[R-sig-hpc] segfault and RunSnowWorker: not found

[Martin Renner]

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
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Homer, AK 99603, USA
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