Hello everyone,
I am using the "parallel" R package for parallel computation.
Code:
# set number of cores
cl <- makeCluster(8, type = "PSOCK") # Mac/Linux need to set
as "FORK"
# pass functions and objects to the cluster environment and set seed
# all the items exported need to stay in the global environment!!
clusterCall(cl, function() { source("xx.R" )})
clusterExport(cl, list("a", "b", "c",
"d",
"5"))
clusterSetRNGStream(cl, 1)
While parallel processing, I receive the following warning signs. Do I
need to ignore these signs or do they potentially slow the whole process?
* Warning signs:*
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 19
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 18
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 17
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 16
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 15
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 14
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 13
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 12
Best regards,
Shah Alam
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Hi Shah, The error usually means you started a cluster and forgot to close it. From the code you post, I cannot see any problem. Maybe you run `makeCluster` twice by accident? Best, Jiefei On Thu, Mar 4, 2021 at 5:53 PM Shah Alam <dr.alamsolangi at gmail.com> wrote:> Hello everyone, > > I am using the "parallel" R package for parallel computation. > > Code: > > # set number of cores > cl <- makeCluster(8, type = "PSOCK") # Mac/Linux need to set as "FORK" > > # pass functions and objects to the cluster environment and set seed > # all the items exported need to stay in the global environment!! > clusterCall(cl, function() { source("xx.R" )}) > clusterExport(cl, list("a", "b", "c", "d", > "5")) > clusterSetRNGStream(cl, 1) > > While parallel processing, I receive the following warning signs. Do I > need to ignore these signs or do they potentially slow the whole process? > > * Warning signs:* > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 19 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 18 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 17 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 16 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 15 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 14 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 13 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 12 > > Best regards, > Shah Alam > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
To avoid the warnings from gc(), call parallel::stopCluster(cl) before removing or overwriting cl. -Bill On Thu, Mar 4, 2021 at 1:52 AM Shah Alam <dr.alamsolangi at gmail.com> wrote:> > Hello everyone, > > I am using the "parallel" R package for parallel computation. > > Code: > > # set number of cores > cl <- makeCluster(8, type = "PSOCK") # Mac/Linux need to set as "FORK" > > # pass functions and objects to the cluster environment and set seed > # all the items exported need to stay in the global environment!! > clusterCall(cl, function() { source("xx.R" )}) > clusterExport(cl, list("a", "b", "c", "d", > "5")) > clusterSetRNGStream(cl, 1) > > While parallel processing, I receive the following warning signs. Do I > need to ignore these signs or do they potentially slow the whole process? > > * Warning signs:* > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 19 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 18 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 17 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 16 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 15 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 14 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 13 > Warning in for (i in seq_len(Ne + echo)) { : > closing unused connection 12 > > Best regards, > Shah Alam > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.