Jim Maas Jim Maas - 3 years ago 263
Linux Question

loading Rmpi with openmpi 3.0.0 on Ubuntu throwing error

I've got some sore of a library problem when trying to install Rmpi, having installed openmpi 3.0.0 from source to /usr/local on Ubuntu 16.04.

open mpi seems to be installed correctly,

--version works

When I try to install Rmpi using this command

sudo R CMD INSTALL ./Downloads/Rmpi_0.6-6.tar.gz --configure-args="--with-Rmpi-type={OPENMPI}"

It compiles fine, and finds the libraries

I am here /usr/local and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/local/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/local/lib
checking for orted... yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status

but when it does the load test I get

** testing if installed package can be loaded
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)

I've tried many things but still no luck. How can I track down the error in the connection to mpi?

Answer Source

Per the various exchanges in the comment section, it appears there is an issue when Open MPI is used as a plugin by Rmpi.

The solution/workaround was to rebuild Open MPI from scratch and configure with the --disable-dlopen parameter.

This might be related to the issue discussed in Open MPI

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