在Ubuntu 16.04 VirtualBox上安装Rmpi

Question

I created a new ubuntu-16.04.2-desktop-amd64 machine on VM VirtualBox and I want to be able to use the R environment with Rmpi.

Both of the below approaches gives a similar error.

Updated simplified pre-build binary approach:

When Ubuntu had installed I opened a terminal and executed the following commands:

~$ sudo apt-get update
~$ sudo apt-get install openmpi-bin
~$ sudo apt-get install r-base
~$ sudo apt-get install r-cran-rmpi
~$ R

This opened the R terminal and I invoking the follow function which resulted in an error:

> library(Rmpi)
libmpi.so: cannot open shared object file: No such file or directory
Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
call: fun(libname, pkgname)
error: Cannot start MPI_Init(). Exit
Error: package or namespace load failed for ‘Rmpi’

Alternative approaches that I have attempted include using a local OpenMPI installation and using the R function install.packages to install the Rmpi package (see below). These all resulted in the same error.

I have also tried using MPICH by substituting ~$ sudo apt-get install mpich as the second command in the above procedure (including using the R function for installing the package) which results in an even more onerous runtime error.

Does anyone know what I have done wrong or what I can do to resolve this installation error?

Or alternatively, have anyone been able to successfully install a VirtualBox machine with Rmpi using any Linux distro or an image with pre-installed components?

Original local installation approach:

I have followed the instructions on this blog to download OpenMPI version 2.1.0, compile and install it. However when I try to install the package in R with:

> install.packages("Rmpi", configure.args =
  c("--with-Rmpi-include=/home/jormunr/openmpi/include",
    "--with-Rmpi-libpath=/home/jormunr/openmpi/lib",
    "--with-Rmpi-type=OPENMPI",
    "--with-mpi=/home/jormunr/openmpi/"))

it gives the following error

Error: .onLoad failed in loadNamespace() for 'Rmpi', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/jormunr/R/x86_64-pc-linux-gnu-library/3.2/Rmpi/libs/Rmpi.so':
libmpi.so.20: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

I can see that the 'libmpi.so.20' file is in the /home/jormunr/openmpi/lib that I provided as one of the parameter to the installation.

Answer 1

[Disclaimer: I am not a Linux expert and merely have user level skills. Any contributions or corrections from an expert will be greatly appreciated.]

Pre-build Binary Approach

Although trying various ways to install the prebuilt binaries I did not manage to get this option to work. This involved executing in the terminal the command 'sudo apt-get install r-cran-rmpi' to install the r-cran-rmpi prebuilt packages which also automatically installs the libopenmpi1.10 package that is a listed prerequisite. However, it appears that the file 'libmpi.so' is not included in the libopenmpi1.10 package but expected by the Rmpi library which causes an error in the R environment that it cannot find this file.

Local Installation Approach

The local installation did eventually succeed with a few amendments. I created a new ubuntu-16.04.2-desktop-amd64 VirtualBox image with default settings, except for 2048MB of memory and 32GB of hard drive space. When installed I opened a terminal and executed the commands from the Jovinge Lab website with the inclusion of the penultimate command which amends the run-time link editor's path and enables the install.package() function of R to find the 'libmpi.so' file. (also changed the version to 1.10.6 as this is the latest version release of version 1 – see below for version 2)

~$ cd /home/jormunr
~$ wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz
~$ tar -zxvf openmpi-1.10.6.tar.gz
~$ cd openmpi-1.10.2
~$ ./configure --prefix=/home/jormunr
~$ make
~$ make install
~$ sudo apt-get install r-base
~$ export LD_LIBRARY_PATH=/home/jormunr/lib:$LD_LIBRARY_PATH
~$ R

This opens an R terminal and I invoked the function:

> install.packages("Rmpi", configure.args =
+ c("--with-Rmpi-include=/home/jormunr/include/",
+   "--with-Rmpi-libpath=/home/jormunr/lib/",
+   "--with-Rmpi-type=OPENMPI",
+   "--with-mpi=/home/jormunr/"))

This now executed without errors and I could test it with the following R statements:

> library("Rmpi")
> mpi.spawn.Rslaves()
master (rank 0, comm. 1) of size 2 is running on: Valhalla
slave1 (rank 1, comm. 1) of size 2 is running on: Valhalla
> mpi.close.Rslaves()
[1] 1
> mpi.quit()

When I tried this process with the OpenMPI Version 2.1.0 the installation completed successfully but the above test had issues; the mpi.spawn.Rslaves() function completed but mpi.close.Rslaves() did not complete – it never returned and the terminal was left hanging.

Answer 2

I experienced similar challenges. I landed on this solution where libopenmpi-dev was the secret.

sudo apt-get install openmpi-common openmpi-bin libopenmpi-dev r-base
sudo apt-get install r-cran-rmpi
sudo su
R
install.packages("doMPI", dependencies=TRUE)