Contact: [email protected]
Contact: [email protected]
The content of this folder was tested on Feb 2023 on the purpose to fulfill the HPC best practices Hands-on for the Ciencia de los Datos (Data Science), Aplicaciones en Biología y Medicina con Python y R UB IL-3 course
Your username is curs$NUM and your initial password will be provided online.
Check the docu: How to connect to Pirineus III
NUM=[1..23].
At the first access you have set a new password with the following rules:
- 8 characters
- 1 upper case
- 1 lower case
- 1 number
- 1 special character
CSUC_USER=curs<INSERT YOUR NUM HERE>
ssh -p2122 [email protected]
- Insert the temporary password.
- Insert the new password - remember it!!!
- Insert again the new password.
git clone https://github.com/kErica/UB-DataScience.git
scp -rp -P 2122 UB-DataScience-master [email protected]:/home/curs<insert number here>
## or
cd UB-DataScience
sftp –oPort=2122 [email protected]
mput -R *
Then ssh to the system
ssh -p2122 [email protected]
pwd
df -h
ls
ls -ld .
ls -l /
sacct ## Displays accounting data for all jobs.
salloc ## Allocate resources for interactive use.
sbatch ## Submit a job script to a queue
scancel ## Signal jobs or job steps that are under the control of SLURM (cancel jobs or job steps)
scontrol ## View SLURM configuration and state
sinfo ## View information about SLURM nodes and partitions
sjstat ## Display statistics of jobs ( data from sinfo, squeue and scontrol).
smap ## Graphically view information about SLURM jobs, partitions, and set config. param
squeue ## View information about jobs located in the SLURM scheduling queue.
srun ## Run a parallel job
NOTE: This is not going to work as your user cannot allocate resources.
salloc -t 0-01:00 -n 4
NOTE: You can open a second terminal and have a current view of your queue jobs.
watch squeue -u $USER
cd UB-DataScience-master/01-Serial
sbatch serial.sh
## check your jobs and outputs
ls -lthr
sbatch --array=0-9 serial-array.sh
cd ../02-OpenMP
ls
sbatch openmp.sh
cat hello.log