From mwkimpel at gmail.com  Thu Dec 20 04:38:35 2007
From: mwkimpel at gmail.com (Mark W Kimpel)
Date: Wed, 19 Dec 2007 22:38:35 -0500
Subject: [Rd] Problem compiling R 3.6.1 on POWER 570 system
In-Reply-To: <47697CB9.5020407@hms.harvard.edu>
References: <47697CB9.5020407@hms.harvard.edu>
Message-ID: <4769E3BB.20703@gmail.com>

Mark,

My sysadmin has helped me install R on our Power cluster. This is not my 
area of expertise, but I will pass along his directions, which got me up 
and running:

To quote him, "Our machine, BigRed runs SuSE Linux Enterprise Server 9, 
Service Pack 3.  The OS
is 64-bit, but there are 32-bit compatibility libraries, and many
(perhaps most) of the system utilities are 32-bit.  The processors on
the user and compute blades are PowerPC 970MP (dual-core)."

Here is the script I used, your install directories and location of 
x-libraries of course may need to be changed.

Good luck and let the list know what ends up working for you.
Mark Kimpel

cd ~/R_HOME
wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.bz2
tar -xjvf R-devel.tar.bz2
cd ~/R_HOME/R-devel
mkdir R-build
cd R-build
LDFLAGS=-m64 FFLAGS="-m64 -mpowerpc64" FCFLAGS="-m64 -mpowerpc64" 
CFLAGS="-m64 -mpowerpc64" ../configure 
--prefix='/N/hd03/mkimpel/BigRed/R_HOME/R-devel/R-build' 
--x-libraries=/usr/X11R6/lib64
make
make install

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)

mwkimpel<at>gmail<dot>com

******************************************************************


Mark Komarinski wrote:
> I've for a RHEL 4 box on a P570 system.  My end user wants to have a 
> 64-bit version of R compiled due to the large amount of memory they 
> require (this image has 16GB allocated to it).
> 
> I can compile R fine in 32-bit mode, but it can't use more than 2.4GB of 
> RAM before it falls over and dies.
> 
> Compiling in 64-bit mode for POWER systems "should" be as easy as adding 
> a CFLAGS="-m64" FFLAGS="-m64" ./configure --without-x .
> 
> It's not, and unfortunately I'm at a loss to what the problem is. 
> Here's the last few lines of the above configure command:
> 
> checking for Fortran 77 libraries of g77...  -L/usr/local/lib64 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6/64 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6/../../../../lib64 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6/../../.. -L/lib/../lib64 
> -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s_64
> checking how to get verbose linking output from gcc -std=gnu99... -v
> checking for C libraries of gcc -std=gnu99...  -L/usr/local/lib64 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6/64 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6/../../../../lib64 
> -L/usr/lib/gcc/ppc64-redhat-linux/3.4.6/../../.. -L/lib/../lib64 
> -L/usr/lib/../lib64 -lgcc_s_64
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... lower case, underscore, 
> extra underscore
> checking whether g77 appends underscores to external names... yes
> checking whether g77 appends extra underscores to external names... yes
> checking whether mixed C/Fortran code can be run... configure: WARNING: 
> cannot run mixed C/Fortran code
> configure: error: Maybe check LDFLAGS for paths to Fortran libraries?
> 
> Here's what looks to be the relevant part from config.log:
> configure:32383: checking whether mixed C/Fortran code can be run
> /usr/bin/ld: skipping incompatible 
> /usr/lib/gcc/ppc64-redhat-linux/3.4.6/libgcc_s_64.so when searching for 
> -lgcc_s_64
> /usr/bin/ld: skipping incompatible 
> /usr/lib/gcc/ppc64-redhat-linux/3.4.6/libgcc_s_64.so when searching for 
> -lgcc_s_64
> /usr/bin/ld: cannot find -lgcc_s_64
> collect2: ld returned 1 exit status
> configure:32447: WARNING: cannot run mixed C/Fortran code
> configure:32449: error: Maybe check LDFLAGS for paths to Fortran libraries?
> 
> This implies that configure is compiling the code in 32 bit mode (which 
> is why it's skipping libgcc_s_64.o
> 
> I guess my questions are: has anyone compiled this for this system?  And 
> if so, how did you do it?
> 
> -Mark
>



[Rd] Problem compiling R 3.6.1 on POWER 570 system
Mark W Kimpel