15 Jul
2013
15 Jul
'13
2:18 p.m.
Hi Jacalyn,
It's difficult to know exactly what the problem is, but it might have to do
with the interaction of PBS with the parallel package (which Amelia uses).
You might try to see if you can run the example scripts on PBS:
library(parallel)
example(mclapply)
If those don't work, there might be an issue between parallel and PBS.
Cheers,
Matt
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Political Science
University of Rochester
url: http://www.mattblackwell.org
On Fri, Jul 12, 2013 at 2:11 PM, Jacalyn Huband <jmh5ad(a)virginia.edu> wrote:
I have been able to run the "multicore"
option of amelia on a single
(Linux) computer with 8 cores, but I am having problems porting my program
to a (Linux) cluster.
Specifically, I have requested (through the PBS resource management
software) a single node with 16 cores. My program appears to run
correctly, but then gets killed by PBS (error message: ncpus 4.01 exceeded
limit 1). In the amelia function, I'm setting m = 5, parallel =
"multicore", and ncpus = 1. I've tried other values for ncpus (including
5, 10, and 16), but the job still gets killed. (Note: It does not get
killed if m = 1, but that defeats the purpose of using multiple cores.)
Is the amelia function trying to spawn threads of which I am unaware?
J. Huband
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