R devel - Oct 2011 - R CMD INSTALL configure.args and CC customization

One way to deal with this is to install R itself with mpicc. Then all 
packages are installed with mpicc and get the required MPI libraries and 
includes by default. I have done this with R-2.13.0 on an Opteron 
cluster running CentOS-5 a while ago and so far it has worked out great.

I crosspost to r-sig-hpc and welcome others to comment if there are 
potential downsides to this solution.

George

> Michael Spiegel michael.m.spiegel at gmail.com 
>
<mailto:r-devel%40r-project.org?Subject=Re%3A%20%5BRd%5D%20R%20CMD%20INSTALL%20configure.args%20and%20CC%20customization&In-Reply-To=%3CCANwu5-rGUYrC73vRo04GJCdW_ZQerycbVU4K_2Dun1ytqNXQ7g%40mail.gmail.com%3E>
> /Fri Sep 9 20:40:42 CEST 2011/ 
> I am running into the following issue that has been previously
> reported on the R-devel mailing list. The short version is that I'm
> writing a package for MPI, and I'd like to change CC and SHLIB_LD to
> "mpicc". Trying to change them in Makevars.in has no effect,
because
> the values are clobbered by /etc/R/Makeconf. Will the following
> changes to Makeconf.in introduce any problems?
>
> --Michael
-- 
George Ostrouchov
Statistics and Data Sciences Group
Computer Science and Mathematics Division
Oak Ridge National Laboratory
(865) 574-3137  http://www.csm.ornl.gov/~ost


	[[alternative HTML version deleted]]

Thanks! This is a possible solution, but I would argue not a preferable
solution. I'd advocate a mechanism that provides transparent support for
MPI, analogous to the way that R 2.13.0 and upwards provides transparent support
for OpenMP. Expressing a personal opinion, I would stress the importance of
providing both shared memory and message parallel parallelism out-of-the-box in
the R interpreter. To use OpenMP or MPI the user would need to have runtime
libraries pre-installed on their system. This patch would make it easier for a
library to auto-detect an MPI implementation, assuming mpicc is in the path.

My initial post on r-devel had a bug, sorry about that. I've posted a new
patch on r-sig-hpc that behaves as intended. It is available here:
https://stat.ethz.ch/pipermail/r-sig-hpc/2011-September/001104.html.

-----Original Message-----
From: r-sig-hpc-bounces at r-project.org [mailto:r-sig-hpc-bounces at
r-project.org] On Behalf Of George Ostrouchov
Sent: Tuesday, October 11, 2011 9:59 AM
To: michael.m.spiegler at gmail.com
Cc: r-sig-hpc at r-project.org; r-devel at r-project.org
Subject: Re: [R-sig-hpc] R CMD INSTALL configure.args and CC customization

One way to deal with this is to install R itself with mpicc. Then all packages
are installed with mpicc and get the required MPI libraries and includes by
default. I have done this with R-2.13.0 on an Opteron cluster running CentOS-5 a
while ago and so far it has worked out great.

I crosspost to r-sig-hpc and welcome others to comment if there are potential
downsides to this solution.

George

> Michael Spiegel michael.m.spiegel at gmail.com 
> <mailto:r-devel%40r-project.org?Subject=Re%3A%20%5BRd%5D%20R%20CMD%20I
> NSTALL%20configure.args%20and%20CC%20customization&In-Reply-To=%3CCANw
> u5-rGUYrC73vRo04GJCdW_ZQerycbVU4K_2Dun1ytqNXQ7g%40mail.gmail.com%3E>
> /Fri Sep 9 20:40:42 CEST 2011/
> I am running into the following issue that has been previously 
> reported on the R-devel mailing list. The short version is that I'm 
> writing a package for MPI, and I'd like to change CC and SHLIB_LD to 
> "mpicc". Trying to change them in Makevars.in has no effect,
because
> the values are clobbered by /etc/R/Makeconf. Will the following 
> changes to Makeconf.in introduce any problems?
>
> --Michael
--
George Ostrouchov
Statistics and Data Sciences Group
Computer Science and Mathematics Division Oak Ridge National Laboratory
(865) 574-3137  http://www.csm.ornl.gov/~ost


	[[alternative HTML version deleted]]

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