R help - May 2008 - trouble installing Rmpi on 64-bit Ubuntu 8.04 with openmpi

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_ADDRESS=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]]

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... at 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.