Installing Rmpi on LAM/MPI cluster

Question

I'm trying to install `Rmpi` package on a LAM MPI cluster machine. Previously I had been compiling and testing some stuff (`mpi4py` and small C++ programs) so I'm sure the MPI itself works. However installing `Rmpi` package fails when linking libraries. My main suspect is a call to `gcc` instead of `mpicc` in makefile (I'm trying to find the line in configuration to change this but so far could not locate it). Does somebody have experience with installing Rmpi on LAM, and how did you manage that? Architecture - LAM MPI (or maybe PBS MPI if such exist, how do I check?). One thing for sure, I have mpicpp file wich I don't think is common to all mpi implementations - R-2.15.2 - Rmpi_0.6-1 - CentOS release 5.5 (Final), x86_64 Command called from R ``` install.packages("Rmpi") ``` Log ``` trying URL 'http://cran.at.r-project.org/src/contrib/Rmpi_0.6-1.tar.gz' Content type 'application/x-gzip' length 92977 bytes (90 Kb) opened URL ================================================== downloade…

Accepted Answer

We have a very similar setup. I haven't touched it recently enough to be able to speak to your particular situation, but I can pass along a few of the commands that got us up-and-running...

The first step for us, as Dirk mentioned, was to get OpenMPI running. Once that's setup, you'll need to be sure your `LD_LIBRARY_PATH` is properly set:

```
export LD_LIBRARY_PATH=/opt/openmpiv2/lib/:$LD_LIBRARY_PATH
```

The command that finally got Rmpi installed for us (after running the above command and starting R) was:

```
install.packages("Rmpi", configure.args = c("--with-Rmpi-include=/opt/openmpiv2/include/", "--with-Rmpi-libpath=/opt/openmpiv2/lib/", "--with-Rmpi-type=OPENMPI", "--with-mpi=/opt/openmpiv2/"))
```

Which installed the package successfully for us. Then we can run jobs using commands such as:

```
qsub -I -l nodes=2:ppn=12
/opt/openmpiv2/bin/mpirun --hostfile $PBS_NODEFILE -n 1 R --slave -f rmpitest.R
```

These commands may be so specific to our setup that they may not be useful, but hopefully something in here can save you some time!

As @Sergej proposes below, a more general solution may be:

```
install.packages(
  "Rmpi", 
  configure.args = c(
   "--with-Rmpi-include=/usr/include/", # This is where LAM's mpi.h is located
   "--with-Rmpi-libpath=/usr/lib/",     # This is where liblam.so is located (actually as I type it mine was located in /usr/lib64/liblam.so.0, so maybe this is not needed at all)
   "--with-Rmpi-type=LAM"               # This says that the type is LAM (there is also OPENMPI and MPICH)
))
```

Our setup: RHEL 5, Rmpi 0.5-9, OpenMPI 1.4.3., R 2.15.0

Installing Rmpi on LAM/MPI cluster

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