Page Comparison

Two BRCF research pods have NVIDIA GPU servers; however their use is restricted to the groups who own those pods. 

...

• Dell PowerEdge R750XA
• dual 24-core/48-thread CPUs (48 cores, 96 hyperthreads total)
• 512 GB system RAM
• 2 NVIDIA Ampere A100 GPUs w/32GB onboard RAM each

...

• GIGABYTE MC62-G40-00 workstation
  
• AMD Ryzen 5975WX CPU (32 cores, 64 hyperthreads total)
• 512 GB system RAM
• 1 4 NVIDIA RTX 6000 Ada GPUs

GPU-enabled software

Resources

Tests

Use nvidia-smi to verify access to the server's GPUs

AlphaFold

The AlphaFold protein structure solving software is available on all AMD GPU servers. The /stor/scratch/AlphaFold directory has the large required database, under the data.3 sub-directory. There is also an AMD example script /stor/scratch/AlphaFold/alphafold_example_amd.shand an alphafold_example_nvidia.sh script if the POD also has NVIDIA GPUs, (e.g. the Hopefog pod). Interestingly, our timing tests indicate that AlphaFold performance is quite similar on all the AMD and NVIDIA GPU servers.

TensorFlow and PyTorch examples

Two Python scripts are located in /stor/scratch/GPU_info that can be used to ensure you have access to the server's GPUs from TensorFlow or PyTorch. Run them from the command line using time to compare the run times.

• Tensor Flow
  • time ( python3 /stor/scratch/GPU_info/tensorflow_example.py )
    • should take 30s or less with GPU, > 1 minute with CPUs only
    • this is a simple test, and on CPU-only servers multiple cores are used but only 1 GPU, one reason why the times are not more different
• PyTorch
  
  • time ( python3 /stor/scratch/GPU_info/pytorch_example.py )
    • takes ~30s or less to complete on wilkcomp03
    • takes ~1m to complete on hfogcomp04.

If GPUs are available and accessible, the output generated will indicate they are being used.

Resources

Use nvidia-smi to verify access to the server's GPUs

CUDA

Both hfogcomp04 has and wilkcomp03 have both CUDA 11 and CUDA 12 installed. wilkcomp03 has only CUDA 12, and needs CUDA 11 installed.

AlphaFold

Native AlphaFold for NVIDIA CPUs has not yet been installed; however AlphaFold databases are available in /stor/scratch/AlphaFold.