search for: makempiclust

...on:~> but I basically cannot get anything more complicated to work yet. R / Rmpi just seem to hang, in particular snow and and getMPIcluster() just sit there: > cl <- makeSOCKcluster(c("localhost", "localhost")) > stopCluster(cl) > library(Rmpi) > cl <- makeMPIcluster(n=3) Error in makeMPIcluster(n = 3) : no nodes available. > I may be overlooking something simple here, in particular the launching of apps appears to be different for Open MPI than it was with LAM/MPI (or maybe I am just confused be...

...minimal example is given below. It runs perfectly fine on my MacBook but when I submit it as a batch job via ... > bsub -n 3 -R "select[model==Opteron8380]" mpirun R --no-save -q -f doSNOW_minimal.R > ... it does not work. The output is also given below. The error is "Error in makeMPIcluster(spec, ...) : a cluster already exists 1". The only similar thing I found on the web is http://www.mail-archive.com/r-help at stat.math.ethz.ch/msg35501.html > but unfortunately, it was not answered. > I also contacted the maintainers of the cluster, however, they couldn't really he...

...ster: launch failed: CreateProcess(/usr/bin/env "RPROG="C:\Programme\R\R-2.5.1\bin\R" "OUT=/dev/null" "R_LIBS=" C:/Programme/R/R-2.5.1/library/snow/RMPInode.sh) on 'cl1' failed, error 3 - Das System kann den angegbenen Pfad nicht finden. I looked into makeMPIcluster. It could not work, mpi.comm.spawn gets the shell command for unix to start the slaves. A simple solution is to use the windows-code from mpi.spawn.rslaves, then it looks like this. And is working on our windows-cluster. (small failures on stopping cluster) # Fro windows if (.Platform$OS==&qu...

...unable to load shared library '/home/apps/R-2.2.0/lib/R/library/Rmpi/libs/Rmpi.so': libmpi.so.0: cannot open shared object file: No such file or directory Error in dyn.unload(x) : dynamic/shared library '/home/apps/R-2.2.0/lib/R/library/Rmpi/libs/Rmpi.so' was not loaded Error in makeMPIcluster(spec, ...) : the `Rmpi' package is needed for MPI clusters. The Rmpi.so exists and the permissions are fine. I also did a lamboot, and its running in the backround fine as well. Any suggestions? Thanks.

Dear Luke and others, I have many R versions on my machine and want to start a particular one when snow builds its cluster. (The same version I start snow from.) It seems that everything is set up correctly in defaultClusterOptions: > mget(ls(defaultClusterOptions), defaultClusterOptions) $homogeneous [1] TRUE $manual [1] FALSE $master nodename "maya.unil.ch" $outfile [1]

Hi, I'm testing affyPara on Debian lenny with R 2.7 from unstable, and the corresponding bioconductor packages from bioconductor.org downloaded using biocLite as per usual. The command cl = makeMPIcluster(k) succeeds, but spawns k R slaves which promptly soak up all available CPU, which is odd since they are not doing anything yet. This looks like a bug to me. Similar behaviour is shown by a different machine, also running lenny, This is probably an issue with rmpi/snow. I notice that the Debi...

...ried again on my system. I was able to build the thing, but not actually get it working. The two obvious difficulties were that, first, I had to manually load the serialize library (which now conflicts with the name of something in the base package) and, second, that whenever I say makeCluster or makeMPIcluster the thing just hangs up. I've tried various permutations of running or not running lamboot first. I am able to to lamboot and lamexec, and I also tried setting LAMRSH to use ssh on the master. My "network" is just my dual-CPU machine. Tony Rossini's notes (http://www.analyti...

...ed process to recreate exactly the same random numbers that it did before; I assume SPRNG assures the streams are independent betweeen processes. Here's what I did, trying to stick within SNOW to avoid trouble (from memory): lamboot start up R library(snow) library(rsprng) library(rmpi) cl<-makeMPIcluster(11) clusterSetupSPRNG(cl, seed=123) clusterEvalQ(cl, source("mycode.R")) r<-parSapply(cl, seq(1000), function(i) doMyThing())) Any comments on that? For example, would sticking to Rmpi and using parSim make sense (I'm not using seq(1000) for anything but getting that many repet...

...do and a for loop. In the directory containing rtest.R it is run from the command line with: > "mpirun -n --hostfile /home/hostfile --no-save -f rtest.R" > > Here is the code for rtest.R: > > ################# > library(doSNOW) > library(panel) > > cl<-makeMPIcluster(3) > registerDoSNOW(cl) > > clusterEvalQ(cl,library(panel)) > > res<-clusterCall(cl, function(){Sys.info()["nodename"]}) > print(do.call(rbind,res)) > > sme<- matrix(rnorm(100),10,10) > clusterExport(cl,"sme") > > myfun<-functio...

We have spent some time setting up Sun Grid Engine and OpenMPI on a group of linux boxes. I have created a parallel environment and everything seems to be working. I have Rmpi 0.5.5-5 installed on all machines. I would like to start an interactive R session using, say, 8 processors and then start the Rmpi cluster. I haven't been able to find what needs to be done in order to accomplish