Difference between revisions of "Biotime machine"

From wiki
Jump to: navigation, search
Line 1: Line 1:
 
 
 
= R installation =
 
= R installation =
  
Line 32: Line 30:
  
 
Will probably do a better job.
 
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 =
 
= 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

Links