Question

Usinig BiocParallel package in R with M1 MAC

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me.achleitner • 0

@a57b51bf

Last seen 2.1 years ago

Austria

Hey there, I got an Macbook Pro with M1 Max Chip. I will analyse RNA Seq data and use the OUTRIDER package. Always when I try to run this code with MulticoreParam() I get an Error log:

ods <- OUTRIDER(ods, BPPARAM = MulticoreParam(as.integer(8))) Error in serialize(data, node$con) : error writing to connection

As soon as I try SerialParam() it works but very very slow of cause!

Do anyone has an idea what I can do?

Thank you in advance! Best, Melanie

RStudio R M1 BiocParallel Mac • 1.5k views

ADD COMMENT • link updated 23 months ago by Christian Mertes • 0 • written 2.1 years ago by me.achleitner • 0

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Can you reproduce the problem with a simpler example, e.g.,

unlist(bplapply(1:8, sqrt, BPPARAM = MulticoreParam(8)))

What about the simpler example and your more complicated example with SnowParam(8).

Can you provide the output of systemInfo() and BiocManager::valid() (the latter should return TRUE).

I do not know the details of the OUTRIDER package. What type of object is ods?

ADD REPLY • link 2.1 years ago Martin Morgan 25k

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I guess this is the same underlying error as you described in another thread.

To pinpoint the error, could you please run it in steps? Use a small test set to speed it up.

dimQ <- 3
BPPARAM <- SerialParam()

dim(ods)
message(date(), ": SizeFactor estimation ...")
ods <- estimateSizeFactors(ods)

message(date(), ": Controlling for confounders ...")
ods <- controlForConfounders(ods, q=dimQ, BPPARAM=BPPARAM)

message(date(), ": P-value calculation ...")
ods <- computePvalues(ods, BPPARAM=BPPARAM)

message(date(), ": Zscore calculation ...")
ods <- computeZscores(ods, peerResiduals=FALSE)

ADD REPLY • link 23 months ago Christian Mertes • 0