[R] Install Rmpi on Fedora with mpich2 installed.

Ye, Bin yeb at karmanos.org
Tue Dec 20 21:45:36 CET 2005

Thank you very much, Martin! I've tried that already, but it still can't find the mpi.h file.

Any other suggestions?


-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: Tue 12/20/2005 2:58 PM
To: Ye, Bin
Subject: Re: [R] Install Rmpi on Fedora with mpich2 installed.
Hi Bin,

I don't have direct experience installing Rmpi on mpich2, but you can
specify the location of the mpi.h files with commands like

./configure --with-mpi=/usr/local/mpich2

when in the unpacked Rmpi packate, or

R CMD INSTALL Rmpi_... --configure-args=--with-mpi=/usr/local/mpich2

when installing the package from the command line.  The ... are the
results of tab completion to the Rmpi tarball, and the path
/usr/local/mpich2 should lead to a direcotry hierarchy such that mpi.h
will be found in something like /usr/local/mpich2/include/mpi.h (some
insight into what is going on is in the configure.in file).

Hope that helps!


"Ye, Bin" <yeb at karmanos.org> writes:

> Hi, everyone,
> I want to install Rmpi on a cluster with Fedora linux. It already installed mpich2, but not lam-mpi. I installed R-2.2.0 on it already.
> And I got error as below:
> * Installing *source* package 'Rmpi' ...
> Try to find mpi.h ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> 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 mpi.h ...
> Cannot find mpi head file
> Please check if --with-mpi=/usr/local/mpich2/bin/ is right
> ERROR: configuration failed for package 'Rmpi'
> ** Removing '/usr/local/R-2.2.0/library/Rmpi'
> Somehow it can not find the mpi.h which is in usr/local/mpich2. Can anyone kindly give me some hint on what should be done? Will installing lam-mpi solve the problem? If so, should mpich2 be uninstalled first? Or just modify the path will do?
> Thanks a lot!
> Bin
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