Using GPUs with Slurm

For general advice on job scheduling, see Running jobs.

Available hardware

These are the GPUs currently available:

Cluster	# of Nodes	Slurm type specifier	Default?	Per node			GPU model	GPU mem (GiB)	Notes
				CPU cores	CPU memory	GPUs
Béluga	172	v100	default	40	191000M	4	V100-SXM2	16	All GPUs associated with the same CPU socket, connected via NVLink
Cedar	114	p100	default	24	128000M	4	P100-PCIE	12	Two GPUs per CPU socket
	32	p100l		24	257000M	4	P100-PCIE	16	All GPUs associated with the same CPU socket
	192	v100l		32	192000M	4	V100-SXM2	32	Two GPUs per CPU socket; all GPUs connected via NVLink
Graham	160	p100	default	32	127518M	2	P100-PCIE	12	One GPU per CPU socket
	7	v100		28	183105M	8	V100-PCIE	16	See Graham: Volta GPU nodes
	2	v100l		28	183105M	8	V100-?	32	See Graham: Volta GPU nodes
	30	t4		44	192000M	4	Tesla T4	16	Two GPUs per CPU socket
	6	t4		16	192000M	4	Tesla T4	16
Hélios	15	k20	default	20	110000M	8	K20	5	Four GPUs per CPU socket
	6	k80		24	257000M	16	K80	12	Eight GPUs per CPU socket
Mist	54	(none)	default	32	256GiB	4	V100-SXM2	32	See Mist specifications
Arbutus	9	(none)		80	384GiB	4	V100	32	Cloud resource, not schedulable via Slurm, included here for completeness

Specifying the type of GPU to use

Some clusters have more than one GPU type available (Cedar, Graham, Hélios), and some clusters only have GPUs on certain nodes (Béluga, Cedar, Graham). You can choose the type of GPU to use by supplying to Slurm the type specifier given in the table above, e.g.:

#SBATCH --gres=gpu:p100:1

If you do not specify a type, Slurm will send your GPU job to a type designated "default" in the table above.

Mist

Mist is a cluster comprised of IBM Power9 CPUs (not Intel x86!) and NVIDIA V100 GPUs. Users with access to Niagara can also access Mist. To specify job requirements on Mist, please see the specific instructions on the SciNet web site.

Single-core job

If you need only a single CPU core and one GPU:

File : gpu_serial_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --gres=gpu:1              # Number of GPUs (per node)
#SBATCH --mem=4000M               # memory (per node)
#SBATCH --time=0-03:00            # time (DD-HH:MM)
./program                         # you can use 'nvidia-smi' for a test

Multi-threaded job

For GPU jobs asking for multiple CPUs in a single node:

File : gpu_threaded_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --gres=gpu:1              # Number of GPU(s) per node
#SBATCH --cpus-per-task=6         # CPU cores/threads
#SBATCH --mem=4000M               # memory per node
#SBATCH --time=0-03:00            # time (DD-HH:MM)
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
./program

For each GPU requested on:

• Béluga, we recommend no more than 10 CPU cores.
• Cedar, we recommend no more than 6 CPU cores per P100 GPU (p100 and p100l) and no more than 8 CPU cores per V100 GPU (v100l).
• Graham, we recommend no more than 16 CPU cores.

MPI job

File : gpu_mpi_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --gres=gpu:4              # Number of GPUs per node
#SBATCH --nodes=2                 # Number of nodes
#SBATCH --ntasks=48               # Number of MPI process
#SBATCH --cpus-per-task=1         # CPU cores per MPI process
#SBATCH --mem=120G                # memory per node
#SBATCH --time=0-03:00            # time (DD-HH:MM)
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun ./program

Whole nodes

If your application can efficiently use an entire node and its associated GPUs, you will probably experience shorter wait times if you ask Slurm for a whole node. Use one of the following job scripts as a template.

Requesting a GPU node on Graham

File : graham_gpu_node_job.sh

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:2
#SBATCH --ntasks-per-node=32
#SBATCH --mem=127000M
#SBATCH --time=3:00
#SBATCH --account=def-someuser
nvidia-smi

Requesting a P100 GPU node on Cedar

File : cedar_gpu_node_job.sh

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:p100:4
#SBATCH --ntasks-per-node=24
#SBATCH --exclusive
#SBATCH --mem=125G
#SBATCH --time=3:00
#SBATCH --account=def-someuser
nvidia-smi

Requesting a P100-16G GPU node on Cedar

There is a special group of GPU nodes on Cedar which have four Tesla P100 16GB cards each. (Other P100 GPUs in the cluster have 12GB and the V100 GPUs have 32G.) The GPUs in a P100L node all use the same PCI switch, so the inter-GPU communication latency is lower, but bandwidth between CPU and GPU is lower than on the regular GPU nodes. The nodes also have 256GB RAM. You may only request these nodes as whole nodes, therefore you must specify --gres=gpu:p100l:4. P100L GPU jobs up to 28 days can be run on Cedar.

File : p100l_gpu_job.sh

#!/bin/bash
#SBATCH --nodes=1 
#SBATCH --gres=gpu:p100l:4   
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24    # There are 24 CPU cores on P100 Cedar GPU nodes
#SBATCH --mem=0               # Request the full memory of the node
#SBATCH --time=3:00
#SBATCH --account=def-someuser
hostname
nvidia-smi

Packing single-GPU jobs within one SLURM job

If you need to run four single-GPU programs or two 2-GPU programs for longer than 24 hours, GNU Parallel is recommended. A simple example is given below:

cat params.input | parallel -j4 'CUDA_VISIBLE_DEVICES=$(({%} - 1)) python {} &> {#}.out'

In this example the GPU ID is calculated by subtracting 1 from the slot ID {%}. {#} is the job ID, starting from 1.

A params.input file should include input parameters in each line, like this:

code1.py
code2.py
code3.py
code4.py
...

With this method, users can run multiple tasks in one submission. The -j4 parameter means GNU Parallel can run a maximum of four concurrent tasks, launching another as soon as each one ends. CUDA_VISIBLE_DEVICES is used to ensure that two tasks do not try to use the same GPU at the same time.

Message Passing Interface