[R] Debugging segfault in foreach

[Rainer M Krug]

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On 11/16/2010 04:53 AM, 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.

Have you tried using mclapply instead? Does that work? If yes, the
problem is in foreach and I would contact revolution analytics - if no,
the problem is in multicore (or your code ...)

I don't think you can go much further then that, unless you want to
debug foreach (or multicore) to that effect.

Cheers,

Rainer


> 
> 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()
> 
> ======== 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
> 


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

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