Re: [R] Debugging segfault in foreach
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-8LC_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_1.2.1multicore_0.1-3 foreach_1.3.0
[10] codetools_0.2-2 iterators_1.0.3 data.table_1.5.1
[13] plyr_1.2.1GenomeGraphs_1.10.0 biomaRt_2.6.0
[16] bitops_1.0-4.1Rsamtools_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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Debugging segfault in foreach
-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-8LC_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_1.2.1multicore_0.1-3 foreach_1.3.0
[10] codetools_0.2-2 iterators_1.0.3 data.table_1.5.1
[13] plyr_1.2.1GenomeGraphs_1.10.0 biomaRt_2.6.0
[16] bitops_1.0-4.1Rsamtools_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: rai...@krugs.de
Skype: RMkrug
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
