MASAMUNE-II User manual

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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）
  • 1.6. （Reference）How to transfer file with WinSCP（Windows）
• 2. Storage configuration and usage
  • 2.1. Storage configuration
  • 2.2. How to check /home usage
• 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 execution order
  • 3.6. Job management command
  • 3.7. Display information about used and remained time of job execution
  • 3.8. How to execute a MPI job
  • 3.9. List of queues
• 4. Compilers and Libraries
  • 4.1. Intel Compiler
  • 4.2. NVIDIA HPC Compiler
  • 4.3. CUDA toolkit
  • 4.4. GNU Compilers and OpenMPI
  • 4.5. 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. CP2K
  • 5.18. Wannier90
  • 5.19. GROMACS
  • 5.20. TOMBO
  • 5.21. OpenMX
  • 5.22. SALMON
  • 5.23. SMASH
  • 5.24. ELK
  • 5.25. ALAMODE
  • 5.26. XCrySDen
  • 5.27. Keras
  • 5.28. TensorFlow
  • 5.29. PyTorch
  • 5.30. 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 Operation Manual
  • 7.1. How to Connect to CCMS JupyterLab Environment
  • 7.2. How to Login
  • 7.3. How to Use CCMS JupyterLab
  • 7.4. How to Create a Conda Environment