Hi Simon, Thanks for the reply. Using the Sys.getenv() function, I get the following paths: ================== LD_LIBRARY_PATH "/home/bs/R-2.14.0/lib64/R/lib:/usr/local/lib64:/usr/X11R6/lib64:/home/bs/openmpi-1.4.4/lib:" R_HOME "/home/bs/R-2.14.0/lib64/R" =================== Which seem to be ok. On Sun, Dec 4, 2011 at 5:35 PM, Simon Urbanek wrote: > Brian, > > I don't think .bashrc/.bash_profile has anything to do with it - I'm not > sure how you start MPI on the cluster, but typically .bashrc is only for > the login session, it's not used for non-interactive sessions. Check the > LD_LIBRARY_PATH value in R (via Sys.getenv()) on the cluster to make sure > it is actually set properly. Note that probably the most reliable way is to > either set it using Sys.setenv() or edit etc/ldpaths in $R_HOME. > > Cheers, > Simon > > > On Dec 4, 2011, at 2:54 PM, Brian Smith wrote: > > > Hi Simon, > > > > Thanks for the response. My .bash_profile is: > > ========================== > > > > # .bash_profile > > > > # Get the aliases and functions > > if [ -f ~/.bashrc ]; then > > . ~/.bashrc > > fi > > > > # User specific environment and startup programs > > > > PATH=$PATH:$HOME/openmpi-1.4.4/bin/ > > > > export LD_LIBRARY_PATH="/home/bs/openmpi-1.4.4/lib:$LD_LIBRARY_PATH" > > > > > > export PATH > > unset USERNAME > > > > ======================= > > > > On changing the PATH and restarting the shells and executing the R > script, I still get the following error: > > > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object > '/home/bs/R-2.14.0/lib64/R/library/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 > > > > > > :( > > > > > > > > > > > > > > On Sun, Dec 4, 2011 at 2:33 PM, Simon Urbanek < > simon.urbanek@r-project.org> wrote: > > > > On Dec 4, 2011, at 2:00 PM, Brian Smith wrote: > > > > > 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 ŚRmpi‚ > > > Execution halted > > > > > > > It seems that you don't have /home/bs/openmpi-1.4.4/lib (or wherever mpi > lives on the cluster) in LD_LIBRARY_PATH on the cluster. You probably want > something like > > export LD_LIBRARY_PATH="/home/bs/openmpi-1.4.4/lib:$LD_LIBRARY_PATH" > > > > Also note that R_HOME is ignored by R - it is overridden by the R script > regardless so there is no point setting it in .bashrc (unless it's for some > other scripts...) > > > > Cheers, > > Simon > > > > > > > > > Other details of my attempts at the installation are given below. Any > help > > > would be greatly appreciated! > > > > > > many thanks! > > > > > > PS: I have read the previous threads on difficulties in installation of > > > Rmpi and have tried to follow the advice/example... > > > > > > > > > > > > > > > > > > ####################################################### > > > #### INSTALL RMPI WITH INTERACTIVE R SESSION ##### > > > ####################################################### > > > > > > [bs@server library]$ 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 > > > Ś/home/bs/R/x86_64-unknown-linux-gnu-library/2.14‚ > > > (as Ślib‚ is unspecified) > > > inferring 'repos = NULL' from the file name > > > * installing *source* package ŚRmpi‚ ... > > > 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 ŚRmpi‚ > > > 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/ > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > R-sig-hpc mailing list > > > R-sig-hpc@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc > > > > > > [[alternative HTML version deleted]]