Many packages can take advantage of GPUs to perform computations faster. To request GPUs, you should specify an additional option ngpus in the resource limits specification in your batch script (batch jobs) or qsub command (interactive jobs). All GPU nodes on Palmetto have 2 GPUs per node, so the value for ngpus can only be 1 or 2. In addition, you can also specify the option gpu_model (m2075, k20, k40, p100 or v100) to request a specific GPU type.

$ qsub -I  -l select=1:ncpus=1:ngpus=1:gpu_model=k20:mem=2gb,walltime=2:00:00

To confirm whether your application is using the GPU, you can SSH into the node that you currently have a job running on, and run the nvidia-smi command, which will list all the processes running on the node that are using the GPU. In addition to /usr/bin/X, if you see your application in this list, then it is using the GPU:

$ ssh node1800
$ nvidia-smi

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 396.26                 Driver Version: 396.26                    |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla K20m          Off  | 00000000:24:00.0 Off |                    0 |
| N/A   42C    P0    75W / 225W |    114MiB /  4743MiB |     76%      Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K20m          Off  | 00000000:27:00.0 Off |                    0 |
| N/A   21C    P8    16W / 225W |     16MiB /  4743MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID   Type   Process name                             Usage      |
|=============================================================================|
|    0      3034      G   /usr/bin/X                                     4MiB |
|    0     30903      C   gmx                                           98MiB |
|    1      3034      G   /usr/bin/X                                     4MiB |
+-----------------------------------------------------------------------------+