search for: nslaves

...rocessor (and later a High-performance clusters (HPC) ) by using the Rmpi, snow, snowfall, ... packages, but I am struggling at the beginning, i.e. to initialise the "cluster" on my dual core computer. Whenever I try to initialize it (via sfInit(parallel=TRUE, cpus=2) or mpi.spawn.Rslaves(nslaves=2) ), I get an error message: > sfInit(parallel=TRUE, cpus=2) Forced parallel. Using session: XXXXXXXXR_rkrug_143706_092708 Error in mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves = count, : MPI_Comm_spawn is not supported. Error in sfInit(parallel = TRUE, cpus = 2) : Starting o...

Hi everybody! I have the next code which makes a reduction of the *a *variable in two slaves, using the Rmpi package. library(Rmpi) mpi.spawn.Rslaves(nslaves=2) reduc<-function(){ a<-mpi.comm.rank()+2 mpi.reduce(a,type=2, op="prod") return(paste("a=",a)) } mpi.bcast.Robj2slave(reduc) mpi.remote.exec(reduc()) cat("Product: ") mpi.reduce(1,op="prod") mpi.close.Rslaves() I want to use the function...

Hi everybody! I have the next code which makes a reduction of the *a *variable in two slaves, using the Rmpi package. library(Rmpi) mpi.spawn.Rslaves(nslaves=2) reduc<-function(){ a<-mpi.comm.rank()+2 mpi.reduce(a,type=2, op="prod") return(paste("a=",a)) } mpi.bcast.Robj2slave(reduc) mpi.remote.exec(reduc()) cat("Product: ") mpi.reduce(1,op="prod") mpi.close.Rslaves() I want to use the function...

...mpi was finally installed (basically I just added the flags "-lmpl -lopa" to the definition of PKG_LIBS in the configure script, and in the R CMD INSTALL call, I passed the configure.args as the correct paths to my MPICH2 installation). However, when I call the "mpi.spawn.Rslaves(nslaves=1)" command, I get the following errors: ################## > mpi.spawn.Rslaves(nslaves=1) *** caught segfault *** address 0x2df0c9f, cause 'memory not mapped' Traceback: 1: .Call("mpi_comm_spawn", as.character(slave), as.character(slavearg),...

According to ?parCapply: parRapply and parCapply always return a vector. This appears not to be the case in the following minimal reproducible example: > library(parallel) > nslaves <- 2 > cl <- makeCluster(nslaves) > X <- matrix(2,nrow=3,ncol=4) > X <- rbind(c(1,1,0,1),X) > tv <- parCapply(cl,X,FUN=function(x){ + ind <- x[1] + y <- x[-1] + if(ind==1){ + r1 <- sum(y) +...

..._ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rmpi_0.5-6 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 > mpi.spawn.Rslaves(nslaves=5, needlog=TRUE) Fehler in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), : MPI_Error_string: error spawning process > traceback() 3: .Call("mpi_comm_spawn", as.character(slave), as.character(slavearg), as.integer(nslaves), as.intege...

...localhost, mapdrive, remotepath) #Rscript,R_HOME,WDrive,WDir,WorkTmp,TmpDir,Master,MapDrive,RemotePath print("super") count<-mpi.comm.spawn( slave=system.file("Rslaves.bat", package="Rmpi"), slavearg=arg, nslaves=count) } else{ # for unix count <- mpi.comm.spawn(slave = "/usr/bin/env", slavearg = args, nslaves = count, intercomm = intercomm) } Doing some work, there should be a better and nice...

...the tutorial website. However, I keep getting the following error: > # Load the R MPI package if it is not already loaded. > if (!is.loaded("mpi_initialize")) { + library("Rmpi") + } > > # Spawn as many slaves as possible > mpi.spawn.Rslaves(nslaves=4) 4 slaves are spawned successfully. 0 failed. Error in unserialize(obj) : unknown input format Calls: mpi.spawn.Rslaves ... mpi.bcast.Robj -> .mpi.unserialize -> unserialize - > .Call Execution halted # Load the R MPI package if it is not already loaded. if (...

Has anybody tried to use Rmpi with the OpenMPI library instead of LAM/MPI? LAM appears to be somewhat hardcoded in the Rmpi setup. Before I start to experiment with changing this, has anybody else tried Rmpi with non-LAM MPI implementations? Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison

...in /home, in fact, it seems work OK. Editing the openmpi-default-hostfile and run "mpirun -np 3 hostname" I can see the hostname of all nodes in my cluster. But my problem comes when I want to spawn several nodes in R. I have installed R 2.6.1 and Rmpi 0.5.5. When I run mpi.spawn.Rslaves(nslaves=3) for example, it only spawn 3 processors in the same node, in fact, the local node. How I can tell to Rmpi that there are 2 o more nodes in the cluster? This problem can be solved passing a hostfile like an argument? Thanks for all [[alternative HTML version deleted]]

Hi, I'm testing the efficiency of the Rmpi package regarding parallelization using a cluster. I've found and tried the task pull programming method, but even if it is described as the best method, it seems to cause deadlock, anyone could help me in using this method? here is the code I've found and tried: # Initialize MPI library("Rmpi") # Notice we just say "give us

...times equal to the number of slaves. I am trying to print out the slave number to a file (once), but it is printing it 4 times (since the number of slaves is 4). The code is as follows: # Initialize the Rmpi environment library("Rmpi") # We are spawning four slaves mpi.spawn.Rslaves(nslaves=4) if (mpi.comm.size() != 5) { print("Please initialize an MPI cluster of at least 5 processors.") print("Then, try again") mpi.quit() } .Last <- function() { if (is.loaded("mpi_initialize")) { if (mpi.comm.size...

...t;COB_4" "CNJ_4" and that works more or less fine to produce a list of length 6 which I've named with the elements of the subsets vector. names(out) <- subsets Now, when I use mpi.apply, I make the trees, folds and minob available to all slaves thus: mpi.spawn.Rslaves(nslaves=6) mpi.bcast.Robj2slave(trees) mpi.bcast.Robj2slave(folds) mpi.bcast.Robj2slave(minob) but, I can't work out what sort of 'array' is required for the first argument to mpi.apply. out.mpi <- mpi.apply(subsets.l, lr.gbm) What should subsets.l look like? I tried a list of le...

...o world' program that's available at http://math.acadiau.ca/ACMMaC/Rmpi/sample.html. The code is as follows; # Load the R MPI package if it is not already loaded. if (!is.loaded("mpi_initialize")) { library("Rmpi") } # Spawn as many slaves as possible mpi.spawn.Rslaves(nslaves=3) # In case R exits unexpectedly, have it automatically clean up # resources taken up by Rmpi (slaves, memory, etc...) .Last <- function(){ if (is.loaded("mpi_initialize")){ if (mpi.comm.size(1) > 0){ print("Please use mpi.close.Rslaves() to close slaves.") mpi.c...

I'm invoking R from withing a shell script like this R --no-save --no-restore --gui=none > `hostname` 2>&1 <<BYE # various commands here BYE I would like to regain control from the invoking terminal at some point. I tried source(stdin()) but got a syntax error, presumably stdin is the little shell here snippet (the part between <<BYE and BYE). Is there some way to

...performance clusters (HPC) ) by using the Rmpi, snow, snowfall, >> ... packages, but I am struggling at the beginning, i.e. to initialise >> the "cluster" on my dual core computer. Whenever I try to initialize >> it (via sfInit(parallel=TRUE, cpus=2) or mpi.spawn.Rslaves(nslaves=2) >> ), I get an error message: >> >>> sfInit(parallel=TRUE, cpus=2) >> Forced parallel. Using session: XXXXXXXXR_rkrug_143706_092708 >> >> Error in mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves = count, : >> MPI_Comm_spawn is not supporte...

Hello R users and developers, I would like to install Rmpi so that I may take advantage of all of the CPUs in my computer, but I cannot get it to install and I am not very good with linux so it is adding to the headache. I have looked through the help archive, but I have not been successful at getting Rmpi to work. I am not sure if I am even installing openMPI correctly in linux. I would really