Leginon

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 ingestion or buffer server to process frames before it goes to gpfs primary storage.  This is reserved to the person using the scope.

{{include(NRAMM buffer server hardware)}}

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]]