Re: [R] trouble installing Rmpi on 64-bit Ubuntu 8.04 with openmpi

From: Paul Hewson <paul.hewson_at_plymouth.ac.uk>
Date: Thu, 05 Jun 2008 08:23:11 +0100

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

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From: r-help-bounces_at_r-project.org [r-help-bounces_at_r-project.org] On Behalf Of tub78 [stu.andrews_at_gmail.com] Sent: 04 June 2008 21:11
To: r-help_at_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" <mwkim..._at_gmail.com> 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)
>
> ******************************************************************
>
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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. Received on Thu 05 Jun 2008 - 08:36:51 GMT

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