Also FWIW changing things like (there are a number of these changes)
sum(unlist(lapply(data, length)))/1e+06
to
sum(lengths(data)) / 1e6
actually has measurable effect on the speed of your code.
Martin
On 04/18/2018 10:47 AM, Carmen M. Livi wrote:
Dear Martin Morgan,
ok, I will switch back to parallel then. Thank you very much for your
reply.
Kind regards,
Carmen
On 18/04/2018 15:30, Martin Morgan wrote:
I'm sorry not to respond to your first email. This is a problem in
BiocParallel that I am working on. In your particular case, where you
are relying on a third-party package that uses parallel::mclapply, I
think you should revert to using that.
Martin
On 04/18/2018 09:22 AM, Carmen M. Livi wrote:
Hi all,
I was using parallel::mclapply() but have been encouraged to substitute
it with BiocParallel::bplapply().
BiocParallel::bplapply(data,
BPPARAM = BiocParallel::MulticoreParam(workers =x ),
FUN =...)....
I never had problems with the code. Now the package got accepted and
moved to the bioconductor-repository and suddenly I am getting errors in
the vignette build when asking for 5 workers:
"Error in serialize(data, node$con, xdr = FALSE) : error writing to
connection"
After reducing the number of requested workers to 3 my package passed
under linux (malbec2 and malbec1) but still fails under OS X (merida2):
"Error : failed to stop ‘SOCKcluster’ cluster: error writing to
connection"
https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/ChIC/merida2-buildsrc.html
Does anyone have an idea what is going on? Am I not supposed to ask for
more then 1 worker in the vignette?
What if I just switch back to parallel::mclapply?
Thank you,
Carmen
//
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