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.
