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.