Hi,
While I suspect that this is an issue peculiar to my machine (Debian squeeze
amd64, R version 3.0.1, up-to-date packages), I'm hoping that somebody on this
list may be able to give me suggestions on how to troubleshoot and fix the
following:
> library (snow)
> cl <- makeSOCKcluster(c("localhost","localhost"))
sh: 1: RunSnowWorker: not found
I presume/hope that this may be related to an (even more pressing) issue I have
with mclapply (package 'parallel'). While
> example (mclapply)
works as expected, any of my longer parallel jobs result in segfaults:
*** caught segfault ***
address 0x7f0aeed649d0, cause 'memory not mapped'
Traceback:
1: mcexit(0L)
2: mcparallel(FUN(X[[i]], ...), mc.set.seed = mc.set.seed, silent = mc.silent)
3: FUN(1:8[[2L]], ...)
4: lapply(jobid, function(i) mcparallel(FUN(X[[i]], ...), mc.set.seed =
mc.set.seed, silent = mc.silent))
5: mclapply(sppDaysL, predDist, mc.cores = 8)
aborting ...
To add to the puzzle: the first couple of iterations sometimes finish
successfully, but on other runs segfaults start to appear with the first
iteration. The reported address seems to be always the same. htop indicates
that there is still sufficient RAM available and memtester came out clean.
Running the code with mc.cores=1 works fine -- run times are just not practical
when I can't take advantage of my 8 cores. Likewise, no problems running in
parallel under Mac OS X.
I tried the cran binaries R version 3.0.1 (2013-05-16) as well as my locally
compiled version with the same result. I also tried a blank user account, again
with the same issue. Any suggestions how I could troubleshoot this seqfault or
RunSnowWorker: not found issue would be much appreciated.
Best wishes,
Martin
Martin Renner
Tern Again Consulting
388 E. Bayview Ave.
Homer, AK 99603, USA
phone: +1 907 235 0728
cell: 299 6152
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