Dear all, I have used the Rmpi package many times before however this time I've installed it as I always do with openMPI tar.gz file direct from the website. I'm installing on my ubuntu 8.10. Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux All i get is:> library(Rmpi)Segmentation fault :~$ Which dumps me back into the shell, and doens't give me much to work with. I've included my install of Rmpi that went fine as far as I could see. Is this a openMPI problem or Rmpi or even an R problem? Any help would be great. Also is there a way beside 'make test' to test my install of openMPI? Cheers, Paul ------Rmpi install -------------------------- ~$ sudo R CMD INSTALL Rmpi_0.5-6.tar.gz * Installing to library '/usr/local/lib64/R/library' * 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 I am here /usr/local and it is OpenMPI Try to find mpi.h ... Found in /usr/local/include Try to find libmpi.so or libmpich.a Found libmpi in /usr/local/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/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c conversion.c -o conversion.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/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 RegQuery.o Rmpi.o -L/usr/local/lib -lmpi -lutil -lpthread -fPIC ** 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)
Dear all, I have used the Rmpi package many times before however this time I've installed it as I always do with openMPI tar.gz file direct from the website. I'm installing on my ubuntu 8.10, R version 2.8.1. Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux All i get is:> library(Rmpi)Segmentation fault :~$ Which dumps me back into the shell, and doens't give me much to work with. I've included my install of Rmpi that went fine as far as I could see. Is this a openMPI problem or Rmpi or even an R problem? Any help would be great. Also is there a way beside 'make test' to test my install of openMPI? Cheers, Paul ------Rmpi install -------------------------- ~$ sudo R CMD INSTALL Rmpi_0.5-6.tar.gz * Installing to library '/usr/local/lib64/R/library' * 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 I am here /usr/local and it is OpenMPI Try to find mpi.h ... Found in /usr/local/include Try to find libmpi.so or libmpich.a Found libmpi in /usr/local/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/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c conversion.c -o conversion.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/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 RegQuery.o Rmpi.o -L/usr/local/lib -lmpi -lutil -lpthread -fPIC ** 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)
Dear all, I have used the Rmpi package many times before however this time the installation doesn't work :(. I've installed it as I always do with openMPI tar.gz file direct from the website. I'm installing on my ubuntu 8.10, R version 2.8.1. Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux All i get is:> library(Rmpi)Segmentation fault :~$ Which dumps me back into the shell, and doesn't give me much to work with. I've included my install of Rmpi that went fine as far as I could see. Is this a openMPI problem or Rmpi or even an R problem? Any help would be great. Also is there a way beside 'make test' to test my install of openMPI? Cheers, Paul ------Rmpi install -------------------------- ~$ sudo R CMD INSTALL Rmpi_0.5-6.tar.gz * Installing to library '/usr/local/lib64/R/library' * 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 I am here /usr/local and it is OpenMPI Try to find mpi.h ... Found in /usr/local/include Try to find libmpi.so or libmpich.a Found libmpi in /usr/local/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/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c conversion.c -o conversion.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/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 RegQuery.o Rmpi.o -L/usr/local/lib -lmpi -lutil -lpthread -fPIC ** 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) [[alternative HTML version deleted]]