SouthernMethodistUniversity/mp_testing

Notes

All code in this repo is for testing. The code may not work and may change. Pull requests and issues welcome.

See Quick Start Notes for a short overview of MP usage.

Usage Example

git clone https://github.com/SouthernMethodistUniversity/mp_testing.git
cd mp_testing/demos/00_nemo
./submit_jobs.sh

Applications

• LAMMPS (NGC)
• AMBER
• NAMD (NGC)
• OpenMM
• Gaussian
• VASP
• CRYSTAL
• Q-Chem
• Quantum Espresso

Analysis Tools

• Memory profiling
• Performance profiling

Libraries/APIs

• Raja
• Magma
• heFFTe
• Pandas
• NumPy
• TensorFlow
• PyTorch
• DALI

Languages

• C
• C++
• Python
• Some custom layer in C++/CUDA
• Fortran
• CUDA Fortran
• Julia

Molecular Dynamics

• OpenMM
• AMBER
• Desmond
• GROMACS
• Mentioned MIC modes?
• NGC for Keras/TF and Pytorch

Issues

• Can't run enroot images directly via enroot start hello_world.sqsh. The OS needs squashfuse and fuse-overlayfs installed. I installed these on Easley and it works.
• Custom build and final images for containerized Spack environments fails due to apparently assuming that Spack already exists. See: 01_spack/spack_nvhpc.yaml.
• Spack-blessed NVIDIA container fails to build due to public key error. See: 01_spack/spack_lammps.yaml.
• export ENROOT_MOUNT_HOME=1 to bind $HOME.
• Default flags and target=zen2 gave LAMMPS run times of 4:44, while target=zen2 cppflags=-O3
• Running containers or non-hpc-x MPI produces warnings about Unknown interface name / An invalid value was given for btl_tcp_if_include. It appears not to see the Mellanox / IB correctly?

Maybe Useful

• https://www.nvidia.com/content/dam/en-zz/Solutions/Data-Center/tesla-product-literature/gpu-applications-catalog.pdf
• https://docs.nvidia.com/deeplearning/frameworks/support-matrix/index.html
• https://docs.nvidia.com/deeplearning/dali/user-guide/docs/index.html
• https://secure.cci.rpi.edu/wiki/

Things we need to plan for

• How and when do we decide we're updating Nvidia Drivers / Cuda. I think we need to be very clear about this if we're not going to maintain the latest and greatest. (we're currently on 11.4, but 11.7 and associated drivers are available)