Rockfish Tutorial

This is the repo for the tutorial of runing tasks on Rockfish. Rockfish is a community-shared cluster, i.e., everyone can use any nodes within the limits of their allocated utilization. Every quarter you request a certain amount of GPU hours (i.e., number of cores x wall time) and provide justification for them. These assigned limits will be reset on a quarterly basis (use it or lose it).

To start, create an account here with your JHED.

IMPORTANT:

• It is important for you to use JHED otherwise the system will have difficulty authenticating you.
• If you're a student, you need to get access through your PI (usually you advisor).

Repository Content

• test_gpus shows how to run a simple script on the GPU processor. You can run sbatch test_gpus.sh to submit the job and make sure that you have access to GPU nodes.
• classification-example shows how to run a simple classification task on the GPU processor. You can run sbatch train_on_rockfish.sh to train a classifier on Rockfish.

FAQ

• How do I find what the queue of a partition?
  • Type the command sinfo -s to get a list of the partitions.
  • sinfo -p partition-name will display the utilization for this partition.
• How do I know what nodes are available?
  • Type the command sinfo -N to get a list of the nodes.
  • sinfo -N -p partition-name will display the utilization for this partition.
• How do I interpret "states"?
  • idle: The node is available for use.
  • alloc: The node is currently being used by a job.
  • mix: Some of the node's processors are currently being used by a job.
  • Further details here: https://slurm.schedmd.com/sinfo.html
• How do I see how many GPUs are available on each node?
  • Type the command sinfo -N -p a100 to get a list of the nodes and the number of GPUs available on each node.
• How do I submit multiple jobs with this different parameters?
  • See this page: https://www.osc.edu/book/export/html/4046
• How do I submit a job to a specific node?
  • You can submit a job to a specific node by using the --nodelist flag.
  • For example, sbatch --nodelist=node1 job.sh will submit the job to node1.
  • You can also use the --exclude flag to exclude a node.
  • For example, sbatch --exclude=node1 job.sh will submit the job to any node except node1.
• How do I create interactive session?
  • You can create an interactive session by using the salloc command.
  • For example, salloc -p a100 --gres=gpu:1 --time=00:30:00 will create an interactive session with 1 GPU for 30 minutes.
  • You can also interact command which internally makes call to salloc command.
• How do I see the queue of my jobs?
  • You can see the queue of your jobs by using the squeue command.
  • You can specialize it for a partition: squeue -p a100
  • For example, squeue -u userid will show the queue of your jobs.
• What do status labels mean in the output of squeue?
  • PD: Pending. The job is awaiting resource allocation.
  • R: Running. The job currently has an allocation.
  • CG: Completing. The job is in the process of completing. Some processes on some nodes may still be active.
  • CD: Completed. The job has terminated all processes on all nodes.
  • F: Failed. The job terminated with non-zero exit code or other failure condition.
  • TO: Timeout. The job terminated upon reaching its time limit.
  • NF: Node Failure. The job terminated due to failure of one or more allocated nodes.
  • CA: Canceled. The job was explicitly canceled by the user or system administrator. The job may or may not have been initiated.
  • SE: Special Exit. The job was requeued in a special state by the scheduler; it may or may not have been initiated.
  • ST: Suspended. The job has an allocation, but execution has been suspended and CPUs have been released for other jobs.
  • S: Suspended by user. The job has an allocation, but execution has been suspended and CPUs have been released for other jobs at the request of the user.
  • PR: Preempted. The job was preempted.
• How do I cancel a job?
  • You can cancel a job by using the scancel command.
  • For example, scancel jobid will cancel the job with the given jobid.
• How do I check the statistics of a finished job?
  • You can check the statistics of a finished job by using the sacct command.
  • For example, sacct -j jobid will show the statistics of the job with the given jobid.

Additional Resources

• Tracking the accounts/usage: https://coldfront.rockfish.jhu.edu/
• Login node: ssh userid@login.rockfish.jhu.edu
• Help desk: help@rockfish.jhu.edu if you face any issues, email these folks! :)
• User Guide: https://www.arch.jhu.edu/access/user-guide/
• System configuration: https://www.arch.jhu.edu/about-rockfish/system-configuration/
• Tutorials: https://marcc.readthedocs.io/
• FAQs: https://www.arch.jhu.edu/access/faq/
• A useful collection of slides on Rockfish.
• Debugging with TotalView

If you struggle with SLURM, these are useful cheatsheets:

• Slurm queueing system
• Slurm basics
• Tutorial: Using Slurm Workload Manager
• Job submit commands with examples