[R-SIG-Mac] png() segfaults inside a parallel::mclapply loop?

[Simon Urbanek]

Steve,

you can't use certain graphics devices/backends in forked processes (see multicore docs).  What is known to work is the Cairo package.

Cheers,
Simon



On May 1, 2012, at 12:30 PM, Steve Lianoglou <mailinglist.honeypot at gmail.com> wrote:

> Hi,
> 
> I can't figure this out -- I have to (slightly different) OSX boxes
> running the same version of R that I grabbed from r.research.att.com a
> little while ago:
> 
> R version 2.15.0 Patched (2012-04-18 r59079)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> Simply calling png() w/in a parallel loop always crashed the
> subprocesses on one machine. This code, for example:
> 
> library(parallel)
> mclapply(1:10, function(i) {
>  png(paste("~/tmp/p", i, "png", sep="."))
>  plot(1:10)
>  dev.off()
> }, mc.cores=8)
> 
> The error (from each subprocess) is pasted below, however swapping out
> the png() call to pdf() works on both.
> 
> The machine that png() fails on is a ~ 2008 2x4-core mac pro. The one
> that doesn't have a problem is a late 2010 core2duo macbook pro 13"
> 
> Both are running OSX.6.8
> 
> Anybody else have this problem?
> 
> -steve
> 
> Error from one process:
> 
> *** caught segfault ***
> address 0x108, cause 'memory not mapped'
> 
> Traceback:
> 1: png(paste("~/tmp/p", i, "png", sep = "."))
> 2: FUN(7L[[1L]], ...)
> 3: lapply(X = S, FUN = FUN, ...)
> 4: doTryCatch(return(expr), name, parentenv, handler)
> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 6: tryCatchList(expr, classes, parentenv, handlers)
> 7: tryCatch(expr, error = function(e) {    call <- conditionCall(e)
> if (!is.null(call)) {        if (identical(call[[1L]],
> quote(doTryCatch)))             call <- sys.call(-4L)        dcall <-
> deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")
>  LO
> NG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg,
> "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
> type = "w")        if (is.na(w))             w <- 14L + nchar(dcall,
> type = "b") + nchar(sm[1L],                 type = "b")
>  if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }
> else prefix <- "Error : "    msg <- paste0(prefix,
> conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if
> (!silent && identical(getOption("show.error.messages"),         TRUE))
> {        ca
> t(msg, file = stderr())        .Internal(printDeferredWarnings())    }
>   invisible(structure(msg, class = "try-error", condition = e))})
> 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
> 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
> 10: FUN(1:8[[7L]], ...)
> 11: lapply(seq_len(cores), inner.do)
> 12: mclapply(1:10, function(i) {    png(paste("~/tmp/p", i, "png", sep
> = "."))    plot(1:10)    dev.off()}, mc.cores = 8)
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
> 
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