Goal: List some common issues and how to resolve.
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How do I know what number of nodes, cores, memory etc to ask for my jobs?
Understand your software and application.
Read the docs – look at the help for commands/options.
Can it run multiple threads - use multi cores (OpenMP) / nodes (MPI)?
Can it use a GPU? Nvidia cuda.
Are their suggestions on data and memory requirements?
How do I find out whether a cluster/partition supports these resources?
How do I find out whether these resources are available on the cluster?
Consult the wiki: Medicine Hardware Summary Table
How long will I have to wait in the queue before my job starts?
How busy is the cluster?
Current Cluster utilization: Commands
sinfo/arccjobs/pestatand OnDemand’s MedicineBow System Status page.
How do I monitor the progress of my job?
Slurm commands:
squeue
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Common Issues
Not defining the
accountandtimeoptions.The
accountis the name of the project you are associated with. It is not your username.Requesting combinations of resources that can not be satisfied: Medicine Hardware Summary Table
For example, you can not request 40 cores on a compute node with a max of 32.
Requesting too much memory, or too many GPU devices with respect to a partition.
My job is pending? Why?
Because the resources are currently not available.
Be mindful of specialized nodes (such as our huge mem with 4T of RAM) we might only have a few of them.
Have you unnecessarily defined a specific partition (restricted yourself) that is busy?
We only have a small number of GPUs.
This is a shared resource - sometimes you just have to be patient…
Check current cluster utilization.
What ever resources you are asking for are currently not available. Slurm will start you job when they become available.
We do empathize and under the frustration, but this is a shared resource, and sometimes we just have to be patient and wait in the queue.
Preemption: Users of an investment get priority on their hardware.
We have the
non-investorpartition.
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Pending Jobs and Scheduled Cluster Maintenance
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When we have schedule maintenance on the cluster, an announcement will go out and indicate the date/time that this is schedules to start. All jobs currently running on the cluster are allowed to finish, and we can aspect further jobs if Slurm can complete them before the maintenance starts. |
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Be conscious of: If an announcement goes out on a Monday that maintenance is to start on the following Friday, there is only a window of four days that any new job must complete within. If you submit a job with a wall time of seven days, then this can not and will not be started since it can not complete before Friday. You job will be accepted by Slurm, queued, have a status of pending, and automatically started once maintenance is completed and Slurm is restarted. |
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Required: Account and Walltime
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