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

Simon Urbanek simon.urbanek at r-project.org
Sun Dec 4 20:33:37 CET 2011 

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/
> 
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> 
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