Displaying 20 results from an estimated 3000 matches similar to: "socket clusters on snow dies easily"
2018 Mar 09
2
parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
BACKGROUND:
While troubleshooting random, occasionally occurring, errors from
parallel::makePSOCKcluster("localhost", port = 11000);
Error in socketConnection("localhost", port = port, server = TRUE,
blocking = TRUE, :
cannot open the connection
I had another look at parallel:::newPSOCKnode(), which is used
internally to set up each background worker. It is designed to,
2018 Mar 09
2
parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
A solution is to have parallel:::.slaveRSOCK() attempt to connect
multiple times before failing, e.g.
makeSOCKmaster <- function(master, port, timeout, useXDR, maxTries
= 10L, interval = 1.0) {
port <- as.integer(port)
for (i in seq_len(maxTries)) {
con <- tryCatch({
socketConnection(master, port = port, blocking = TRUE,
2018 Mar 10
1
parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
Great.
For the record of this thread, I've submitted patch PR17391
(https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17391). I've
patched it against the latest R-devel on the SVN, passes 'make
check-all', and I've verified it works with the above tests.
/Henrik
On Fri, Mar 9, 2018 at 4:37 AM, <luke-tierney at uiowa.edu> wrote:
> I'm happy to look at a
2012 Aug 02
2
parallel SNOW slower than single core?
Dear All,
I am learning parallel in R and start with the package "snow". I did a test
about running time and the parallel version is much slower than the regulat
code. My laptop is X200s with dual core intel L9400 cpu.
Should I make more clusters than 2? Or how to improve the performance?
# install.packages("snow")
library(snow)
cl <- makeCluster(2)
t1 <- proc.time()
a
2019 Jun 07
1
Parallel number stream: clusterSetRNGStream
Dear All,
Is the following expected behaviour?
set.seed(1)
library(parallel)
cl = makeCluster(5)
clusterSetRNGStream(cl, iseed = NULL)
parSapply(cl, 1:5, function(i) sample(1:10, 1))
# 7 4 2 10 10
clusterSetRNGStream(cl, iseed = NULL)
# 7 4 2 10 10
parSapply(cl, 1:5, function(i) sample(1:10, 1))
stopCluster(cl)
The documentation could be read either way, e.g.
* iseed: An integer to be
SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()
2019 Mar 18
2
SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()
(Bcc: CRAN)
This is a proposal helping CRAN and alike as well as individual
developers to avoid stray R processes being left behind that might be
produced when an example or a package test fails to set up a
parallel::makeCluster().
ISSUE
If a package test sets up a PSOCK cluster and then the master process
dies for one reason or the other, the PSOCK worker processes will
remain running for 30
2006 Mar 13
1
Parallel computing with the snow package: external file I/O possible?
Hello,
I am trying to do model autocalibration using the snow and rgenoud
packages. The function I want to run in task-parallel fashion across
multiple machines is one that pre- and post-processes data and runs an
external model code. My problem is that external file I/O is happening
only in the master node and not in the slaves. I have followed Jasjeet
Sekhon's suggestion to test the
2007 Apr 24
2
Error in clusterApply(): recursive default argument reference
Hi,
I want to compute a distribution of the intersection of a graph and
'randomized' graphs induced by the permutations of node labels (to
preserve the graph topology).
Since I ll have many permutations to perform, I was thinking of using
the snow package and in particular "parSapply" to divide the work
between my 4 CPUs.
But I get the following error message :
Error in
2006 Apr 20
1
Parallel computing with the snow package: external file I/O possible?
Hello,
After getting help to solve part of my problem and some delay on my
part, I am posting a more refined version to see if someone can help me
further. I am trying to autocalibrate a model in my subject area using
the snow and rgenoud packages. I want to use the key function "fn" that
is called by genoud() to finalize input, run the model executable, and
compute the objective
2018 Mar 04
3
Random Seed Location
On Mon, Feb 26, 2018 at 3:25 PM, Gary Black <gwblack001 at sbcglobal.net>
wrote:
(Sorry to be a bit slow responding.)
You have not supplied a complete example, which would be good in this
case because what you are suggesting could be a serious bug in R or a
package. Serious journals require reproducibility these days. For
example, JSS is very clear on this point.
To your question
>
2013 Apr 18
1
parSapply can't find function
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (n>k) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n)
2009 Jan 09
1
snow and different R versions
Dear Luke and others,
I have many R versions on my machine and want to start a particular
one when snow builds its cluster. (The same version I start snow
from.) It seems that everything is set up correctly in
defaultClusterOptions:
> mget(ls(defaultClusterOptions), defaultClusterOptions)
$homogeneous
[1] TRUE
$manual
[1] FALSE
$master
nodename
"maya.unil.ch"
$outfile
[1]
2013 Oct 03
1
Problem with makePSOCKcluster R3.0.1
Hello,
I am using function makePSOCKcluster to make parallel computation on 3 EC2
Amazon machines.
I have a passwordless between machines and ssh is correct.
In the R 2.15.1 release this function works correctly.
Installing R 3.0.1 on my EC2 machines makePSOCKcluster does not produce the
cluster.
If I run the function with outfile="" option, I obtain this message
Error in
2016 Jan 15
1
Error in socketConnection(master, port = port, blocking = TRUE, open = "a+b", : cannot open the connection
Dear All
I have sucessfully created cluster of four nodes using localhost in my local machine by executing the following command
> cl<-makePSOCKcluster(c(rep("localhost",4)),outfile='',homogeneous=FALSE,port=11001)
starting worker pid=4271 on localhost:11001 at 12:12:26.164
starting worker pid=4280 on localhost:11001 at 12:12:26.309
starting worker pid=4289 on
2018 Mar 04
2
Random Seed Location
The following helps identify when .GlobalEnv$.Random.seed has changed:
rng_tracker <- local({
last <- .GlobalEnv$.Random.seed
function(...) {
curr <- .GlobalEnv$.Random.seed
if (!identical(curr, last)) {
warning(".Random.seed changed")
last <<- curr
}
TRUE
}
})
addTaskCallback(rng_tracker, name = "RNG tracker")
EXAMPLE:
>
2018 Mar 04
0
Random Seed Location
Thank you, everybody, who replied! I appreciate your valuable advise! I will move the location of the set.seed() command to after all packages have been installed and loaded.
Best regards,
Gary
Sent from my iPad
> On Mar 4, 2018, at 12:18 PM, Paul Gilbert <pgilbert902 at gmail.com> wrote:
>
> On Mon, Feb 26, 2018 at 3:25 PM, Gary Black <gwblack001 at sbcglobal.net>
>
2006 Oct 13
3
Rmpi performance
Dear R users,
we are trying to do some parallel computing using library(snow).
In particular we have a cluster with 3 nodes
>cl <- makeCluster(3, type = "MPI")
3 slaves are spawned successfully. 0 failed.
and we want to compute the function op_mat (see below) first with the
master and then with the cluster using system.time for checking the
computational performance.
2011 Sep 16
1
package snow/parallel doesnt make any clusters
I am running R.And I want to make parallel computations.
When using the snow package under R-2.13.1patched or the parallel package
under R 2.14.0dev, R isn't able to create a cluster. When typing:
cl <- makeCluster(4)
R doesn't respond. It doesn't crash either.
specs:
OS: 32 bit, Windows XP Prof, SP3.
Processor: Intel Core i3 cpu, quad core.
My colleague works on exactly the
2012 Oct 04
1
(minor) R syntax error in help page to the function makeCluster of library(snow)
Dear list,
I just realized that one of the examples given in the help page to the
function makeCluster of the library(snow) has a small syntax error :
## to get started
library(snow)
?makeCluster
.. will open a halp page containing the command towards the end of the
examples :
cl <- makeCluster(c(rep(list(macOptions), 2), rep(list(lnxOptions), 2),
rep(list(winOptions),
2013 Feb 26
1
parallel execution in R
Dear all,
I have a piece of code that I want to run in parallel (I am working in system of 16 cores)
foreach (i=(seq(-93,-73,length.out=21))) %dopar%
{
threshold<-i
print(i)
do_analysis1(i,path)
do_analysis2(i,path)
do_something_else_analysis1(i,path)
something_else_now(i,path)
}
as you can see I have already tried to make