Hi,

There seems to be a problem with bplapply() on Windows in BiocParallel for version 1.2.9 and higher (I tested up to 1.3.41). While the code below works fine on BiocParallel version 1.0.3 it causes the system to hang on newer versions. Can anybody reproduce this problem or else tell me what I got wrong...

Minimal test code:

library(parallel)
cl<-makeCluster(2, 'SOCK')
parLapply(cl, 1:4, function(i) Sys.sleep(1))
stopCluster(cl)

library(BiocParallel)
register(SnowParam(workers = 2, type = 'SOCK'), default = TRUE)
bpparam()
bplapply(1:4, function(i) Sys.sleep(1))

While the first snippet works fine on Linux, OSX and Windows, the second one hangs up on Windows. When stopping execution, I get the following warning:

Warning message:
running command 'env MASTER=localhost PORT=11521 OUT=/dev/null RPROG=C:/PROGRA~1/R/R-32~1.1/bin/R R_LIBS= C:/Users/loge/Documents/R/win-library/3.2/BiocParallel/RSOCKnode.sh' had status 127

Cheers

Lorenz

When I install cygwin and put it on the path everything works. 

Lorenz

Hi Lorenz,

I can't reproduce this error but that doesn't mean there isn't a problem. BiocParallel always uses a shell script (inst/RSOCKnode.sh) to launch the workers whereas snow launches via an R script or shell script (default is R script). The cluster arg that controls this behavior is useRscript. 

Can you try running both a shell and R script created cluster on your machine? This may at least identify if the problem is due to the system call -

library(snow) cl1 <- makeCluster(2, "SOCK", useRscript=TRUE, outfile=NULL) cl2 <- makeCluster(2, "SOCK", useRscript=FALSE, outfile=NULL) parLapply(cl1, 1:2, Sys.sleep) parLapply(cl2, 1:2, Sys.sleep)

Here is my output:

> cl1 <- makeCluster(2, "SOCK", useRscript=TRUE, outfile=NULL)
starting worker for localhost:11270
starting worker for localhost:11270
> cl2 <- makeCluster(2, "SOCK", useRscript=FALSE, outfile=NULL)
> parLapply(cl1, 1:2, Sys.sleep)
Type: EXEC
Type: EXEC
[[1]]
NULL

[[2]]
NULL

> parLapply(cl2, 1:2, Sys.sleep)
[[1]]
NULL

[[2]]
NULL

Valerie