Hi,

I was trying to install the Rmpi package on a cluster (running SGE). I
first installed the openmpi package in my directory, and then installed the
Rmpi package (after downloading tarball from cran) by an interactive R
session.

If I load Rmpi within an R interactive session everything seems to be fine.
However, if I try to use the SGE then I get errors:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/home/bs/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs/Rmpi.so':
  libmpi.so.0: cannot open shared object file: No such file or directory
Error: package/namespace load failed for ‘Rmpi’
Execution halted

Other details of my attempts at the installation are given below. Any help
would be greatly appreciated!

many thanks!

PS: I have read the previous threads on difficulties in installation of
Rmpi and have tried to follow the advice/example...





#######################################################
####         INSTALL RMPI  WITH INTERACTIVE R SESSION        #####
#######################################################

[bs@server library]$ cd ~/R-2.14.0/bin
[bs@server bin]$ ./R
>
install.packages("/home/bs/R-2.14.0/library/Rmpi_0.5-9.tar.gz",configure.args=c("--with-Rmpi-include=/home/bs/openmpi-1.4.4/include","--with-Rmpi-libpath=/home/bs/openmpi-1.4.4/lib","--with-Rmpi-type=OPENMPI"))
Installing package(s) into
‘/home/bs/R/x86_64-unknown-linux-gnu-library/2.14’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from the file name
* installing *source* package ‘Rmpi’ ...
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** Creating default NAMESPACE file
** libs
gcc -std=gnu99 -I/home/bs/R-2.14.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/home/bs/openmpi-1.4.4/include  -DMPI2 -DOPENMPI
-I/usr/local/include    -fpic  -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/home/bs/R-2.14.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/home/bs/openmpi-1.4.4/include  -DMPI2 -DOPENMPI
-I/usr/local/include    -fpic  -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/home/bs/R-2.14.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/home/bs/openmpi-1.4.4/include  -DMPI2 -DOPENMPI
-I/usr/local/include    -fpic  -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/home/bs/R-2.14.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/home/bs/openmpi-1.4.4/include  -DMPI2 -DOPENMPI
-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/home/bs/openmpi-1.4.4/lib -lmpi
installing to /home/bs/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Rmpi)
> library(Rmpi)
>
> mpi.spawn.Rslaves(nslaves=2)
        2 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 3 is running on: server
slave1 (rank 1, comm 1) of size 3 is running on: server
slave2 (rank 2, comm 1) of size 3 is running on: server
> x <- c(10,20)
> mpi.apply(x,runif)
[[1]]
 [1] 0.5279140 0.6070291 0.5367963 0.2028148 0.3930856 0.2121955 0.3994963
 [8] 0.4322645 0.6733323 0.4020272

[[2]]
 [1] 0.39267299 0.48316984 0.88169217 0.15594098 0.81789819 0.40163353
 [7] 0.25264554 0.52592001 0.72461786 0.16952091 0.52862589 0.05710565
[13] 0.48598241 0.34414770 0.62858189 0.42895010 0.88796806 0.93477003
[19] 0.82415421 0.73289008

>


############################
###### MY loadRmpi.R file #####
############################
library(snow)
library(Rmpi)
print('loaded...')

############################
###### eerror.out file   ##########
############################

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/home/bs/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs/Rmpi.so':
  libmpi.so.0: cannot open shared object file: No such file or directory
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/home/bs/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs/Rmpi.so':
  libmpi.so.0: cannot open shared object file: No such file or directory
Error: package/namespace load failed for ‘Rmpi’
Execution halted

##############################
############# R CMD ldd  Rmpi.so  ######
##############################

[bs@server Rmpi]$ R CMD ldd
~/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs/Rmpi.so
        libmpi.so.0 => /home/bs/openmpi-1.4.4/lib/libmpi.so.0
(0x0000002a95662000)
        libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a9582b000)
        libopen-rte.so.0 => /home/bs/openmpi-1.4.4/lib/libopen-rte.so.0
(0x0000002a95a65000)
        libopen-pal.so.0 => /home/bs/openmpi-1.4.4/lib/libopen-pal.so.0
(0x0000002a95bb0000)
        libdl.so.2 => /lib64/libdl.so.2 (0x0000002a95d03000)
        libnsl.so.1 => /lib64/libnsl.so.1 (0x0000002a95e06000)
        libutil.so.1 => /lib64/libutil.so.1 (0x0000002a95f1f000)
        libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a96022000)
        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a961a8000)
        /lib64/ld-linux-x86-64.so.2 (0x000000552aaaa000)
[bs@server Rmpi]$



########################
######## added to  .bashrc file #######
#########################

R_HOME=$HOME/R/x86_64-unknown-linux-gnu-library/2.14/

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