[R-sig-hpc] Rmpi installation with openmpi (on local directory)

Simon Urbanek simon.urbanek at r-project.org
Sun Dec 4 23:35:26 CET 2011 

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:$LD_LIBRARY_PATH"
> 
> 
> export PATH
> unset USERNAME
> 
> =======================
> 
> On changing the PATH and restarting the shells and executing the R script, I still get the following error:
> 
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object '/home/bs/R-2.14.0/lib64/R/library/Rmpi/libs/Rmpi.so':
>   libmpi.so.0: cannot open shared object file: No such file or directory
> Error: package/namespace load failed for ‘Rmpi’
> Execution halted
> 
> 
> :(
> 
> 
> 
> 
> 
> 
> On Sun, Dec 4, 2011 at 2:33 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> 
> On Dec 4, 2011, at 2:00 PM, Brian Smith wrote:
> 
> > Hi,
> >
> > I was trying to install the Rmpi package on a cluster (running SGE). I
> > first installed the openmpi package in my directory, and then installed the
> > Rmpi package (after downloading tarball from cran) by an interactive R
> > session.
> >
> > If I load Rmpi within an R interactive session everything seems to be fine.
> > However, if I try to use the SGE then I get errors:
> >
> > Error in dyn.load(file, DLLpath = DLLpath, ...) :
> >  unable to load shared object
> > '/home/bs/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs/Rmpi.so':
> >  libmpi.so.0: cannot open shared object file: No such file or directory
> > Error: package/namespace load failed for ŒRmpi‚
> > Execution halted
> >
> 
> It seems that you don't have /home/bs/openmpi-1.4.4/lib (or wherever mpi lives on the cluster) in LD_LIBRARY_PATH on the cluster. You probably want something like
> export LD_LIBRARY_PATH="/home/bs/openmpi-1.4.4/lib:$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 at server library]$ cd ~/R-2.14.0/bin
> > [bs at 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
> > Œ/home/bs/R/x86_64-unknown-linux-gnu-library/2.14‚
> > (as Œlib‚ is unspecified)
> > inferring 'repos = NULL' from the file name
> > * installing *source* package ŒRmpi‚ ...
> > 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 ŒRmpi‚
> > Execution halted
> >
> > ##############################
> > ############# R CMD ldd  Rmpi.so  ######
> > ##############################
> >
> > [bs at 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 at server Rmpi]$
> >
> >
> >
> > ########################
> > ######## added to  .bashrc file #######
> > #########################
> >
> > R_HOME=$HOME/R/x86_64-unknown-linux-gnu-library/2.14/
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > R-sig-hpc at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
> 
>

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