CODEWITHSUNDEEP
linuxrparallel-processingmpi
Rich
Rich

Reputation: 169

Rmpi: cannot use MPI_Comm_spawn API

I installed Rmpi on my linux machine and it successfully loads in R. There are two versions of MPICH on my machine, and I (believe) have installed Rmpi with the latest version. I also had to update my LD_LIBRARY_PATH. I primarily followed the installation instructions here.

After loading Rmpi in R, I run mpi.spawn.Rslaves(nslaves=4) and get the following error message:

Error in mpi.spawn.Rslaves(nslaves = 2) : 
You cannot use MPI_Comm_spawn API

Does anyone know how I can get Rmpi working?

Thanks!

Upvotes: 1

Views: 1100

Answers (1)

Steve Weston
Steve Weston

Reputation: 19677

You need to use MPICH2 for spawn support. If you have MPICH2 installed, you may still need to specify --with-Rmpi-type=MPICH2 when installing Rmpi. If you used --with-Rmpi-type=MPICH instead, it would disable functions such as mpi.spawn.Rslaves.

Also note that MPICH2 apparently does not support spawning workers unless the program is launched using a command such as mpiexec. This basically means that you can't execute mpi.spawn.Rslaves from an interactive R session using MPICH2, although this is possible using Open MPI. To be clear, this is not the issue that you're reporting, but you may encounter this after you have correctly installed Rmpi using MPICH2.

I was able to install Rmpi 0.6-5 using MPICH 3.1.3 with the command:

$ R CMD INSTALL Rmpi_0.6-5.tar.gz --configure-args='--with-mpi=$HOME/mpich-install --with-Rmpi-type=MPICH2'

To debug a configuration problem, you should install Rmpi from a directory rather than a tar file. That will allow you to examine the "config.log" file afterwards which will provide important information. Here is how I did that on my Linux box:

$ tar xzvf Rmpi_0.6-5.tar.gz 
$ R CMD INSTALL Rmpi --configure-args='--with-mpi=$HOME/mpich-install --with-Rmpi-type=MPICH2'

In order to get spawn support, the MPI2 macro needs to be defined when compiling the C code in Rmpi. You can check if that is happening by searching for "PKG_CPPFLAGS" in config.log:

$ grep PKG_CPPFLAGS Rmpi/config.log
PKG_CPPFLAGS='-I/home/steve/mpich-install/include  -DMPI2 -DMPICH2'

I have found "config.log" to be very useful for debugging configuration and build problems.

Note that you can use Rmpi without spawn support. You'll need to start all of the workers using mpirun (or mpiexec, etc) and it will be much more difficult, if not impossible, to use functions such as mpi.apply, mpi.applyLB, etc. But if you just need to initialize MPI so you can use MPI from functions implemented in C or Fortran, you will probably need to start all of the workers via mpirun.

Upvotes: 2

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