search for: rslaves

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 f...

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 f...

...u/Rmpi/) With MPICH2 I managed to connect my computers so that I was able to remotely launch Rgui on both machines but R hanged when calling "library(Rmpi)". If only one Rgui was launched on the localhost, "library(Rmpi)" worked without errors, but trying to use "mpi.spawn.Rslaves()" resulted in an error message, and so did "mpi.universe.size()". (In my current setup I can not reproduce this error message, but I can go back to this setup if this seems to be an important piece of information) After that I removed MPICH2 from the system and installed DeinoMPI...

Hello, I try to write parts of my code in C to accelerate the for-loops. But basic operations I want to do in R (e.g. start cluster). My R code looks something like this: library(Rmpi) mpi.spawn.Rslaves() mpi.remote.exec(....) dyn.load("test.so") erg <- .Call("test", ....) .... mpi.close.Rslaves() mpi.quit() And my C function looks something like this: #include <mpi.h> #include <R.h> #include <Rdefines.h> #include <Rinternals.h> SEXP test (SEXP a, ....

...l core processor (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) : St...

I am running R 2.7.0 on a Suse 9.1 linux cluster with a job scheduler dispatching jobs and openmpi-1.0.1. I have tried running one of the examples at http://ace.acadiau.ca/math/ACMMaC/Rmpi/examples.html in Rmpi and they seem to be working, except mpi.close.Rslaves() hangs. The slaves are closed, but the master doesn't finish its script. Below is the example script and the call to R. The job is being run on a single 4 processor machine. Any suggestions? Also is Rmpi using rexec to communicate? Can it use ssh if it doesn't already? mpirun -...

...e server. However, it's a little harder convincing myself which nodes are doing what. When looking directly in Rmpi, lamhosts() reports all the hosts correctly, unfortunately mpi.universe.size reports 1 node (I think this is as documented). More importantly, I have the issue with mpi.spawn.Rslaves() freezing. This has been mentioned before: http://tolstoy.newcastle.edu.au/R/e2/help/07/06/18573.html I wondered if anyone would mind supplying pointers. I'm specifically wondering if I need to check the version of openmpi, and whether at the moment it would be better to use another flavo...

...ow from 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 loade...

...g 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 all the slaves you've got." mpi.spawn.Rslaves() if (mpi.comm.size() < 2) { print("More slave processes are required.") mpi.quit() } .Last <- function(){ if (is.loaded("mpi_initialize")){ if (mpi.comm.size(1) > 0){ print("Please use mpi.close.Rslaves() to close slaves.&quot...

Hi, I am using a cluster with LAM 7.1.3/MPI 2 and R 2.6.0. Rmpi version 0.5-5 is working very well. Now I have tested "Rmpi 0.5-6". During spawning the Rslaves I get an error: MPI_Error_string: error spawning process > sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;L...

...tml npRmpi 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(slave...

...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=="windows"){ workdrive <- unlist(strsplit(getwd(),":"))[1] tmpdrive <- unlist(strsplit(tempdir(),":"))[1] worktmp &l...

...mber of 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.c...

...#39;hello 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.")...

Hi, I try use Rmpi package to my compute. In my work I'm using eclipse version 3.6.2 and statEt version 0.10.0 (launch Rterm or RJ). Actually I observed strange behavior, when I try loading Rmpi directly I don't have any problem i.e.: library("Rmpi") mpi.spawn.Rslaves() 8 slaves are spawned successfully. 0 failed. master (rank 0, comm 1) of size 9 is running on: marcin-HP slave1 (rank 1, comm 1) of size 9 is running on: marcin-HP slave2 (rank 2, comm 1) of size 9 is running on: marcin-HP slave3 (rank 3, comm 1) of size 9 is running on: marcin-HP mpi.remo...

Hi, I asked the question on stackexchange (http://unix.stackexchange.com/questions/264931/centos-7-unable-to-cleanly-umount-a-bind-mount-using-rbind-and-rslave) and CentOS 7 bug report (https://bugs.centos.org/view.php?id=10414) but didn't get any useful response, so I am thinking if I can get some help here. The problem arose when I tried to rbind mount /dev and /proc to a chroot sandbox

Hello: Anybody knows how to run Rmpi through PBS (Portable Batch System) on a cluster computer. I'm using a supercomputer which require to submit jobs to PBS queue for dispatching. I tried use mpirun in my PBS script. But all my Rslaves are spawned to the same node. This is not desired. Any suggestions are welcome! Thanks in advance. ======================================== Shengqiao Li Research Associate The Department of Statistics PO Box 6330 West Virginia University Morgantown, WV 26506-6330 Phone: (304) 285-5960

Hi I have managed to install MPICH2 and Rmpi on my Windows 7 machine. I can also run the following code > library(Rmpi) > mpi.spawn.Rslaves() 4 slaves are spawned successfully. 0 failed. master (rank 0, comm 1) of size 5 is running on: MyMaster slave1 (rank 1, comm 1) of size 5 is running on: MyMaster slave2 (rank 2, comm 1) of size 5 is running on: MyMaster slave3 (rank 3, comm 1) of size 5 is running on: MyMaster sl...

Hi I have managed to install MPICH2 and Rmpi on my Windows 7 machine. I can also run the following code > library(Rmpi) > mpi.spawn.Rslaves() 4 slaves are spawned successfully. 0 failed. master (rank 0, comm 1) of size 5 is running on: MyMaster slave1 (rank 1, comm 1) of size 5 is running on: MyMaster slave2 (rank 2, comm 1) of size 5 is running on: MyMaster slave3 (rank 3, comm 1) of size 5 is running on: MyMaster slave4 (...

...OpenMPI 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]]