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

[Steve Lianoglou]

Ahh .. I see. Thanks for the pointer.

-steve

On Tue, May 1, 2012 at 2:26 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>



-- 
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