Warning messages while parallel computing

cl <- parallel::makeCluster(3, type="PSOCK")
invisible(gc())
rm(cl)
invisible(gc())

cl <- parallel::makeCluster(3, type="PSOCK")
invisible(gc())
parallel::stopCluster(cl)
invisible(gc())
rm(cl)
invisible(gc())

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

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