cloudyr
Does it work with Sun Grid Engine?
This repository looks fantastic. Would be great to use it at work, but unfortunately after SSHing onto the remote cluster I have to log onto one of our nodes to do the work. I followed your tutorial and suspect that this additional step could be the reason why I can't get it to work at the moment. Instead, in R I get this kind of output after reloading the localhost:4321 website (which doesn't refresh on its own for me):
> channel 5: open failed: connect failed: Connection refused
channel 5: open failed: connect failed: Connection refused
channel 5: open failed: connect failed: Connection refused
Just asking in case you have some experience with this kind of environment. I apologise if this is not enough information to understand what the problem is. If so, let me know and I'll explain in a bit more detail later.
Thanks!
I have done multi-hop ssh with forwarding in the past but it's been a while. This should be possible - see, for example, the second answer to this question here: https://superuser.com/questions/96489/an-ssh-tunnel-via-multiple-hops
Hi,
I got it to work with the SGE cluster I have access by taking advantage of the names of the compute machines in our SGE cluster. All nodes start with compute. So this is what I have:
Local machine ~./ssh/config:
Host sge
User my_username
Hostname my_cluster@somewhere
LocalForward 4321 localhost:4321
ForwardX11 yes
ForwardX11Trusted yes
I guess that forwarding X11 is there for historical reasons, or in case that rmote fails and you don't want to have to restart your terminal.
ForwardX11 yes
ForwardX11Trusted yes
~/.ssh/config at SGE cluster
Set up local forwarding for all compute nodes in my SGE cluster. This http://pentestmonkey.net/cheat-sheet/ssh-cheat-sheet was useful to me btw because I tried first with RemoteForward.
Host compute*
LocalForward 4321 localhost:4321
~/.Rprofile at SGE
Force all different terminal windows to use the same server_dir for start_rmote() so that they all update in the same location.
## rmote for images
# https://github.com/cloudyr/rmote
installed <- require('rmote')
if(!installed) {
cat('install.packages("rmote", repos = c(CRAN = "http://cran.rstudio.com",
tessera = "http://packages.tessera.io"))')
} else {
start_rmote(port = 4321, server_dir = '/users/my_username/rmote/rmote_server')
## This also works
# start_rmote(port = 4321, server_dir = paste0('/users/my_username/rmote/rmote_server_', Sys.Date()))
}
rm(installed)
In reality I chose a different number from 4321 for the port, so that it won't conflict with other users if they use the default value in rmote::start_rmote().
Best, Leo
Session info
> options(width = 120); devtools::session_info()
Session info ----------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.3 Patched (2018-01-20 r74142)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz US/Eastern
date 2018-02-16
Packages --------------------------------------------------------------------------------------------------------------
package * version date source
base * 3.4.3 2018-01-20 local
colorout * 1.1-2 2017-08-10 Github (jalvesaq/colorout@020a14d)
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.1)
compiler 3.4.3 2018-01-20 local
datasets * 3.4.3 2018-01-20 local
devtools 1.13.4 2017-11-09 CRAN (R 3.4.2)
digest 0.6.15 2018-01-28 cran (@0.6.15)
ggplot2 2.2.1 2016-12-30 CRAN (R 3.4.1)
graphics * 3.4.3 2018-01-20 local
grDevices * 3.4.3 2018-01-20 local
grid 3.4.3 2018-01-20 local
gtable 0.2.0 2016-02-26 CRAN (R 3.4.1)
htmltools 0.3.6 2017-04-28 CRAN (R 3.4.1)
htmlwidgets 0.9 2017-07-10 CRAN (R 3.4.1)
httpuv 1.3.5 2017-07-04 CRAN (R 3.4.1)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.2)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.1)
methods * 3.4.3 2018-01-20 local
mime 0.5 2016-07-07 CRAN (R 3.4.1)
munsell 0.4.3 2016-02-13 CRAN (R 3.4.1)
pillar 1.1.0 2018-01-14 CRAN (R 3.4.2)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.1)
png 0.1-7 2013-12-03 CRAN (R 3.4.1)
Rcpp 0.12.14 2017-11-23 CRAN (R 3.4.2)
rlang 0.1.6 2017-12-21 CRAN (R 3.4.2)
rmote * 0.3.4 2018-02-16 deltarho (R 3.4.3)
scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
servr 0.8 2017-11-06 CRAN (R 3.4.3)
stats * 3.4.3 2018-01-20 local
tibble 1.4.1 2017-12-25 CRAN (R 3.4.2)
tools 3.4.3 2018-01-20 local
utils * 3.4.3 2018-01-20 local
withr 2.1.1 2017-12-19 CRAN (R 3.4.2)
PS I found about this project thanks to https://community.rstudio.com/t/feature-request-send-plots-from-r-in-terminal-to-plots-pane/1877/3
