[Rd] R CMD INSTALL configure.args and CC customization

From: Paul Johnson <pauljohn32_at_gmail.com>
Date: Wed, 20 Jan 2010 13:31:07 -0600


Hi, everybody.

I hope the new year is treating you well.

In a Rocks Cluster Linux system (that's Centos 5.2 based), I have built R-2.10 and it runs well.

While fiddling with MPI libraries and R packages, I've noticed a few little wrinkles.

This comes as no surprise to the veteran R programmers, but let me share to the new guys the following gem:

There is a difference between . and -

Simple, and yet so vital!

install.packages inside R takes a period between "configure" and "args", as in "configure.args=", while in the shell, the same option specified to R CMD INSTALL wants a dash, as in "--configure-args=". The "period" versus the "hyphen" was killing me all morning!

When building Rmpi, I had to specify configure options to let R know which MPI library to use. I *tried* to avoid that by forcing the compiler to be "mpicc", not "gcc". I believe that if one uses mpicc, then the compiler really is gcc, but it is initiated with the INC and LIB dirs set so that the configure can find what it needs. But gcc seems to be deeply glued to R installation of packages.

I find various posts in the r-help list in which people claim this should work:

CC=mpicc R CMD INSTALL ...

but it doesn't make a difference for me. The compiler that gets used is gcc, no matter how many different ways I try to say it should be mpicc:

$ CC=mpicc R CMD INSTALL
--configure-args=--with-mpi=/usr/lib64/openmpi/1.2.7-gcc
--configure-vars=CC=mpicc Rmpi_0.5-8.tar.gz
Password:
* installing to library '/share/apps/lib/R/site-library' * installing *source* package 'Rmpi' ... checking for gcc... gcc -m64 -std=gnu99
checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables...
checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed Trying to find mpi.h ...
Found in /usr/lib64/openmpi/1.2.7-gcc/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /usr/lib64/openmpi/1.2.7-gcc/lib checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.2.7-gcc/include
-DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c RegQuery.c -o
RegQuery.o
gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.2.7-gcc/include
-DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rmpi.c -o Rmpi.o
gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.2.7-gcc/include
-DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c conversion.c -o
conversion.o
gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.2.7-gcc/include
-DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c internal.c -o
internal.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi/1.2.7-gcc/lib
-lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR

** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (Rmpi)
======================

The same effect (or lack thereof) can be had with configure.vars in install.packages:

> install.packages("Rmpi", configure.args="--with-mpi=/usr/lib64/openmpi/1.2.7-gcc", configure.vars="CC=mpicc") Warning in install.packages("Rmpi", configure.args = "--with-mpi=/usr/lib64/openmpi/1.2.7-gcc", :   argument 'lib' is missing: using '/share/apps/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.mirrors.hoobly.com/src/contrib/Rmpi_0.5-8.tar.gz' Content type 'application/x-gzip' length 87528 bytes (85 Kb) opened URL



downloaded 85 Kb

--

Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas



R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Wed 20 Jan 2010 - 19:34:37 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 20 Jan 2010 - 20:20:20 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive