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

New R

A new R installation was compiled by hand and resides in /opt/R-3.5.1


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


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.

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


Vital machine details

  • Remote control (DRAC/IPMI) ip: (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, as can the remote console application.
  • Remote console is a JNLP/javaws program which is a deprecated technology. It requires Java 6 and the method for settign up should follow this.
  • Remote console will allow you login as root using the password for the machine which is the same as above.
  • when updating and rebooting this machine has a tendency (albeit a rare one) to hang at BIOS: simply try rebooting.
  • this machine mostly reboots smoothly, the above statement may be over cautious.
  • Faye Moyes at Ecology is official maintainer. Maria Dornelas is the PI for this machine.
  • IT Security do external scans on the 5th of every month between 6pm and 5am, and they take a couple of days.