On 15/11/2010 10:53 PM, Steve Lianoglou wrote:
Hi,
I'm using R-2.12 on a linux 64bit machine.
When I run a chunk of code inside a foreach() %do% { ...} or %dopar%
{...} (with doMC backend) I keep getting a segfault. Running the
*same* code within lapply(something, function(x) ... ) doesn't result
in any segfaults. I'll paste the output below, but I'm not sure it
would be helpful.
I'm more curious how to go about smoking out what's causing this, as
getting back "into" the code block that is crashing is tricky inside
the code block executed by foreach().
If anybody has any suggestions on how they debug with foreach, I'd be
happy to hear them. Setting .veborse=TRUE isn't providing anything
informative.
Anyway, I'll paste the segfault bomb below, followed by sessionInfo()
I have very little experience debugging on Linux, but presumably what
you want to do is to use a post-mortem debugger to analyze the core dump
(no idea how to do that), or run R under gdb or another debugger to
catch things at the time the segfault occurs. There's a command line
option to do that; try R --help to see it. (But it won't give you help
on gdb, you'll need other sources of info for that.)
Duncan Murdoch
======== Segfault dump ==========
result of evaluating expression:
*** caught segfault ***
address 0x30, cause 'memory not mapped'
Traceback:
1: format(x[[i]], ..., justify = justify)
2: format.data.frame(x, digits = digits, na.encode = FALSE)
3: as.matrix(format.data.frame(x, digits = digits, na.encode = FALSE))
4: print.data.frame(r)
5: print(r)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({ repeat { args<- nextElem(it) if
(obj$verbose) { cat(sprintf("evaluation # %d:\n", i))
print(args) } for (a in names(args)) assign(a\
, args[[a]], pos = envir, inherits = FALSE) r<-
tryCatch(eval(expr, envir = envir), error = function(e) e) if
(obj$verbose) { cat("result of evaluating expression\
:\n") print(r) }
tryCatch(accumulator(list(r), i), error = function(e) {
cat("error calling combine function:\n") print(e)
NULL }) \
i<- i + 1 }}, error = function(e) { if
(!identical(conditionMessage(e), "StopIteration"))
stop(simpleError(conditionMessage(e), expr))})
10: doSEQ(obj, substitute(ex), parent.frame())
11: foreach(chr = chrs, .packages = "GenomicFeaturesX", .verbose =
TRUE) %do% { .gc<- duplicate(gcache, pre.load = NULL)
on.exit(dispose(.gc)) cat("===", chr, "===\n") \
apaSummary(expt, .gc, chr, pvd.policy, utr.index, polya.variants,
gene.collapse) }
12: apaSummaryCrank(bpm[[1]], gcr, chrs[21:22], gene.collapse = "longest")
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
============= sessionInfo ==============
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] reshape2_1.0 ShortRead_1.8.0 lattice_0.19-13
[4] ggplot2_0.8.8 proto_0.3-8 reshape_0.8.3
[7] doMC_1.2.1 multicore_0.1-3 foreach_1.3.0
[10] codetools_0.2-2 iterators_1.0.3 data.table_1.5.1
[13] plyr_1.2.1 GenomeGraphs_1.10.0 biomaRt_2.6.0
[16] bitops_1.0-4.1 Rsamtools_1.2.0 RSQLite_0.9-2
[19] DBI_0.2-5 Biostrings_2.18.0 GenomicFeaturesX_0.2
[22] GenomicFeatures_1.2.0 GenomicRanges_1.2.1 IRanges_1.8.2
loaded via a namespace (and not attached):
[1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0
[4] BSgenome_1.18.0 hwriter_1.2 RCurl_1.4-3
[7] rtracklayer_1.10.2 stringr_0.4 XML_3.2-0
[10] xtable_1.5-6
-steve
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