[R-sig-hpc] locating mpi directories for RMPI installation

Dirk Eddelbuettel edd at debian.org
Thu Sep 19 16:19:13 CEST 2013

On 19 September 2013 at 08:40, Ben Weinstein wrote:
| Hi all,
| I'm trying to install Rmpi locally on NSF Xsede stampede cluster.

Can you explain in plain English what a 'NSF Xsede stampede cluster' is? Is
it Linux based? If so, what distro?  What compiler does it use?
| I'm following the layout as given here:
| http://www.stats.uwo.ca/faculty/yu/Rmpi/
| However, i can't seem to find exactly where the mpi lib and include
| directories are stored.

There are two things here.  

You need to understand first which MPI version you have (typically: Open MPI,
or MPICH) and where it is stored. At this point I recommend a very simple
plain C program (no R) to just include MPI headers and library and get it
work, and run across more than one machine.  At this point we have MPI.

Next is to get into to work with Rmpi.  In its configure script, a simple
shell script loop runs over a number of candidate locations. Yours are
seemingly not part of this; so you need to adjust this. It is not hard, but
involves a few minutes with a new 'language' (ie autoconf).  We can help.
But try to get the first step sorted out first, please.

| i've tried locate mpi.h, which returned hundreds of header files and locate
| mpi/lib finds the python mpi files. Any suggestions for how to go about
| finding the directories i need? The admins have been extremely unhelpful.

If it works for Python you could learn from Python what it does during the
build process.  


| I've looked under /usr/lib64 and explored all obvious options, but it may
| be named something i'm not familiar with.
| Thanks for your help
| Ben Weinstein
| -- 
| Ben Weinstein
| PhD Candidate
| Ecology and Evolution
| Stony Brook University
| http://benweinstein.weebly.com/
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Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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