On Mon, 14 Mar 2011, Brian Smith wrote:
Hi,
I was trying to install the package Rmpi on a hpc cluster running SGE. The
Which is what? (If Sun Grid Engine, not relevant and it is your
unstated OS that we needed to know. Not just 'Linux', but the
precise distro.))
Please do note the posting guide: your R is several versions old, for
example, and this was an R-devel question (most questions about
installing wrapper packages will be, since they are almost nothing to
do with the R language).
The symptoms you post are those of finding a 32-bit libmpi on a 64-bit
install. Please consult the documentation for Rmpi and set the RMPI*
environment variables appropriately for your installed 64-bit libmpi
(regratably Rmpi does not use the recommended methods and so often
needs to be overridden). Also, most modern OSes use OpenMPI and not
lam, so see if you can use the former.
One guess is that it needs to be told to look in /usr/lib64/lam.
OTOH, for x86_64 Fedora 14 I am using
setenv RMPI_INCLUDE /usr/include/openmpi-x86_64
setenv RMPI_LIB_PATH /usr/lib64/openmpi/lib
setenv RMPI_TYPE OPENMPI
command, and the sessionInfo() is as follows:
===========================================
install.packages("Rmpi",dependencies=TRUE)
also installing the dependency ?rsprng?
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz'
Content type 'application/x-gzip' length 35916 bytes (35 Kb)
opened URL
==================================================
downloaded 35 Kb
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/Rmpi_0.5-9.tar.gz'
Content type 'application/x-gzip' length 87953 bytes (85 Kb)
opened URL
==================================================
downloaded 85 Kb
* installing *source* package ?rsprng? ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ANSI C... none needed
Try to find sprng.h ...
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sprng.h usability... no
checking sprng.h presence... no
checking for sprng.h... no
Cannot find sprng 2.0 header file.
ERROR: configuration failed for package ?rsprng?
* removing ?/home/bs/R_home/R-2.11.1/library/rsprng?
Well, first you need to install sprng-2.0b
* installing *source* package ?Rmpi? ...
checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr/lib/lam and it is LAM
Trying to find mpi.h ...
Found in /usr/lib/lam/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib/lam/lib
Try to find liblam.so ...
Found liblam in /usr/lib/lam/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include -fpic -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o
conversion.o internal.o -L/usr/lib/lam/lib -lmpi -llam -lutil -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so when searching
for -lmpi
/usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.a when searching
for -lmpi
/usr/bin/ld: cannot find -lmpi
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
ERROR: compilation failed for package ?Rmpi?
* removing ?/home/bs/R_home/R-2.11.1/library/Rmpi?
The downloaded packages are in
?/tmp/RtmpShmM5e/downloaded_packages?
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("Rmpi", dependencies = TRUE) :
installation of package 'rsprng' had non-zero exit status
2: In install.packages("Rmpi", dependencies = TRUE) :
installation of package 'Rmpi' had non-zero exit status
sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.11.1
Is there something else that I need to do to install this, and other
parallel R packages?
thanks!
[[alternative HTML version deleted]]
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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