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Question: doParallel with Bumphunter gives Error in mcfork()
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4.7 years ago by
Guest User12k
Guest User12k wrote:
modified 4.7 years ago by Tim Triche4.2k • written 4.7 years ago by Guest User12k
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4.7 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
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4.7 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
Hi, Not related to the methylation analysis at all, but: On Sun, Apr 13, 2014 at 4:31 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > 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. I'm curious why you'd suggest that? I thought the general consensus was that the multicore package has "passed the baton" to the parallel package, so people who want to use "it" via foreach should then prefer doParallel ... no? -steve -- Steve Lianoglou Computational Biologist Genentech
I just checked and they both use the 'parallel' package as a backend. In the past, I've had issues with doParallel locking up on seemingly trivial jobs, whereas I've never had that happen with doMC. This may have long since been resolved, but once bitten, twice shy. Statistics is the grammar of science. Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> On Sun, Apr 13, 2014 at 10:23 PM, Steve Lianoglou <lianoglou.steve@gene.com>wrote: > Hi, > > Not related to the methylation analysis at all, but: > > On Sun, Apr 13, 2014 at 4:31 PM, Tim Triche, Jr. <tim.triche@gmail.com> > wrote: > > 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. > > I'm curious why you'd suggest that? I thought the general consensus > was that the multicore package has "passed the baton" to the > parallel package, so people who want to use "it" via foreach > should then prefer doParallel ... no? > > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech > [[alternative HTML version deleted]]
Tim, On Mon, Apr 14, 2014 at 11:37 AM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > I just checked and they both use the 'parallel' package as a backend. In > the past, I've had issues with doParallel locking up on seemingly trivial > jobs, whereas I've never had that happen with doMC. This may have long > since been resolved, but once bitten, twice shy. Since we're talking about methylation here, I think it's important to remember that the third time is the CHARM ... ... I think my job here is done. -steve -- Steve Lianoglou Computational Biologist Genentech

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