Current NRAMM setup » History » Revision 4
Revision 3 (Anchi Cheng, 03/11/2019 03:27 PM) → Revision 4/5 (Anchi Cheng, 03/11/2019 03:28 PM)
h1. Current NRAMM setup (9/14/17) NRAMM is located at Simons Electron Microscopy Center (SEMC) at New York Structural Biology Center. We currently have 6 TEM. 1 x JEOL 1230 with Gatan UltraScan 4000 1 x FEI T-12 with TVIPS F416 1 x FEI F20 with DE-20 camera and TVIPS F416 3 x FEI Krios with Falcon |||, Ceta, and Gatan K2 Summit 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. h2. Network All hardware mentioned below as well as the instruments are on a local 10 GB copper network. h2. Leginon control or processing work station One station per scope. For example, CPU 8 x Intel i7-6700 @ 3.40GHz MemoryL 16 GB Storage: 50G HDD h2. Database server Dell R730 with (2) Intel E5-2689 3.1GHz, lOCore CPUs, Memory: 128GB of RAM, Storage: (2) 120GB HDD, (1) 800GB SSD h2. Web server 1. For local network only * CPU 4 x Intel Xeon @ 3.00GHz * Memory: 4 GB * Storage 700GB HDD 2. For local network only (This is one of the node on our processing cluster. Rather under used this way) * CPU 24 Intel Xeon E5-2670 v3 @2.30GHz * Memory: 265 MB 3. Internet accessible: for guests and member institution to use from outside the building * CPU: 8 x Intel Xeon L5410 @ 2.33GHz * Memory: 8 GB + 8 GB swap h2. Frame processing server (One per microscope) h3. K2/Falcon ||| An injection or buffer server to process frames before it goes to gpfs primary storage. This is reserved to the person using the scope. {{include(NRAMM [[NRAMM buffer server hardware)}} hardware]] * Network: ** To local network: 1x Dual 10GE SFP+ cards (2 ports) ** To the camera computer: 10 GB Fiber direct connection - SFP+ optical module for 10GBASE-LR ** To gpfs RAID: inifiniband - ConnectX-3 VPI adapter card, dual-port QSFP, FDR IB (56Gb/s) / 40GigE, PCIe 3.0 x8 8GT/s * CPU: 2U Dual 2.1GHz Intel E5-2620 v4 * Memory: 128GB memory (8x 16GB) * Storage: 9x 8TB 7.2K SATA drives, 1x 120GB SSD drive * GPU: 2x NVIDIA PNY GeForce GTX 1080. h3. DE20 Direct Electron frame alignment program runs on CPUs. It has its dedicated computer. * CPU: 32 x Intel Xeon E5-2640 v2 @ 2.00 GHz * Memory: 132 GB RAM * Job scheduler Torque installed. h2. Primary Storage GPFS 1 pB h2. [[SEMC file storage policy]]