[Bioc-devel] error related to kmp_runtime.cpp(6480)

Martin Morgan martin.morgan at roswellpark.org
Tue Apr 25 00:28:17 CEST 2017

On 04/24/2017 04:43 PM, Vladislav Petyuk wrote:
> My package passes all the builds except OS X.
> http://www.bioconductor.org/checkResults/devel/bioc-LATEST/MSnID/veracruz2-buildsrc.html
> Interestingly, the build goes just fine (with the same arguments) on my
> laptop, which is OS X 10.12.3.
> Given that kmp_runtime.cpp is from OpenMP and chunk 25 in the vignette
> indirectly engages `mclapply`, my hunch is that this is something to do
> with parallel processing.  Is multithreading not allowed on this OS X
> machine?  Is simply forcing mc.cores = 1 going to solve the problem?  Any
> other suggestions on what is this error about and how to handle it?

is this nested parallelism -- mclapply() (forked process) then in the 
parallel chunks invoking OpenMP code? This probably at least partly 
defeats the parallelism, since threads are competing with one another 
for forked resources.

Just a guess,


> Thanks,
> Vlad
> 	[[alternative HTML version deleted]]
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