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Getting Started
This section shows how to login to the the system and submit a basic job on the cluster. If you do no have an account already, please apply for one by following the link applying_for_an_account
Logging In
To connect to the cluster, ssh to ranger.zamren.zm using the username and password you registered during account application. Once you login, you will be asked to reset the password.
Environmental Variables To see the variables in your environment execute the command: env
Modules
The Environment Modules package provides for the dynamic modification of a user’s environment via modulefiles. To see available modules type the command
module avail
—————-/path/toModules——————————————————————————-
cmake/3.5.0 FFTW/3.3.4 gmp/4.3.2 gromacs/5.1.0 mpich/3.1 mvapich/2.1 openmpi/1.10.1 FFTW/2.1.5 gcc/4.4.7 gotoblas2/2 gsl/1.9 mpich/3.2 openblas/0.2.15
Submitting a Job
The cluster uses SLURM for scheduling and resource management. Key commands to view the status of the cluster are
sinfo reports the state of partitions and nodes managed by SLURM. It has a wide variety of filtering, sorting, and formatting options
squeue reports the state of jobs or job steps. It has a wide variety of filtering, sorting, and formatting options. By default, it reports the running jobs in priority order and then the pending jobs in priority order.
srun is used to submit a job for execution or initiate job steps in real time. srun has a wide variety of options to specify resource requirements, including: minimum and maximum node count, processor count, specific nodes to use or not use, and specific node characteristics (so much memory, disk space, certain required features, etc.). A job can contain multiple job steps executing sequentially or in parallel on independent or shared nodes within the job's node allocation.
sbatch is used to submit a job script for later execution. The script will typically contain one or more srun commands to launch parallel tasks.
scancel is used to cancel a pending or running job or job step. It can also be used to send an arbitrary signal to all processes associated with a running job or job step.
More information can be obtained from Slurm Quick User Guide
