[Bioc-devel] error related to kmp_runtime.cpp(6480)
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, Martin
Thanks, Vlad [[alternative HTML version deleted]]
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