[R] Installing Rmpi on hpc
Hi, I was trying to install the package Rmpi on a hpc cluster running SGE. The command, and the sessionInfo() is as follows: === install.packages(Rmpi,dependencies=TRUE) also installing the dependency rsprng trying URL ' http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz' Content type 'application/x-gzip' length 35916 bytes (35 Kb) opened URL == downloaded 35 Kb trying URL ' http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/Rmpi_0.5-9.tar.gz' Content type 'application/x-gzip' length 87953 bytes (85 Kb) opened URL == downloaded 85 Kb * installing *source* package rsprng ... 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 Try to find sprng.h ... 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 sprng.h usability... no checking sprng.h presence... no checking for sprng.h... no Cannot find sprng 2.0 header file. ERROR: configuration failed for package rsprng * removing /home/bs/R_home/R-2.11.1/library/rsprng * installing *source* package Rmpi ... checking for gcc... gcc -std=gnu99 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 -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed I am here /usr/lib/lam and it is LAM Trying to find mpi.h ... Found in /usr/lib/lam/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /usr/lib/lam/lib Try to find liblam.so ... Found liblam in /usr/lib/lam/lib 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/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c RegQuery.c -o RegQuery.o gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c Rmpi.c -o Rmpi.o gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c conversion.c -o conversion.o gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c internal.c -o internal.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib/lam/lib -lmpi -llam -lutil -lpthread /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so when searching for -lmpi /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.a when searching for -lmpi /usr/bin/ld: cannot find -lmpi collect2: ld returned 1 exit status make: *** [Rmpi.so] Error 1 ERROR: compilation failed for package Rmpi * removing /home/bs/R_home/R-2.11.1/library/Rmpi The downloaded packages are in /tmp/RtmpShmM5e/downloaded_packages Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages(Rmpi, dependencies = TRUE) : installation of package 'rsprng' had non-zero exit status 2: In install.packages(Rmpi, dependencies = TRUE) : installation of package 'Rmpi' had non-zero exit status sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils
Re: [R] Installing Rmpi on hpc
On Mon, 14 Mar 2011, Brian Smith wrote: Hi, I was trying to install the package Rmpi on a hpc cluster running SGE. The Which is what? (If Sun Grid Engine, not relevant and it is your unstated OS that we needed to know. Not just 'Linux', but the precise distro.)) Please do note the posting guide: your R is several versions old, for example, and this was an R-devel question (most questions about installing wrapper packages will be, since they are almost nothing to do with the R language). The symptoms you post are those of finding a 32-bit libmpi on a 64-bit install. Please consult the documentation for Rmpi and set the RMPI* environment variables appropriately for your installed 64-bit libmpi (regratably Rmpi does not use the recommended methods and so often needs to be overridden). Also, most modern OSes use OpenMPI and not lam, so see if you can use the former. One guess is that it needs to be told to look in /usr/lib64/lam. OTOH, for x86_64 Fedora 14 I am using setenv RMPI_INCLUDE /usr/include/openmpi-x86_64 setenv RMPI_LIB_PATH /usr/lib64/openmpi/lib setenv RMPI_TYPE OPENMPI command, and the sessionInfo() is as follows: === install.packages(Rmpi,dependencies=TRUE) also installing the dependency ?rsprng? trying URL ' http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz' Content type 'application/x-gzip' length 35916 bytes (35 Kb) opened URL == downloaded 35 Kb trying URL ' http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/Rmpi_0.5-9.tar.gz' Content type 'application/x-gzip' length 87953 bytes (85 Kb) opened URL == downloaded 85 Kb * installing *source* package ?rsprng? ... 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 Try to find sprng.h ... 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 sprng.h usability... no checking sprng.h presence... no checking for sprng.h... no Cannot find sprng 2.0 header file. ERROR: configuration failed for package ?rsprng? * removing ?/home/bs/R_home/R-2.11.1/library/rsprng? Well, first you need to install sprng-2.0b * installing *source* package ?Rmpi? ... checking for gcc... gcc -std=gnu99 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 -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed I am here /usr/lib/lam and it is LAM Trying to find mpi.h ... Found in /usr/lib/lam/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /usr/lib/lam/lib Try to find liblam.so ... Found liblam in /usr/lib/lam/lib 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/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c RegQuery.c -o RegQuery.o gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c Rmpi.c -o Rmpi.o gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c conversion.c -o conversion.o gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/lib/lam/include -DMPI2 -DLAM -I/usr/local/include-fpic -g -O2 -c internal.c -o internal.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib/lam/lib -lmpi -llam -lutil -lpthread /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so when searching
