Cluster Theory
You require a cluster to run molecular docking at scale.
Non-Scalable Cluster
You can just take a bunch of computers, new or used, and put them together to make a cluster. That's mostly what we've done for the last 15 years. It works ok, but as you scale it becomes unwieldy. If you can afford it, we recommend starting with a scalable design, below.
Minimalist Scalable Cluster - One computer - $20K
You can begin a scalable cluster with as few as one computer, albeit a biggish one. We recommend using a hypervisor so you can run multiple virtual machines on a single computer. You can get away without a rack, just put the machine in a sound-proof room.
We would buy:
- a) 1 x 128 core / 256 GB / 16 TB disk @ $20K
Starter Scalable Cluster - $40K
If you can afford it, starting with a few more computers will be easier to scale up.
We would buy:
- a) 1 x 96 TB NAS server, $18K
- b) 1 x 128 core / 512 GB @ $20K
- c) switch, cables, economy workstation: $2K
You do not need a rack, but you need a sound proof room with normal room air conditioning.
- 2 x 15A circuits.
Small Scaleable Cluster - $92K
If you had around $100K to spend, we would buy:
- a) 1 x 96 TB NAS server, $18K
- b) 3 x 128 core / 512 GB @ $20K
- c) barebones rack, switch, cables: $1K
- d) 4 workstations @ $2K = $8K
- e) spare parts (disks, switch) $4K
- f) ssh portal machine / firewall $1K
Sound proof room, 1 T of cooling = 12,000 Btu/h = 3.516 KW
- 30 A @ 208V (e.g. 1 x L6-30)
Bigger Scaleable Cluster - $250K
If you had around $250K to spend, we would buy:
- a) 2 x 96 TB NAS server @ $18K = $36K
- b) 10 x 128 core / 512 GB @ $20K = $200K
- c) barebones rack, switch, cables: $1K
- d) 4 workstations @ $2K = $8K
- e) spare parts (disks, switch) $4K
- f) ssh portal machine / firewall $1K
- Sound proof room, 5 T of cooling
- 90 A @ 208V (e.g. 3 L6-30s)
Back to So you want to set up a lab.