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
No direct experience with mpich2 on Fedora, but I think you can use ./configure --with-mpi=/usr/local/mpich2 from within the unpacked Rmpi tarball, or R CMD INSTALL Rmpi_... --configure-args=--with-mpi=/usr/local/mpich2 from the command line. ... is the tab-completion to the tarball, and /usr/local/mpich2 should be a path such that mpi.h is in /usr/local/mpichs/include/mpi.h. Some insight is in the configure.in file of Rmpi. Hope that helps! Sorry for the repost, Bin, meant this originally to reply to the newsgroup. Martin "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 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Thank you very much, Martin! I've tried that already, but it still can't find the mpi.h file. Any other suggestions? Bin -----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! Martin "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 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html