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<P><FONT SIZE=2>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.<BR>
Here's the problem I'm having:<BR>
<BR>
> library(Rmpi)<BR>
> library(snow)<BR>
> setwd("/home/john/LREWI15_TIO")<BR>
> dyn.load("./swat2009_i64_calibrate.so")<BR>
Error in dyn.load("./swat2009_i64_calibrate.so") :<BR>
unable to load shared library '/home/john/LREWI15_TIO/./swat2009_i64_calibrate.so':<BR>
libifport.so.5: cannot open shared object file: No such file or directory<BR>
><BR>
<BR>
I've also attached the makefile I used to generate swat2009_i64_calibrate.so, if it helps.<BR>
<BR>
Any guidance would be much appreciated. <BR>
<BR>
John Joseph<BR>
<BR>
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.<BR>
<BR>
-----Original Message-----<BR>
From: r-sig-hpc-bounces@r-project.org on behalf of Kevin.Buckley@ecs.vuw.ac.nz<BR>
Sent: Sun 11/21/2010 4:11 PM<BR>
To: r-sig-hpc@r-project.org<BR>
Subject: Re: [R-sig-hpc] trouble installing Rmpi<BR>
<BR>
><BR>
> Thanks for your help, Kevin.<BR>
><BR>
> These instructions look very helpful, and I've begun studying them.<BR>
> I'm such a newbie that I understand little of it. I'm learning a<BR>
> little by reading the documentation, but I'm just not getting all of<BR>
> it. It seems that the idea is to make a file called "Makevars" that<BR>
> is stored in certain directories. I did the first three lines, but<BR>
> can't find where Makevars went...Well, I did find a Makevars and<BR>
> Makevars.win file several directories deep into the R directory that<BR>
> was already there, but I don't know if these two files were created<BR>
> by the 3 lines I wrote or were already there...Anyway, as you can<BR>
> see, I'm struggling with the basics.<BR>
><BR>
> Another thing is that when I go to etc/profile.d I do not find<BR>
> openmpi.sh within it.<BR>
><BR>
> In any case, I appreciate this help you gave.<BR>
><BR>
> John Joseph<BR>
<BR>
hey John,<BR>
<BR>
it seems as though I forgot to copy the list into my "advice/experience"<BR>
so am now doing so (see below for original)<BR>
<BR>
In respect of the issues you raise, the /etc/profile.d/openmpi.sh<BR>
is a LOCAL thing, which merely gives the users, at login time, the<BR>
correct environment (paths, etch) for OpenMPI.<BR>
<BR>
Chances are that that's being handled for you in some way because<BR>
you installed OpenMPI from a package.<BR>
<BR>
The inclusion of that line there was just me running things explicitly<BR>
as a "hedge" against a user who might not have had such an environment<BR>
set up. Apologies, I should have tailored the commands to remove the<BR>
"local" bits.<BR>
<BR>
As to the R Makevars file I referred to, again the syntax of my<BR>
suggestions is creating it as though it was not there (I should<BR>
have, of course, suggested checking to see if the user account<BR>
being used for the installation already had such a file as my<BR>
"instructions" trample all over it).<BR>
<BR>
That ties in with the note about removing the Makevars file<BR>
afterwards: if you already had one and moved it out of the<BR>
way, or otherwise appended the variables that Rmpi seemed to<BR>
need, you'ld want to simply remove them or replace the old file,<BR>
rather than bin it.<BR>
<BR>
But basically, you won't see that file ~/.R/Makevars (you might<BR>
not even see the directory ~/.R) unless it had already been created<BR>
beneath the home directory of the user doing the installtion.<BR>
<BR>
Kevin<BR>
<BR>
PS<BR>
<BR>
Just in case it is something you have not seen before, the ~ (tilde)<BR>
character at the start of the path to the Makevears referred to<BR>
is a shorthand for the home directory of the user, in case the user<BR>
doing the install.<BR>
<BR>
<BR>
> -----Original Message-----<BR>
> From: Kevin.Buckley@ecs.vuw.ac.nz<BR>
> Sent: Thu 11/18/2010 3:35 PM<BR>
> To: John Joseph<BR>
> Subject: Re: [R-sig-hpc] trouble installing Rmpi<BR>
><BR>
><BR>
> Not directly addressing your install methodology issues, John, but<BR>
><BR>
> "the way it worked for me"<BR>
><BR>
> was to install from outside of R itself, but still using R, so as<BR>
> to have some control over the paths to our OpenMPI installtion.<BR>
><BR>
> Note the use of the R "Makevars" file to override some<BR>
> of the defaults R might be picking up if left to its own<BR>
> devices:<BR>
><BR>
> The "mpicc" is the OpenMPI-aware C compiler wrapper<BR>
><BR>
> You might need to tweak the paths for Ubuntu's OpenMPI package<BR>
> setup.<BR>
><BR>
> This was for Rmpi_0.5-8.tar.bz2<BR>
><BR>
> mkdir ~/.R<BR>
> echo CC=mpicc > ~/.R/Makevars<BR>
> echo SHLIB_LD=mpicc >> ~/.R/Makevars<BR>
> . /etc/profile.d/openmpi.sh<BR>
><BR>
> /opt/R/bin/R CMD INSTALL \<BR>
> --library=/opt/Rlibs \<BR>
> /path/to/Rmpi_0.5-8.tar.bz2 \<BR>
> --configure-args=--with-Rmpi-type=OPENMPI \<BR>
> --configure-args=--with-Rmpi-libpath=/opt/openmpi/1.4.2/lib \<BR>
> --configure-args=--with-Rmpi-include=/opt/openmpi/1.4.2/include<BR>
><BR>
> Oh yeah, once you have built the package, (assuming you do!),<BR>
> remove the file<BR>
><BR>
> ~/.R/Makevars<BR>
><BR>
> unless you want all future R packages you build by hand, to be built<BR>
> against OpenMPI that is !<BR>
><BR>
> Kevin<BR>
<BR>
--<BR>
Kevin M. Buckley Room: CO327<BR>
School of Engineering and Phone: +64 4 463 5971<BR>
Computer Science<BR>
Victoria University of Wellington<BR>
New Zealand<BR>
<BR>
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