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Batch Submission and Schedulers

A batch system will track the resources available on a system and determine when jobs can run on compute nodes. This is often conducted through separate applications of a resource manager (which tracks what resources are available on each compute node) and a job scheduler (which determines when jobs can run).
On the Spartan HPC system we use the Slurm Workload Manager, which combines both tasks into a single application.
To submit jobs to the cluster one needs to provide a job submission script.
The script consists of two sets of directives:

  • The first set are the resource requests that one is making to the scheduler. This includes how many nodes are needed, how many cores per node, what partition the job will run on, and how long these resources are required (walltime).


These scheduler directives must come first.

  • The second set is the batch of commands that are understood by the computer's operating system environment, the shell. This includes any modules that are being loaded, and the commands, including invoking other scripts, that will be run.

When a job is submitted to Slurm, it will go the scheduler which will receive information from the resource manager daemons that run on the compute nodes. The resource requests of the job are compared with the resources available and evaluated by a policy-based "Fair Share" system. When the jobs are available on the partition requested and the job has priority, it will run for as long as the time that the resources have been requested for. When the job completes (or aborts) the scheduler will write an output file, and the application may as well.

Spartan's Partitions

HPC systems often are built around queues or partitions representing homogenous hardware or administrative restrictions. With Slurm on Spartan, one can view the list of partitions with the sinfo -s command, like the following:

cascade*            up 30-00:00:0        3/78/0/81 spartan-bm[001-029,039-046,049,053-066,087-115]
rhel7             down 30-00:00:0        0/10/0/10 spartan-bm[116-125]
long                up 90-00:00:0          0/2/0/2 spartan-bm[031-032]
bigmem              up 14-00:00:0          0/5/0/5 spartan-bm[030,033-034,037-038]
argali              up 30-00:00:0        0/21/2/23 spartan-argali[01-23]
msps2               up 30-00:00:0          0/2/0/2 spartan-bm[047-048]
punim0396           up 30-00:00:0          0/1/0/1 spartan-bm050
gpu-a100            up 7-00:00:00        0/29/0/29 spartan-gpgpu[099-127]
gpu-a100-short      up    4:00:00          0/2/0/2 spartan-gpgpu[128-129]
gpu-a100-preempt    up 7-00:00:00        0/23/0/23 spartan-gpgpu[098,131,144-159,161-165]
gpu-v100-preempt    up 7-00:00:00          0/4/0/4 spartan-gpgpu[084-085,089-090]
feit-gpu-a100       up 7-00:00:00        0/21/0/21 spartan-gpgpu[144-159,161-165]
deeplearn           up 30-00:00:0        0/31/7/38 spartan-gpgpu[065-071,078-082,086-088,091-096,132-143,160,166-169]
interactive         up 2-00:00:00          0/4/0/4 spartan-bm[083-086]
extremecfd          up 14-00:00:0          0/1/0/1 spartan-gpgpu097
feit-geoandco       up 14-00:00:0          0/1/0/1 spartan-gpgpu131
mig                 up 30-00:00:0        0/10/0/10 spartan-bm[067-076]
turbsim             up 30-00:00:0          0/6/0/6 spartan-bm[077-082]
mig-gpu             up 30-00:00:0          0/2/0/2 spartan-gpgpu[084-085]
gpgputest           up 30-00:00:0          0/4/0/4 spartan-gpgpu[089-090,098,130]
physicaltest        up 30-00:00:0          0/2/0/2 spartan-bm[035-036]
physicaltest-amd  down 30-00:00:0          0/1/0/1 spartan-bm128
adhoc             down 14-00:00:0          0/0/0/0 
debug               up 30-00:00:0      3/233/9/245 spartan-argali[01-23],spartan-bm[001-050,053-125,128],spartan-gpgpu[065-071,078-082,084-169]

This provides the partition name (e.g., cascade, long, gpgpu, etc).
Some of the partitions are restricted to particular projects (e.g., punim0396, deeplearn, etc) and will require membership to a relevant group and an additional scheduler directive to access.
Others (e.g., cascade, long) have general access.
In addition to the name, the output lists the Availability of the partition (up, down), and the maximum walltime that is available for job submission. Normally, this is 30-00:00:0, or 30 days for most partitions. If it is less than 30 days this indicates that a planned outage is pending, with the maximum walltime decrementing as the day of the outage approaches.  
Following this is a summary status of nodes in the partition. These are either Allocated, Idle, Out, and Total. Finally, the list of nodes in the partition with hostnames and ranges. Note that individual nodes can belong to multiple partitions.

Partition Utilisation

Before submitting a job it may be worthwhile to check the utilisation of a partition. Whilst the sinfo -s command gives a high-level overview of the status of all the partitions, the sinfo -O cpusstate command can be used to specify the status of a partitular partition, e.g., sinfo -O cpusstate -p cascade, sinfo -O cpusstate -p gpgpu etc).

For example  

$ sinfo -p cascade -O cpusstate

As can be seen from the example, cascade has 5904 CPU cores, 5648 are being used, and 256 cores are currently idle.

Job Priority

Spartan is a very busy system, with 100% worker node allocation on most days. Demand for HPC resources typically surpasses supply. Because no system has an infinite number of cores there needs to be some sort of method which establishes an order when a job can run.  
By default, the scheduler allocates on a simple "first-in, first-out" (FIFO) approach. However the applications of rules and policies can change the priority of a job, which will be expressed as a number to the scheduler. Some of the main factors are:

  • Job size : The number of nodes, cores, or memory that a job is requesting. A higher priority is given to larger jobs.
  • Wait time : The priority of a job increases the longer it has been in the queue.
  • Fairshare : Fairshare takes into account the resources used by a project's jobs in the last 14 days. The more resources used by a project's jobs in the last 14 days, the lower the priority of the new jobs for that project.
  • Backfilling: This allows lower priority jobs to run as long as the batch system knows they will finish before the higher priority job needs the resources. This makes it very important that the users specify their CPU, memory and walltime requirements accurately, to make best use of the backfilling system.
  • Partition and QoS: A factor associated with each node partition.

On Spartan, the calculated priority is dominated by the fairshare component (aside from QoS restrictions), so the most common reason for a job taking a long time to start is because of the amount of resources consumed in the last 14 days.
You can see your job priority, and what makes up the priority, by using the sprio command

# sprio -j 12409951
       12409951 cascade        4240       3000       1233          6          1          0
Note: Users with COVID-19 projects may gain an additional priority with the directive --qos=covid19 at job submission