Thanks to all for the advice. Took me a bit to get back to this, but the following worked just fine for me with my 64-bit Ubuntu 8.04 OS: R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi
On Thu, Jun 5, 2008 at 3:23 AM, Paul Hewson <[EMAIL PROTECTED]> wrote: > Or (more simply?) install it from the bash prompt using: > > R CMD INSTALL Rmpi_0.5-5.tar.gz > --configure-args=--with-mpi=/opt/openmpi/include/ > (or whatever your path to openmpi might be). > > I missed this as well and confused myself for a bit, but it is mentioned in > the R news article on Rmpi H.Yu (2002) "Rmpi: Parallel Statistical Computing > in R" Vol 2(2) page 10-14 > > Our cluster has a variety of forms of mpi running, and I also had to follow > the readme in the Rmpi library carefully to make sure it didn't spawn stray > lam-mpi processes as well. > > Best > > Paul > > -=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > Paul Hewson > Lecturer in Statistics > University of Plymouth > Drake Circus > Plymouth PL4 8AA > > tel ++44(0)1752 232778 > email [EMAIL PROTECTED] > web http://www.plymouth.ac.uk/staff/phewson > > ________________________________________ > From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of tub78 [EMAIL PROTECTED] > Sent: 04 June 2008 21:11 > To: r-help@r-project.org > Subject: Re: [R] trouble installing Rmpi on 64-bit Ubuntu 8.04 with openmpi > > The problem here is that the compiler cannot find the include files > for mpi. Notice that the first checks that fail are: > >> checking mpi.h usability... no >> checking mpi.h presence... no >> checking for mpi.h... no > > One solution is to create a file named "~/.R/Makevars" with the > following line: > > PKG_CPPFLAGS = -I/opt/openmpi/include > > ... where /opt/openmpi/include/ contains the necessary mpi.h include > file. > > Then, try to recompile. > > Hope this helps, > - Stu > > > > On May 6, 12:52 pm, "Mark Kimpel" <[EMAIL PROTECTED]> wrote: >> Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy >> Heron, have openmpi installed, and get the following error message with >> attempted install of Rmpi. sessionInfo() follows. >> >> Mark >> >> checking for ANSI C header files... yes >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking mpi.h usability... no >> checking mpi.h presence... no >> checking for mpi.h... no >> Try to find libmpi.so or libmpich.a >> checking for main in -lmpi... yes >> 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/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include >> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" >> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 >> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 >> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 >> -DHAVE_UNISTD_H=1 -DUNKNOWN -fPIC -I/usr/local/include -fpic -g -O2 -c >> conversion.c -o conversion.o >> In file included from conversion.c:18: >> Rmpi.h:1:17: error: mpi.h: No such file or directory >> In file included from conversion.c:18: >> Rmpi.h:14: error: expected '=', ',', ';', 'asm' or '__attribute__' before >> 'mpitype' >> make: *** [conversion.o] Error 1 >> chmod: cannot access `/home/mkimpel/R_HOME/site-library-2.7.0/Rmpi/libs/*': >> No such file or directory >> ERROR: compilation failed for package 'Rmpi' >> ** Removing '/home/mkimpel/R_HOME/site-library-2.7.0/Rmpi' >> >> The downloaded packages are in >> /tmp/RtmppcK0FI/downloaded_packages >> Warning message: >> >> > sessionInfo() >> >> R version 2.7.0 Patched (2008-05-04 r45620) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF- >> 8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_A >> DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] graph_1.18.0 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.10 tcltk_2.7.0 tools_2.7.0 >> >> -- >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> ****************************************************************** >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > 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. > > ______________________________________________ > 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. > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ______________________________________________ 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.
