(no subject)
On 12/12/2011 04:47 PM, Christoph Knapp wrote:
Hi all, I'm trying to get the snow package with mpi working on my linux ubuntu 10.04 machine. When I tried to install it (see below) it already had problems with the dependencies.
I am going to point you to my PPA, c2d4u. It has a version of Rmpi
rebuilt that solves the "NAMESPACE" issue. Once you have added the PPA
to you system ('sudo add-apt-repository ppa:marutter/c2d4u'),
update/install r-cran-rmpi and r-cran-snow from apt or synaptic. They
should work fine.
Here is the PPA:
https://launchpad.net/~marutter/+archive/c2d4u
Michael
R version 2.14.0 (2011-10-31) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
install.packages("Rmpi")
Installing package(s) into ?/home/christoph/R/x86_64-pc-linux-gnu-library/2.14? (as ?lib? is unspecified) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.stat.auckland.ac.nz/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 ?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 checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/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... no checking mpi.h presence... no checking for mpi.h... no configure: error: "Cannot find mpi.h header file" ERROR: configuration failed for package ?Rmpi? * removing ?/home/christoph/R/x86_64-pc-linux-gnu-library/2.14/Rmpi? The downloaded packages are in ?/tmp/RtmplPStE5/downloaded_packages? Warning message: In install.packages("Rmpi") : installation of package ?Rmpi? had non-zero exit status
q()
Save workspace image? [y/n/c]: n christoph at dell-desktop:~$ sudo apt-get install r-cran-rmpi Reading package lists... Done Building dependency tree Reading state information... Done r-cran-rmpi is already the newest version. The following packages were automatically installed and are no longer required: r-cran-catools r-cran-gdata r-cran-gtools r-cran-gmodels libvpx0 r-cran-bitops r-cran-gplots Use 'apt-get autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. christoph at dell-desktop:~$ dpkg -s r-cran-rmpi Package: r-cran-rmpi Status: install ok installed Priority: optional Section: gnu-r Installed-Size: 408 Maintainer: Ubuntu Developers<ubuntu-devel-discuss at lists.ubuntu.com> Architecture: amd64 Source: rmpi Version: 0.5-8-1 Depends: libc6 (>= 2.4), libopenmpi1.3, r-base-core (>= 2.10.1), mpi-default-bin Suggests: r-cran-rsprng Description: GNU R package interfacing MPI libraries for distributed computing This CRAN package provides an interface to the MPI (Message-Passing Interface) API. It also provides an interactive R slave environment in which distributed statistical computing can be carried out. Original-Maintainer: Dirk Eddelbuettel<edd at debian.org> christoph at dell-desktop:~$ R R version 2.14.0 (2011-10-31) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
library(Rmpi)
Error in library(Rmpi) : package ?Rmpi? does not have a NAMESPACE and should be re-installed
q()
Save workspace image? [y/n/c]: n christoph at dell-desktop:~$ R R version 2.14.0 (2011-10-31) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
install.packages("snow",dependencies=T)
Installing package(s) into ?/home/christoph/R/x86_64-pc-linux-gnu-library/2.14? (as ?lib? is unspecified) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done also installing the dependencies ?rpvm?, ?rsprng? trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/rpvm_1.0-4.tar.gz' Content type 'application/x-gzip' length 66497 bytes (64 Kb) opened URL ================================================== downloaded 64 Kb trying URL 'http://cran.stat.auckland.ac.nz/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://cran.stat.auckland.ac.nz/src/contrib/snow_0.3-8.tar.gz' Content type 'application/x-gzip' length 22893 bytes (22 Kb) opened URL ================================================== downloaded 22 Kb * installing *source* package ?rpvm? ... 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 ISO C89... none needed Check if PVM_ROOT is defined... no I'll try to build rpvm but you need set PVM_ROOT before use pvm. See pvm_intro(1PVM) Try to guess if pvm is installed somewhere ... Cannot find pvm. If pvm is installed, set PVM_ROOT to where pvm is. Otherwise, please install pvm first. ERROR: configuration failed for package ?rpvm? * removing ?/home/christoph/R/x86_64-pc-linux-gnu-library/2.14/rpvm? * 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/christoph/R/x86_64-pc-linux-gnu-library/2.14/rsprng? * installing *source* package ?snow? ... ** package ?snow? successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (snow) The downloaded packages are in ?/tmp/RtmprRxhVG/downloaded_packages? Warning messages: 1: In install.packages("snow", dependencies = T) : installation of package ?rpvm? had non-zero exit status 2: In install.packages("snow", dependencies = T) : installation of package ?rsprng? had non-zero exit status
I have installed openmpi and tried to set the MPI_ROOT, but I'm not sure I picked the right path. christoph at dell-desktop:~$ whereis openmpi openmpi: /etc/openmpi /usr/lib/openmpi /usr/lib64/openmpi /usr/share/openmpi For now I set it to christoph at dell-desktop:~$ $MPI_ROOT bash: /etc/openmpi: is a directory I tried all of them but without any luck. I also googled the problem and found a lot but nothing really which solved the problem. Any ideas where I'm going wrong? I'm mainly interested in using snow with mpi. Thanks in advance Christoph [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Debian mailing list R-SIG-Debian at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter