o.heil at dkfz.de
2010-Feb-03 12:55 UTC
[Rd] mclapply on a set not divisible by number of cores (PR#14205)
Full_Name: Oliver Heil
Version: 2.10.0
OS: debian squeeze
Submission from: (NULL) (193.174.58.251)
When running mclapply on a list of strings with a length of 618 on 10 cores the
resulting data is wrong every 10 entries starting with the 6th. Our machine has
16 cores.
You may reproduce the error using data provided here:
<http://www.dkfz.de/gpcf/tmp_535434fsfd/>
Together with the following code (R --vanilla):
# foreach probeid(618 Probeids) get the data points from the
# dataframes control and group
# calculate mean, standard deviation and detection p value for group and
control
# calculate the p value, that mean of control and mean of group are different
#
# The result is a list (length 618) of 7 tuples
#
# Have a look at x_sd_p.test[[6]], x_sd_p.test[[16]], ...
# It works fine using lapply or doing the function "by
# hand" for example with factor=probeids[6]
#
load("df.control.R")
load("df.group.R")
load("negative_bead.R")
load("probeids.R")
library("multicore")
x_sd_p.test=mclapply(probeids,function(factor){
idxg=which(df.group$Factor %in% factor);
mg=NA;sdg=NA;pg=1.0;
if(length(idxg)>0){
lg=df.group$x[idxg];
mg=mean(lg,,TRUE);
sdg=sd(lg,TRUE);
t=wilcox.test(lg,negative_bead,alternative="g",exact=TRUE);
pg=t$p.value;
}
idxc=which(df.control$Factor %in% factor);
mc=NA;sdc=NA;pc=1.0
if(length(idxc)>0){
lc=df.control$x[idxc];
mc=mean(lc,,TRUE);
sdc=sd(lc,TRUE);
t=wilcox.test(lc,negative_bead,alternative="g",exact=TRUE);
pc=t$p.value;
}
p=1.0;
if(length(idxg)>0&&length(idxc)>0){
t=wilcox.test(lg,lc,alternative="t",exact=TRUE);
p=t$p.value;
}
c(mg,sdg,pg,mc,sdc,pc,p);
},mc.cores=10)
l=lapply(x_sd_p.test,function(x){length(x)})
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] multicore_0.1-3
loaded via a namespace (and not attached):
[1] tools_2.10.0
> version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 10.0
year 2009
month 10
day 26
svn rev 50208
language R
version.string R version 2.10.0 (2009-10-26)