Merge pull request #74 from Danzelot/various

Various additions, mostly section about tmux

README.md

@@ -4,9 +4,10 @@
 
 Served via http://hpc-uit.readthedocs.org.
 
-Copyright (c) 2018
+Copyright (c) 2019
 Radovan Bast,
 Mathias Bockwoldt,
+Jørn Dietze,
 Roy Dragseth,
 Stig Rune Jensen,
 Dan Jonsson,

jobs/interactive.rst

@@ -3,6 +3,8 @@
 Interactive jobs
 ================
 
+Starting an interacitve job
+---------------------------
 You can run an interactive job like this::
 
   $ srun --nodes=1 --ntasks-per-node=1 --time=01:00:00 --pty bash -i
@@ -28,3 +30,38 @@ Some users have experienced problems with the command, then it has helped to spe
   $ srun --account=<NAME_OF_MY_ACCOUNT> --nodes=1 --ntasks-per-node=1 --time=01:00:00 --pty bash -i 
   
   
+
+Keeping interactive jobs alive
+------------------------------
+Interactive jobs die when you disconnect from the login node either by choice or by
+internet connection problems. To keep a job alive you can use a terminal multiplexer
+like ``tmux``.
+
+tmux allows you to run processes as usual in your standard bash shell 
+
+You start tmux on the login node before you get a interactive slurm session with
+``srun`` and then do all the work in it. In case of a disconnect you simply reconnect 
+to the login node and attach to the tmux session again by typing::
+
+  tmux attach
+
+or in case you have multiple session running::
+
+  tmux list-session
+  tmux attach -t SESSION_NUMBER
+
+As long as the tmux session is not closed or terminated (e.g. by a server restart) your 
+session should continue. One problem with our systems is that the tmux session is bound 
+to the particular login server you get connected to. So if you start a tmux session on 
+stallo-1 and next time you get randomly connected to stallo-2 you first have to connect
+to stallo-1 again by::
+
+  ssh login-1
+
+To log out a tmux session without closing it you have to press CTRL-B (that the Ctrl key 
+and simultaneously "b", which is the standard tmux prefix) and then "d" (without the
+quotation marks). To close a session just close the bash session with either CRTL-D or
+type exit. You can get a list of all tmux commands by CTRL-B and the ? (question mark).
+See also `this page <https://www.hamvocke.com/blog/a-quick-and-easy-guide-to-tmux/>`_
+for a short tutorial of tmux.
+Otherwise working inside of a tmux session is almost the same as a normal bash session.

software/applications.rst

@@ -57,6 +57,9 @@ not used by other users of Stallo, so a systemwide installation doesn't make muc
 To see if your software is available via the EasyBuild system have a look into the
 `easyconfig github repository <https://github.com/easybuilders/easybuild-easyconfigs>`_.
 if you can find a version of your software there.
+Alternatively use the search function of EasyBuild::
+
+    eb -S REGEX
 
 Let's assume you want to install the genome aligner Kraken2.
 We find a easyconfig file with the name `Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb <https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb>`_