Hi guys, I've spent a few days trying to install Rmpi with no luck. I originally tried using mpich, moved on to mpich2, and then to openmpi. I've gotten the furthest with openmpi, though am still running into this problem and can't figure it out. Can someone help!? Thanks so much in advanced.
I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the error at the bottom. link@Ubuntu12-04:~/Downloads$ R CMD INSTALL Rmpi_0.6-1.tar.gz --configure-args="--with-mpi=/usr/local/ --with-Rmpi-type=OPENMPI" * installing to library ‘/home/link/R/x86_64-pc-linux-gnu-library/2.15’ * installing *source* package ‘Rmpi’ ... ** package ‘Rmpi’ successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed Trying to find mpi.h ... Found in /usr/local//include Trying 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/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c RegQuery.c -o RegQuery.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c Rmpi.c -o Rmpi.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c conversion.c -o conversion.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c internal.c -o internal.o gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/local//lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR installing to /home/link/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded [Ubuntu12-04:03523] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_paffinity_hwloc: /usr/local/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol: opal_hwloc_topology (ignored) [Ubuntu12-04:03523] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_shmem_posix: /usr/local/lib/openmpi/mca_shmem_posix.so: undefined symbol: opal_shmem_base_output (ignored) [Ubuntu12-04:03523] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_hnp: /usr/local/lib/openmpi/mca_ess_hnp.so: undefined symbol: orte_timing_output (ignored) [Ubuntu12-04:03523] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_singleton: /usr/local/lib/openmpi/mca_ess_singleton.so: undefined symbol: orte_local_cpu_model (ignored) [Ubuntu12-04:03523] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_slurm: /usr/local/lib/openmpi/mca_ess_slurm.so: undefined symbol: orte_orted_exit_with_barrier (ignored) [Ubuntu12-04:03523] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_slurmd: /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_pmap_t_class (ignored) [Ubuntu12-04:03523] [[INVALID],INVALID] ORTE_ERROR_LOG: Unknown error: -1 in file ../../../orte/runtime/orte_globals.c at line 176 input in flex scanner failed ERROR: loading failed * removing ‘/home/link/R/x86_64-pc-linux-gnu-library/2.15/Rmpi’ -- Kind regards, Linh Tran, MPH ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
