Biotime machine

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R installation

R-3.4.1 was installed in /usr/local/bin. Rstudio is told to use this version via:

cat /etc/rstudio/rserver.conf

# Server Configuration File
rsession-which-r=/usr/local/bin/R

Administration

The executable is rstudio-server. Documentation is available but for the professional version, whihc nonetheless may be useful (see the links section).

There is no manpage, but there is this very concise help which nonethless is useful:

root@biotime:/etc/rstudio# rstudio-server --help
$Usage: rstudio-server {status|start|stop|restart|test-config|verify-installation|suspend-session|suspend-all|force-suspend-session|force-suspend-all|kill-session|kill-all|offline|online|active-sessions|version}

For example to kill a certain session, first find out the PID

rstudio-server active-sessions <PID>

then try and suspend

rstudio-server force-suspend-session <PID>

However, suspend does not sound quite aggressive enough, so

rstudio-server kill-session <PID>

Will probably do a better job.

Hanging user sessions

As well as killing the session, getting rid of the following file

~/.rstudio/suspended-session/environment 

which can often be quite big, will cure the hanging. There is a link to this post in the links section.

Memory-style errors

These used to happen quite often with marvin.

nutria@biotime:/mnt/rdrive/Bioinformatics$
Message from syslogd@biotime at Apr  3 14:56:59 ...
 kernel:[5173414.766503] [Hardware Error]: Corrected error, no action required.

Message from syslogd@biotime at Apr  3 14:56:59 ...
 kernel:[5173414.766566] [Hardware Error]: CPU:24 (15:2:0) MC4_STATUS[-|CE|MiscV|-|AddrV|-|Poison|CECC]: 0x9c664880011c017b

Message from syslogd@biotime at Apr  3 14:56:59 ...
 kernel:[5173414.766664] [Hardware Error]: MC4_ADDR: 0x0000003a066ab700 

Message from syslogd@biotime at Apr  3 14:56:59 ...
 kernel:[5173414.766712] [Hardware Error]: MC4 Error (node 3): L3 data cache ECC error.

Message from syslogd@biotime at Apr  3 14:56:59 ...
 kernel:[5173414.766767] [Hardware Error]: cache level: L3/GEN, tx: GEN, mem-tx: EV

Links

Vital machine details

  • Remote control (DRAC/IPMI) ip: 138.251.13.226 (simply type as URL in browser. Note there may be security warnings from modern browsers: carry on regardless).
  • User: root
  • Password, the same as IPMI for marvin (obviously cannot write that here).
  • Some basic functions are available on DRAC, such as power on and power cycle, but Remote Console is the most interesting.
  • DRAC can also load an live Linux iso from your local computer and boot it instead of the resident OS
  • Remote console is a JNLP program (java) which can be downloaded and run with the latest version of javaws. Or, the browser may launch it automatically
  • Remote console will allow you login using the password.
  • when updating and rebooting this machine has a tendency (albeit a rare one) to hang at BIOS: simply try rebooting.