• Table of contents
• Bash tricks
  • Get disk usage
  • Get CPU and RAM usage
  • Start a Job without a queue
  • Start a mpi code:
  • Start a openMP code:
  • Abort a Job:

Bash tricks¶

Get disk usage¶

df -h

Will give you something like this:

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

Get CPU and RAM usage¶

htop

Will give you something like this:

To get more information about htop see here

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), it will block the SIGTERM signal. To start your application with screen:

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

To reconnect to your previous session:

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

Start a mpi code:¶

Please note that the default mpi distribution on Bender /Flexo /Jakolass is a custom one compiled with intel compiler 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/...). 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.

mpirun -np 32 /path_to_myapp/myapp
#to run myapp with 32 MPI processes 

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.

export OMP_NUM_THREADS=32
/path_to_myapp/myapp
#to run myapp with 32 openMP threads

Abort a Job:¶

To stop a running job you can use the kill command in different ways

• You have just on Job running on the machine and you know its name

 killall TheNameOfTheJob

• You have multiple jobs running, you have first to get the Process ID of the job

ps ax # will list the running processes 
# You can filter, for example if you have started your job with mpi
ps ax | grep mpi

The first number you get is the Process ID

To kill it

kill -9 123456 # if 123456 is your Process ID