/*====================================================================== * R-ScaLAPACK version 0.6.x: ScaLAPACK interface to R * Oak Ridge National Laboratory, Oak Ridge TN. * Authors: David Bauer, Guruprasad Kora, Nagiza. F. Samatova, * Srikanth Yoginath. * Contact: Nagiza F. Samatova; (865) 241-4351; samatovan@ornl.gov * Contact: Guruprasad Kora; (865) 576-6210; koragh@ornl.gov * Computer Science and Mathematics Division * Oak Ridge National Laboratory, Oak Ridge TN 37831 * (C) 2004 All Rights Reserved * * NOTICE * * Permission to use, copy, modify, and distribute this software and * its documentation for any purpose and without fee is hereby granted * provided that the above copyright notice appear in all copies and * that both the copyright notice and this permission notice appear in * supporting documentation. * * Neither the Oak Ridge National Laboratory nor the Authors make any * representations about the suitability of this software for any * purpose. This software is provided ``as is'' without express or * implied warranty. * * RScaLAPACK (http://www.aspect-sdm.org/Parallel-R) was funded * as part of the Scientific Data Management Center * (http://sdm.lbl.gov/sdmcenter) under the Department of Energy's * Scientific Discovery through Advanced Computing (DOE SciDAC) program * (http://www.scidac.org ). =========================================================================*/ RScaLAPACK (v0.6.1) ------------------------------- I - INSTALLATION Instructions ------------------------------- System requirements: GNU – gcc toolchain (4.0.0 or higher) – Standard on most Linux distributions. R (R-2.0 or higher) OpenMPI (System provided) - /sw/ewok/ompi/1.2.8/sl5.2_gnu4.1.2 ScaLAPACK (Current version) - http://www.netlib.org/scalapack/scalapack_installer.tgz (BLAS, BLACS, LAPACK will be installed as part of ScaLAPACK.) 1. Instructions to install R ---------------------------- Download http://cran.cnr.berkeley.edu/src/base/R-2/R-2.9.1.tar.gz wget http://cran.cnr.berkeley.edu/src/base/R-2/R-2.9.1.tar.gz Unzip R-2.9.1.tar.gz tar zxvf R-2.9.1.tar.gz Change in to the unzipped directory Execute ./configure --prefix=<path to install> --enable-R-shlib make make install Add the above <build directory>/lib to your LD_LIBRARY_PATH export LD_LIBRARY_PATH=<build directory>/lib:$LD_LIBRARY_PATH Add the above <build directory>/bin to your PATH export PATH=<build directory>/bin:$PATH Create R_HOME environment variable. export R_HOME=<build_directory> 2. Instructions to install OpenMPI ---------------------------------- Download http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.3.tar.gz wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.3.tar.gz Unzip openmpi-1.3.3.tar.gz tar zxvf openmpi-1.3.3.tar.gz Change in to the unzipped directory Execute ./configure --prefix=<path to install> make make install Add the above <build directory>/lib to your LD_LIBRARY_PATH export LD_LIBRARY_PATH=<build directory>/lib:$LD_LIBRARY_PATH Add the above <build directory>/bin to your PATH export PATH=<build directory>/bin:$PATH 3. Instructions to install ScaLAPACK ------------------------------------ Download http://www.netlib.org/scalapack/scalapack_installer.tgz wget http://www.netlib.org/scalapack/scalapack_installer.tgz Unzip scalapack_installer.tgz tar zxvf scalapack_installer.tgz Change in to the unziped directory Execute ./setup.py --prefix=<path to install> --downblas --downblacs --downlapack --f90=gfortran Add the above <build directory>/lib to your LD_LIBRARY_PATH export LD_LIBRARY_PATH=<build directory>/lib:$LD_LIBRARY_PATH 4. Instructions to install RScaLAPACK Download RScaLAPACK through CRAN wget http://cran.cnr.berkeley.edu/src/contrib/RScaLAPACK_0.6.1.tar.gz R CMD INSTALL --configure-args="--with-f77 --with-mpi=<MPI install home directory> --with-blacs=<scalapack build>/lib --with-blas=<scalapack build>/lib --with-lapack=<scalapack build>/lib --with-scalapack=<scalapack build>/lib" RScaLAPACK_0.6.1.tar.gz =========================================================================================================== FAQs ---- 1. I get the following error when I try to run RScaLAPACK functions on a cluster with OpenMPI. [system:13400] pls:tm: failed to poll for a spawned proc, return status = 17002 [system:13400] [0,0,0] ORTE_ERROR_LOG: In errno in file rmgr_urm.c at line 462 [system:13400] [0,0,0] ORTE_ERROR_LOG: In errno in file communicator/comm_dyn.c at line 608 o Try executing R with mpirun, like mpirun –np 1 R --vanilla 2. I get the following error when I exit R after using RScaLAPACK library (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null o You get this message when you are using MPICH mpi implementation. Try executing R with mpirun, like mpiexec –np 1 R --vanilla 3. I get MPI_Finalize error after exiting R when I use RScaLAPACK library o Its a MPICH2 issue. Known bug, waiting for the MPICH team to fix it. In the meantime, please execute "PA.exit()" to gracefully exit RScaLAPACK before you quit R. ======================================================================================================= CONTACT: Write to parallel_r@mailhub.ornl.gov ======================================================================================================== ------------------------- II - Usage Instructions ------------------------- Testing RScaLAPACK ------------------ Start R R Execute 1. Load the RScaLAPACK library in the R-environment library(RScaLAPACK) 2. Prepare data rnorm(100)->x dim(x)=c(10,10) c(1,0*(1:9))->y dim(y)=c(10,1) 3. Execute RScaLAPACK's parallel solve routine sla.solve(x,y) 4. To find help for a function in R, use > ?sla.solve 5. To get to know the details of a package > help (package=RScaLAPACK) DEMO: ---- To invoke the demo scripts, provided along with the package > demo (RScaLAPACK) This will provide you with a list of demo routines provided with this package. To view the demo, you can call any of the listed function. For example: > slaSolveDemo() This command will run the R script demonstrating the usage of "sla.solve" function. ======================================================================================================= CONTACT: Write to parallel_r@mailhub.ornl.gov ========================================================================================================