Slurm: Common Questions and Issues and How to Resolve
Goal: List some common issues and how to resolve.
- 1 Common Questions
- 2 Common Issues
- 3 Pending Jobs and Scheduled Cluster Maintenance
- 4 Required: Account and Walltime
- 5 Correct Partitions
- 6 Timeouts
- 7 My Jobs Need to Run Longer than 7 Days
- 8 Requested node configuration is not available
- 9 OUT-OF-MEMORY: Segmentation Fault
- 10 My Job Stopped and Re-Started: Preemption
- 11 Why Is My Job One-of-Many on a Compute Node?
- 12 Can I Submit Jobs from within a Script?
- 13 Closing a Linux Session while Running an salloc
Common Questions
How do I know what number of nodes, cores, memory etc to ask for my jobs?
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?
How long will I have to wait in the queue before my job starts? How busy is the cluster?
How do I monitor the progress of my job?
My job finished before the wall time - what happens?
Common Questions: Suggestions
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
/pestat
and OnDemand’s MedicineBow System Status page.
How do I monitor the progress of my job?
Slurm commands:
squeue
My job finished before the wall time - what happens?
If your job has completely finished before the wall time you requested (e.g. it finished in two hours and you requested four hours) i.e. it’s status is no longer running, then Slurm will remove the job from the queue, release any requested resources back to the cluster, and allow other jobs to start running. Your job is not sitting idle on the cluster waiting for the wall time to run down.
Common Issues
Not defining the
account
andtime
options.The
account
is 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-investor
partition.
Pending Jobs and Scheduled Cluster Maintenance
Required: Account and Walltime
[]$ salloc
salloc: error: You didn't specify a project account (-A,--account). Please open a ticket at arcc-help@uwyo.edu for help.
salloc: error: Job submit/allocate failed: Invalid account or account/partition combination specified
[]$ salloc -A <project-name>
salloc: error: You didn't specify a walltime (-t, --time=) for the job. Please open a ticket at arcc-help@uwyo.edu for help.
salloc: error: Job submit/allocate failed: Requested time limit is invalid (missing or exceeds some limit)
[]$ salloc -t 10:00
salloc: error: You didn't specify a project account (-A,--account). Please open a ticket at arcc-help@uwyo.edu for help.
salloc: error: Job submit/allocate failed: Invalid account or account/partition combination specified
# The bare minimum:
[]$ salloc -A <project-name> -t 10:00
salloc: Granted job allocation 1250349
salloc: Nodes mbcpu-025 are ready for job
Correct Partitions
[]$ salloc -A <project-name> -t 10:00 --partition=mb-l40
salloc: error: invalid partition specified: mb-l40
salloc: error: Job submit/allocate failed: Invalid partition name specified
Timeouts
My Jobs Need to Run Longer than 7 Days
Requested node configuration is not available
Too many cores on a node:
Must define a GPU enabled partition:
OUT-OF-MEMORY: Segmentation Fault
My Job Stopped and Re-Started: Preemption
Why Is My Job One-of-Many on a Compute Node?
Can I Submit Jobs from within a Script?
Closing a Linux Session while Running an salloc
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