Displaying 20 results from an estimated 1000 matches similar to: "Fwd: Re: [R-sig-hpc] Working doSNOW foreach openMPI example"
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
2011 Feb 25
1
Question about foreach (with doSNOW), is that a bug?
Hi all,
Within a foreach loop with doSNOW, we cant call functions which come from
the non-default package. We need to load(require/library) the package once
more within the foreach loop. Anyone knows why would happen like this? Is it
caused by the snow package and something happened when "snow" parallelize
the job?
Other than load the package once more with in the foreach loop, is
2013 Dec 09
3
compat-openmpi issues after upgrade to CentOS 6.5
Just wondering if anyone can shed some light into an issue we are having
with compat-openmpi after upgrading CentOS to version 6.5
Some of our cluster applications are dependent on an older version of
OpenMPI, so we are using compat-openmpi. Up to CentOS 6.4 this was
version 1.4.3:
% /usr/lib64/compat-openmpi/bin/mpirun -V
mpirun (Open MPI) 1.4.3
but after the upgrade to CentOS 6.5 it
2009 May 25
1
lam vs. openmpi
Dear R Debian Users:
I wrote a quick C program (eventually to become R code) and compiled it as:
mpicc -o greet greet.c
So far so good. Now when I run mpirun, this happens:
erin at erin-laptop:~$ mpirun -np 2 greet
-----------------------------------------------------------------------------
It seems that there is no lamd running on the host erin-laptop.
This indicates that the LAM/MPI
2012 Jul 24
1
untaring files in parallel with foreach and doSNOW?
Hello,
I'm running some code that requires untaring many files in the first step.
This takes a lot of time and I'd like to do this in parallel, if possible.
If it's the disk reading speed that is the bottleneck I guess I should not
expect an improvement, but perhaps it's the processor. So I want to try this
out.
I'm working on windows 7 with R 2.15.1 and the latest foreach
2007 Oct 04
1
Rmpi_0.5-4 and OpenMPI questions
Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make
the changes to support Open MPI.
I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under
R 2.6.0 but I cannot convince myself yet whether it works or not. Simple
tests work. E.g. on my Debian testing box, with Rmpi installed directly
using Open Mpi 1.2.3-2 (from Debian) and using 'r' from
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
2009 Jul 14
1
Snow/openmpi
I'm running R/snow on a small cluster with opensuse, openmpi, and openshh. I
start up R with "mpirun -n 1 R --no-save". That works but it strikes me how
easily I get kicked out of R whenever I run into syntax errors. Is there a
way to avoid this, for instance, by starting up a regular R session and
invoking/activating(?) openmpi within R, e.g. by passing on extra arguments
to the
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)
2015 Feb 10
0
R CMD check: Uses the superseded package: ‘doSNOW’
The CRAN package snow is superseded by the parallel package which is
distributed with R since version 2.14.0. Here are the release notes
\item There is a new package \pkg{parallel}.
It incorporates (slightly revised) copies of packages
\CRANpkg{multicore} and \CRANpkg{snow} (excluding MPI, PVM and NWS
clusters). Code written to use the higher-level API functions in
those packages should
2015 Feb 10
1
R CMD check: Uses the superseded package: ‘doSNOW’
Oh, I completely missed that one.
It's very neat as it seems to work both on Windows and Unix.
Thanks!
Xavier
On 10/02/15 10:52, Martyn Plummer wrote:
> The CRAN package snow is superseded by the parallel package which is
> distributed with R since version 2.14.0. Here are the release notes
>
> \item There is a new package \pkg{parallel}.
>
> It incorporates (slightly
2015 Feb 09
2
R CMD check: Uses the superseded package: ‘doSNOW’
Dear list,
When I run an R CMD check --as-cran on my package (pROC) I get the
following note:
> Uses the superseded package: ?doSNOW?
The fact that it uses the doSNOW package is correct as I have the
following example in an .Rd file:
> #ifdef windows
> if (require(doSNOW)) {
> registerDoSNOW(cl <- makeCluster(2, type = "SOCK"))
> ci(roc2,
2011 Nov 07
1
Strange behaviour of ssh
Hello together!
I've Debian 6.0.3 with OpenSSH_5.5p1 and problem with the execution of remote commands via ssh.
It seems as if the first command isn't looked up in all "$PATH" dirs.
Here normally I should get the version information of mpirun twice but the first one fails:
$ ssh cluster2 mpirun --version ; mpirun --version
bash: mpirun: command not found
mpirun (Open MPI) 1.4.3
2012 May 08
1
revolution foreach oddity
I know this is not a revolution support forum, but as anyone noticed the
following?
I have a foreach loop to generate random samples. If I run the exact code
below in normal r (2.14.1) it works as expected, but if I run it from
revolution 4.2.0 each loop returns the same numbers.
The only way I can get revolution to give different numbers is using 1
instead of 8 in
registerDoSNOW(makeCluster(8,
2013 Nov 06
0
MPICH2 Rmpi and doSNOW
Hi
I have managed to install MPICH2 and Rmpi on my Windows 7 machine. I can
also run the following code
> library(Rmpi)
> mpi.spawn.Rslaves()
4 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 5 is running on: MyMaster
slave1 (rank 1, comm 1) of size 5 is running on: MyMaster
slave2 (rank 2, comm 1) of size 5 is running on: MyMaster
slave3
2012 Jan 18
0
makeCluster() function in doSNOW package hangs
Dear R help,
I am trying to set up a cluster for parallel computing on a machine
running 64-bit windows XP, using the doSNOW package on R 2.14.1.
However, the command makeCluster() consistently makes the computer hang.
No R processes are started, no CPU consumed, R just becomes
unresponsive. ESC still terminates the command, but I cannot start the
cluster. There seems to be quite a lot of posts
2013 Nov 06
0
MPICH2 Rmpi and doSNOW
Hi
I have managed to install MPICH2 and Rmpi on my Windows 7 machine. I can
also run the following code
> library(Rmpi)
> mpi.spawn.Rslaves()
4 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 5 is running on: MyMaster
slave1 (rank 1, comm 1) of size 5 is running on: MyMaster
slave2 (rank 2, comm 1) of size 5 is running on: MyMaster
slave3 (rank 3, comm
2013 Jun 16
2
Problem in linking a library in R package
1.I have a library fpmpi . I made the shared library fpmpi.so from this
library.I am using ubuntu .
2.Now, I want to use in my R package .My R package has src folder the there
is makevars.in file
### Setup R source code and objects.
PKG_CPPFLAGS = @PKG_CPPFLAGS@
PKG_LIBS = -L/home/g/Desktop/Project -fpmpip
### For user configuration.
USER_CONF = Makeconf
### Start making here.
all:
2009 Sep 22
0
snowfall: missing MPI node
Hello,
I don't know if the question pertains to Rmpi, snow or snowfall.
I run my job by:
mpirun -np N -hostfile $PBS_NODEFILE RMPISNOW -f my-script.r --slave
In the snowfall sfInit call I have to specify one less CPU respect to
the mpirun call
sfInit(parallel=TRUE, cpus=N-1, type="MPI")
otherwise I receive an error similar to: "cluster size N-1 already
2010 Jun 16
2
Parallel computing on Windows (foreach) (Sergey Goriatchev)
foreach (or virtually anything you might use for concurrent programming)
only really makes sense if the work the "clients" are doing is substantial
enough to overwhelm the communication overhead. And there are many ways to
accomplish the same task more or less efficiently (for example, doing blocks
of tasks in chunks rather than passing each one as an individual job).
But more to the