High Performance Computing
High Performance Computing (HPC) uses distributed computational cycles to decrease the amount of time a single job would take. HPC processing jobs typically consist of searching or time and process jobs. Processing string searching for genomic data comparisons assists with the speed-up of “needle” and “haystack” processing and analysis
Researchers utilize custom and open software to analyze, distribute, and calculate large data sets. Utilizing best practices users can decrease job run time several fold by using distribution and cluster related protocols such as MPI.
Examples of HPC distribution include: Monte Carlo computations, time and space computations, and string (over DNA, etc.) matching algorithms. Users can create programs, and scripts, on the cluster here at UMASS for pattern matching and general search based needs; for example using HG18 we can create simple shell scrip(s) using the Perl scripting language for effective pattern matching. We, ARCS, can assist with these needs and help you create optimal routines and searing as needed.
Resources
Priority Queues for faculty/labs.
- PI or Campus purchases equipment with agreement of 5-year life span.
- PI retains access to the 15,000+ core shared cluster.
- PI has priority queue on purchased equipment.
- Jobs from short queue (<=4 hrs) are allowed to backfill when priority queues are idle. Backfilled jobs will not be preempted (comparable to the large queue).
- Electricity, Rent, Software and Hardware maintenance, and cluster administration are all included in the capital purchase cost.
- All software modules available to the Shared Cluster will be available to your Priority Queue cluster nodes
How to procure a Priority Queue.
- Contact either:
- The UMass MGHPCC Support Team: hpcc-admins@umassmed.edu
- The UMass MGHPCC Director: paul.langlois@umassmed.edu
- Give your hardware requirements (cores, memory, storage) to the MGHPPC Support team
- HPC team will prepare a quote for you & order the hardware for you, using UMass’ deep discounts with DELL and Lenovo.
- HPC team will rack and administer your hardware for you.
- Sign a Memorandum of Understanding. The key conditions are:
- Your hardware will be attached to the Shared Cluster.
- A new queue will be created giving your team priority access to those cores.
- Your hardware will be removed in five years.
The HPC environment runs the IBM LSF scheduling software for job management. The High Performance Computing Cluster (HPCC) consists of the following hardware:
Networking:
- EDR/FDR based Infiniband (IB) network
- 10 Gigabit Ethernet network for the storage environment
Storage:
- Dell/EMC high performance Isilon storage with 1,585TB of Isilon H500
- Dell/EMC high performance Isilon storage with 2,457 TB of NL410
- Dell/EMC high performance Isilon storage with 162 TB of NL400
Data storage and pricing details
Computing:
Scheduling Software:
- The HPC environment runs the IBM LSF scheduling software for job management.
MGHPCC Facility:
- The Massachusetts Green High Performance Computer Center (MGHPCC) facility has space, power, and cooling capacity to support 680 racks of computing and storage equipment, drawing up to 15MW of power.
- High speed network connections to the facility are available via dark fiber, the Northern Crossroads, and Internet 2.
- The MGHPCC facility has been awarded LEED Platinum status.
Resources:
MGHPCC Web Site: Official web site of the Massachusetts Green High Performance Computing Center
UMass HPCC Wiki: Detailed information for users of the UMass Shared HPC Cluster
Account Request: Form to request an account on the UMass Shared HPC Cluster
ghpcc-discsussion list: Email discussion list for users of the UMass Shared HPC Cluster
HPC Accounts and Training:
If you are interested in an HPC account, please use this link to request access. Individual support for cluster usage is available. For more information please contact hpcc-support@umassmed.edu.
