Send your sessionInfo().

While you're doing that, here are some suggestions:

1) use fewer processes.  minfi will kill a machine with 64GB of RAM using
as few as 4 processes for bumphunting. Plus, you probably want to use
doMC() instead of doParallel().  Try setting options("mc.cores") to
something like 4 and gradually increasing it as you successfully run
analyses on this machine/cluster/whatever.

2) look into using DMRcate if it's a simple 1:1 comparison. It's faster
than bumphunter.

3) the real drag here is that it looks like your run actually completes!!
 You have a huge number of candidate bumps but when the permutation testing
is being run, you run out of memory for at least one of the child
processes, and that's all she wrote.  So, back to #1, use fewer processes
for the time being.  If you can put more RAM into the machine, by all means
do so, but until that is done, try using a relatively small number of
processes.

Best,

--t



Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>


On Sat, Apr 12, 2014 at 7:42 PM, Brad Ruzicka [guest] <
guest@bioconductor.org> wrote:

>
> I'm trying to run bumphunter within the minfi package on a linux cluster,
> and when I use doParallel with bumphunter it consistently errors out with
> "Error in mcfork() : unable to fork, possible reason: Cannot allocate
> memory"
> I haven't been able to find a solution searching the web or working with
> our support staff.
> Has anyone seen this before or know where the problem is?
> Any help will be greatly appreciated.
> - Brad
>
>
>  -- output of sessionInfo():
>
> Loading module hpc/intel-mkl-11.0.0.079.
>
>         JDK 1.6 module
>         ****************************************************
>
>           This module sets up the following environment
>           variables for JDK 1.6:
>               PATH /n/app/jdk1.6.0_11/bin
>
>         ****************************************************
>
> Loading module centos6/tcl-8.5.14.
> Loading module centos6/tk-8.5.14.
> Loading module centos6/fftw-3.3_gcc-4.4.7.
> Loading module centos6/gsl-1.16_gcc-4.4.7.
> Loading module centos6/hdf5-1.8.11_gcc-4.4.7.
> Loading module centos6/netcdf-4.3.0_gcc-4.4.7.
> Loading module centos6/R-3.0.2.
> Loading required package: minfi
> Loading required package: methods
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: Ã¢â'¬ËoeBiocGenericsÃ¢â'¬â"¢
>
> The following objects are masked from Ã¢â'¬Ëoepackage:parallelÃ¢â'¬â"¢:
>
>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>     clusterExport, clusterMap, parApply, parCapply, parLapply,
>     parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following object is masked from Ã¢â'¬Ëoepackage:statsÃ¢â'¬â"¢:
>
>     xtabs
>
> The following objects are masked from Ã¢â'¬Ëoepackage:baseÃ¢â'¬â"¢:
>
>     anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
>     duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
>     lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
>     pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
>     sapply, setdiff, sort, table, tapply, union, unique, unlist
>
> Loading required package: Biobase
> Welcome to Bioconductor
>
>     Vignettes contain introductory material; view with
>     'browseVignettes()'. To cite Bioconductor, see
>     'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: lattice
> Loading required package: reshape
> Loading required package: plyr
>
> Attaching package: Ã¢â'¬ËoereshapeÃ¢â'¬â"¢
>
> The following objects are masked from Ã¢â'¬Ëoepackage:plyrÃ¢â'¬â"¢:
>
>     rename, round_any
>
> Loading required package: GenomicRanges
> Loading required package: IRanges
>
> Attaching package: Ã¢â'¬ËoeIRangesÃ¢â'¬â"¢
>
> The following objects are masked from Ã¢â'¬Ëoepackage:reshapeÃ¢â'¬â"¢:
>
>     expand, rename
>
> The following objects are masked from Ã¢â'¬Ëoepackage:plyrÃ¢â'¬â"¢:
>
>     desc, rename
>
> Loading required package: XVector
>
> Attaching package: Ã¢â'¬ËoeXVectorÃ¢â'¬â"¢
>
> The following object is masked from Ã¢â'¬Ëoepackage:plyrÃ¢â'¬â"¢:
>
>     compact
>
> Loading required package: Biostrings
> Loading required package: bumphunter
> Loading required package: foreach
> Loading required package: iterators
> Loading required package: locfit
> locfit 1.5-9.1   2013-03-22
>
> Attaching package: Ã¢â'¬ËoelocfitÃ¢â'¬â"¢
>
> The following objects are masked from Ã¢â'¬Ëoepackage:GenomicRangesÃ¢â'¬â"¢:
>
>     left, right
>
> Loading required package: IlluminaHumanMethylation450kmanifest
> Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> [bumphunterEngine] Parallelizing using 64 workers/cores (backend:
> doParallel, version: 1.0.6).
> [bumphunterEngine] Computing coefficients.
> [bumphunterEngine] Performing 1000 permutations.
> [bumphunterEngine] Computing marginal permutation p-values.
> [bumphunterEngine] cutoff: 0.05
> [bumphunterEngine] Finding regions.
> [bumphunterEngine] Found 175279 bumps.
> [bumphunterEngine] Computing regions for each permutation.
> Loading required package: rngtools
> Loading required package: pkgmaker
> Loading required package: registry
>
> Attaching package: Ã¢â'¬ËoepkgmakerÃ¢â'¬â"¢
>
> The following object is masked from Ã¢â'¬Ëoepackage:IRangesÃ¢â'¬â"¢:
>
>     new2
>
> Error in mcfork() :
>   unable to fork, possible reason: Cannot allocate memory
> Calls: bumphunter ... %dopar% -> <Anonymous> -> mclapply -> lapply -> FUN
> -> mcfork
> Execution halted
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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