SSH banner causes submitJobs to fail?

[alexvorobiev]

I am trying to use SSH cluster and it looks like the banner that gets printed when an ssh connection is established confuses submitJobs.

submitJobs(reg)
OS cmd: ssh host03 '/path/to/R/library/BatchJobs/bin/linux-helper list-jobs "/tmp/RtmpeFOD8J/file46824cd97f9e"'
OS result:
$exit.code
[1] 0

$output
[1] "14 lines of SSH banner"
...
[15] "last line of the banner"

Saving conf: /tmp/RtmpeFOD8J/file46824cd97f9e/conf.RData
Submitting 50 chunks / 50 jobs.
Cluster functions: SSH.
Auto-mailer settings: start=none, done=none, error=none.
Writing 50 R scripts...
SubmitJobs |+ | 0% (00:00:00)OS cmd: ssh host03 '/path/to/R/library/BatchJobs/bin/linux-helper status "/opt/revr/tmp/RtmpeFOD8J/file46824cd97f9e"'
OS result:
$exit.code
[1] 0

$output
[1] "14 lines of SSH banner"
...
[15] "last line of the banner"
[16] "20.47 0 0 0"

Warning in as.list(as.numeric(strsplit(res, " +")[[1L]])) :
NAs introduced by coercion

Error in if (worker$status$n.jobs >= worker$max.jobs) return("J") :
missing value where TRUE/FALSE needed
6: stop(e)
5: value[3L]
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
for (i in seq_along(ids)) {
...
1: submitJobs(reg)
Sending 0 submit messages...
Might take some time, do not interrupt this!

[mllg]

I've added new options in a9fad27 to configure the ssh command and its arguments. Can you please try if setting

options(BatchJobs.ssh.args = "-q")

solves your problem?

@berndbischl AFAIR you had a similar problem on a system in Munich?