findPeaks.centwave appears to run single-threaded on a virtual Windows machine. about xcms HOT 3 CLOSED

Could you please provide the output of your sessionInfo? In the devel branch of xcms we switched from the old parallel processing setup (which was quite cumbersome in xcms) to BiocParallel, i.e. BiocParallel takes care of the correct parallel processing setup (whether snow Rmpi or parallel are used) which can be configured system-wide.

If you're using the release branch you might still be with the old setup. Eventually you're lacking one of the required packages for parallel processing. Try installing snow, parallel, Rmpi on your windows machine. I can't remember which one, but only one of those works on Windows, so don't be surprised if not all are available or can be installed:

library(BiocInstaller)
biocLite(c("snow", "parallel", "Rmpi"))

from xcms.

sessionInfo() revealed that "parallel" was already attached; as you said, apparently it is not effective for XCMS.

I did find that adding

library("snow")
to my script did result in parallel processing, e.g.,
Starting snow cluster with 12 sockets
Detecting features in file # 1: foo.mzXML
Detecting features in file # 2: bar.mzXML
etc.

Page 81 of the package manual
http://bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
documents nSlaves as

nSlaves - number of slaves/cores to be used for parallel peak detection. MPI is used if installed, otherwise the snow package is employed for multicore support. If none of the two packages is available it uses the parallel package for parallel processing on multiple CPUs of the current machine.

Perhaps this could be very slightly more explicit for the naive user, e.g.:

nSlaves - number of slaves/cores to be used for parallel peak detection.
Requires at least one of the additional libraries: Rmpi, snow, parallel.
If several are loaded, the order of preference is: Rmpi > snow > parallel.

Thank you very much for your quick response!

from xcms.

Thanks for your suggestion. Note however that the use of nSlaves is deprecated in the next release. As noted above we'll switch to BiocParallel for parallel processing; I'll try to enhance the documentation and eventually add a specific section to the vignette.

from xcms.