High performance computing (HPC)
Collectively, HP&RC’s support team has significant expertise in multiple areas of computational biology including molecular modeling, genomics, drug design and other bioinformatics disciplines. Most members of the scientific team have earned a Ph.D in one of the life sciences or a complementary physical science and have accumulated significant experience applying state-of-the-art cyberinfrastructure to the solution of demanding research problems. It is this human resource that is a most valuable asset in a research endeavor navigating the cutting edge of a complex scientific problem.
HP&RC operates two facilities that comprise its main computational arsenal, although external resources such as commercial cloud services or university/government research networks are used in situations in which the requisite software or computing capability is not locally available or realistic with regard to the time course of a calculation.
Specifically, HP&RC maintains the newton Linux cluster comprising 62, 8 core nodes. Nodes have a minimum of 12 Gbytes RAM (the majority have 16 Gbytes) and 1 Terabyte of on board scratch space. Project storage is maintained by a 30 Terabyte Gluster file system with each node supplying one Terabyte of storage to the ensemble. Longer term storage is provisioned through standard RAID technology. Access to newton is through a job interface supported by the cluster login node (newton.umdnj.edu). An overview of newton can be found at newton linux cluster. Complete information about the Linux cluster, available scientific applications and other usage specific information can be found at newton wiki (under construction).
Sirius2 (bioinformatics server) is a 24 core Linux SMP machine provisioned with 128 Gbytes of memory and 20 Terabytes of user storage. Sirius2 supports a comprehensive set of bioinformatics tools through interactive and batch interfaces. Complete information about sirius2, available scientific applications and other usage specific information can be found at sirius2 wiki.
HP&RC’s computational resources are managed through a partnership with IST’s Core Services and Technologies. HP&RC retains one of the country’s leading cluster specialists, Dr. Douglas Eadline, to help us keep the cluster resource highly available and optimized for demanding computational problems. Improvements to the cluster in terms of manageability, reliability and performance are made on a continuing basis as research computing requirements evolve.
Large File Transfer service (LiFT): Information Services and Technology supports file & folder transfers up to 30 Gbytes between members of the UMDNJ research community and their external collaborators. LiFT and documentation for its use are located at LiFT service.
UMDNJ is a member and network participant Internet2, a consortium of academic, government and industrial partners. Internet2 access is restricted to member access for the purpose of research and education. Commercial traffic is not permitted. Internet2 provides advanced network technologies to support the cutting-edge challenges in science, technology and education.
Normally, UMDNJ network traffic destined for an Internet2 institution is automatically routed through UMDNJ’s Internet2 link. Educators and researchers with specific network or performance requirements relating to Internet2 are encouraged to contact the HP&RC Office at 973-972-4973 or a member of the scientific staff. Please refer to the following link for detail Internet2 information and related links: