Re: [R] Problem installing Rmpi with lam on SGI SLES9
On 24/04/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Tue, 24 Apr 2007, Hendrik Fuß wrote: Hi, I've been trying here to install Rmpi on an SGI IA-64 machine with 64 processors, running SuSE Linux Enterprise Server 9, R 2.4.0 and lam-mpi 7.1.3. While I've read of similar problems on this list, I think I've got an entirely new set of error messages to contribute (see below). I'm not sure what the actual error is and what the @gprel relocation message is about. Any help greatly appreciated. I don't know for sure, but on many 64-bit OSes you cannot link code from static libraries into dynamic shared libraries, and that seems to be the case with ia64 Linux. Almost certainly you need to re-compile LAM with -fPIC flags. Yes, thanks a million, this solved the problem. While Rmpi now works, there is another issue connected with this one: I'm trying to use the papply package. However, when I do: library(papply) papply(list(1:10, 1:15, 1:20), sum) 1 slaves are spawned successfully. 0 failed. master (rank 0, comm 1) of size 2 is running on: behemoth slave1 (rank 1, comm 1) of size 2 is running on: behemoth [1] Running serial version of papply\n Papply only spawns one slave and then decides to run the serial version instead. I'm not sure how to tell it to use all the 64 processors available. Hendrik -- Hendrik Fuß PhD student Systems Biology Research Group University of Ulster, School of Biomedical Sciences Cromore Road, Coleraine, BT52 1SA, Northern Ireland __ 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.
Re: [R] Problem installing Rmpi with lam on SGI SLES9
Hendrik, Are you starting the lam daemons before starting R? % lamboot You might need to specify a 'hosts' argument to lamboot. The default way Rmpi calls lamboot is with no arguments, and this might simply create a single lam daemon. I don't usually use papply, but glancing at it's code suggests that it does require(Rmpi) and then decides based on the result of mpi.comm.size what to do. So to debug, load Rmpi and try mpi.comm.size. As a work-around, I think it should be possible to library(Rmpi) mpi.spawn.Rslaves(nslaves=64) # maybe a little bold, initially! before making your first papply call. Hope that helps Martin Hendrik Fuß [EMAIL PROTECTED] writes: On 24/04/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Tue, 24 Apr 2007, Hendrik Fuß wrote: Hi, I've been trying here to install Rmpi on an SGI IA-64 machine with 64 processors, running SuSE Linux Enterprise Server 9, R 2.4.0 and lam-mpi 7.1.3. While I've read of similar problems on this list, I think I've got an entirely new set of error messages to contribute (see below). I'm not sure what the actual error is and what the @gprel relocation message is about. Any help greatly appreciated. I don't know for sure, but on many 64-bit OSes you cannot link code from static libraries into dynamic shared libraries, and that seems to be the case with ia64 Linux. Almost certainly you need to re-compile LAM with -fPIC flags. Yes, thanks a million, this solved the problem. While Rmpi now works, there is another issue connected with this one: I'm trying to use the papply package. However, when I do: library(papply) papply(list(1:10, 1:15, 1:20), sum) 1 slaves are spawned successfully. 0 failed. master (rank 0, comm 1) of size 2 is running on: behemoth slave1 (rank 1, comm 1) of size 2 is running on: behemoth [1] Running serial version of papply\n Papply only spawns one slave and then decides to run the serial version instead. I'm not sure how to tell it to use all the 64 processors available. Hendrik -- Hendrik Fuß PhD student Systems Biology Research Group University of Ulster, School of Biomedical Sciences Cromore Road, Coleraine, BT52 1SA, Northern Ireland __ 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.
Re: [R] Problem installing Rmpi with lam on SGI SLES9
On 25/04/07, Martin Morgan [EMAIL PROTECTED] wrote: Hendrik Fuß [EMAIL PROTECTED] writes: I'm trying to use the papply package. However, when I do: library(papply) papply(list(1:10, 1:15, 1:20), sum) 1 slaves are spawned successfully. 0 failed. master (rank 0, comm 1) of size 2 is running on: behemoth slave1 (rank 1, comm 1) of size 2 is running on: behemoth [1] Running serial version of papply\n Papply only spawns one slave and then decides to run the serial version instead. I'm not sure how to tell it to use all the 64 processors available. Hendrik, Are you starting the lam daemons before starting R? % lamboot You might need to specify a 'hosts' argument to lamboot. The default way Rmpi calls lamboot is with no arguments, and this might simply create a single lam daemon. Thanks, that was a pointer in the right direction. The solution is to edit the file /etc/lam/lam-bhost.def and specify the number of cpus (see man bhost) cheers Hendrik -- Hendrik Fuß PhD student Systems Biology Research Group University of Ulster, School of Biomedical Sciences Cromore Road, Coleraine, BT52 1SA, Northern Ireland __ 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.
Re: [R] Problem installing Rmpi with lam on SGI SLES9
On Tue, 24 Apr 2007, Hendrik Fuß wrote: Hi, I've been trying here to install Rmpi on an SGI IA-64 machine with 64 processors, running SuSE Linux Enterprise Server 9, R 2.4.0 and lam-mpi 7.1.3. While I've read of similar problems on this list, I think I've got an entirely new set of error messages to contribute (see below). I'm not sure what the actual error is and what the @gprel relocation message is about. Any help greatly appreciated. I don't know for sure, but on many 64-bit OSes you cannot link code from static libraries into dynamic shared libraries, and that seems to be the case with ia64 Linux. Almost certainly you need to re-compile LAM with -fPIC flags. thanks Hendrik behemoth:~/Rmpi # R CMD INSTALL /home/hfuss/build/Rmpi_0.5-3.tar.gz --configure-args=--with-mpi=/usr/local/lam-mpi * Installing *source* package 'Rmpi' ... Try to find mpi.h ... Found in /usr/local/lam-mpi/include Try to find libmpi or libmpich ... Found libmpi in /usr/local/lam-mpi/lib Try to find liblam ... Found liblam in /usr/local/lam-mpi/lib checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include-fpic -g -O2 -std=gnu99 -c RegQuery.c -o RegQuery.o gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include-fpic -g -O2 -std=gnu99 -c Rmpi.c -o Rmpi.o gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include-fpic -g -O2 -std=gnu99 -c conversion.c -o conversion.o gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include-fpic -g -O2 -std=gnu99 -c internal.c -o internal.o gcc -shared -L/usr/local/lib -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/local/lam-mpi/lib -lmpi -llam /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_comms /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_argv0 /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_mpi_ao /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_ger /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_c2c /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_appnum /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_universe_size /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_jobid /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_jobid /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_mpi_ao /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_ger /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_c2c /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_appnum /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_universe_size /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_mpi_ao
