Computing Facilities

The Center’s IT infrastructure consists of over 300 Linux workstations and 150 Windows and Macintosh desktops in offices and labs owned by individual research groups. There is a server farm with over 25 Linux servers that handles central storage, email, web, print, specialized processing and other shared services. The overall storage capacity of the center, including disks in local workstations and central storage, exceeds 2 petabytes.

The Center has a 126-node computing cluster for batch analysis jobs. Each node consists of two Quad Core Xeon E5472 3.0 GHz CPUs with 32GB of RAM, which together equal a total of 1024 compute cores available for batch jobs. Each node is connected by both a 1 GBit/s Ethernet link and a 20 GBit/s DDR Infiniband backplane. The Infiniband connection is used by parallelized jobs using MPI (message passing interface) to utilize multiple cores.

A 1.8 Petabyte storage cluster was installed and went online in May 2010. This storage cluster uses IBM DCS9900 storage arrays with 1200 SATA hard disks. The array controllers connect via redundant Fibre-Channel fabric to nine IBM HS22 Blade Servers running RedHat Enterprise Linux and the GPFS cluster file system. The 126-node computing cluster accesses the storage directly via GPFS client software while the rest of the workstations in the center use NFS. Backup is provided using a IBM TS3500 Tape Library with 1760 Cartridge Slots and four LTO-4 tape drives.

The IT facilities are supported by a small IT staff comprising one full-time PhD-level manager, who directs two full-time system administrators and a part-time support technician. The Center also has three full-time programmers who support in-house-developed software for data analysis and management. Available commercial software includes AVS (Advanced Visual Systems, Waltham, MA), MATLAB (The MathWorks, Natick, MA) and MEDx (Sensor Systems, Sterling, VA) for general-purpose computation, simulation and image analysis; and XWIN-NMR (Bruker BioSpin), Origin (OriginLab Corp., Northampton, MA), Nuts (Acorn NMR, Livermore, CA) for analysis of NMR spectra and the Siemens IDEA development environment for pulse sequences and image reconstruction software (Siemens, Erlangen, Germany). A substantial level of internal software development for image and data analysis is ongoing, using LAMP, C, C++, Java, FORTRAN, Ruby, Python, Perl and TCL/TK.

For high-performance image reconstruction the center is equipped with a custom-designed ScaleMP vSMP computer equipped with sixteen 8-core Xeon E5472 and 1TB shared RAM. In April 2013 the Center added a Dell PowerEdge R910 server with four 10-core Intel Xeon E7-4850 processors and 1TB of quad ranked, DDR3 RAM. The center also has three Dell PowerEdge R910 with four 8-core Intel Xeon X7560 processors and 256GB of RAM.

Advanced Computational Image Processing and Analysis Center

The Advanced Computational Image Processing and Analysis Center (ACIPAC) is a satellite of the Martinos Center on the MIT campus, established in collaboration with the MIT Artificial Intelligence (AI) Laboratory. The closely affiliated ACIPAC has extensive resources and expertise for solving practical image processing and analysis issues relevant to biomedical imaging. This Center is an important bridge to affiliated MIT research community, and allows MIT students a direct avenue to engage in biomedical imaging research at the Martinos Center.