[BioC] Install Rmpi on Fedora with mpich2 installed.
binye at med.wayne.edu
Wed Dec 21 15:58:41 CET 2005
Thank you very much, Li! With my limited knowledge about MPI and linux, I don't know how to set up the MPI_INSTALL, could you please give me more details or some reference about this?
Thank you again!
From: Li Long [mailto:lilong at isb-sib.ch]
Sent: Wed 12/21/2005 5:31 AM
To: Ye, Bin
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Install Rmpi on Fedora with mpich2 installed.
This is probably something you could consider, might be a bit out-dated...
(I haven't done it recently)
(1) the current Rmpi wants LAMMPI, I had a lot of trouble getting it to
work with MPICH more than a year ago, and finally gave up on it;
(2) you could try setting MPI_INSTALL in the environment (I had it) as well,
the install script might wants it;
(3) it's not a problem to have both MPICH and LAMMPI on the same system, as
far as you could keep them separated from each other (you could double-
check the scripts to make sure)
> 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!
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
More information about the Bioconductor