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GPU computing

GPU job

To run GPU calculation, the user needs to:

  1. specify number of GPU cards (parameter ngpus), and
  2. choose one of the gpu queues explicitly.

name of GPU queue must be specified

Contrary to normal job, the GPU jobs will not be routed into appropriate queue according to parameter ngpus only. The name of the queue (parameter -q) has to be specified, too.

GPU queue name Walltime range
gpu@meta-pbs.metacentrum.cz 00:00:00 - 24:00:00
gpu_long@meta-pbs.metacentrum.cz 00:00:00 - 336:00:00
gpu@cerit-pbs.cerit-sc.cz 00:00:00 - 24:00:00

GPU jobs on the konos cluster can be also run via the priority queue iti@meta-pbs.metacentrum.cz (queue for users from ITI - Institute of Theoretical Informatics, Univ. of West Bohemia).

Example

qsub -I -q gpu -l select=1:ncpus=1:ngpus=1:scratch_local=10gb -l walltime=24:0:0

Specific PBS resources

gpu mem

PBS parameter gpu_mem specifies minimum amount of memory that the GPU card will have.

qsub -q gpu -l select=1:ncpus=1:ngpus=1:gpu_mem=10gb ...

gpu_cap

PBS parameter gpu_cap is Cuda compute capability as defined on this page.

cuda_version

PBS parameter cuda_version is version of CUDA installed.

Specific system variables

IDs of GPU cards are stored in CUDA_VISIBLE_DEVICES variable.

These IDs are mapped to CUDA tools virtual IDs. Though if CUDA_VISIBLE_DEVICES contains value 2, 3 then CUDA tools will report IDs 0, 1.