Displaying 20 results from an estimated 1000 matches similar to: "SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()"
SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()
2019 Mar 27
0
SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()
The problem causing the stray worker processes when the master fails to
open a server socket to listen to connections from workers is not
related to timeout in socketConnection(), because socketConnection()
will fail right away. It is caused by a bug in checking the setup
timeout (PR 17391).
Fixed in 76275.
Best
Tomas
On 3/18/19 2:23 AM, Henrik Bengtsson wrote:
> (Bcc: CRAN)
>
>
2019 Jun 04
2
MacOS parallel::makeCluster fails
Hi all,
The call parallel::makeCluster(1L) hangs infinitely on my MacOS machine which seems to be already reported by some people (e.g., https://stat.ethz.ch/pipermail/r-devel/2018-February/075565.html).
However, the solutions posted on SO, GH or R-devel do not work in my case.
So far, I unsuccessfully tested ?
1. Couple of reboots
2. Adding 192.0.0.1 to /etc/hosts
3. Using R.app
2017 Dec 04
2
PSOCK cluster and renice
Hi all,
Is it possible to use the 'renice' option together with parallel
clusters of type 'PSOCK'? The help page for parallel::makeCluster is
not specific about which options are supported on which types and I am
getting the following message when passing renice = 19 :
> cl <- parallel::makeCluster(2, renice = 19)
nice: ?+19?: No such file or directory
Kind regards,
2017 Dec 04
1
PSOCK cluster and renice
Hi Henrik,
Thanks for the detailed in fast reply!
My guess would be that the confusion comes from the different use of nice and renice.
The workraund you provided work fine! Thanks a lot.
Best,
Andreas
Henrik Bengtsson <henrik.bengtsson at gmail.com> writes:
> Looks like a bug to me due to wrong assumptions about 'nice'
> arguments, but could be because a
2019 Jul 12
1
MacOS parallel::makeCluster fails
Hi Thomas,
thanks for your reply (and thanks for your patience...).
I am now using the following minimal reprex:
> library(parallel)
> cl <- makeCluster(2L)
I freshly started the machine and did not open any other app. Just R.app (3.6.1).
After executing the second line of code, R seems to hang infinitely and does not respond.
The R process itself uses almost no CPU.
Unfortunately,
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,
2017 Dec 04
0
PSOCK cluster and renice
Looks like a bug to me due to wrong assumptions about 'nice'
arguments, but could be because a "non-standard" 'nice' is used. If
we do:
> trace(system, tracer = quote(print(command)))
Tracing function "system" in package "base"
we see that the system call used is:
> cl <- parallel::makePSOCKcluster(2L, renice = 19)
Tracing system(cmd, wait
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
2013 Oct 28
3
speed of makeCluster (package parallel)
Hi all,
I am quite new in the world of parallelization and I wonder if there is a
way to increase the speed of creation of a parallel socket cluster. The
time spend to include threads increase exponentially with the number of
thread considered and I use of computer with two 8 cores CPU and thus
showing a total of 32 threads in windows 7.
Currently, I use the default parameters (type =
2020 Nov 04
2
parallel PSOCK connection latency is greater on Linux?
I'm not sure the user would know ;). This is very system-specific issue just because the Linux network stack behaves so differently from other OSes (for purely historical reasons). That makes it hard to abstract as a "feature" for the R sockets that are supposed to be platform-independent. At least TCP_NODELAY is actually part of POSIX so it is on better footing, and disabling
2020 Nov 02
3
parallel PSOCK connection latency is greater on Linux?
On Mon, 2 Nov 2020 at 02:22, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>
> It looks like R sockets on Linux could do with TCP_NODELAY -- without (status quo):
How many network packets are generated with and without it? If there
are many small writes and thus setting TCP_NODELAY causes many small
packets to be sent, it might make more sense to set TCP_QUICKACK
instead.
2019 Jun 05
0
MacOS parallel::makeCluster fails
Hi Dominik,
from the output, the master process could not "listen" on the port where
it expects a connection from the worker. We need to find out why. I'd
recommend first to create a minimal reproducible example (and one that
does not use future, only parallel, and a minimal number of threads,
ideally just 2). Then I'd recommend to check if the problem still exists
with
2016 Oct 31
1
BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)
On Mon, 31 Oct 2016, Henrik Bengtsson wrote:
> Thank you for looking into this Luke.
>
> On Thu, Oct 27, 2016 at 9:26 AM, <luke-tierney at uiowa.edu> wrote:
>> On unix, unless event polling is enabled Sys.sleep just waits in a
>> select() call (with a SIGINT handler in place) so the elapsed time
>> isn't checked until after the select call is complete.
2018 Mar 09
0
parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
I just noticed that parallel:::.slaveRSOCK() passes 'timeout' to
socketConnection() as a character, i.e. there's a missing timeout <-
as.integer(timeout), cf. port <- as.integer(port) and useXDR <-
as.logical(value):
> parallel:::.slaveRSOCK
function ()
{
makeSOCKmaster <- function(master, port, timeout, useXDR) {
port <- as.integer(port)
con
2018 Mar 09
0
parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
I'm happy to look at a patch that does this. I'd start with a small
interval and increase it by 50%, say, on each try wit a max retry time
limit. This isn't eliminating the problem,only reducing the
probability, but still worth it. I had considered doing something like
this but it didn't seem necessary at the time. You don't want to retry
indefinitely since the connection
2012 Dec 19
1
problem with opening more than one SOCK cluster with package snow
Dear list,
i have some problems using the snow package to create a SOCK cluster.
The errors just occour irregularly but it seems to me that they occour
when I try to create more than one cluster on the same machine via
different R instances started via submitting LSF jobs to a cluster. Does
anyone have an idea how to solve this or where to start digging for
solutions?
The error messages
2020 Nov 01
2
parallel PSOCK connection latency is greater on Linux?
I'm exploring latency overhead of parallel PSOCK workers and noticed
that serializing/unserializing data back to the main R session is
significantly slower on Linux than it is on Windows/MacOS with similar
hardware. Is there a reason for this difference and is there a way to
avoid the apparent additional Linux overhead?
I attempted to isolate the behavior with a test that simply returns
2019 Apr 13
3
SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()
Hi Inaki,
> "Performant"... in terms of what. If the cost of copying the data
> predominates over the computation time, maybe you didn't need
> parallelization in the first place.
Performant in terms of speed. There's no copying in that example
using `mclapply` and so it is significantly faster than other
alternatives.
It is a very simple and contrived example, but
2018 Mar 14
2
clusterApply arguments
Hi!
I recognized that the argument matching of clusterApply (and therefore parLapply) goes wrong when one of the arguments of the function is called "c". In this case, the argument "c" is used as cluster and the functions give the following error message "Error in checkCluster(cl) : not a valid cluster".
Of course, "c" is for many reasons an unfortunate