Re: [R] Problem about spawn nodes with Rmpi
2008/10/22 Markus Schmidberger <[EMAIL PROTECTED]> > > Hi Marce, > > there is a new mailing list for R and HPC: [EMAIL PROTECTED] > This is probably a better list for your question. > > Probably Rmpi does not find the correct Rmpi implementation. Have you > installed a second mpi implementation (lammpi)? > How do you have installed Rmpi? > Did you compiled it to the mpi libraries? > R CMD INSTALL --configure-args="--with-mpi=MPIPATH" Rmpi > > Best > Markus > > -- > Dipl.-Tech. Math. Markus Schmidberger > > Ludwig-Maximilians-Universität München > IBE - Institut für medizinische Informationsverarbeitung, > Biometrie und Epidemiologie > Marchioninistr. 15, D-81377 Muenchen > URL: http://www.ibe.med.uni-muenchen.de > Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de > Tel: +49 (089) 7095 - 4599 Oh thanks, I don't know the existence of this mail list :p. I have just subscribe. About your answer, I don't have more implementations of MPI, just OpenMPI. When I install Rmpi I did like you say: "/home/R/bin/R CMD INSTALL Rmpi --configure-args--with-mpi=/home/openmpi/. I think that installation went OK, after that in logs Rmpi recognize MPI directory..all OK. Now I'm not in my computer, tomorrow I'll do again to see more logs. Thanks again for all Markus. ((PD: I will send this post both list, sorry for the duplicated messages) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem about spawn nodes with Rmpi
Hi Marce, there is a new mailing list for R and HPC: [EMAIL PROTECTED] This is probably a better list for your question. Probably Rmpi does not find the correct Rmpi implementation. Have you installed a second mpi implementation (lammpi)? How do you have installed Rmpi? Did you compiled it to the mpi libraries? R CMD INSTALL --configure-args="--with-mpi=MPIPATH" Rmpi Best Markus Marce wrote: > Hi all, > now I'm testing R in a "virtual cluster", made it with VirtualBox. This one > has 3 nodes, running CentOS 5 and OpenMPI 1.2.8, and the principal node > (called "server") exports the /home to other nodes. > I have installed R and 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]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universität München IBE - Institut für medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem about spawn nodes with Rmpi
Hi all, now I'm testing R in a "virtual cluster", made it with VirtualBox. This one has 3 nodes, running CentOS 5 and OpenMPI 1.2.8, and the principal node (called "server") exports the /home to other nodes. I have installed R and 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]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
