Server: ponyo

ponyo is a standalone server (cvlkrcompute1.utdallas.edu).

Direct Commands (Testing & Debugging)

Unlike cortex, you can run tests and debug scripts directly in your shell session on ponyo.

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 (Sun Grid Engine)

ponyo features the Sun Grid Engine (SGE) queue scheduler.

First, load the SGE module:

module load sge

Common SGE commands:

qsub <script>    # Submit a job
qstat            # View statuses of jobs
qdel <jobid>     # Cancel a job
qhold <jobid>    # Hold a queued job to prevent it from running

Standard SGE template header:

# ------------------------------------------------------------------------------
# sge settings
# ------------------------------------------------------------------------------
#$ -V
#$ -S /bin/bash
#$ -o jid-$JOB_ID-$TASK_ID_jname-$JOB_NAME.log
#$ -j y
#$ -m a \
#$ -M ${USER}@utdallas.edu

Submit an SGE batch job script with arguments:

qsub /path/to/script.sh --airc_id 3tb1111 --sub 0001 --date 20230101 --ses 3

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For templates and code files, see the Script Template.