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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

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.

Warning

With the introduction of new PBS server running on OpenPBS, the specification of gpu_cap parameter is done in two distinct ways depending whether you submit to PBS Pro or OpenPBS scheduler.

OpenPBS (new scheduler)

The user can specify a minimal required architecture (compute_XY), or a minimal required version within a given architecture (sm_XY).

Minimal architecture:

gpu_cap=compute_70   # will give you 7.0, 7.1, ... 7.5, but also 8.0, 9.0 ...

Minimal version of a chosen architecture, e.g. 7 ("Volta"):

gpu_cap=sm_72        # will give you 7.2 till 7.5, but not 8.0 and higher

The requirements can be combined in a comma-separated string.

Note

The commas are evaluated as an OR operand.

Example:

qsub -l select=1:ngpus=1:gpu_cap=\"sm_65,compute_70\":mem=4gb   # 6.5 or 7.0 and higher
qsub -l 'select=1:ngpus=1:gpu_cap="sm_65,compute_70":mem=4gb'   # dtto

Note

Note that the quotes enclosing the gpu_cap options must be protected against shell expansion either by escaping them or by enclosing the whole qsub command into single quotes.

PBS Pro (old schedulers)

qsub -q gpu -l select=1:ncpus=1:ngpus=1:gpu_cap=cuda70 ...

cuda_version

PBS parameter cuda_version is version of CUDA installed.

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.