similar to: Rmpi on Linux (SuSE) with OpenMPI

Dear knowledgeable experts :-), I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM cluster. I'm not an IT expert, but I surely could use a working installation of Rmpi and SNOW. I try to load the Rmpi library and get the following: > library(Rmpi) [master:07230] mca: base: component_find: unable to open osc pt2pt: file not found (ignored)

Hi guys, I've spent a few days trying to install Rmpi with no luck. I originally tried using mpich, moved on to mpich2, and then to openmpi. I've gotten the furthest with openmpi, though am still running into this problem and can't figure it out. Can someone help!? Thanks so much in advanced. I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the error at the

Guys, I'm running LAM 7.1.4 and R/Rmpi on a SuSE 9.3 box. When I do >library(Rmpi) The whole thing crashes with the following message: ----------------------------------------------------------------------------- No SSI RPI modules said that they were available to run. This should only happen if you request an MPI thread level that is too high (for example, none of the SSI RPI modules

Hello, I'm using R on a 10 blade dual quad core Rocks Cluster, and trying to use Rpmi and snow. I basically wondered if at the moment I ought to install Rmpi against another form of mpi (not openmpi) and wondered whether anyone could pass on any experience. I'm mainly worried about (a) the R server taking up 100% cpu time (I think this is a known issue with Rmpi and openmpi) and (b)

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

Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy Heron, have openmpi installed, and get the following error message with attempted install of Rmpi. sessionInfo() follows. Mark checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes

Greetings. I see a warning message while compiling OpenMPI and would appreciate it if you tell me what it means. This warning happens with any OpenMPI > 1.6.5. Even before starting a cluster, just "sessionInfo" triggers this warning. I'm pasting in the message from R-3.3.2 (this is MRO). Do the R parallel package cluster functions violate the warnings described here? >

Hi, I appreciate any help that can be given. For the life of me, I cannot create a writeable share on a specific box - a fairly new install of Fedora Core 5. I have posted on several forums over the past 2 weeks, but haven't gotten anywhere with the advice given, so I'm turning to this list as my last hope. This box runs as an NIS client, but I have had no problems with NIS. The problem

Guys, I'm running R on both Windows & Linux. I'm looking at a number of packages for parallel execution. It seems that the most used packages are "snow" and "Rmpi". snow seems more user friendly, but it doesn't run on windows. I see from searching the mailing list that I'm not the first one to try it on Windows. There was a message that kind of shed some

I am trying to install the R package "Rmpi" which needs libmpi. I've installed openmpi and lam in Centos 5.2: [root at rab45-1 /]# rpm -qv openmpi openmpi-1.2.5-5.el5 openmpi-1.2.5-5.el5 [root at rab45-1 /]# rpm -qv lam lam-7.1.2-14.el5 lam-7.1.2-14.el5 But I get the following error message when trying to install Rmpi: /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so

Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make the changes to support Open MPI. I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under R 2.6.0 but I cannot convince myself yet whether it works or not. Simple tests work. E.g. on my Debian testing box, with Rmpi installed directly using Open Mpi 1.2.3-2 (from Debian) and using 'r' from

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

Hi AllThis is NOT specifically related to CentOS per se.? I have 2 servers that are on two networks.? I did NOT set this up.? The NIC went bad and it has been replaced.? I knew enough to update the HW address in the ifcfg-* files.? The network service restarts successfully without errors.? However I cannot connect via ping or ssh with the pt2pt network setup on 192.168.x.*.? When I use our

Hello, We have R working with Rmpi/openmpi, but I'm a little worried. Specifically, (a) the -np flag doesn't seem to override the hostfile (it works fine with fortran hello world) and (b) I appear to have twice as many processes running as I think I should. Rmpi version 0.5.5 Openmpi version 1.1 Viglen HPC with (effectively) 9 blades and 8 nodes on each blade. myhosts file contains

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

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

I try to install Rmpi as root with install.packages("Rmpi"). It fails with: ... checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO C89... none needed I am here /usr and it is OpenMPI Trying to find mpi.h ... Found in /usr/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /usr/lib checking for openpty in -lutil... yes checking for main in -lpthread...

I got Rmpi to compile with little difficulty, but had a tricky time setting the LD_LIBRARY_PATH to use the OpenMPI libs. I now get a different error when I try to load Rmpi > require(Rmpi) Loading required package: Rmpi librdmacm: couldn't read ABI version. librdmacm: assuming: 4 libibverbs: Fatal: couldn't read uverbs ABI version. CMA: unable to open

Hi Folks, I've recently transitioned to Debian 8.0 and was having a hard time getting Rmpi to work. I believed I'd successfully installed dependencies via > sudo apt-get install r-cran-rmpi > apt-show-versions r-cran-rmpi r-cran-rmpi:amd64/jessie 0.6-5-1 uptodate but when installing the package I was still getting checking mpi.h presence... no checking for mpi.h... no

I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the following without errors: "R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi" Immediately at library(Rmpi) I get the segfault displayed in my complete output below. My first thought is that perhaps I used the wrong library for openmpi, but with my 64 bit install it seemed like a logical