High Performance Computing (HPC)

The Clark Science Center’s Computing and Technical Services group (CATS) maintains and supports an on-campus High Performance Computing (HPC) infrastructure consisting of two separate systems described below. CATS is also affiliated with the Massachusetts Green High Performance Computing Center (MGHPCC) in Holyoke, MA, enabling us to leverage additional computing nodes as needed.

Available Computational Resources

  1. A Virtual HPC cluster consisting of three high-end Dell and one MacPro server each hosting numerous HPC Virtual Machines (VM). The virtualization and higher amount of RAM on these servers (VM hosts) allow the flexibility of running either Windows or Linux VMs at the same time. This permits us to allocate only the resources that are needed.
      • HPC-VM1 Server: 512GB RAM, 2 processors with 18 cores (72 total)
      • HPC-VM2 Server: 512GB RAM, 2 processors with 18 cores (72 total), 1 NVIDIA Tesla M60 GPU with 16GB of Ram and 4096 GPU cores.
      • HPC-VM3 Server: 2TB RAM, 2 processors with 26 cores (104 total)
      • HPC-MAC: 384GB RAM, 2.5GHz 28‑core Intel Xeon W processor, Radeon Pro W5700X 16GB of GDDR6 memory 

 

  1. A Bright Cluster consists of a management node, twelve compute nodes, and one RAM server. Software is loaded onto the management node by CATS using the EasyBuild module manager and shared throughout the compute nodes. The cluster uses the Slurm Workload Manager to schedule and run the jobs. The Bright infrastructure is fully scalable and can accommodate additional compute nodes as needed.
      • Management Node: 384GB RAM, 2 processors with 32 cores
      • Compute Nodes (12): 192GB RAM, 2 processors with 32 cores each
      • RAM Node: 1500GB RAM, 2 processors with 35 cores each

 

Cluster management tools:  Hadoop, VMware, Bright Computing, Slurm, Easybuild

Current Uses

Bioinformatics
Biopython (https://biopython.org/)
DendroPy (https://dendropy.org/)
P4 (http://p4.nhm.ac.uk/)
Bioperl (https://bioperl.org/)
MAFFT (https://mafft.cbrc.jp/alignment/software/)
USEARCH (https://www.drive5.com/usearch/)
Guidance (http://guidance.tau.ac.il/)
trimAl (http://trimal.cgenomics.org/)
RAxML (https://cme.h-its.org/exelixis/web/software/raxml/index.html)
wt2dbg (https://github.com/ruanjue/wtdbg2/)
ABySS (https://www.bcgsc.ca/resources/software/abyss)

Other Computational Software

    • Biology — bioinformatics and genetic analyses using: Seqman NGen, Muscle, SOAPDenovo, SPAdes and other packages
    • Chemistry — calculational chemistry using: Gaussian, ORCA, ADF
    • Economics — Monte Carlo and other modeling simulations using: Matlab, Mathematica, NetLogo, Stata
    • Engineering —  modeling using Ansys
    • Physics — Monte Carlo simulations using: Matlab
    • Statistics and Data Sciences — R