Bash tricks » History » Revision 10
Revision 9 (Alexis Jeandet, 30/03/2014 03:57 PM) → Revision 10/14 (Alexis Jeandet, 30/03/2014 03:58 PM)
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h1. Bash tricks
h2. Get disk usage
<pre><code class="bash">
df -h
</code></pre>
Will give you something like this:
<pre>
Sys. de fichiers Taille Utilisé Dispo Uti% Monté sur
/dev/sde1 110G 8,1G 97G 8% /
devtmpfs 126G 0 126G 0% /dev
tmpfs 126G 0 126G 0% /dev/shm
tmpfs 126G 920K 126G 1% /run
tmpfs 126G 0 126G 0% /sys/fs/cgroup
tmpfs 126G 4,0K 126G 1% /tmp
/dev/mapper/ddf1_DATA2 15T 7,7G 14T 1% /home
</pre>
h2. Get CPU and RAM usage
<pre><code class="bash">
htop
</code></pre>
Will give you something like this:
p=. !{width: 80%}htop.png(htop screenshot example)!
To get more information about htop see "here":http://htop.sourceforge.net/index.php?page=main
h2. Start a Job without a queue
All process started from ssh are terminated when you close the ssh connection, even if you fork them
(./app &). They are closed because when a process is closed the system send the SIGTERM signal
to all its children, it’s done to avoid zombies process on a machine. To keep your task alive when
you disconnect from ssh, you should use screen ("tutorial":http://www.rackaid.com/blog/linux-screen-tutorial-and-how-to/), it will block the SIGTERM signal. To
start your application with screen:
<pre><code class="bash">
screen # to start screen
./your_app #to start your application or any other command
#type ’ Ctrl-A’ d to leave screen with your application running in background
</code></pre>
To reconnect to your previous session:
<pre><code class="bash">
screen -ls # to list running sessions
screen -r 33287.pts-36.bender # to reconnect to 33287.pts-36.bender session
exit # to close your screen session
</code></pre>
h2. Start a mpi code:
Please note that the default mpi distribution on "Bender":https://hephaistos.lpp.polytechnique.fr/redmine/projects/hpc/wiki/Computers#Bender /"Flexo":https://hephaistos.lpp.polytechnique.fr/redmine/projects/hpc/wiki/Computers#Flexo /"Jakolass":https://hephaistos.lpp.polytechnique.fr/redmine/projects/hpc/wiki/Computers#Jakolass is a custom one compiled with intel com-
piler and libraries, to use the gcc one you should call mpi(cc/f90/run/...) with the full path /usr/lib64/openmpi/bin/mpi(cc/f90/run/...). /us-
r/lib64/openmpi/bin/mpi(cc/f90/run/...). To run a software compiled with mpi (mpic/cxx/fortran),
uses mpirun with -np to set the number of mpi processes you want to start.
<pre><code class="bash">
mpirun -np 32 /path_to_myapp/myapp
#to run myapp with 32 MPI processes
</code></pre>
h2. Start a openMP code:
When you run a software compiled with openMP library, you can tune the number of openMP threads your
code will run. To do this you just have to set the OMP_NUM_THREADS environment variable.
<pre><code class="bash">
export OMP_NUM_THREADS=32
/path_to_myapp/myapp
#to run myapp with 32 openMP threads
</code></pre>