MASAMUNE-II User manual

The trial period will continue until the end of June 2025, and consumed node hours will be added in July. Please note that the manual may be updated during the trial period as needed. If you encounter any issues with how to use the system or with the content of the manual, we would appreciate it if you could report them to us.

Contents:

• 1. How to Login
  • 1.1. Node name of the supercomputing system in CCMS
  • 1.2. Register SSH Public Key
  • 1.3. How to login servers
  • 1.4. How to use SSH relay server
  • 1.5. （Reference）How to login with Tera Term（Windows）
• 2. Configuration of storage
• 3. Job submit/management commands
  • 3.1. Job submit command（qsub command）
  • 3.2. Format of an execution script
  • 3.3. Interactive mode
  • 3.4. Submitting jobs to Shared-Queue
  • 3.5. Job management command
  • 3.6. Display information about used and remained time of job execution
  • 3.7. How to execute a MPI job
  • 3.8. List of queues
• 4. Compilers and Libraries
  • 4.1. Intel Compiler
  • 4.2. NVIDIA HPC Compiler
  • 4.3. CUDA toolkit
  • 4.4. Usage of Library
• 5. Usage of applications
  • 5.1. Applications
  • 5.2. Gaussian
  • 5.3. GaussView 6
  • 5.4. AVS/Express Developer
  • 5.5. Materials Studio
  • 5.6. CRYSTAL17
  • 5.7. VASP 5
  • 5.8. VASP 6
  • 5.9. WIEN2k
  • 5.10. ADF
  • 5.11. ADF GUI
  • 5.12. SIESTA
  • 5.13. ABINIT
  • 5.14. CPMD
  • 5.15. QUANTUM ESPRESSO
  • 5.16. LAMMPS
  • 5.17. XCrySDen
  • 5.18. Keras
  • 5.19. TensorFlow
  • 5.20. PyTorch
  • 5.21. Japanese-compatible TeX
• 6. Usage of Python
  • 6.1. About using Python
  • 6.2. Install pyenv
  • 6.3. Backing up the pyenv environment from the previous system
  • 6.4. Setting environment variables
  • 6.5. Operational check
  • 6.6. Basic usage
  • 6.7. Execution method
• 7. CCMS JupyterLab