High Performance
Computing Research

at UMass Amherst

Research, collaboration & community

Get Started

Section last updated: 08/13/2018

The Massachusetts Green High Performance Computing Center (MGHPCC) provides state-of-the-art high-performance computing resources for UMass Amherst faculty and researchers pursuing a diverse body of research.

Located in Holyoke, MA and featuring a green design, the MGHPCC supports the computing research needs of five of the most research-intensive Universities in the Northeast (Boston University, Harvard University, MIT, Northeastern University, and the University of Massachusetts).

With high-end computing equipment and storage, including thousands of CPU cores and GPU cards, UMass Amherst operates one of the biggest GPU clusters in the nation in the MGHPCC. This includes the UMass System Shared Cluster, available for general use to UMass Amherst researchers and researchers from other UMass campuses.

UMass Amherst researchers can use this page to get started using the data center and its high-end computational infrastructure for research in science, engineering, and other areas of academic scholarship as well as learn what resources and additional clusters are available to them.

Request Access to the Shared Cluster

  • To request access to the UMass Shared Cluser, fill out an application form at www.umassrc.org/hpc/ to get immediate access and 50GB of storage - with no initial commitment (PIs can request more storage via an email to hpcc-support@umassmed.edu).
  • Note: you must be connected to the UMass Amherst network (i.e., have a UMass Amherst address for your computer) to access this form.
  • You'll be notified by email when your account is ready. You will also automatically be added to the MGHPCC user group mailing list (moderated): ghpcc@list.umassmed.edu, which is used for announcement purposes. There is also an opt-in email list: https://www.umassrc.org/hpc/ghpcc-discussion.php. These are great resources for asking and answering user questions about the UMass MGHPCC shared cluster.

Cost: Researchers utilizing the Shared Cluster will be provided an annual level of computing subsidized by the university (up to 10 CPU years). Groups using over 10 CPU years will be assessed a charge of $59 per CPU year. This charge will be assessed on a quarterly basis once you have exceeded the CPU years subsidized by the university.

Contribute Equipment (Optional):

  • UMass Amherst researchers may contribute equipment or help finance equipment for the System Shared Cluster and/or the Amherst Priority-Shared Cluster (see below).
  • If you choose to contribute physical equipment, the equipment must be consistent with the current facility standards and should have a useful lifetime in the cluster of four years.
  • For more information on contributing to the shared cluster, contact hpc@it.umass.edu.

Exclusive use of your own equipment

Obtain your own computing equipment (e.g., from a research grant) and place it in the MGHPCC for your exclusive use alone; this is referred to as the UMass-colo model.

Status: Available

To request access: Contact hpc@it.umass.edu

Cost: No charge (other than the cost of equipment). There is no charge to place your equipment in the MGHPCC.

Notes:

  • If you are a faculty member/ principal investigator and have equipment you would like to place in the MGHPCC for your own exclusive use, you may do so as long as the equipment meets the current facility standards. For more information on facility standards, please contact Jim Mileski (james.mileski@umass.edu).
  • UMass Information Technology will manage the physical aspects of the equipment. Generally, you will not have access to your equipment and you will need to contact OIT staff when physical changes are necessary.
  • MGHPCC staff are on-site at some hours of the day to “push buttons” if you instruct them to do so.
  • Only the minimal services mentioned above are avaialble. Except the installation and physical changes, you will have to manage all other aspects of your equipment.

Questions? See the Get Help section of this site.

F.A.Q.

Section last updated: 09/21/2018
  • What is the MGHPCC?

    The Massachusetts Green High Performance Computing Center (MGHPCC) is a collaboration of five most research-intensive Universities in Massachusetts (Boston University, Harvard, MIT, Northeastern and the University of Massachusetts), state government and private industry (Cisco and EMC). The center showcases the most significant collaboration among government, industry, and public and private Universities in the history of the Commonwealth of Massachusetts. Legally, the MGHPCC is a 501c3 non-profit organization owned by the five Universities. For more information, see www.mghpcc.org

  • What does the MGHPCC do?

    The MGHPCC has two primary roles. First, it operates the MGHPCC data center in Holyoke MA, which houses research computing equipment owned by the five Universities. In this first role, the MGHPCC acts like a collocation (colo) center to the five Universities; each University occupies one-fifth of the MGHPCC’s data center space. The MGHPCC owns and operates the building, and the electrical, cooling and network services (“ping, power and pipe”) to the racks. Note: The MGHPCC does not own the research computing equipment housed in the MGHPCC; this equipment is owned and operated by the individual Universities.

    The second role of the MGHPCC is to help foster research collaborations among the MGHPCC Universities in computational science, engineering, applications, and beyond. In addition, the MGHPCC represents a partnership with Holyoke, the Pioneer Valley, and the Commonwealth. The MGHPCC has worked closely with the Holyoke Innovation District Task Force to leverage the benefits of the facility’s location in Holyoke, and is partnering with K-12 public schools and community colleges on new educational and workforce development initiatives.

  • Can I get computing equipment from the MGHPCC?

    No. The MGHPCC does not own any of the computers in the facility and does not provide computing equipment. The individual Universities supply computing equipment to their constituents.

  • How big is the facility?

    The facility size is 90,300 square feet, with 10 Megawatts (MW) of power available for computing and another 5MW available for other functions such as cooling and lighting. The site is 8.6 acres, allowing room for expansion. The machine room floor has built-out capacity that can house roughly 10,000 high-end computers, and expansion capabilities in the building for a further 10, 000 computers. For more information, see these frequently-asked questions.

  • How much did it cost to build the facility?

    The MGHPCC was completed several million dollars below its original budget of $95M.

  • Who paid for the MGHPCC?

    The five MGHPCC Universities, the Commonwealth of Massachusetts, Cisco, EMC, and the Federal New Markets Tax Credit program provided the initial funding for this project. The Universities are funding its ongoing operation.

  • How much does it cost for a researcher to contribute to the shared cluster(s)?

    This depends on how many computing cores (for which you will have priority access) and how much storage (which will be yours) you want to buy. A rough rule is approximately $400/core, which includes storage and minimal software licenses. This is just a ballpark figure, and prices change constantly; for details, please contact hpc@it.umass.edu.

  • I am writing a grant and I would like to include a letter about the MGHPCC in my proposal. Where is that letter available?

    If you are in the process of applying for a grant: For letters regarding the MGHPCC infrastucture, integrating your proposal equipment into the shared cluster(s), placing equipment in the MGHPCC, or standard cost and billing information and statements, contact hpc@it.umass.edu.
    If you already have a grant: For guidance on purchasing equipment and the latest facility standards your equipment must adhere to, please contact hpc@it.umass.edu.

    I don't have a grant or other funding. Can I still get access the computing equipment in the MGHPCC?

    Yes. Please consider the UMass System Shared Cluster, available to researchers from all five UMass campuses.

    Can I make a request for additional software?

    Installing software above the base software noted below is the responsibility of the individual researcher or research groups using the system. There is a system-wide user group that may be able to provide expertise. The Amherst member of the group is Michael Zink (zink@ecs.umass.edu)

More…

Hardware & Software

Section last updated: 08/13/2018

The following is a breakdown of the computing resources available at MGHPCC:

UMass Shared Cluster

  • 15,000-core system, including 140 Graphics Processing Unit (GPU) nodes for rapid calculations & data-heavy processing.
  • EMC Isilon storage for easy management and protection of unstructured data.
  • Available for general use to UMass Amherst researchers at no charge, with no initial commitment.
  • Amherst Priority Shared Cluster

  • Supplements shared access as a part of the UMass Shared Cluster.
  • Includes 1,152 Central Processing Unit (CPU) cores needed for high performance computing.
  • For a fee, researchers receive dedicated access to a set of nodes and unused CPU cycles.
  • UMass IALS Computational Core Facility

  • 32 nodes, 4x GPUs per node for demanding computational modeling and simulations.
  • The Institute for Applied Life Sciences (IALS) facility provides expert consultative and collaborative services to academic and industry partners.
  • Expertise includes molecular dynamics and chemistry simulation applications. More information at umass.edu/ials/computational-modeling.
  • Includes a fee-for-service computational modeling facility using the IALS GPU cluster.
  • Gypsum GPU Cluster (CICS)

  • 153 nodes, 4-8x GPU’s per node, 824 GPU cards total.
  • Mix of NVIDIA Tesla, Titan X, 1080Ti GPUs
  • Available to Computer Science researchers and affiliated faculty.
  • C3DDB

  • 133 computer nodes, with a total of 7,200 cores.
  • The Commonwealth Computational Cloud for Data Driven Biology (C3DDB) is a computer system dedicated to life sciences research supported by innovative big data analytics.
  • Available to all UMass Principal Investigators.
  • Open to anyone conducting life science research or development at a university or research institute, including software tool developers.
  • Easy to sign up. More information at umass.edu/it/c3ddb.
  • Available Software for System Wide Fair Shared Cluster

    Bioinformatics

    • CLUSTAL 2.1 Multiple Sequence Alignments
    • EMBOSS
    • ImageJ
    • ImageMagick
    • Iprscan - unique, non-redundant characterization of a given protein family, domain or functional site
    • Meme
    • Miranda - microRNA Target Scanning Algorithm
    • Miropeats - Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically
    • NCBI Blast
    • MPIBlast
    • PAML - phylogenetic analyses of DNA or protein sequences using maximum likelihood
    • R
    • Ranfold - compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE)
    • RepeatMasker - RepeatMasker uses a sequence search engine to perform it's search for repeats
    • ViennaRNA - examine RNA folding and structure

    Next Gen Sequencing

    • abyss
    • BEDTools
    • BFast
    • Bisulfite
    • brat and brat_bw
    • bismark
    • bsmap
    • methylcode
    • BLAT
    • BioScope
    • Bowtie
    • BWA
    • CuffLinks
    • Genomics Software
    • Hapsembler Software
    • HTSeq
    • IlluminaPipeline
    • FastX Toolkit
    • spliceSites
    • MACS
    • MAQ
    • Novoalign
    • RNA_pipeline
    • SAMtools
    • PySam
    • Shrimp
    • SoapSNP
    • SOLiDTools
    • TopHat
    • Velvet

    General Software

    • AMD Open X64 Compiler Suite
    • gcc
    • Java
    • ddd
    • gnuplot
    • graphviz
    • apache-ant
    • Perl
    • PHP
    • Python

    Libraries

    • libgmp
    • libmpfr
    • ITKToolKit
    • libseq
    • Boost
    • zlbilb

    Molecular Mechanics

    • amber
    • charm
    • charmd
    • NAMD
    • vmd
    • gaussian
    • Desmond

    Utility Based (Linux) Software

    • MD5deep
    • Aspera
    • cmake
    • Bison/Lex/Yacc

    Physics Software

    • Gate
    • Ecat
    • Geant
    • Root
    • LMF
    • CLHep
    • Galaxy
    • SBGrid
    • Signalp
    • Trinity
    • IGV
    • MEV

    To see a full listing of available software, see the UMass MGHPCC Wiki, located at: wiki.umassrc.org. Or, after logging into the cluster, type "-> modules avail"

    Facility

    Section last updated: 11/26/2013

    The Massachusetts Green High Performance Computing Center (MGHPCC) facility is a two-story, 90,300-square-foot data center. It is located on an 8.6 acre site between Cabot and Appleton Streets in Holyoke, Massachusetts.

    The operating model for the MGHPCC is as a specialized landlord for computers from the five Universities, providing state-of-the-art facilities to house, power, climate-control and connect, tailored to the needs of users on different campuses.

    Completed in November 2012, the building features outside transformer capacity to deliver power from both Holyoke Gas and Electric (HG&E) and backup generators. There is extra power capacity and open space for later staged expansion.

    The second floor computer room is the highlight of the MGHPCC facility. Close to an acre in area, this is where all production computing, storage, and networking equipment is housed. The computer room floor is divided into a matrix of “pods,” each containing a set of custom designed racks supplying the necessary power, cooling, and communication support to the installed computing hardware.

    More about the MGHPCC facility

    About High Performance Computing Research

    Section last updated: 11/26/2013

    High Performance Computing (HPC) uses multiple computers working closely together to solve complex computational problems too large or too extensive for stand-alone desktops or servers to solve. HPC provides the computational science infrastructure for scientific discovery, advanced research, and scholarship.

    Clusters of high performance computers, such as the ones in the Massachusetts Green High Performance Computing Center (MGHPCC) achieve high computational rates by using the power of massive numbers of processors.

    The applications of HPC span across disciplines, including science, engineering, and social sciences. Examples include:

    • Energy (e.g., fuel cells)
    • Smart grid analytics
    • Materials (e.g., high temperature superconductors)
    • Astronomy
    • Financial modeling
    • Industrial design
    • And much more...

    High Performance Computing Research at UMass Amherst

    The University of Massachusetts and the MGHPCC provide UMass Amherst researchers with a high-performance computing environment and, in the future, training and support for ground-breaking research in a wide range of disciplines, from engineering to biological and physical sciences.

    UMass Amherst researchers have the unique opportunity to pioneer competitive research with the help of advanced computing technology, establish new collaborations, and become part of a new, vibrant research community. In doing so, their contributions support the research mission of the University.

    Get Help

    Section last updated: 11/26/2013

    For all requests:
    Contact hpc@it.umass.edu.

    Wiki for University researchers using the UMass System Shared Cluster:
    http://wiki.umassrc.org/wiki/index.php/Main_Page