Current NRAMM setup » History » Version 2
Anchi Cheng, 09/14/2017 07:56 PM
| 1 | 1 | Anchi Cheng | h1. Current NRAMM setup (9/14/17) |
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| 2 | |||
| 3 | NRAMM is located at Simons Electron Microscopy Center (SEMC) at New York Structural Biology Center. |
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| 4 | We currently have 6 TEM. |
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| 5 | |||
| 6 | 1 x JEOL 1230 with Gatan UltraScan 4000 |
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| 7 | 1 x FEI T-12 with TVIPS F416 |
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| 8 | 1 x FEI F20 with DE-20 camera and TVIPS F416 |
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| 9 | 3 x FEI Krios with Falcon |||, Ceta, and Gatan K2 Summit |
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| 10 | |||
| 11 | All 6 microscopes use Leginon for data collection and Appion for preprocessing (defined as frame alignment/ctf estimation/particle picking) and on the same database server and together has 3 web servers to serve the images for users to view and/or as Appion gui to construct the preprocessing commands. What is listed does not include infrastructure for 2D/3D classification and other post-processing. |
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| 12 | |||
| 13 | h2. Network |
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| 14 | |||
| 15 | All hardware mentioned below as well as the instruments are on a local 10 GB copper network. |
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| 16 | |||
| 17 | h2. Leginon control or processing work station |
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| 18 | |||
| 19 | One station per scope. For example, |
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| 20 | |||
| 21 | CPU 8 x Intel i7-6700 @ 3.40GHz |
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| 22 | MemoryL 16 GB |
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| 23 | Storage: 50G HDD |
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| 24 | |||
| 25 | |||
| 26 | h2. Database server |
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| 27 | |||
| 28 | Dell R730 with (2) Intel E5-2689 3.1GHz, lOCore CPUs, |
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| 29 | Memory: 128GB of RAM, |
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| 30 | Storage: (2) 120GB HDD, (1) 800GB SSD |
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| 31 | |||
| 32 | h2. Web server |
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| 33 | |||
| 34 | 1. For local network only |
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| 35 | * CPU 4 x Intel Xeon @ 3.00GHz |
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| 36 | * Memory: 4 GB |
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| 37 | * Storage 700GB HDD |
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| 38 | |||
| 39 | 2. For local network only (This is one of the node on our processing cluster. Rather under used this way) |
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| 40 | * CPU 24 Intel Xeon E5-2670 v3 @2.30GHz |
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| 41 | * Memory: 265 MB |
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| 43 | |||
| 44 | 3. Internet accessible: for guests and member institution to use from outside the building |
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| 45 | * CPU: 8 x Intel Xeon L5410 @ 2.33GHz |
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| 46 | * Memory: 8 GB + 8 GB swap |
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| 47 | |||
| 48 | h2. Frame processing server (One per microscope) |
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| 49 | |||
| 50 | h3. K2/Falcon ||| |
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| 51 | |||
| 52 | An injection or buffer server to process frames before it goes to gpfs primary storage. This is reserved to the person using the scope. |
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| 53 | * Network: |
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| 54 | ** To local network: 1x Dual 10GE SFP+ cards (2 ports) |
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| 55 | ** To the camera computer: 10 GB Fiber direct connection - SFP+ optical module for 10GBASE-LR |
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| 56 | ** To gpfs RAID: inifiniband - ConnectX-3 VPI adapter card, dual-port QSFP, FDR IB (56Gb/s) / 40GigE, PCIe 3.0 x8 8GT/s |
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| 57 | * CPU: 2U Dual 2.1GHz Intel E5-2620 v4 |
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| 58 | * Memory: 128GB memory (8x 16GB) |
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| 59 | * Storage: 9x 8TB 7.2K SATA drives, 1x 120GB SSD drive |
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| 60 | * GPU: 2x NVIDIA PNY GeForce GTX 1080. |
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| 61 | |||
| 62 | h3. DE20 |
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| 63 | |||
| 64 | Direct Electron frame alignment program runs on CPUs. It has its dedicated computer. |
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| 65 | * CPU: 32 x Intel Xeon E5-2640 v2 @ 2.00 GHz |
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| 66 | * Memory: 132 GB RAM |
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| 67 | * Job scheduler Torque installed. |
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| 68 | |||
| 69 | h2. Primary Storage |
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| 70 | |||
| 71 | GPFS 1 pB |
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| 72 | 2 | Anchi Cheng | |
| 73 | h2. [[SEMC file storage policy]] |