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@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@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-disc...@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<e...@debian.org>
christoph@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@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@dell-desktop:~$ whereis openmpi
openmpi: /etc/openmpi /usr/lib/openmpi /usr/lib64/openmpi /usr/share/openmpi
For now I set it to
christoph@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
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--
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
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