Hi,
I was trying to install the package Rmpi on a hpc cluster running SGE. The
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
* 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!
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