[R-sig-hpc] trouble installing Rmpi

Tue Nov 30 02:46:44 CET 2010

Thanks, Kevin and Dirk, for the help you've given me.  I uninstalled (COMPLETELY unistalled) all of R, and then re-installed Rmpi, using the simple command Dirk had recommended: sudo apt-get install r-cran-rmpi.I am no longer getting errors when entering the script "library(Rmpi)", but I'm still having trouble associated with dyn.load().  I haven't found clarity by reading the documentation.  Maybe someone can at least help me focus my search among what I've looked at already: makefile flags/options, installation of the fortran compiler software (Intel Composer, latest edition), R manuals.
Here's the problem I'm having:

> library(Rmpi)
> library(snow)
> setwd("/home/john/LREWI15_TIO")
> dyn.load("./swat2009_i64_calibrate.so")
Error in dyn.load("./swat2009_i64_calibrate.so") : 
  unable to load shared library '/home/john/LREWI15_TIO/./swat2009_i64_calibrate.so':
  libifport.so.5: cannot open shared object file: No such file or directory
> 

I've also attached the makefile I used to generate swat2009_i64_calibrate.so, if it helps.

Any guidance would be much appreciated.  

John Joseph

P.S.  Thanks for the added clarity regarding what worked for you for Rmpi.  If you think the instructions are still relevant to my new situation, I would be happy to still try to work them out.  But I have a little fear of digging myself into a deeper hole, so I'll need to ask you a couple of things first.

-----Original Message-----
From: r-sig-hpc-bounces at r-project.org on behalf of Kevin.Buckley at ecs.vuw.ac.nz
Sent: Sun 11/21/2010 4:11 PM
To: r-sig-hpc at r-project.org
Subject: Re: [R-sig-hpc] trouble installing Rmpi

>
> Thanks for your help, Kevin.
>
> These instructions look very helpful, and I've begun studying them.
> I'm such a newbie that I understand little of it.  I'm learning a
> little by reading the documentation, but I'm just not getting all of
> it.  It seems that the idea is to make a file called "Makevars" that
> is stored in certain directories.  I did the first three lines, but
> can't find where Makevars went...Well, I did find a Makevars and
> Makevars.win file several directories deep into the R directory that
> was already there, but I don't know if these two files were created
> by the 3 lines I wrote or were already there...Anyway, as you can
> see, I'm struggling with the basics.
>
> Another thing is that when I go to etc/profile.d I do not find
> openmpi.sh within it.
>
> In any case, I appreciate this help you gave.
>
> John Joseph

hey John,

it seems as though I forgot to copy the list into my "advice/experience"
so am now doing so (see below for original)

In respect of the issues you raise, the /etc/profile.d/openmpi.sh
is a LOCAL thing, which merely gives the users, at login time, the
correct environment (paths, etch) for OpenMPI.

Chances are that that's being handled for you in some way because
you installed OpenMPI from a package.

The inclusion of that line there was just me running things explicitly
as a "hedge" against a user who might not have had such an environment
set up. Apologies, I should have tailored the commands to remove the
"local" bits.

As to the R Makevars file I referred to, again the syntax of my
suggestions is creating it as though it was not there (I should
have, of course, suggested checking to see if the user account
being used for the installation already had such a file as my
"instructions" trample all over it).

That ties in with the note about removing the Makevars file
afterwards: if you already had one and moved it out of the
way, or otherwise appended the variables that Rmpi seemed to
need, you'ld want to simply remove them or replace the old file,
rather than bin it.

But basically, you won't see that file ~/.R/Makevars (you might
not even see the directory ~/.R) unless it had already been created
beneath the home directory of the user doing the installtion.

Kevin

PS

Just in case it is something you have not seen before, the ~ (tilde)
character at the start of the path to the Makevears referred to
is a shorthand for the home directory of the user, in case the user
doing the install.

> -----Original Message-----
> From: Kevin.Buckley at ecs.vuw.ac.nz
> Sent: Thu 11/18/2010 3:35 PM
> To: John Joseph
> Subject: Re: [R-sig-hpc] trouble installing Rmpi
>
>
> Not directly addressing your install methodology issues, John, but
>
>  "the way it worked for me"
>
> was to install from outside of R itself, but still using R, so as
> to have some control over the paths to our OpenMPI installtion.
>
> Note the use of the R "Makevars" file to override some
> of the defaults R might be picking up if left to its own
> devices:
>
> The "mpicc" is the OpenMPI-aware C compiler wrapper
>
> You might need to tweak the paths for Ubuntu's OpenMPI package
> setup.
>
> This was for Rmpi_0.5-8.tar.bz2
>
> mkdir ~/.R
> echo CC=mpicc > ~/.R/Makevars
> echo SHLIB_LD=mpicc >> ~/.R/Makevars
> . /etc/profile.d/openmpi.sh
>
> /opt/R/bin/R CMD INSTALL \
>  --library=/opt/Rlibs \
>  /path/to/Rmpi_0.5-8.tar.bz2 \
>  --configure-args=--with-Rmpi-type=OPENMPI  \
>  --configure-args=--with-Rmpi-libpath=/opt/openmpi/1.4.2/lib \
>  --configure-args=--with-Rmpi-include=/opt/openmpi/1.4.2/include
>
> Oh yeah, once you have built the package, (assuming you do!),
> remove the file
>
>  ~/.R/Makevars
>
> unless you want all future R packages you build by hand, to be built
> against OpenMPI that is !
>
> Kevin

-- 
Kevin M. Buckley                                  Room:  CO327
School of Engineering and                         Phone: +64 4 463 5971
 Computer Science
Victoria University of Wellington
New Zealand

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