Question

BiocParallel not proceeding

1

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petyuk ▴ 70

@petyuk-7261

Last seen 5.1 years ago

United States

After refreshing my R installation and the packages, this simple example of BiocParallel::bplapply doesn't work properly. It looks like it starts, but never finishes.

Thanks for taking a look into it!

Vlad

> library(BiocParallel)
> fun <- function(v) {
+     message("working") ## 10 tasks
+     sqrt(v)
+ }
> bplapply(1:10, fun)

# it does not finish (at least in a minute or so)

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

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

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   
>

software error • 2.9k views

ADD COMMENT • link updated 9.0 years ago by Martin Morgan 25k • written 9.1 years ago by petyuk ▴ 70

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upgrading to BiocParallel_1.7.9 didn't help
works fine on windows machine though

ADD REPLY • link 9.1 years ago petyuk ▴ 70

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It hits a snag at this line in bplapply

BPPARAM <- bpstart(BPPARAM, length(X))

ADD REPLY • link 9.1 years ago petyuk ▴ 70

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Within bpstart the issue is at

bpbackend(x) <- .bpmakeForkCluster(nnodes, bptimeout(x), getOption("ports", NA_integer_))

ADD REPLY • link 9.1 years ago petyuk ▴ 70

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A likely candidate is that ports on the Mac are not accessible; I'm not familiar enough with how things work, but I think the overall strategy would be to identify open ports and use these via options(ports=123).

ADD REPLY • link 9.1 years ago Martin Morgan 25k

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Not sure if this is relevant but this is what I get (regardless of the port). Although may be this is what is supposed to be since there is no process communicating to the 11709 port. Anyway, BiocParallel:::.bpmakeForkCluster is not cooperating with me today.

> port <- 11000L + sample(1000L, 1L)
> port
[1] 11709
> socketConnection("localhost", port=port, TRUE, TRUE, "a+b", timeout = 3)
Error in socketConnection("localhost", port = port, TRUE, TRUE, "a+b",  : 
  cannot open the connection
In addition: Warning message:
In socketConnection("localhost", port = port, TRUE, TRUE, "a+b",  :
  problem in listening on this socket

ADD REPLY • link 9.1 years ago petyuk ▴ 70

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What is odd it starts with MulticoreParam(), that is FORK type, but later switches to SOCK type. I thought SOCK is for Windows, but not POSIX systems.

ADD REPLY • link 9.1 years ago petyuk ▴ 70

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The 'SOCK' class of the return value is a red herring here. A simple fork isn't rich enough to support the BiocParallel behavior, which requires communication between the forked and master process. Sockets are used for that communication.

ADD REPLY • link 9.1 years ago Martin Morgan 25k

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If I intercept the execution and rename the host from "WE25743" (the name of my machine) to "localhost", then .bpmakeForkCluster proceeds just fine. Hope that helps.

debugging in: BiocParallel:::.bpmakeForkCluster(8, 10, NA_integer_)
debug: {
    nnodes <- as.integer(nnodes)
    if (is.na(nnodes) || nnodes < 1L)
        stop("'nnodes' must be >= 1")
    if (is.na(port))
        port <- 11000L + sample(1000L, 1L)
    else if (length(port) != 1L)
        stop("'port' must be integer(1)")
    host <- Sys.info()[["nodename"]]
    cl <- vector("list", nnodes)
    for (rank in seq_len(nnodes)) {
        .bpmakeForkChild(host, port, rank, timeout)
        cl[[rank]] <- .bpconnectForkChild(host, port, rank, timeout)
    }
    class(cl) <- c("SOCKcluster", "cluster")
    cl
}

ADD REPLY • link 9.1 years ago petyuk ▴ 70

score 1 · Answer 1 · 2016-10-29

Sorry for the delay and thanks for debugging. I can sort of guess at the issue and have provided a patched version in BiocParallel 1.8.1 (current Bioc release version 3.4) and 1.9.1 (bioc devel), available with either

BiocInstaller::biocLite("Bioconductor-mirror/BiocParallel@release-3.4")  ## if you're using Bioconductor v. 3.4, release
BiocInstaller::biocLite("Bioconductor-mirror/BiocParallel")  ## if you're using Bioconductor v. 3.5, devel

or after the next build (likely Sunday afternoon, eastern time) via biocLite("BiocParallel").

The workaround lets you set the host using a global option

options(bphost="localhost")

instead of the default Sys.info()[["nodename"]]. Set the option any time before calling bplapply(), bpvec(), or bpstart(). I'd appreciate hearing whether this works for you (and others), and if so will make a more permanent change.