Server: cortex

cortex (cortex.cvl.utdallas.edu) is a High-Performance Computing (HPC) server managed by CVL Tech.

Interactive Commands (Testing & Debugging)

To run commands, compile software, or debug code interactively, you must launch an interactive session inside a partition (dev or kenrod).

Warning

Do not run computations on the login node. Running heavy jobs on the login node will slow down the server for all users and may crash the system.

Entering a Compute Node

Note

The dev partition is preferred for testing and debugging interactive sessions.

Launch an interactive session on the dev partition:

srun --partition=dev --nodes=1 --ntasks=1 --cpus-per-task=1 --mem=4G --pty /bin/bash

Launch an interactive session on the kenrod partition:

srun --partition=kenrod --nodes=1 --ntasks=1 --cpus-per-task=1 --mem=4G --pty /bin/bash

Alternatively, rather than memorizing or typing or memorizing the full srun command, you can run the interactive prompt helper:

srun-prompt

Running the Code

Once inside the allocated partition, execute scripts and commands normally.

For example, to run a bash script:

bash /path/to/script.sh

For example, to run an AFNI command using its container:

module load afni
afni-exec 3dinfo /path/to/nifti/file

Batch Jobs (SLURM)

cortex is managed by the SLURM workload manager. To schedule parallel batch jobs, write a shell script featuring SLURM directives and submit it using sbatch.

Common SLURM commands:

sbatch <script>          # Submit a job
squeue                   # View pending and running jobs
scancel <jobid>          # Cancel a specific job
scancel -u <username>    # Cancel all jobs for your user

Standard SLURM template header:

# ------------------------------------------------------------------------------
# slurm settings
# ------------------------------------------------------------------------------
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1        # can be increased if needed
#SBATCH --mem=4G                 # can be increased if needed
#SBATCH --partition=kenrod
#SBATCH --output=jid-%A_jname-%x.log
#SBATCH --mail-type=FAIL
#SBATCH --time=2-00:00:00        # day-hours:minutes:seconds format
#SBATCH --export=NONE            # export no environment variables

Submit a batch job script:

sbatch /path/to/script.sh

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For templates and code files, see the Script Template.