Rmpi installation with openmpi (on local directory)
R cannot find libmpi.so in /usr/lib64/openmpi/1.4-gcc/lib. You have to tell R where to find it. There are two ways to do it: 1. Modify the env var LD_LIBRARY_PATH to include /usr/lib64/openmpi/1.4-gcc/lib. 2. Modify R in R/bin to add a line (at third line) like LD_LIBRARY_PATH=/usr/lib64/openmpi/1.4-gcc/lib Recompile Rmpi or load Rmpi to see if this works. Hao
Rodney Sparapani wrote:
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 ?Rmpi? Execution halted 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...
Hi Brian et al.: I'm seeing pretty much the same thing with R 2.14.0 on RHEL 5.7 with GCC 4.4.4 20100726 (Red Hat 4.4.4-13). I didn't see a solution in this thread. Any ideas? Thanks in advance. /opt/local/src/R/Rmpi:$ R CMD INSTALL Rmpi_0.5-9.tar.gz \ --configure-args=--with-mpi=/usr/lib64/openmpi/1.4-gcc * installing to library '/opt/local/lib64/R/library' * installing *source* package 'Rmpi' ... checking for gcc... gcc44 -std=gnu99 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 gcc44 -std=gnu99 accepts -g... yes checking for gcc44 -std=gnu99 option to accept ISO C89... none needed Trying to find mpi.h ... Found in /usr/lib64/openmpi/1.4-gcc/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /usr/lib64/openmpi/1.4-gcc/lib checking for openpty in -lutil... yes checking for main in -lpthread... yes configure: creating ./config.status config.status: creating src/Makevars ** Creating default NAMESPACE file ** libs gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -c RegQuery.c -o RegQuery.o gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -c Rmpi.c -o Rmpi.o gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -c conversion.c -o conversion.o gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -c internal.c -o internal.o gcc44 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi/1.4-gcc/lib -lmpi -lutil -lpthread installing to /opt/local/lib64/R/library/Rmpi/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/opt/local/lib64/R/library/Rmpi/libs/Rmpi.so': libmpi.so.0: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failed * removing '/opt/local/lib64/R/library/Rmpi' /opt/local/src/R/Rmpi:# yum info openmpi openmpi-devel Loaded plugins: rhnplugin, security Installed Packages Name : openmpi Arch : i386 Version : 1.4 Release : 4.el5 Size : 300 k Repo : installed Summary : Open Message Passing Interface URL : http://www.open-mpi.org/ License : BSD Description: Open MPI is an open source, freely available implementation of both the : MPI-1 and MPI-2 standards, combining technologies and resources from : several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in : order to build the best MPI library available. A completely new MPI-2 : compliant implementation, Open MPI offers advantages for system and : software vendors, application developers, and computer science : researchers. For more information, see http://www.open-mpi.org/ . Name : openmpi Arch : x86_64 Version : 1.4 Release : 4.el5 Size : 316 k Repo : installed Summary : Open Message Passing Interface URL : http://www.open-mpi.org/ License : BSD Description: Open MPI is an open source, freely available implementation of both the : MPI-1 and MPI-2 standards, combining technologies and resources from : several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in : order to build the best MPI library available. A completely new MPI-2 : compliant implementation, Open MPI offers advantages for system and : software vendors, application developers, and computer science : researchers. For more information, see http://www.open-mpi.org/ . Name : openmpi-devel Arch : i386 Version : 1.4 Release : 4.el5 Size : 3.9 M Repo : installed Summary : Development files for openmpi URL : http://www.open-mpi.org/ License : BSD Description: Contains development headers and libraries for openmpi Name : openmpi-devel Arch : x86_64 Version : 1.4 Release : 4.el5 Size : 3.9 M Repo : installed Summary : Development files for openmpi URL : http://www.open-mpi.org/ License : BSD Description: Contains development headers and libraries for openmpi -- Rodney Sparapani, PhD Center for Patient Care and Outcomes Research Sr. Biostatistician http://www.mcw.edu/pcor 4 wheels good, 2 wheels better! Medical College of Wisconsin (MCW) WWLD?: What Would Lombardi Do? Milwaukee, WI, USA
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