NVIDIA GPU servers

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

Servers

Hopefog pod

hfogcomp04.ccbb.utexas.edu compute server on the Hopefog pod (Ellington/Marcotte):

• Dell PowerEdge R750XA

• dual 24-core/48-thread CPUs (48 cores, 96 hyperthreads total)

• 512 GB system RAM

• 2 NVIDIA Ampere A100 GPUs w/80GB onboard RAM each

• 1.8 TB NVMe drive mounted as /NVMe1 for fast local I/O – not backed up

hfogcomp05.ccbb.utexas.edu

• GIGABYTE MC62-G40-00

• 32-core/64-thread AMD Ryzen CPU

• 512 GB system RAM

• 4 NVIDIA RTX 6000 Ada GPUs, 48G RAM each

• 1 TB NVMe drive mounted as /NVMe1 for fast local I/O – not backed up

Wilke pod

wilkcomp03.ccbb.utexas.edu compute server

• GIGABYTE MC62-G40-00 workstation

• AMD Ryzen 5975WX CPU (32 cores, 64 hyperthreads total)

• 512 GB system RAM

• 4 NVIDIA RTX 6000 Ada GPUs

• 14 TB NVMe drive mounted as /ssd1 for fast local I/O – not backed up

Marcotte/Gilpin pod

gilpcomp01.ccbb.utexas.edu compute server 

• ThinkMate GPU server

• dual AMD EPYC 9654 96-core CPUs

• 768 GB system RAM

• 4 NVIDIA GH100 GPUs, 96G RAM each

• 4 NVMe drives for fast local I/O – not backed up

  • /ssd1, /ssd2 – 13 TB,  OS is on separate mirrored partitions

  • /ssd3, /ssd4 - 14 TB

GPU-enabled software

AlphaFold2

The AlphaFold2 protein structure solving software is available on all NVIDIA GPU servers. The /stor/scratch/AlphaFold directory has the large required database under the data.3 sub-directory. There is also an NVIDIA example script alphafold_example_nvidia.sh script. 

TensorFlow and PyTorch

Two Python example 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 like this:

• Tensor Flow

  • python3 /stor/scratch/GPU_info/tensorflow_example.py 

• PyTorch

  • python3 /stor/scratch/GPU_info/pytorch_example.py

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

Note that our system-wide CUDA-enabled TensorFlow and PyTorch versions are available in both the default Python 3 command-line environment (e.g. python3 or python3.12 on the command line) and also in the global JupyterHub environment that uses the Python 3.12 kernel. If you need a different combination of Python and  TensorFlow/PyTorch versions, you'll need to construct an appropriate custom conda environment (e.g. miniconda3 or anaconda).

GROMACS

An NVIDIA GPU-enabled version of the Molecular Dynamics (MD) GROMACS program is available on all NVIDIA GPU servers, and a CPU-only version is installed also.

The /stor/scratch/GROMACS directory has several useful resources:

• benchmarks/ - a set of MD benchmark files from https://www.mpinat.mpg.de/grubmueller/bench

• gromacs_nvidia_example.sh - a simple GROMACS example script taking advantage of the GPU, running the benchMEM.tpr benchmark by default.

• gromacs_cpu_example.sh - an GROMACS example script using the CPUs only.

Resources

CUDA

Both hfogcomp04 and wilkcomp03 have both CUDA 11.8 and CUDA 12.9 installed, under version-specific subdirectories of /usr/local. 

To ensure CUDA 11 is made active:

To ensure CUDA 12 is made active:

Neither version is specified by default, and some (but not all) programs rely on these environment variables. So you should activate one or the other before running software that uses GPUs.

After setting these environment variables, type nvcc --version to ensure you have access to the desired version.

CUDA drivers are installed under /usr/lib/x86_64-linux-gnu/. To see what version is currently installed:
ls /usr/lib/x86_64-linux-gnu/libnvidia-gl*. See https://saturncloud.io/blog/where-did-cuda-get-installed-in-my-computer/.

Command-line diagnostics

Use nvidia-smi to verify access to the server's GPUs and to monitor GPU usage.

Sharing resources

Since there's no batch system on BRCF POD compute servers, it is important for users to monitor their resource usage and that of other users in order to share resources appropriately.

• Use top to monitor running tasks (or top -i to exclude idle processes)

  • commands while top is running include:

  • M - sort task list by memory usage

  • P - sort task list by processor usage

  • N - sort task list by process ID (PID)

  • T - sort task list by run time

  • 1 - show usage of each individual hyperthread

    • they're called "CPUs" but are really hyperthreads

    • this list can be long; non-interactive mpstat may be preferred

• Use mpstat to monitor overall CPU usage

  • mpstat -P ALL to see usage for all hyperthreads

  • mpstat -P 0 to see specific hyperthread usage

• Use free -g to monitor overall RAM memory and swap space usage (in GB)

• Use nvidia-smi to  monitorGPU usage