Cryo-EM Cluster Resources
- Rashad Ahmed
- Meghan Netterville
Generally Available Cryo-EM Resources
Two institutional high-performance computing (HPC) clusters, hosted and managed by Weill Cornell Medical College’s Scientific Computing Unit, are reserved for Cryo-EM researchers on a slurm-based queuing system. All nodes within each cluster are connected with a high-speed infiniband interconnect. The first HPC cluster is equipped with 548 physical cores distributed over 14 CPU nodes and 5 GPU nodes. 4 of which contain 4 Tesla P100 cards and one of which contains 4 Tesla V100 cards. The newest HPC cluster has 2 compute nodes and 6 GPU nodes, each of which is comprised of dual Intel Xeon CPUs with 16 physical CPU cores in each running at 2.90 GHz, 384 GB of RAM, and four Nvidia Quadro RTX 6000 GPU cards in each of the 6 GPU nodes.
SCU - Weill Greenberg Cluster
| Node | Count | Cores | RAM | GPU | Processor |
|---|---|---|---|---|---|
| node163-174 | 14 | 28 (No HT) | 256GB | NA | 2x Xeon E5-2680 v4 |
| node175-177 | 3 | 56 (HT) | 256GB | 4x P100 | 2x Xeon E5-2680 v4 |
| node180 | 1 | 64 (HT) | 384GB | 4x P100 | 2x Xeon Gold 6130 |
| node183 | 1 | 80 (HT) | 384GB | 4x V100 | 2x Xeon Gold 6148 |
| Total CPU | 14 | 392 Logical 392 Physical | 3584 GB | NA | 28x Xeon E5-2680 v4 |
| Total GPU | 5 | 312 Logical 156 Physical | 1536 GB | 16x P100 4x V100 | 6x Xeon E5-2680 v4 2x Xeon Gold 6130 2x Xeon Gold 6148 |
| Total | 19 | 704 Logical 548 Physical | 5120 GB | 16x P100 4x V100 | 34x Xeon E5-2680 v4 2x Xeon Gold 6130 2x Xeon Gold 6148 |
SCU - BRB Cluster
| Node | Count | Cores | RAM | GPU | Processor |
|---|---|---|---|---|---|
| scu-node001-002 | 2 | 64 (HT) | 383GB | NA | 2x Xeon Gold 6226R |
| scu-node003-008 | 6 | 64 (HT) | 383GB | 4x RTX6000 | 2x Xeon Gold 6226R |
| scu-node063-074 | 12 | 28 | 256GB | NA | -- |
| Total CPU | 14 | 464 Logical 64 Physical | 8946GB | NA | 4x Xeon Gold 6226R |
| Total GPU | 6 | 384 Logical 192 Physical | 2304GB | 24x RTX6000 | 12x Xeon Gold 6226R |
| Total | 20 | 848 Logical 256 Physical | 11250GB | 24x RTX6000 | 16x Xeon Gold 6226R |
Total Generally Available Cryo-EM Resources
| Type | Count | Cores | RAM | GPU | Processor |
|---|---|---|---|---|---|
| CPU | 28 | 856 Logical 456 Physical | 12530GB | NA | 28x Xeon E5-2680 v4 4x Xeon Gold 6226R |
| GPU | 11 | 696 Logical 348 Physical | 3840 GB | 16x P100 4x V100 24x RTX6000 | 6x Xeon E5-2680 v4 2x Xeon Gold 6130 2x Xeon Gold 6148 12x Xeon Gold 6226R |
| Total | 39 | 1552 Logical 804 Physical | 16370 GB | 16x P100 4x V100 24x RTX6000 | 34x Xeon E5-2680 v4 2x Xeon Gold 6130 2x Xeon Gold 6148 16x Xeon Gold 6226R |
Lab Specific Cryo-EM Resources
In addition to the generally available Cryo-EM resources, several labs have procured additional resources for private use
Accardi Lab
| Node | Count | Cores | RAM | GPU | Processor |
|---|---|---|---|---|---|
| scu-node017 | 1 | 64 (HT) | 384 GB | NA | 2x Xeon Gold 6226R |
| scu-node013-016 | 4 | 64 (HT) | 384 GB | 4x RTX6000 | 2x Xeon Gold 6226R |
| node178 (shared) | 1 | 64 (HT) | 384 GB | 4x P100 | 2x Xeon Gold 6130 |
| Total CPU | 1 | 64 Logical 32 Physical | 384 GB | NA | 2x Xeon Gold 6226R |
| Total GPU | 5 | 320 Logical 160 Physical | 1920 GB | 16x RTX6000 4x P100 | 8x Xeon Gold 6226R 2x Xeon Gold 6130 |
| Total | 6 | 384 Logical 192 Physical | 2304 GB | 16x RTX6000 4x P100 | 10x Xeon Gold 6226R 2x Xeon Gold 6130 |
Boudker Lab
| Node | Count | Cores | RAM | GPU | Processor |
|---|---|---|---|---|---|
| scu-node009-010 | 2 | 64 (HT) | 384 GB | NA | 2x Xeon Gold 6226R |
| scu-node011-012 | 2 | 64 (HT) | 384 GB | 4x RTX6000 | 2x Xeon Gold 6226R |
| node179 | 1 | 64 (HT) | 384 GB | 4x P100 | 2x Xeon Gold 6130 |
| node184-185 | 2 | 80 (HT) | 384 GB | 4x V100 | 2x Xeon Gold 6148 |
| Total CPU | 2 | 128 Logical 64 Physical | 768 GB | NA | 4x Xeon Gold 6226R |
| Total GPU | 5 | 352 Logical 176 Physical | 1920 GB | 8x RTX6000 4x P100 8x V100 | 8x Xeon Gold 6226R 2x Xeon Gold 6130 4x Xeon Gold 6148 |
| Total | 7 | 480 Logical 240 Physical | 2688 GB | 8x RTX6000 4x P100 8x V100 | 12x Xeon Gold 6226R 2x Xeon Gold 6130 4x Xeon Gold 6148 |
XYHuanglab
| Node | Count | Cores | RAM | GPU | Processor |
|---|---|---|---|---|---|
| node178 (shared) | 1 | 64 (HT) | 384 GB | 4x P100 | 2x Xeon Gold 6130 |
| Total | 1 | 64 Logical 32 Physical | 384 GB | 4x P100 | 2x Xeon Gold 6130 |
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