Displaying 20 results from an estimated 10000 matches similar to: "parallel computing"
2008 May 30
1
R and Openmpi
Hello,
We have R working with Rmpi/openmpi, but I'm a little worried. Specifically, (a) the -np flag doesn't seem to override the hostfile (it works fine with fortran hello world) and (b) I appear to have twice as many processes running as I think I should.
Rmpi version 0.5.5
Openmpi version 1.1
Viglen HPC with (effectively) 9 blades and 8 nodes on each blade.
myhosts file contains
2008 Jun 11
3
Rmpi segfault after install on Ubuntu Hardy Heron
I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the
following without errors:
"R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi"
Immediately at library(Rmpi) I get the segfault displayed in my
complete output below. My first thought is that perhaps I used the
wrong library for openmpi, but with my 64 bit install it seemed like a
logical
2010 Dec 17
1
[R-sig-hpc] Error in makeMPIcluster(spec, ...): how to get a minimal example for parallel computing with doSNOW to run?
Shouldn't -n be 4 in the bsub command?
One master+3 slaves. This was required for snowfall, but I think doSNOW
is similar.
Hope it helps
mario
On 16-Dec-10 23:09, Marius Hofert wrote:
> Dear expeRts,
>
> I try to get a minimal example for parallel computing via "foreach" + "doSNOW" to run on a computer cluster (Brutus from
2008 Oct 22
1
Problem about spawn nodes with Rmpi
Hi all,
now I'm testing R in a "virtual cluster", made it with VirtualBox. This one
has 3 nodes, running CentOS 5 and OpenMPI 1.2.8, and the principal node
(called "server") exports the /home to other nodes.
I have installed R and OpenMPI in /home, in fact, it seems work OK. Editing
the openmpi-default-hostfile and run "mpirun -np 3 hostname" I can see the
2010 Jan 20
0
R CMD INSTALL configure.args and CC customization
Hi, everybody.
I hope the new year is treating you well.
In a Rocks Cluster Linux system (that's Centos 5.2 based), I have
built R-2.10 and it runs well.
While fiddling with MPI libraries and R packages, I've noticed a few
little wrinkles.
This comes as no surprise to the veteran R programmers, but let me
share to the new guys the following gem:
There is a difference between . and -
2009 Jun 11
1
help installing Rmpi
Hello R users and developers,
I would like to install Rmpi so that I may take advantage of all of
the CPUs in my computer, but I cannot get it to install and I am not
very good with linux so it is adding to the headache. I have looked
through the help archive, but I have not been successful at getting
Rmpi to work. I am not sure if I am even installing openMPI correctly
in linux. I would really
2012 Aug 29
2
Problem installing Rmpi with Open MPI
Hi guys,
I've spent a few days trying to install Rmpi with no luck. I originally
tried using mpich, moved on to mpich2, and then to openmpi. I've gotten
the furthest with openmpi, though am still running into this problem and
can't figure it out. Can someone help!? Thanks so much in advanced.
I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the
error at the
2011 Sep 09
1
R CMD INSTALL configure.args and CC customization
I am running into the following issue that has been previously
reported on the R-devel mailing list. The short version is that I'm
writing a package for MPI, and I'd like to change CC and SHLIB_LD to
"mpicc". Trying to change them in Makevars.in has no effect, because
the values are clobbered by /etc/R/Makeconf. Will the following
changes to Makeconf.in introduce any problems?
2010 Apr 26
0
Rmpi installation problems on slave nodes
Hi guys,
I'm trying to install Rmpi on the slave nodes of my cluster. The
installation seems to work with no errors or warnings using this
command:
R CMD INSTALL --configure-args="--with-Rmpi-include=/usr/lib64/openmpi/1.3.2-gcc/include
--with-Rmpi-libpath=/usr/lib64/openmpi/1.3.2-gcc/lib
--with-Rmpi-type=OPENMPI" Rmpi_0.5-8.tar.gz
But when I attempt to load Rmpi I get the
2011 Mar 14
1
Installing Rmpi on hpc
Hi,
I was trying to install the package Rmpi on a hpc cluster running SGE. The
command, and the sessionInfo() is as follows:
===========================================
> install.packages("Rmpi",dependencies=TRUE)
also installing the dependency ‘rsprng’
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz'
Content type
2011 Mar 07
1
Rmpi fails to install
I try to install Rmpi as root with install.packages("Rmpi").
It fails with:
...
checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO
C89... none needed
I am here /usr and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib
checking for openpty in -lutil... yes
checking for main in -lpthread...
2009 Mar 27
2
Installing openmpi & lam for use with R
I am trying to install the R package "Rmpi" which needs libmpi. I've
installed openmpi and lam in Centos 5.2:
[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
2007 Nov 28
0
Rmpi : openmpi and mpi.spawn.Rslaves
Hello,
I'm using R on a 10 blade dual quad core Rocks Cluster, and trying to use Rpmi and snow. I basically wondered if at the moment I ought to install Rmpi against another form of mpi (not openmpi) and wondered whether anyone could pass on any experience.
I'm mainly worried about (a) the R server taking up 100% cpu time (I think this is a known issue with Rmpi and openmpi) and (b)
2011 Dec 12
1
(no subject)
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.
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
2014 Mar 12
1
2 versions of same library loaded
Can anyone help me understand how I got 2 versions of the same library
loaded, how to prevent it, and what the consequences are? Running under
Debian GNU/Linux squeeze.
lsof and /proc/xxx/map both show 2 copies of several libraries loaded:
/home/ross/install/lib/libmpi.so.1.3.0
/home/ross/install/lib/libopen-pal.so.6.1.0
/home/ross/install/lib/libopen-rte.so.7.0.0
2011 Dec 02
0
Rmpi installation problems
Hi all,
I am trying to install the Rmpi package in R and, while the installation
itself works, it breaks down when trying to load the library. I think it
has something to do with shared vs static loading of helper libraries,
or the order in which shared libraries are loaded, but I am not sure.
R version: 2.14.0
Linux version: Gentoo, i686-pc-linux-gnu (32-bit)
GCC version: 4.5.3 (Gentoo 4.5.3-r1
2015 Apr 07
1
Rmpi install issues
Hi Folks,
I've recently transitioned to Debian 8.0 and was having a hard time
getting Rmpi to work.
I believed I'd successfully installed dependencies via
> sudo apt-get install r-cran-rmpi
> apt-show-versions r-cran-rmpi
r-cran-rmpi:amd64/jessie 0.6-5-1 uptodate
but when installing the package I was still getting
checking mpi.h presence... no
checking for mpi.h... no
2008 Apr 07
2
problem with Rmpi 0.5-5 and openmpi
Dear knowledgeable experts :-),
I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM
cluster. I'm not an IT expert, but I surely could use a working
installation of Rmpi and SNOW.
I try to load the Rmpi library and get the following:
> library(Rmpi)
[master:07230] mca: base: component_find: unable to open osc pt2pt: file
not found (ignored)
2009 Feb 06
2
Rmpi Segmentation fault
Dear all,
I have used the Rmpi package many times before however this time I've
installed it as I always do with openMPI tar.gz file direct from the
website. I'm installing on my ubuntu 8.10.
Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux
All i get is:
> library(Rmpi)
Segmentation fault
:~$
Which dumps me back into the shell, and doens't give me much
2017 Jun 19
1
Rmpi, openMPI editions.
Greetings.
I see a warning message while compiling OpenMPI and would appreciate
it if you tell me what it means.
This warning happens with any OpenMPI > 1.6.5. Even before starting a
cluster, just "sessionInfo" triggers this warning.
I'm pasting in the message from R-3.3.2 (this is MRO).
Do the R parallel package cluster functions violate the warnings described here?
>