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

From: Mark Kimpel <mwkimpel_at_gmail.com>
Date: Tue, 10 Jun 2008 20:25:23 -0400

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 <paul.hewson_at_plymouth.ac.uk> 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 paul.hewson_at_plymouth.ac.uk
> web http://www.plymouth.ac.uk/staff/phewson
>
> ________________________________________
> 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)
>>
>> ******************************************************************
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-h...@r-project.org 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_at_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_at_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)

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and provide commented, minimal, self-contained, reproducible code.
Received on Wed 11 Jun 2008 - 00:28:14 GMT

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