Many trees enter.
Fresh analysis ensues.
New insights emerge.
The conference on Informatics for Phylogenetics, Evolution, and Biodiversity
(iEvoBio) is again holding a Challenge competition in 2012, on the theme
Synthesizing Phylogenies. Somewhere, buried in large sets of trees, lies a
Dear all,
I have been trying to come up with easy ways to split diversitree runs
among processors when using multiple trees. It seems that the multicore
package would be a good way of doing it, but I have failed to use
multicore with diversitree functions. Essentially, I cannot figure out
how
Hey Rafael-
Hey, I'm using mclapply right now! What I'm doing with it is a trick I use
often in lapply and sapply statements. If I have, say a list 'A' and a
vector 'B' of the same length that I want to analyze in a lapply statement
which analyzes each corresponding pair, I do the following:
hi Rafael,
I have recently conducted diversitree analysis in a cluster. The only way I got
it to work was using the Rmpi package (I couldn't get multicore to detect cores
in multiple nodes, so it was limited to the number of cores in a single node,
in my case 8; with Rmpi there wasn't such
Hi Rafael,
I'd agree with RM, take a look at some of the explicit parallelization
packages (I find snowfall has less overhead on my typing than Rmpi does) if
you're planning to run over multiple trees. This will let you run on
multiple cores or on clusters. Here's quick example based on my
Hi all,
I am not sure what type of diversitree analysis but there may be some
memory issues if you use mcapply or the likes (this is especially true if
using the mcmc version of QuaSSE). An alternative (albeit slightly more
complicated) way of doing this is to write a bash script which utilizes
Hi Alex,
To fix this, do fix(plot.phylo) and look for this bit (around line #259):
if (phyloORclado direction == downwards)
yy - y.lim[2] - yy
Change the second line for:
yy - max(yy) - yy
This will be in the next release. Thank you for the report.
Cheers,
Emmanuel
-Original
