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

[Lockwood, Glenn]

Err, it looks like I didn't see this second thread.

Ben, the easiest way is to just send an email to help at xsede.org and let them know what you need.  TACC might already have Rmpi installed on Stampede, and if they don't, they will do it for you.  If that fails, I can give you exact instructions on how to do it.  It's our job to do complicated software installs on our XSEDE machines so you don't have to :)

Glenn

On Sep 19, 2013, at 8:11 AM, Jonathan Olmsted <jolmsted at princeton.edu>
 wrote:

> B
> en, I'm going to respond to this same email instead of splitting it up over
> two threads.
> 
> Lots of information about the MPI installation is here:
> https://www.xsede.org/web/guest/tacc-stampede#appdev-compiling-mpi,
> assuming this is your machine. So, is it?
> 
> -Jonathan
> 
> 
> 
> -------------------------------------------------------------------------
> J.P. Olmsted
> 
> 029 Corwin (Office)
> 130 Corwin Hall (Mail)
> 
> Politics Department
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> 
> t: 609.258.6202
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> jolmsted at princeton.edu
> http://about.me/olmjo
> -------------------------------------------------------------------------
> 
> 
> On Thu, Sep 19, 2013 at 11:05 AM, Jonathan Olmsted
> <jolmsted at princeton.edu>wrote:
> 
>> B
>> en, let me just add that you should check to see if whatever version of
>> whatever MPI implementation you are using is managed by
>> http://modules.sourceforge.net/. That will be useful information when it
>> comes time for files to be in your path. After looking at
>> https://www.xsede.org/web/guest/tacc-stampede#overview, if that is the
>> machine you are using, they are clearly using modules to some extent.
>> 
>> -Jonathan
>> 
>> 
>> 
>> -------------------------------------------------------------------------
>> J.P. Olmsted
>> 
>> 029 Corwin (Office)
>> 130 Corwin Hall (Mail)
>> 
>> Politics Department
>> Princeton University
>> Princeton, NJ 08544
>> 
>> 
>> t: 609.258.6202
>> f: 609.258.1110
>> jolmsted at princeton.edu
>> http://about.me/olmjo
>> -------------------------------------------------------------------------
>> 
>> 
>> On Thu, Sep 19, 2013 at 10:19 AM, Dirk Eddelbuettel <edd at debian.org>wrote:
>> 
>>> 
>>> 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.
>>> 
>>> Dirk
>>> 
>>> |
>>> | 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/
>>> |
>>> |       [[alternative HTML version deleted]]
>>> |
>>> | _______________________________________________
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>>> | R-sig-hpc at r-project.org
>>> | https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>> 
>>> --
>>> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>>> 
>>> _______________________________________________
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>>> 
>> 
>> 
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