search for: lmpi

...successfully compiled R 2.4.0 and lam-mpi 7.1.2 on this server using a 64-bit architecture, I have not been able to install Rmpi to interface with lam-mpi, despite success on nearly identical servers in a 32-bit architecture. When trying on the 64-bit server, I receive the error "cannot find -lmpi" during compilation (see below). If anyone has had success in this regards and notice an installation problem that I may have overlooked, I would greatly appreciate any advice. Note that because I do not have root access, all of the lam-mpi and R files were installed locally. Thanks in adva...

...\"\" -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: c...

....2: [root at rab45-1 /]# rpm -qv openmpi openmpi-1.2.5-5.el5 openmpi-1.2.5-5.el5 [root at rab45-1 /]# rpm -qv lam lam-7.1.2-14.el5 lam-7.1.2-14.el5 But I get the following error message when trying to install Rmpi: /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so when searching for -lmpi I'm not sure what else to install/uninstall to fix this. Rick B.

...y, is anybody using snow with Rmpi and Open MPI yet? Also, the Open MPI FAQ is pretty clear on their preference for using mpicc for compiling/linking to keep control of the compiler and linker options and switches. Note that e.g. on my Debian system edd at ron:~> mpicc --showme:link -pthread -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl whereas Rmpi built with just the default from R CMD: gcc-4.2 -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi -lpthread -fPIC -L/usr/lib/R/lib -lR Don't we need libopen-rte and li...

Has anybody tried to use Rmpi with the OpenMPI library instead of LAM/MPI? LAM appears to be somewhat hardcoded in the Rmpi setup. Before I start to experiment with changing this, has anybody else tried Rmpi with non-LAM MPI implementations? Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison

...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 ISO C89... none needed Try to find mpi.h ... Found in /import/home/u1/uaf/ogorman/lam/include Try to find libmpi.so or libmpich.a checking for main in -lmpi... yes Try to find liblam.so ... 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/usr/local/pkg/r/r-2.6.1/lib64/R/include -I/usr/local/pkg...

Hi R Gurus. I'm trying to install the Rmpi package. Here are the errors: 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 libmpi or libmpich ... checking for main in -lmpi... no libmpi not found. exiting... ERROR: configuration failed for package 'Rmpi' ** Removing '/home/Desktop/R-2.5.1/library/Rmpi' The downloaded packages are in /tmp/Rtmp90H1Vp/downloaded_packages Warning messages: 1: installation of package 'rsprng' had non-zero e...

Hi, I want to compute a distribution of the intersection of a graph and 'randomized' graphs induced by the permutations of node labels (to preserve the graph topology). Since I ll have many permutations to perform, I was thinking of using the snow package and in particular "parSapply" to divide the work between my 4 CPUs. But I get the following error message : Error in

...r gcc -m64 -std=gnu99 accepts -g... yes > checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed > I am here /usr/local and it is OpenMPI > Trying to find mpi.h ... > Found in /usr/local/include > Trying to find libmpi.so or libmpich.a ... > checking for main in -lmpi... no > libmpi not found. exiting... > ERROR: configuration failed for package ‘Rmpi’ > * removing ‘/usr/lib64/R/library/Rmpi’ > The downloaded source packages are in > ‘/tmp/RtmpBvTTqc/downloaded_packages’ > Updating HTML index of packages in '.Library' > Making packag...

...e packaged 'snow' and 'Rmpi' for that, however, I get an error while downloading and installing them: When I do a: install.packages("Rmpi", dependencies=T) I get this error: checking for mpi.h... no Try to find libmpi.so or libmpich.a checking for main in -lmpi... no libmpi not found. exiting... However, mpi.h is present via the openmpi-devel package on my RHEL 5.3. Some of those packages need sprng 2.0 (rsprng, for instance, which is a dependency for another MPI-related package). Sprng 2.0, however, isn't in developement for years, I wonder how...

Ive tryed this: R CMD INSTALL Rmpi_0.5-2.tar.gz But occurred this error: gcc -shared -L/usr/local/lib64 -o Rmpi.so conversion.o internal.o RegQuery.o Rmpi.o -lmpi -llam -lutil -lpthread -L/usr/local/lib64/R/lib -lR /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: /usr/local/lib/libmpi.a(infoset.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libmpi.a: could not rea...

...... 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 libmpi.so or libmpich.a checking for main in -lmpi... 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/mkimpel/R_HOME/R-patched/R-build/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"...

...I C... none needed checking for pthread_atfork in -lpthread... yes checking for LAM-MPI... checking LAM-MPI Libraries at /usr/lib/lam... configure: LAM-MPI lib detected @ /usr/lib/lam.. Configured Parameters ... LIBS = -lscalapack -lblacsF77init -lblacsCinit -lblacs -lf77blas -latlas -llamf77mpi -lmpi -llam -lpthread LDFLAGS = -L/usr/lib -L/usr/lib -L/usr/lib/lib -L/usr/lib/lam/lib CFLAGS = -I/usr/lib/lam/include -g -O2 -std=gnu99 PALIBS = -lmpi -llam -lpthread ... *** ... configure: creating ./config.status config.status: creating src/Makefile configure: creating ./config.status config.status:...

...clude -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c internal.c -o internal.o gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi/1.2.7-gcc/lib -lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... * DONE (Rmpi) ====================== The same effect (or lack thereof) can be had with configure.vars in install.packages: install...

...r 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 ... checking for main in -lmpi... yes Try to find liblam ... checking for main in -llam... no liblam not found. Probably not LAM-MPI checking for openpty in -lutil... yes checking for main in -lpthread... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/zzz.R ** libs gcc -I/u...

...CKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -c internal.c -o internal.o x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR installing to /usr/lib64/R/library/Rmpi/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded /usr/lib64/R/bin/exec/R: symbol lookup er...

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

...clude -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c internal.c -o internal.o gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi/1.2.7-gcc/lib -lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... * DONE (Rmpi) ====================== The same effect (or lack thereof) can be had with configure.vars in install.packages: > in...

...ON=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC -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 -L/usr/local/lib -lmpi -lutil -lpthread -fPIC ** R ** demo ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'Rmpi' Formats: text html latex example hosts text html latex internal text...

...ON=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c internal.c -o internal.o gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/local/lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR installing to /home/erin/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/libs ** R ** demo ** inst ** preparing package for lazy loading ** help ** help *** installing help indices ** building package indices ** testing if installed package can be loaded libmpi.dylib:...