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