[R-sig-Debian] segfault and RunSnowWorker: not found
Johannes Ranke
jranke at uni-bremen.de
Sun Aug 18 15:25:54 CEST 2013
Hi,
just for the record: On Debian squeeze, amd64, using R 3.0.1 from CRAN I get:
> library(snow)
> cl <- makeSOCKcluster(c("localhost", "localhost"))
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=de_DE at euro LC_NUMERIC=C
[3] LC_TIME=de_DE at euro LC_COLLATE=de_DE at euro
[5] LC_MONETARY=de_DE at euro LC_MESSAGES=de_DE at euro
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE at euro LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] snow_0.3-12
So it seems to be a problem with your installation.
Johannes
Am Freitag, 2. August 2013, 21:29:27 schrieb 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
> 388 E. Bayview Ave.
> Homer, AK 99603, USA
> phone: +1 907 235 0728
> cell: 299 6152
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen
http://chem.uft.uni-bremen.de/ranke
-------------- next part --------------
> library(snow)
> cl <- makeSOCKcluster(c("localhost", "localhost"))
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=de_DE at euro LC_NUMERIC=C
[3] LC_TIME=de_DE at euro LC_COLLATE=de_DE at euro
[5] LC_MONETARY=de_DE at euro LC_MESSAGES=de_DE at euro
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE at euro LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] snow_0.3-12
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