bplapply(1:6, sqrt, BPPARAM = MulticoreParam(3))

But, nothing occurs in the R console and the session is broken. The loop never ends and I need to force de program close. When I checked the cpus usage nothing is running. 

When I run the same example but using the SerialParam with 1 or more than 1 worker or when I use the SerialParam function all is ok.

Can somebody help me? 

Thanks, Gabriela.

sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12 (Sierra)

locale:
[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8

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

other attached packages:
[1] BiocParallel_1.8.0

loaded via a namespace (and not attached):
[1] snow_0.4-2     parallel_3.3.1

 

 

 

 

 

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by gmerino20
Answer: bplapply doesn't work in the multicore mode on mac os x
1
gravatar for Martin Morgan
2.8 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Please see the response and follow up at A: BiocParallel not proceeding and my apologies for the delay.

ADD COMMENTlink written 2.8 years ago by Martin Morgan ♦♦ 23k
Answer: bplapply doesn't work in the multicore mode on mac os x
1
gravatar for gmerino
2.8 years ago by
gmerino20
Argentina
gmerino20 wrote:

Thank you very much. The problem was solved after the BiocParallel updating to 1.8.1 version and the addition of  "options(bphost="localhost") in my R code before to the bplapply use.

ADD COMMENTlink written 2.8 years ago by gmerino20
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