MICDE announces 2017-2018 Fellowship recipients

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MICDE is pleased to announce the recipients of the 2017-2018 MICDE Fellowships for students enrolled in the PhD in Scientific Computing or the Graduate Certificate in Computational Discovery and Engineering. We had 91 applicants from 25 departments representing 6 schools and colleges. Due to the extraordinary number of high quality applications we increased the number of fellowships from 15 to 20 awards. See our Fellowship page for more information.

AWARDEES

Diksha Dhawan, Chemistry
Negar Farzaneh, Computational Medicine & Bioinformatics
Kritika Iyer, Biomedical Engineering
Tibin John, Neuroscience
Bikash Kanungo, Mechanical Engineering
Yu-Han Kao, Epidemiology
Steven Kiyabu, Mechanical Engineering
Christiana Mavroyiakoumou, Mathematics
Ehsan Mirzakhalili, Mechanical Engineering
Colten Peterson, Climate and Space Sciences & Engineering
James Proctor, Chemical Engineering
Evan Rogers, Biomedical Engineering
Longxiu Tian, S. Ross School of Business
Jipu Wang, Nuclear Engineering and Radiological Sciences
Yanming Wang, Chemistry
Zhenlin Wang, Mechanical Engineering
Alicia Welden, Chemistry
Anna White, Industrial & Operations Engineering
Chia-Nan Yeh, Physics
Yiling Zhang, Industrial & Operations Engineering

HONORABLE MENTIONS

Geunyeong Byeon, Industrial & Operations Engineering
Ayoub Gouasmi, Aerospace Engineering
Joseph Kleinhenz, Physics
Jia Li, Physics
Changjiang Liu, Biophysics
Vo Nguyen, Computational Medicine & Bioinformatics
Everardo Olide, Applied Physics
Qiyun Pan, Industrial & Operations Engineering
Pengchuan Wang, Civil & Environmental Engineering
Xinzhu Wei, Ecology & Evolutionary Biology

Early user buy-in available for new Locker large-file storage service

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Advanced Research Computing – Technology Services (ARC-TS) will be deploying a new research storage service aimed at serving faculty in the Big Data era.  This service, called Locker, complements our existing Turbo general purpose storage service and planned archive service Data Den.

Locker is a large-file cost-optimized storage and is not good for general purpose / small file use.

Faculty can now buy in, at a one-time cost to bootstrap the service.  Faculty interested in this option ahead of the general service will need to commit to 200TB un-replicated or 100TB replicated, of space or more, at a one-time cost of $175/TB un-replicated, $350/TB replicated, for 5 years. This would be a minimum purchase of $35,000, with no further costs for 5 years.

If you are interested, please contact ARC-TS by July 10, 2017, at hpc-support@umich.edu.

Locker Service Timeline - Timeline(4)Frequently Asked Questions

Q: When will Locker be ready if I contribute funds to its launch?

A: Locker aims to be on site and ready for data by Fall semester (2017).

 

Q: When will Locker be ready as a monthly service?

A: The current timeline aims for early November 2017.

 

Q: What if I need less than 100TB replicated or 200TB un-replicated?

A: After the early period smaller allocations will be available.  Contact us at hpc-support@umich.edu to discuss your needs.

 

Q: Can I keep data beyond 5 years?

A: Yes. Options will exist beyond the first 5 years with new ongoing costs for support of the system.

 

Q: What is a large file for Locker?

A: A file size averaging 1MB or larger.  If files are smaller than this, Turbo or MiStorage are preferred options due to their SSD and other caching functionality.

 

Q: With what methods does one access Locker?

A: Locker will support NFS (v3/v4) and CIFS/SMB to workstations, servers, and clusters.

 

Q: Can I use Locker with Sensitive Data such as HIPAA/PHI?

A: Locker comes with encryption at rest and will eventually support HIPAA/PHI data and more.  It will NOT support sensitive data during the early user period. Sensitive data clearance work will start once the system is in place, and should be ready 2-3 months later.

 

Q: Can I pay for Locker monthly rather than up front?

A: Locker will eventually be a monthly service similar to Turbo, but during the early period we are looking for faculty to commit to a minimum amount of storage at a one-time cost (hardware only) to bootstrap the service and keep future prices low.

 

Q: Can I add more capacity?

A: Yes, you can request more capacity at any time.  Because of the design, larger requests will require a few weeks lead time.  To keep costs low, Locker does not maintain significant extra capacity idle, but can grow at anytime to sizes in the 10s of PB.

 

Q: What optional features exist?

A: The features are:

  • Optional Geographic Replication
  • Optional Snapshots

 

Q: Can I use this for clinical care / enterprise use cases?

A: No. Locker has a 9:00 a.m. – 5:00 p.m. support window and is not architected for enterprise availability.  We recommend using MiStorage for enterprise or comparable services in HITS for clinical care.

 

Q: Does Locker include backups?

A: Locker does not include backups.  It does include optional geographic replication and snapshots, which provide some protection against user deletion and major disaster but do not protect against software or administrator error the same way backups do.  For backups we recommend MiBackup.

 

Q: Who should use Locker?

A: Researchers whose datasets typical file size exceed 1 MB can use Locker to store their data more cost efficiently than other options at the University.

 

Q: Why should I contribute to the launch of Locker?

A: Locker aims to provide a cost effective solution for big data storage.  To do this a minimum amount of space needs to be allocated.  By contributing you secure the option of low cost storage for research going forward.

ARC-TS seeks input on next generation HPC cluster

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The University of Michigan is beginning the process of building our next generation HPC platform, “Big House.”  Flux, the shared HPC cluster, has reached the end of its useful life. Flux has served us well for more than five years, but as we move forward with replacement, we want to make sure we’re meeting the needs of the research community.

ARC-TS will be holding a series of town halls to take input from faculty and researchers on the next HPC platform to be built by the University.  These town halls are open to anyone and will be held at:

  • College of Engineering, Johnson Room, Tuesday, June 20th, 9:00a – 10:00a
  • NCRC Bldg 300, Room 376, Wednesday, June 21st, 11:00a – 12:00p
  • LSA #2001, Tuesday, June 27th, 10:00a – 11:00a
  • 3114 Med Sci I, Wednesday, June 28th, 2:00p – 3:00p

Your input will help to ensure that U-M is on course for providing HPC, so we hope you will make time to attend one of these sessions. If you cannot attend, please email hpc-support@umich.edu with any input you want to share.

Job Opening: Research Cloud Administrator

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Advanced Research Computing – Technology Services (ARC-TS)  has an exciting opportunity for a Research Cloud Administrator.

This position will be part of a team working on a novel platform for research computing in the university for data science and high performance computing.  The primary responsibilities for this position will be to develop and create a resource sharing environment to enable execution of Data Science and HPC workflows using containers for University of Michigan researchers.

For more details and to apply, visit: http://careers.umich.edu/job_detail/142372/research_cloud_administrator_intermediate

HPC training workshops begin Monday, May 15

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series of training workshops in high performance computing will be held May 15, May 17 and May 24, 2017, presented by CSCAR in conjunction with Advanced Research Computing – Technology Services (ARC-TS). All sessions are held at East Hall, Room B254, 530 Church St.

Introduction to the Linux command Line
This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also known as the “command line.”
• Monday, May 15, 9 a.m. – noon. (full descriptionregistration)

Introduction to the Flux cluster and batch computing
This workshop will provide a brief overview of the components of the Flux cluster, including the resource manager and scheduler, and will offer students hands-on experience.
• Wednesday, May 17, 1 – 4:30 p.m. (full description | registration)

Advanced batch computing on the Flux cluster
This course will cover advanced areas of cluster computing on the Flux cluster, including common parallel programming models, dependent and array scheduling, and a brief introduction to scientific computing with Python, among other topics.
• Wednesday, May 24, 1 – 5 p.m. (full description | registration)

NOTE: Additional workshops may be scheduled if demand warrants. Please sign up for the waiting list if the workshops are full, and you will be given first priority for any additional sessions.

U-M students invited to apply for MICDE fellowships — May 19 deadline

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University of Michigan students are invited to apply for Michigan Institute for Computational Discovery and Engineering (MICDE) Fellowships for the 2017-2018 academic year. These $4,000 fellowships are available to students in both the Ph.D in Scientific Computing and the Graduate Certificate Program in Computational Discovery and Engineering. Applicants should be graduate students enrolled in either program, although students not yet enrolled but planning to do so may simultaneously submit program and fellowship applications.

Fellows will receive a $4,000 research fund that can be used to attend a conference, to buy a computer, or for any other approved activity that enhances the Fellow’s graduate experience. We also ask that Fellows attend at least 8 MICDE seminars between Fall 2017 and Winter 2018, attend one MICDE students’ networking event, and present a poster at the MICDE Symposium on March 22, 2018. For more details and to apply please visit http://micde.umich.edu/academic-programs/micde-fellowships/.

Interested students should download and complete the application form, and submit it with a one-page resume as a SINGLE PDF DOCUMENT to MICDE-apps@umich.edu. The due date for applications is May 19, 2017, 5:00 E.T. We expect to announce the awardees onJune 5, 2017.

We encourage applications from all qualified candidates, including women and minorities.

ARC-TS contributes to successful fNIRS workshop

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The Center for Human Growth and Development (CHGD) held a workshop on functional near-infrared spectroscopy (fNIRS), a form of neuroimaging, with a special focus on pediatric applications. The workshop was sponsored by units at U-M, as well as units from Eastern Michigan University and Gallaudet University. It was attended by 50 people from as far away as Texas, and included research talks, instructional sessions, and hands-on experience with fNIRS data processing. The workshop was the first of its kind at U-M.

CHGD, ARC-TS, and LSA IT staff collaborated to provide a remote neuroimaging computing environment, which included a graphical interface, access to Matlab, and a suite of fNIRS software, that was accessed from participants’s laptops during the workshop. The attendees rated the practice exercises done via the computing environment one of the most important components of the workshop.

ARC-TS was pleased to be able to contribute to training in computational tools needed for emerging methods in neuroimaging. For more information about the fNIRS workshop, please see http://chgd.umich.edu/facilities-resources/developmental-neuroscience-laboratories/fnirs/fnirs-workshop/

New private insurance claims dataset and analytic support now available to health care researchers

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The Institute for Healthcare Policy and Innovation (IHPI) is partnering with Advanced Research Computing (ARC) to bring two commercial claims datasets to campus researchers.

The OptumInsight and Truven Marketscan datasets contain nearly complete insurance claims and other health data on tens of millions of people representing the US private insurance population. Within each dataset, records can be linked longitudinally for over 5 years.  

To begin working with the data, researchers should submit a brief analysis plan for review by IHPI staff, who will create extracts or grant access to primary data as appropriate.

CSCAR consultants are available to provide guidance on computational and analytic methods for a variety of research aims, including use of Flux and other UM computing infrastructure for working with these large and complex repositories.

Contact Patrick Brady (pgbrady@umich.edu) at IHPI or James Henderson (jbhender@umich.edu) at CSCAR for more information.

The data acquisition and availability was funded by IHPI and the U-M Data Science Initiative.

Designing optimal shunts for newborns with heart defects using computational modeling

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shuntFor babies born with hypoplastic left heart syndrome, several open-heart surgeries are required. During Stage I, a Norwood procedure is performed to construct an appropriate circulation to both the systemic and the pulmonary arteries. The pulmonary arteries receive flow from the systemic circulation, often by using a Blalock-Taussig (BT) shunt between the innominate artery and the right pulmonary artery. This procedure causes significantly disturbed flow in the pulmonary arteries.

A group of researchers led by U-M Drs. Ronald Grifka and Alberto Figueroa used computational hemodynamic simulations to demonstrate its capacity for examining the properties of the flow through and near the BT shunt. Initially, the researchers constructed a computational model which produces blood flow and pressure measurements matching the clinical magnetic resonance imaging (MRI) and catheterization data. Achieving this required us to determine the level of BT shunt occlusion; because the occlusion is below the MRI resolution, this information is difficult to recover without the aid of computational simulations. The researchers determined that the shunt had undergone an effective diameter reduction of 22% since the time of surgery. Using the resulting geometric model, they showed that we can computationally reproduce the clinical data. The researchers then replaced the BT shunt by with a hypothetical alternative shunt design with a flare at the distal end. Investigation of the impact of the shunt design revealed that the flare can increase pulmonary pressure by as much as 7%, and flow by as much as 9% in the main pulmonary branches, which may be beneficial to the pulmonary circulation.

Read more in Frontiers in Pediatrics.