Using GPUs¶
The nxg and sbg nodes contain GPU cards that can provide huge acceleration for certain types of parallel computing tasks, via the CUDA and OpenCL frameworks.
Access to GPU nodes
Access to GPU nodes is available for free to QM Researchers. Please contact us if you would like to use these nodes so we can add you to the allowed user list and help you get started with your initial GPU job submission. Note that access to GPU nodes is not permitted for Undergraduate and MSc students
Applications with GPU support¶
There is a
considerable number of
scientific and analytical applications with GPU support. While some have GPU
support out of the box, such as Matlab and
Ansys, others may require specific GPU-ready
builds. These may appear in the module avail list with a -gpu suffix. If
you require GPU support adding to a specific application, please
submit a request for a GPU build and provide some test
data.
Be aware that not every GPU-capable application will run faster on a GPU for your code. For example, CP2K only has a GPU port of the DBCSR sparse matrix library. If you are not using this library in your code then you will not experience a performance boost.
Submitting jobs to GPU nodes¶
To request a GPU the -l gpu=<count> option should be used in your job
submission, and the scheduler will automatically select a GPU node. Note that
requests are handled per node, so a request for 64 cores and 2 GPUs will result
in 4 GPUs across two nodes. Examples are shown below.
Selecting a specific GPU type¶
For compatibility, you may optionally require a specific GPU type. For example,
CUDA version 8 predates the V100 GPU, and is not supported, so
-l gpu_type=kepler would select nodes using the K80 GPU instead. Conversely,
nodes with the V100 GPU may be selected with -l gpu_type=volta.
GPU Card Allocation¶
Ensure you set card allocation
Failure to set card allocation may result in contention with other users jobs and result in your job being killed.
Requesting cards with parallel PE
If using the parallel parallel environment requests will be exclusive,
please ensure that you correctly set slots and gpu to fill the node.
Once a job starts, the assigned GPU cards are listed in the SGE_HGR_gpu
environment variable as a space separated list. To ensure correct use of
allocated GPU cards you need to limit your computation to run only on the
allocated cards.
For Cuda this can be done by exporting the CUDA_VISIBLE_DEVICES environment
variable which should be a comma separated list:
$ echo $SGE_HGR_gpu 0 1 # Set CUDA_VISIBLE_DEVICES, # this converts the space separated list into a comma separated list $ export CUDA_VISIBLE_DEVICES=${SGE_HGR_gpu// /,}
For OpenCL, this can be done via the GPU_DEVICE_ORDINAL environment variable
which should be a comma separated list:
$ echo $SGE_HGR_gpu 0 1 # Set GPU_DEVICE_ORDINAL, # this converts the space separated list into a comma separated list $ export GPU_DEVICE_ORDINAL=${SGE_HGR_gpu// /,}
Checking GPU usage¶
GPU usage can be checked with the nvidia-smi command e.g.:
$ nvidia-smi -l 1 Tue May 1 13:30:11 2018 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 375.26 Driver Version: 375.26 | |-------------------------------+----------------------+----------------------+ | 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 K80 On | 0000:83:00.0 Off | 0 | | N/A 32C P0 147W / 149W | 1211MiB / 11439MiB | 97% Default | +-------------------------------+----------------------+----------------------+ | 1 Tesla K80 On | 0000:84:00.0 Off | 0 | | N/A 31C P8 30W / 149W | 0MiB / 11439MiB | 0% Default | +-------------------------------+----------------------+----------------------+ +-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=============================================================================| | 0 28939 C ...pose/build/examples/openpose/openpose.bin 1207MiB | +-----------------------------------------------------------------------------+
In this example we can see that the process is using GPU 0. We use the -l 1
option which tells nvidia-smi to repeatedly output the status.
Example job submissions¶
Request one GPU (Cuda)¶
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 8 # 8 cores (32 per gpu node) #$ -l h_rt=10:0:0 # 10 hour runtime #$ -l h_vmem=7.5G # 7.5 * 8 = 60G #$ -l gpu=1 # request 1 GPU per host export CUDA_VISIBLE_DEVICES=${SGE_HGR_gpu// /,} ./run_code.sh
Part node requests
When using a single graphics card, you will need to request the
appropriate slots and memory on the node. We recommend requesting
7.5G per core, which may be increased to 11.5G if using the
-l gpu_type=volta complex to ensure the job runs on the sbg nodes.
Request two GPUs on the same box (OpenCL)¶
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 16 # 16 cores (32 per gpu node) #$ -l h_rt=10:0:0 # 10 hour runtime #$ -l h_vmem=7.5G # 7.5 * 16 = 120G #$ -l gpu=2 # request 2 gpu per host export GPU_DEVICE_ORDINAL=${SGE_HGR_gpu// /,} ./run_code.sh
Request four GPUs on the same box (OpenCL)¶
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 32 # 32 cores (32 per gpu node) #$ -l h_rt=10:0:0 # 10 hour runtime #$ -l gpu=4 # request 4 gpu per host #$ -l exclusive # request exclusive access to the node export GPU_DEVICE_ORDINAL=${SGE_HGR_gpu// /,} ./run_code.sh
Request four GPUs across multiple boxes (Cuda)¶
Infiniband
When requesting two GPU nodes, make sure to include the "infiniband_direct" parameter. More information here.
#!/bin/bash #$ -cwd #$ -j y #$ -pe parallel 64 # 64 cores (32 per nxg node) #$ -l h_rt=10:0:0 # 10 hour runtime #$ -l gpu=2 # request 2 gpu per host (2 per nxg node) #$ -l infiniband_direct=nxg3-4 # request nxg3 & nxg4 infiniband direct export CUDA_VISIBLE_DEVICES=${SGE_HGR_gpu// /,} ./run_code.sh