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

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! Bin -----Original Message----- From: Li Long [mailto:lilong@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. Hi, This is probably something you could consider, might be a bit out- dated... (I haven't done it recently) I think (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) Good luck. Li > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi, This is probably something you could consider, might be a bit out- dated... (I haven't done it recently) I think (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) Good luck. Li > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >