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()
======== 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
--
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
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 >
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel: +33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: Rainer at krugs.de Skype: RMkrug -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzigYgACgkQoYgNqgF2egqFWQCcCHb8ZrvUmdT3dtla6NJOvw+3 UCwAn0FxzQI4JE2f8+H5vOaMSxk4TCLc =GaBe -----END PGP SIGNATURE-----