Re: [R] Rmpi and x86
On Tue, 28 Aug 2007, Martin Morgan wrote: > Edna -- > > I'll keep this on the list, so that others will learn, and others will > correct me when I give bad advice! > >> relocation R_X86_64_32 against `lam_mpi_comm_world' can not be used >> when making a shared object; recompile with -fPIC > > This likely means that your lam was not built with the --enable-shared > configure option, as documented in the installation guide. (It might > also mean that R was not configure with --enable-R-shlib; the message > is opaque to me). The line above is /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../lib64/libmpi.a(infoset.o): so it means lam needs to be rebuilt either with --enable-shared or just with -fPIC added to CFLAGS. (Users migrating from i386 Linux to x86_64 Linux got quite used to this quirk.) > I believe others on the list have only had success with specific > versions of LAMMPI, so that would be the next place to look (after > sorting out the shared library issue) > > Martin > > "Edna Bell" <[EMAIL PROTECTED]> writes: > >> Here is what happens: >> Note: lam-7.1.4 >> >> linux-tw9c:/home/bell/Desktop/R-2.5.1/bin # ./R CMD INSTALL --clean >> Rmpi_0.5-3.tar.gz >> * Installing to library '/home/bell/Desktop/R-2.5.1/library' >> * Installing *source* package 'Rmpi' ... >> checking for gcc... gcc >> checking for C compiler default output... 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... yes >> checking mpi.h presence... yes >> checking for mpi.h... yes >> Try to find libmpi or libmpich ... >> checking for main in -lmpi... yes >> Try to find liblam ... >> checking for main in -llam... yes >> 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/bell/Desktop/R-2.5.1/include >> -I/home/hodgesse/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 >> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 >> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 >> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include >> -fpic -g -O2 -c conversion.c -o conversion.o >> gcc -std=gnu99 -I/home/bell/Desktop/R-2.5.1/include >> -I/home/bell/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 >> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 >> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 >> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include >> -fpic -g -O2 -c internal.c -o internal.o >> gcc -std=gnu99 -I/home/bell/Desktop/R-2.5.1/include >> -I/home/bell/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 >> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 >> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 >> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include >> -fpic -g -O2 -c RegQuery.c -o RegQuery.o >> gcc -std=gnu99 -I/home/bell/Desktop/R-2.5.1/include >> -I/home/bell/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 >> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 >> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 >> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include >> -fpic -g -O2 -c Rmpi.c -o Rmpi.o >> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o >> internal.o RegQuery.o Rmpi.o -lmpi -llam -lutil -lpthread >> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld: >> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../lib64/libmpi.a(infoset.o): >> relocation R_X86_64_32 against `lam_mpi_comm_world' can not be used >> when making a shared object; recompile with -fPIC >> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../lib64/libmpi.a: >> could not read symbols: Bad
Re: [R] Rmpi and x86
Edna -- I'll keep this on the list, so that others will learn, and others will correct me when I give bad advice! > relocation R_X86_64_32 against `lam_mpi_comm_world' can not be used > when making a shared object; recompile with -fPIC This likely means that your lam was not built with the --enable-shared configure option, as documented in the installation guide. (It might also mean that R was not configure with --enable-R-shlib; the message is opaque to me). I believe others on the list have only had success with specific versions of LAMMPI, so that would be the next place to look (after sorting out the shared library issue) Martin "Edna Bell" <[EMAIL PROTECTED]> writes: > Here is what happens: > Note: lam-7.1.4 > > linux-tw9c:/home/bell/Desktop/R-2.5.1/bin # ./R CMD INSTALL --clean > Rmpi_0.5-3.tar.gz > * Installing to library '/home/bell/Desktop/R-2.5.1/library' > * Installing *source* package 'Rmpi' ... > checking for gcc... gcc > checking for C compiler default output... 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... yes > checking mpi.h presence... yes > checking for mpi.h... yes > Try to find libmpi or libmpich ... > checking for main in -lmpi... yes > Try to find liblam ... > checking for main in -llam... yes > 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/bell/Desktop/R-2.5.1/include > -I/home/hodgesse/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include > -fpic -g -O2 -c conversion.c -o conversion.o > gcc -std=gnu99 -I/home/bell/Desktop/R-2.5.1/include > -I/home/bell/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include > -fpic -g -O2 -c internal.c -o internal.o > gcc -std=gnu99 -I/home/bell/Desktop/R-2.5.1/include > -I/home/bell/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include > -fpic -g -O2 -c RegQuery.c -o RegQuery.o > gcc -std=gnu99 -I/home/bell/Desktop/R-2.5.1/include > -I/home/bell/Desktop/R-2.5.1/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DMPI2 -I/usr/local/include > -fpic -g -O2 -c Rmpi.c -o Rmpi.o > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o > internal.o RegQuery.o Rmpi.o -lmpi -llam -lutil -lpthread > /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld: > /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../lib64/libmpi.a(infoset.o): > relocation R_X86_64_32 against `lam_mpi_comm_world' can not be used > when making a shared object; recompile with -fPIC > /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../lib64/libmpi.a: > could not read symbols: Bad value > collect2: ld returned 1 exit status > make: *** [Rmpi.so] Error 1 > chmod: cannot access `/home/bell/Desktop/R-2.5.1/library/Rmpi/libs/*': > No such file or directory > ERROR: compilation failed for package 'Rmpi' > ** Removing '/home/bell/Desktop/R-2.5.1/library/Rmpi' > linux-tw9c:/home/bell/Desktop/R-2.5.1/bin # > > > > On 8/28/07, Martin Morgan <[EMAIL PROTECTED]> wrote: >> Hi Edna -- >> >> I have Rmpi 0.5-3 under R 2.5.1
Re: [R] Rmpi and x86
Hi Edna -- I have Rmpi 0.5-3 under R 2.5.1 with LAM 7.1.2 installed on an x86_64 SuSE 10.0. I installed (as a regular user, to my own disc space) LAM and ran through some basic checks (lamboot / lamhalt, checking that I could compile the demo programs) After downloading Rmpi_0.5.3.tar.gz, I did CC=mpicc R CMD INSTALL --clean Rmpi_0.5.3.tar.gz the configure script of Rmpi found libmpi and liblam in my LAMHOME, and also -lutil and -lpthread. Source files compiled without any issues, and the package installed. If I have not issued a lamboot command, inside R, > library(Rmpi) loads the library and indicates that it is starting lam. If I have already issued lamboot, then library(Rmpi) loads as expected. Where do things go wrong for you? Martin "Edna Bell" <[EMAIL PROTECTED]> writes: > Dear R Gurus: > > Is there a problem with Rmpi on x86 with SUSE 10.1, please? > > I've tried everything and it still won't load. > > Has anyone else dealt with this please? > > Thanks, > Edna Bell > > __ > R-help@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 > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-help@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 and provide commented, minimal, self-contained, reproducible code.
[R] Rmpi and x86
Dear R Gurus: Is there a problem with Rmpi on x86 with SUSE 10.1, please? I've tried everything and it still won't load. Has anyone else dealt with this please? Thanks, Edna Bell __ R-help@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 and provide commented, minimal, self-contained, reproducible code.
