Cluster 7

Introduction

A cluster built on Rocky 9 linux distribution which is under the RHEL umbrella.

How to Request for Access

Contact a system administrator.

How to Login

1. Remote

   ssh <user>@epsilon.compbio.ucsf.edu

SLURM Nodes

• To list partitions

  sinfo

• To list all nodes and their information

  sinfo -lNe

CPU Servers

• cpu02 (128 Cores, 256 Threads, 1TB RAM)
• cpu[03-17] (48 Cores, 96 Threads, 256GB RAM)
• I make that 1696 concurrent processes.

GPU Servers

• gpu01 8 x GeForce RTX 2080 Ti 10 GB VRAM. (48 Cores, 96 Threads, 758GB RAM, 8 x RTX 2080 Ti)
• gpu02 4 x GForce RTX 3090 . 24 GB VRAM. (48 Cores, 96 Threads, 758GB RAM, 4 x RTX 3090). 2.4 Ghz. Xeon Gold 6240R.
• gpu03 5 x GeForce GTX 1080 Ti 10 GB VRAM + 3 x Titan Xp 12 GB VRAM. 64 cpus. Xeon E5-2697 v4 @ 2.6 GHz
• gpu04 4 x Titan RTX. 24 GB VRAM. 96 cores. Xeon Gold 6240R @ 2.4 GHz
• gpu05 4 x Titan RTX. 24GB VRAM. 96 cpus. Xeon Gold 6240R 2.4 GHz
• gpu06 4 x GeForce RTX 3090. 24 GB VRAM. 96 cpus. Xeon Gold 6240R 2.4 GHz

• I make that 32 GPUs and 544 cpu processes.

NFS Servers

• home01
• hdd02

Global Modules/Software

• To check the list of available modules

  /* Long version */
  module available 
  
  /* OR */
  
  /* Short version */
  ml av

• To load a module(s)

  /* Single module */
  module load dock 
  
  /* OR */
  
  ml dock 
  
  ==================================
  
  /* Multi-module */
  module load dock python/3.12, schrodinger
  
  /* OR */
  
  ml dock python/3.12 schrodinger

• To list all loaded modules

  module load
  
  /* OR */
  
  ml

• To unload a module

  module unload <module>
  /* OR */
  ml unload <module>

• To unload all modules

  module purge 
  /* OR */
  ml purge

Guidelines and Recommendations

• /nfs/home is for code (backed up to github or gitlab)
• /nfs/hdd01/work/<yourid> and /nfs/hdd02/work/<yourid> are good places to keep docking jobs. write to your sysadmin to set up a folder for you.
• jobs under slurm should write to local /scratch during the job, move back to your work area and clean up when job ends