I don't think 'parallel' is to blame in this case. Those warnings:
Warning in for (i in seq_len(Ne + echo)) { :
closing unused connection 19
come from base::source()
[https://github.com/wch/r-source/blob/9caddc1eaad1f480283f1e98af34a328699d1869/src/library/base/R/source.R#L166-L244].
Unless there's a bug in source() that leaves connections open, which
is unlikely, I think there's something in the 'xx.R' script that
opens
a connection but doesn't close it. Possibly multiple times. A good
check is to see if the same warnings are produced when calling
source("xx.R") sequentially in a for() loop or an lapply() call.
Hope this helps,
Henrik
On Thu, Mar 4, 2021 at 9:58 AM Bill Dunlap <williamwdunlap at gmail.com>
wrote:>
> 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.
>
> ______________________________________________
> 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.