Software

• Overview of Installed Software
  • Libraries, Programming Languages, Developer Tools
  • Molecular dynamics, Quantum Chemistry
  • Mathematical and Simulation Packages
  • Deep Learning and AI
  • Software Tools for Genomic Analyses
  • Software Environments
  • Licence Information
• Environment Modules
• Alphafold2
  • Sequence alignment
  • Running the prediction on the GPU partition
  • Multimer runs
  • Multimer sequence alignment
  • Multimer GPU prediction
• Genomic Analyses
  • Available tools
  • Scheduled analyses (sbatch)
  • Interactive analyses
• Cray Programming Environment
  • Useful Compiler Settings
  • Cray Scientific and Math Libraries (CSML)
  • Cray Message Passing Toolkit (CMPT)
  • Performance Analysis and Optimization
  • Cray Debugger Support Tools (CDST)
  • Reference Manuals:
• Container environment
  • Singularity
  • Building containers
  • Running containers
  • Copying into the container
  • Python environment in the container
  • Nvidia CUDA containers
• Ansys Fluent
  • Creating Journal file in Ansys Fluent
  • Creating a SLURM script
  • Running a job
• OpenFOAM
  • Accessing OpenFOAM binaries @ Komondor
• AMBER
  • Submitting a AMBER calculation
  • Preparing the system for simulation
• GROMACS
  • Submitting a Gromacs calculation
  • Recommended hardware allocation
• ORCA
  • Submitting an ORCA calculation using the ubORKA script
  • Estimating computational requirements
• TeraChem
  • Submitting a TeraChem calculation
• MRCC
  • Submitting an MRCC calculation
  • Estimating computational requirements
• Q-Chem & BrianQC
  • Quick start guide for Q-Chem + BrianQC on HPC komondor
  • Prerequisites for Q-Chem & BrianQC
  • Starting Q-Chem or Q-Chem+BrianQC
  • Examples
• NAMD
  • Submitting a NAMD calculation
• MATLAB
  • Getting Started with Parallel Computing using MATLAB on the Komondor HPC Cluster
  • CONFIGURATION – MATLAB client on the cluster
  • INSTALLATION and CONFIGURATION – MATLAB client on the desktop
  • CONFIGURING JOBS
  • INTERACTIVE JOBS - MATLAB client on the cluster
  • INDEPENDENT BATCH JOB
  • PARALLEL BATCH JOB
  • HELPER FUNCTIONS
  • DEBUGGING
  • TO LEARN MORE
• Wolfram Mathematica
  • Adding license configuration
• Pytorch
  • Licence
  • Preinstalled Pytorch environments
  • Usage of Pytorch container
  • Usage of Pytorch module
  • Parallel jobs with Pytorch (torchrun):
  • Distributed Data Parallel (DDP)
  • Model parallelism
  • DDP + Model Parallelism
  • Solutions for suboptimal GPU usage
  • AI_env module package list
• Jupyter Environment
  • Accessing JupyterHub
  • Using JupyterHub
  • Stopping the Jupyter container
  • List of available containers
  • Using your own container
  • IPython Parallel