Best practices for job submission: Difference between revisions

Much like the case of nodes with a large amount of memory, the nodes with GPUs are relatively uncommon so that any job which asks for a GPU will wait significantly longer in most cases. It's therefore in your interest to be sure that this GPU you had to wait so much longer to obtain is being used as efficiently as possible and that it is really contributing to improved performance in your jobs. A considerable amount of software does have a GPU option, for example such widely used packages as [[NAMD]] and [[GROMACS]], but only a small part of these program's functionality has been modified to make use of GPUs. For this reason, it is wiser to first test a small sample calculation both with and without a GPU to see what kind of speed-up you obtain from the use of this GPU. If your job only finishes 5% or 10% more quickly with a GPU, it's probably not worth the effort of waiting to get a node with a GPU as it will be idle during much of your job's execution.