Difference between revisions of "Biotime machine"
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= R installation = | = R installation = | ||
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Will probably do a better job. | Will probably do a better job. | ||
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| + | == Hanging user sessions = | ||
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| + | As well as killing the session, getting rid of the following file | ||
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| + | ~/.rstudio/suspended-session/environment | ||
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| + | which can often be quite big, will cure the hanging. There is a link to this post in the links section. | ||
= Memory-style errors = | = Memory-style errors = | ||
Revision as of 14:19, 17 October 2017
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
