MASAMUNE-II User manual
getting started
masamune-ii user manual
User manual(日本語)
CCMS
getting started
masamune-ii user manual
User manual(日本語)
CCMS

Index

Contents:

  • Getting Started
    • System Configuration of MASAMUNE-II
    • Logging In to the System
    • Transferring Files
    • Executing Calculations
  • 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
  • 8. How to Use Singularity
    • 8.1. Creating Container Images (pull)
    • 8.2. Cleaning the Cache (cache clean)
    • 8.3. How to Run Containers
    • 8.4. Job Script Examples

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5.1. Applications

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Contents:

  • 5.1. Applications
  • 5.2. Gaussian
    • 5.2.1. Gaussian utilities
  • 5.3. GaussView 6
  • 5.4. AVS/Express Developer
  • 5.5. Materials Studio
    • 5.5.1. Setting for Client PC’s hosts file
    • 5.5.2. SSH port forwarding to the license server and gateway server.
    • 5.5.3. How to set License server
    • 5.5.4. How to set Gateway
    • 5.5.5. How to execute
    • 5.5.6. How to execute CASTEP
    • 5.5.7. How to execute DMol3
    • 5.5.8. How to execute DFTB+
    • 5.5.9. How to execute FlexTS
    • 5.5.10. Confirming Job Status
    • 5.5.11. Canceling Job
  • 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
    • 5.27.1. Preparing Container Image (Frontend Node)
    • 5.27.2. Job Script Format
    • 5.27.3. Example
    • 5.27.4. Reference
  • 5.28. TensorFlow
    • 5.28.1. Preparing Container Image (Frontend Node)
    • 5.28.2. Job Script Format
    • 5.28.3. Example
    • 5.28.4. Reference
  • 5.29. PyTorch
    • 5.29.1. Preparing Container Image (Frontend Node)
    • 5.29.2. Job Script Format
    • 5.29.3. Example
    • 5.29.4. Reference
  • 5.30. Japanese-compatible TeX
  • ← 4.5. Usage of Library
  • 5.1. Applications →
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