[R-sig-hpc] Problem with Rmpi and snow - makeCluster(type="MPI") not working
Rainer M Krug
r.m.krug at gmail.com
Mon Nov 24 17:59:29 CET 2008
On Mon, Nov 24, 2008 at 6:20 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> On 24 November 2008 at 16:57, Rainer M Krug wrote:
> | Sorry - posting reposted at R-sig-hpc
>
> (But pllease don't cross-post)
That's why I said sorry - forgotten about the new hpc list. No
crossposting intended.
>
> | > I managed tio install Rmpi and to load it, but I get the following
> | > errormessage when I try to create an MPI cluster and R hangs (no
> | > response):
> | >
> | > library(Rmpi)
> | > [head001:15781] mca: base: component_find: unable to open osc pt2pt:
> | > file not found (ignored)
>
> Hm, my reading of the error message is different from yours.
>
> I wouldn't be convinced that you managed to install Open MPI correctly. It
> may be worth trying to see if you can build and run a standard 'hello world'
> in C under MPI first.
According to the installation output, Rmpi installed correctly. See
below the procedure I used:
rkrug at head001:~/source> export MPI_ROOT=/usr/local/openmpi_sun/
rkrug at head001:~/source> R CMD INSTALL Rmpi_0.5-5.tar.gz
* Installing to library '/export/home/rkrug/R/x86_64-unknown-linux-gnu-library/2
.7'
* Installing *source* package 'Rmpi' ...
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 ISO C89... none needed
Try to find mpi.h ...
Found in /usr/local/openmpi_sun//include
Try to find libmpi.so or libmpich.a
Found libmpi in /usr/local/openmpi_sun//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/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lo
cal/openmpi_sun//include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -
g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lo
cal/openmpi_sun//include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -
g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lo
cal/openmpi_sun//include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -
g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lo
cal/openmpi_sun//include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -
g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o internal.o Reg
Query.o Rmpi.o -L/usr/local/openmpi_sun//lib -lmpi -lutil -lpthread -fPIC -L/u
sr/lib64/R/lib -lR
** R
** demo
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'Rmpi'
Formats: text html latex example
hosts text html latex
internal text html latex
mpi.abort text html latex
mpi.apply text html latex example
mpi.barrier text html latex
mpi.bcast text html latex
mpi.bcast.Robj text html latex
mpi.bcast.cmd text html latex
mpi.cart.coords text html latex example
mpi.cart.create text html latex example
mpi.cart.get text html latex example
mpi.cart.rank text html latex example
mpi.cart.shift text html latex example
mpi.cartdim.get text html latex example
mpi.comm text html latex example
mpi.comm.disconnect text html latex
mpi.comm.free text html latex
mpi.comm.inter text html latex
mpi.comm.set.errhandler text html latex
mpi.comm.spawn text html latex
mpi.const text html latex
mpi.dims.create text html latex example
mpi.exit text html latex
mpi.finalize text html latex
mpi.gather text html latex example
mpi.gather.Robj text html latex example
mpi.get.count text html latex
mpi.get.processor.name text html latex
mpi.get.sourcetag text html latex
mpi.info text html latex
mpi.init.sprng text html latex
mpi.intercomm.merge text html latex
mpi.parSim text html latex
mpi.parapply text html latex example
mpi.probe text html latex
mpi.realloc text html latex
mpi.reduce text html latex
mpi.remote.exec text html latex example
mpi.scatter text html latex example
mpi.scatter.Robj text html latex example
mpi.send text html latex example
mpi.send.Robj text html latex
mpi.sendrecv text html latex example
mpi.setup.rng text html latex
mpi.spawn.Rslaves text html latex example
mpi.universe.size text html latex
mpi.wait text html latex
** building package indices ...
* DONE (Rmpi)
rkrug at head001:~/source>
I also tried it with
rkrug at head001:~/source> export MPI_ROOT=/usr/local/openmpi_gnu/
but still the same problems.
But I will come back to your questions as soon as I managed to compile
the C_MPI example
Rainer
>
> | >> library(snow)
> | >> cl <- makeCluster(2, type = "MPI")
> | > Rscript execution error: No such file or directory
> | > Rscript execution error: No such file or directory
> | >
> | > I am using the following version:
>
> But which MPI library and version ?
>
> Dirk
>
> --
> Three out of two people have difficulties with fractions.
>
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Faculty of Science
Natural Sciences Building
Private Bag X1
University of Stellenbosch
Matieland 7602
South Africa
More information about the R-sig-hpc
mailing list