Amarel Research Community Forum (ACRF)

We have started a new monthly meeting series focused on getting researchers, OARC cluster support staff, and any interested participants together to discuss issues and ensure that Amarel is configured and developing in a way that best addresses the needs of our growing computational research community. It’s called the Amarel Research Community Forum (ARCF).

These are brief (approximately 1 hr) meetings usually over lunch, “brown bag lunch” style meetings, where we’ll begin each session with a researcher giving a 10-20 min research presentation addressing use of the Amarel cluster.

After the presentation, we’ll have an open forum for discussion of issues, future plans, announcements, suggestions from the community, etc. that will carry-on for 45-90 min, depending on the level of activity.

Please join us! Bring your lunch and any questions or issues you’d like to discuss with our community.

Date, Time, Location Presenter(s) & Affiliation
August 22, 12:00pm
Piscataway, Busch Campus
CoRE 601
Prof. Ronald P. Hart, Director, Stem Cell Program, Human Genetics Institute of New Jersey
RNAseq on Perceval/Amarel Using SLURM Arrays
An overview of concepts and methods to describe how RNA sequencing works, the use of the efficient HISAT2 “splice-aware” genome aligner, and how SLURM arrays easily parallelize sample alignment.

Dr. Timothy Giese, Associate Research Professor, BioMaPS Institute for Quantitative Biology
Ab Initio Quantum Mechanical/Molecular Mechanical Dynamics Simulation: CPU Performance Benchmark Comparison Between Rutgers HPC and XSEDE Clusters
The scaling of a computational chemistry package developed in Dr. Darrin York’s lab is used to compare the performance of various clusters. The development of a new particle mesh Ewald method for ab initio QM/MM simulations is shown to increase resource efficiency.

September 20, 12:00pm
Piscataway, Busch Campus
CoRE 601
Matthew Emerson, Undergraduate Researcher, Edward Castner’s Group, Chemistry and Chemical Biology
GROMACS: The Journey to Amarel


OARC’s Upcoming Training/Education Events
Computing Research & Education (CoRE) Building, Room 601

Rutgers University’s Office of Advanced Research Computing (OARC) offers a recurring series of training and educational opportunities to the Rutgers research computing community. Most workshops are held multiple times, sometimes more than once each semester. Workshops are also conducted at various Rutgers locations: Camden, New Brunswick, Newark, and Piscataway.

Date, Time, Location Event Title Presenter(s) & Affiliation


OARC Office Hours: Summer session, Tuesdays, 12-3pm
Computing Research & Education (CoRE) Building, Room 708

We are currently hosting weekly, general help office hour sessions where questions can be answered, problems can be discussed, and help with troubleshooting is available! There is no sign-up required and visitors will be helped in a first-come first served fashion.


National Strategic Computing Initiative WEBINAR Series Upcoming Events 

The National Strategic Computing Initiative (NSCI), an Executive Order of the President of the United States, is designed to “maximize benefits of high performance computing (HPC) research, development, and deployment” for the United States. As such, the National Institute of Standards and Technology has organized a bi-monthly seminar program to increase the knowledge base of staff and academia in topics of advanced computing and data science as well as computational platforms, measurement and testing science, algorithms and applied mathematics, and neuromorphic and quantum computing.

Rutgers University’s Office of Advanced Research Computing (OARC) and Rutgers Discovery Informatics Institute (RDI2) are pleased to collaborate as one of the nation’s few host sites for this limited-seat WEBINAR series. Unless otherwise noted, all events will take place in Room 601 of the CoRE Building on Busch Campus at 96 Frelinghuysen Road, Piscataway, NJ 08854.

Date & Time Event Title Presenter & Affiliation
No webinars scheduled at this time