Call for Research!

Have the Rutgers Office of Advanced Research Computing or Amarel helped advance your research? Have you published a poster, paper, or presentation highlighting research performed with OARC’s compute clusters (including the former HPCC, Perceval, NM3, Sirius, or Newton)? If so, here’s your chance to have your visual research seen at Supercomputing (SC18), the international conference for high performance computing, where more than 12,000 scientists, engineers, software developers, policy makers, corporate managers, CIOs, and IT administrators from around the world will convene in November. Contact OARC’s Program Coordinator, Janae Baker, today to find out how we can highlight your research at the Rutgers SC18 exhibit booth!


OARC’s Upcoming Training/Education Events

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
Fri, April 27th,
10:00am-1:00pm Piscataway, Busch Campus
CoRE Auditorium, Room 101
Preparing Biological Research Labs for Petascale Computing

F. Alex Feltus
Date, Time, Location Event Title Presenter (s) & Affiliation
Mon, April 16th
MSB C632
Introduction to Research Computing and the Amarel Cluster Muhammad Awan

Date, Time, Location Event Title Presenter (s) & Affiliation
Wed, April 11th
Armitage Hall 101
 Introduction to Research Computing and the Amarel Cluster  Muhammad Awan

Date, Time, Location Event Title Presenter (s) & Affiliation
Thurs, March 22nd,
Piscataway, Busch Campus
LSB Auditorium
Google Genomics On-Site Training OARC’s Research Scientists
Tara Matise
Nina Sanapareddy



 OARC’s Application Workshop Series

Computational Genomics Series: RNA_Seq analysis-Part I, Part II

Date, Time, Location Event Title Presenter (s) & Affiliation
Mon, July 16th
1:00 -4:00 pm
RBHS Newark
MSB C632
Part I
Workshop FULL! Registration closed.
 OARC’s Research Scientists
Thurs, July 19th
1:00 -4:00 pm
RBHS Newark
MSB C632
Part II
Workshop FULL! Registration closed.
OARC’s Research Scientists

Amarel Research Community Forum (ARCF)

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, 2017
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, 2017
Piscataway, Busch Campus
CoRE 601
Matthew Emerson, Undergraduate Researcher, Edward Castner’s Group, Chemistry and Chemical Biology
GROMACS: The Journey to Amarel

OARC Office Hours: Wednesdays, Noon-3pm
Computing Research & Education (CoRE) Building, Room 708, Piscataway
Medical Science Building (MSB), Room C630, Newark

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.