High Performance Computing Facility (CM-HPC) Overview

The facility provides a high-performance computing environment for processing the large datasets generated by Cryo-Electron Microscopy (Cryo-EM). Key features include:

  1. Pre-installed Software
    • Major software is pre-installed and available for all users.
    • Users can access and switch between software environments using environment modules with simple commands (e.g., module load <software>).
  2. Storage and Disk Quota
    • Users are allocated disk space for storage.
    • Disk quota can be increased or decreased as needed.
    • Charges apply for user accounts and storage size. Please refer to the detailed charging policies on the provided website.
  3. Job Submission and Resource Allocation
    • Jobs are submitted via a batch job system (SLURM).
    • Jobs are executed on available compute nodes, subject to constraints on maximum resource usage.
    • If the general job queues do not meet your needs, you can request a customized job queue by submitting details of your job execution plan and resource requirements. Custom queues are created on a short-term basis after review and subject for approval.
    • If you have special requirements, please reach out to us to discuss options. All such requests are subject to resource availability and prior approval.

Key Commands and Usage

  1. Environment Modules
    • Load software: module load <software>
    • Unload software: module unload <software>
    • List available software: module avail
    • List loaded software: module list
  2. Job Submission (SLURM)
    • Submit a job: sbatch <job_script>
    • Check job status: squeue
    • Delete a job: scancel <job_id>

Best Practices

  1. Optimize Resource Usage
    • Request only the resources you need to avoid unnecessary charges.
    • Use efficient algorithms and scripts to minimize computation time.
  2. Monitor Job Status
    • Regularly check the status of your jobs using squeue.
    • Debug and review related log of your failed jobs.
  3. Backup Important Data
    • Regularly back up your data to avoid loss in case of system issues.

If you have specific questions or need further assistance, feel free to contact us: