Cluster 7: Difference between revisions
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Jgutierrez6 (talk | contribs) (Created page with "== 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 == #Remote #: <source>ssh <user>@epsilon.compbio.ucsf.edu</source> #On-premise #: <source>ssh <user>@login02.compbio.ucsf.edu</source>") |
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#Remote | #Remote | ||
#: <source>ssh <user>@epsilon.compbio.ucsf.edu</source> | #: <source>ssh <user>@epsilon.compbio.ucsf.edu</source> | ||
== SLURM Nodes == | |||
*To list partitions | |||
*:<source> | |||
sinfo | |||
</source> | |||
*To list all nodes and their information | |||
*:<source> | |||
sinfo -lNe | |||
</source> | |||
==== 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 | |||
*:<source> | |||
/* Long version */ | |||
module available | |||
/* OR */ | |||
/* Short version */ | |||
ml av | |||
</source> | |||
* To load a module(s) | |||
*: <source> | |||
/* Single module */ | |||
module load dock | |||
/* OR */ | |||
ml dock | |||
================================== | |||
/* Multi-module */ | |||
module load dock python/3.12, schrodinger | |||
/* OR */ | |||
ml dock python/3.12 schrodinger | |||
</source> | |||
*To list all loaded modules | |||
*: <source> | |||
module load | |||
/* OR */ | |||
ml | |||
</source> | |||
*To unload a module | |||
*:<source> | |||
module unload <module> | |||
/* OR */ | |||
ml unload <module> | |||
</source> | |||
*To unload all modules | |||
*:<source> | |||
module purge | |||
/* OR */ | |||
ml purge | |||
</source> | |||
== 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 | |||
* | |||
[[Category:C7]] | |||
Latest revision as of 19:21, 10 September 2026
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
- 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