Rmpi cannot load shared libraries as root user

Question

I have a problem with Rmpi ​​in which I try to download it and I get this error message:

> library('Rmpi') Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/lib64/R/library/Rmpi/libs/Rmpi.so': libmpi.so.0: cannot open shared object file: No such file or directory In addition: Warning message: .Last.lib failed in detach() for 'Rmpi', details: call: dyn.unload(file.path(libpath, "libs", paste("Rmpi", .Platform$dynlib.ext, error: dynamic/shared library '/usr/lib64/R/library/Rmpi/libs/Rmpi.so' was not loaded Error in library("Rmpi") : .First.lib failed for 'Rmpi' 

This error does not occur if I am logged in as root.

This is not a permissions issue. I checked permissions for libmpi.so.0:

 [meehan@cnl10 /]$ ll /usr/lib64/lam/lib/ total 7.4M -rw-r--r-- 1 root root 207 May 25 2008 lam.module -rw-r--r-- 1 root root 885K May 25 2008 liblam.a -rw-r--r-- 1 root root 361K May 25 2008 liblamf77mpi.a lrwxrwxrwx 1 root root 21 Apr 12 2010 liblamf77mpi.so -> liblamf77mpi.so.0.0.0 lrwxrwxrwx 1 root root 21 Apr 12 2010 liblamf77mpi.so.0 -> liblamf77mpi.so.0.0.0 -rwxr-xr-x 1 root root 73K May 25 2008 liblamf77mpi.so.0.0.0 -rw-r--r-- 1 root root 2.2M May 25 2008 liblammpi++.a -rw-r--r-- 1 root root 509K May 25 2008 liblammpio.a lrwxrwxrwx 1 root root 20 Apr 12 2010 liblammpi++.so -> liblammpi++.so.0.0.0 lrwxrwxrwx 1 root root 20 Apr 12 2010 liblammpi++.so.0 -> liblammpi++.so.0.0.0 -rwxr-xr-x 1 root root 167K May 25 2008 liblammpi++.so.0.0.0 lrwxrwxrwx 1 root root 15 Apr 12 2010 liblam.so -> liblam.so.0.0.0 lrwxrwxrwx 1 root root 15 Apr 12 2010 liblam.so.0 -> liblam.so.0.0.0 -rwxr-xr-x 1 root root 332K May 25 2008 liblam.so.0.0.0 -rw-r--r-- 1 root root 2.2M May 25 2008 libmpi.a lrwxrwxrwx 1 root root 15 Apr 12 2010 libmpi.so -> libmpi.so.0.0.0 lrwxrwxrwx 1 root root 15 Apr 12 2010 libmpi.so.0 -> libmpi.so.0.0.0 -rwxr-xr-x 1 root root 655K May 25 2008 libmpi.so.0.0.0 

And Rmpi.so:

 [meehan@cnl10 /]$ ll /usr/lib64/R/library/Rmpi/libs/ total 108K -rwxr-xr-x 1 root root 104K Jan 20 2011 Rmpi.so 

Anyway, I run R as sudo.

Relevant system information: -Linux distribution: CentOS 5.5 -R version: 2.11.1 (2010-05-31) -Rmpi version: 0.5-8 -MPI implementation - openmpi

 [meehan@cnl10 /]$ echo $LD_LIBRARY_PATH /opt/lib:/opt/open-mpi/tcp-`gnu41/lib:/opt/intel/mkl/10.2/lib/em64t:/opt/intel/fce/11.1/lib:/opt/intel/cce/11.1/lib:` 

Any help would be appreciated!

Answer 1

The problem here is that by default, OpenMPI does not register the library catalog with the system linker. That's why some installation guides recommend that you put your directories in your LD_LIBRARY_PATH variable so that libraries can be found at runtime. However, “adding directories to LD_LIBRARY_PATH” should be done every time a new shell is loaded, so these guides suggest putting it in ~/.bashrc or the like so that this setting is restored every time you log in.

However, the ~/.bashrc (or ~/.profile or any such) is the setting for the user. Assuming that one of them is registered as root when installing openmpi and Rmpi, etc., which seems likely, this means that adding to these user files will only set library paths when working as root, and not like a regular runtime user.

The fix, in general, is to tell the linker where these files can be found. On my own system running CentOS 7, OpenMPI 1.10.0 (using RPM Scientific Linux), R 3.2.3, and Rmpi ​​0.6-5, this happens when I cannot set the library path:

 [dchurch@workstation ~]$ R -q -e "library('Rmpi')" > library('Rmpi') Error : .onLoad failed in loadNamespace() for 'Rmpi', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/usr/lib64/R/library/Rmpi/libs/Rmpi.so': libmpi.so.12: cannot open shared object file: No such file or directory Error: package or namespace load failed for 'Rmpi' Execution halted 

If I temporarily set the linker path with a temporary variable, it works for this call:

 [dchurch@workstation ~]$ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib R -q -e "library('Rmpi')" > library('Rmpi') > > 

However, to make this change permanent, the best way to do this is to register the openmpi library directory with the system builder itself, create a new file in /etc/ld.so.conf.d and run ldconfig like this:

 [dchurch@workstation ~]$ sudo sh -c 'echo /usr/lib64/openmpi/lib > /etc/ld.so.conf.d/openmpi.conf; ldconfig' [dchurch@workstation ~]$ R -q -e "library('Rmpi')" > library('Rmpi') > > 

Once you have done this, Rmpi ​​should be downloaded for any user, regardless of the environment variables.