Research Technology Newsletter

Our monthly Research Technology Newsletter updates the research community on current events. These include RT announcements, cluster and storage statistics, software updates on new licenses, feature and version releases, outages, workshops, and other information on RT services.

Research Technology's newsletter is published monthly.

NOTE: Due to the Covid-19 situation, the last issue was published in December 2019.

RT Newsletter December 2019

 

Announcements

HPC Cluster Upgrade from RedHat 6 to 7

ATTENTION: Over the upcoming holiday break, the operating system on Tufts High Performance Compute (HPC) cluster will be upgraded from Redhat 6 to Redhat 7. This will enable upcoming enhancements to gpu management, slurm scheduler, singularity containers, virtualization and remove long standing issues with older version of glibc. While we work to ensure no packages break, there is no way to test every permutation. If there are any questions or concerns before, during or after the upgrade, please let us know.

Mark Lab Upgrade

Stop by the newly upgraded Mark Lab, a Windows OS computer Lab geared towards data intensive research. Located on the first floor of Tisch Library (Room 103), the computer lab is open the same hours as the library and available for use when classes are not in session.

Research Computing By the Numbers

From month to month we will be featuring interesting statistics regarding Research Technology services. Below are the total counts for Cluster account creations, Cluster and Desktop storage requests, LabArchives account requests & activities. The graphs provide a monthly visual. If there are any metrics you are interested in, please let us know.

Total Cluster Account Creation: 436
Total Cluster & Desktop Storage Request: 216
Total LabArchives Account Creation: 200
Total LabArchives Activity: 174,200

cluster account requests
research storage requests
la accounts
la activity

Workshops

Webinar: Using the NVIDIA Rapids Toolkit on Comet

Tufts is looking at installing RAPIDS system wide so please attend the webinar and if it is something people are interested in let us know.

RAPIDS is NVIDIA's new Python-based framework for accelerating end-to-end data science and machine learning pipelines on their GPUs. In this webinar, we'll provide an overview of this new framework and how you can incorporate it in your own research.

In this webinar we will show how to use RAPIDS to accelerate your data science applications utilizing libraries like cuDF (GPU-enabled Pandas-like dataframes) and cuML (GPU-accelerated machine learning algorithms). We will demonstrate how to use Jupyter Notebooks on Comet to accelerate Data Science workflows with RAPIDS using interactive computing methods. In particular, if you use pandas and/or scikit-learn extensively, you'll definitely want to attend this webinar. This webinar will use the Zoom conferencing system.

 

Date: Thursday, 1/16/2020 
    Time: 2:00PM to 3:00PM EST

Register Here

 

You should receive an email with connection details a few days prior to the event. Please send any questions to training-info@sdsc.edu

**About the Instructor:**
Marty Kandes is a Computational and Data Science Research Specialist in the High-Performance Computing User Services Group at SDSC.

 

Past Research Technology Workshops

Thanks to everyone who took the time to attend this year's workshops (see below)! Research Technology provides hundreds of hours of training every year and your participation is greatly appreciated. Please email us for any feedback or requests for other topics. 

  • Petascale Computing Institute 2019
  • XSEDE HPC Monthly Workshops 2019:

        - HPC Summer Boot Camp - OpenACC, OpenMP and MPI
        - Big Data using Python and Spark 
        - GPU Programming Using OpenACC 
        - Multicore/Multinode Programming in C and Fortran using MPI
        - Multicore programming in C and Fortran using OpenMP

  •  Intro to Basic Linux Workshops
  • Intro to HPC Cluster Workshops
  • Intro to Bioinformatics Workshops

 

Opportunities

International HPC Summer School 2020

Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States are invited to apply for the 11th International HPC Summer School, to be held July 12-17, 2020 in Toronto, Canada, hosted by the SciNet HPC Consortium. Applications are due January 27, 2020. The summer school is sponsored by the Partnership for Advanced Computing in Europe (PRACE), the Extreme Science and Engineering Discovery Environment (XSEDE), the RIKEN Center for Computational Science (R-CCS) and the SciNet HPC Consortium.


Dates: July 12-17, 2020
     Location: Toronto, Canada
                             More Informationhttps://ss20.ihpcss.org/

 

NSF Computational Social Science REU

Within the Computational Social Science (CSS) REU program, ten students select from a wide variety of computational social science projects at the University of Notre Dame and work collaboratively with expert mentors. Computational social science as an approach to analyzing the social world is growing rapidly. An increasing number of social interactions are taking place in the virtual world via social media, mobile phones, and other electronic means. The digital traces of such interactions and the greater availability and detail of CSS data sets (e.g. surveys, census data, historical records) yield an exponential growth in data available for analysis. New cyberinfrastructure tools and methodologies for data analytics are needed to capitalize on this resource and enhance American economic competitiveness. This REU training program develops multidisciplinary social scientists with the appropriate expertise to answer the computational social science data growth challenges and opportunities.

Applications are now open for the summer 2020 cohort.
More Information: https://crc.nd.edu/outreach/reu-program/

 

Improving Scientific Software conference -- call for talks, tutorials and papers

The 2020 annual SEA’s Improving Scientific Software conference will take place in Boulder, CO at the NCAR Center Green Campus from the afternoon of Monday April 27th to Friday May 1st.

We are soliciting talks, tutorials and papers on Improving Scientific Software related to any of the following:

  • Influence of computer architecture on scientific software design
  • Modern tools for Data Analysis, Processing and Visualization
  • Scientific Workflows: Purpose and Product Review.
  • Machine learning for Scientific Computing
  • Containers in scientific software
  • Leveraging Cloud Computing Resources for HPC Development and Operations


Please see https://sea.ucar.edu/conference/2020 for further details and submit your talks, tutorials and papers!
 

 

LabArchives Digital Notebook

Labarchives is a cloud-based Digital Notebook solution that has commonly been refer to as Electronic Lab Notebook or ELN. Designed with academic researchers in mind, Labarchives gives faculty, staff and students the ability to digitally manage information in the cloud and offers secure collaboration for research groups.

Want to start using or try out LabArchives? Request LOGIN Access

RT Newsletter December 2019

 

Announcements

HPC Cluster Upgrade from RedHat 6 to 7

ATTENTION: Over the upcoming holiday break, the operating system on Tufts High Performance Compute (HPC) cluster will be upgraded from Redhat 6 to Redhat 7. This will enable upcoming enhancements to gpu management, slurm scheduler, singularity containers, virtualization and remove long standing issues with older version of glibc. While we work to ensure no packages break, there is no way to test every permutation. If there are any questions or concerns before, during or after the upgrade, please let us know.

Mark Lab Upgrade

Stop by the newly upgraded Mark Lab, a Windows OS computer Lab geared towards data intensive research. Located on the first floor of Tisch Library (Room 103), the computer lab is open the same hours as the library and available for use when classes are not in session.

Research Computing By the Numbers

From month to month we will be featuring interesting statistics regarding Research Technology services. Below are the total counts for Cluster account creations, Cluster and Desktop storage requests, LabArchives account requests & activities. The graphs provide a monthly visual. If there are any metrics you are interested in, please let us know.

Total Cluster Account Creation: 436
Total Cluster & Desktop Storage Request: 216
Total LabArchives Account Creation: 200
Total LabArchives Activity: 174,200

cluster account requests
research storage requests
la accounts
la activity

Workshops

Webinar: Using the NVIDIA Rapids Toolkit on Comet

Tufts is looking at installing RAPIDS system wide so please attend the webinar and if it is something people are interested in let us know.

RAPIDS is NVIDIA's new Python-based framework for accelerating end-to-end data science and machine learning pipelines on their GPUs. In this webinar, we'll provide an overview of this new framework and how you can incorporate it in your own research.

In this webinar we will show how to use RAPIDS to accelerate your data science applications utilizing libraries like cuDF (GPU-enabled Pandas-like dataframes) and cuML (GPU-accelerated machine learning algorithms). We will demonstrate how to use Jupyter Notebooks on Comet to accelerate Data Science workflows with RAPIDS using interactive computing methods. In particular, if you use pandas and/or scikit-learn extensively, you'll definitely want to attend this webinar. This webinar will use the Zoom conferencing system.

 

Date: Thursday, 1/16/2020 
    Time: 2:00PM to 3:00PM EST

Register Here

 

You should receive an email with connection details a few days prior to the event. Please send any questions to training-info@sdsc.edu

**About the Instructor:**
Marty Kandes is a Computational and Data Science Research Specialist in the High-Performance Computing User Services Group at SDSC.

 

Past Research Technology Workshops

Thanks to everyone who took the time to attend this year's workshops (see below)! Research Technology provides hundreds of hours of training every year and your participation is greatly appreciated. Please email us for any feedback or requests for other topics. 

  • Petascale Computing Institute 2019
  • XSEDE HPC Monthly Workshops 2019:

        - HPC Summer Boot Camp - OpenACC, OpenMP and MPI
        - Big Data using Python and Spark 
        - GPU Programming Using OpenACC 
        - Multicore/Multinode Programming in C and Fortran using MPI
        - Multicore programming in C and Fortran using OpenMP

  •  Intro to Basic Linux Workshops
  • Intro to HPC Cluster Workshops
  • Intro to Bioinformatics Workshops

 

Opportunities

International HPC Summer School 2020

Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States are invited to apply for the 11th International HPC Summer School, to be held July 12-17, 2020 in Toronto, Canada, hosted by the SciNet HPC Consortium. Applications are due January 27, 2020. The summer school is sponsored by the Partnership for Advanced Computing in Europe (PRACE), the Extreme Science and Engineering Discovery Environment (XSEDE), the RIKEN Center for Computational Science (R-CCS) and the SciNet HPC Consortium.


Dates: July 12-17, 2020
     Location: Toronto, Canada
                             More Informationhttps://ss20.ihpcss.org/

 

NSF Computational Social Science REU

Within the Computational Social Science (CSS) REU program, ten students select from a wide variety of computational social science projects at the University of Notre Dame and work collaboratively with expert mentors. Computational social science as an approach to analyzing the social world is growing rapidly. An increasing number of social interactions are taking place in the virtual world via social media, mobile phones, and other electronic means. The digital traces of such interactions and the greater availability and detail of CSS data sets (e.g. surveys, census data, historical records) yield an exponential growth in data available for analysis. New cyberinfrastructure tools and methodologies for data analytics are needed to capitalize on this resource and enhance American economic competitiveness. This REU training program develops multidisciplinary social scientists with the appropriate expertise to answer the computational social science data growth challenges and opportunities.

Applications are now open for the summer 2020 cohort.
More Information: https://crc.nd.edu/outreach/reu-program/

 

Improving Scientific Software conference -- call for talks, tutorials and papers

The 2020 annual SEA’s Improving Scientific Software conference will take place in Boulder, CO at the NCAR Center Green Campus from the afternoon of Monday April 27th to Friday May 1st.

We are soliciting talks, tutorials and papers on Improving Scientific Software related to any of the following:

  • Influence of computer architecture on scientific software design
  • Modern tools for Data Analysis, Processing and Visualization
  • Scientific Workflows: Purpose and Product Review.
  • Machine learning for Scientific Computing
  • Containers in scientific software
  • Leveraging Cloud Computing Resources for HPC Development and Operations


Please see https://sea.ucar.edu/conference/2020 for further details and submit your talks, tutorials and papers!
 

 

LabArchives Digital Notebook

Labarchives is a cloud-based Digital Notebook solution that has commonly been refer to as Electronic Lab Notebook or ELN. Designed with academic researchers in mind, Labarchives gives faculty, staff and students the ability to digitally manage information in the cloud and offers secure collaboration for research groups.

Want to start using or tryout LabArchives? Request LOGIN Access

Announcements

Thanks to everyone who took the time to attend the following workshops:

  • XSEDE on Multicore programming in C and Fortran using OpenMP
  • Intro to Basic Linux
  • Intro to HPC Cluster

Research Technology provides hundreds of hours of training every year and your participation is greatly appreciated! Please email us for any feedback or requests for other topics.

 

Workshops

Ingenuity Pathway Analysis Hands-On Training 

Come learn about how IPA can help you model, analyze, and understand complex Omics data. For more information about using IPA at tufts, visit http://go.tufts.edu/ipa. All faculty, student and staff are welcome!

Date: Tuesday 11/19/2019

Schedule: 10 am - 12:30 pm Hands-On Training, 12:30 - 1 pm Lunch + Q&A

Location: Sackler rm 514 (Boston campus)

Instructor: Eric Seiser, PhD | Field Application Scientist

Register Here

 

XSEDE Workshop: Big Data Using Python and Spark

This workshop is in conjunction with the Pittsburgh Supercomputer Center (PSC). Seats will go fast, so sign up early and join the Research Technology (RT) staff for two excellent days of free training! These workshops are sponsored by the National Science Foundation (NSF) funded eXstreme Science and Engineering Discovery Environment (XSEDE). All faculty, students and staff are welcome!

Dates: Tuesday 12/03/2019 and Wednesday 12/04/2019

Time: 11 am - 5 pm (both days)

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

Register Here

 

Intro to Bioinformatics for NGS Data Using Tufts Compute Cluster

This course will cover some examples of using the Tufts High Performance Compute Cluster (HPC) to manipulate Next Generation Sequencing (NGS) data. Tufts HPC hosts many different tools and datasets to facilitate analysis of sequencing data. Basic knowledge of Linux and an account on the Tufts Compute Cluster are required.

Medford

Date: Friday 12/06/2019

Register Here

Boston

Date: Tuesday 12/10/2019

Register Here

LabArchives Digital Notebook

Labarchives is a cloud-based Digital Notebook solution that has commonly been refer to as Electronic Lab Notebook or ELN. Designed with academic researchers in mind, Labarchives gives faculty, staff and students the ability to digitally manage information in the cloud and offers secure collaboration for research groups.

Interested in having your research team to use or tryout Labarchives? Click here to request LOGIN access.

Announcements

Thanks to everyone who took the time to attend our successful series of workshops:

  • Petascale Computing Institute 2019
  • XSEDE: Summer Boot Camp
  • XSEDE: Multicore Programming in C and Fortran Using OpenMP

Research Technology provides hundreds of hours of training every year and your participation is greatly appreciated. Please email us for any feedback or requests for other topics!

Workshops

XSEDE Workshop: Big Data Using Python and Spark

This workshop is in conjunction with the Pittsburgh Supercomputer Center (PSC). Seats will go fast, so sign up early and join the Research Technology (RT) staff for two excellent days of free training! These workshops are sponsored by the National Science Foundation (NSF) funded eXstreme Science and Engineering Discovery Environment (XSEDE). All faculty, students and staff are welcome!

Dates: Tuesday 10/01/2019 and Wednesday 10/02/2019

Time: 11 am – 5 pm (both days)

Location: Collaborative Learning and Innovation Complex rm 316 (Medford campus)

Register Here

 

Introduction To Basic Linux Workshop

This is designed to be an introductory level workshop on Basic Linux (the command line environment and some useful commands).

Medford

Date: 10/11/2019

Register Here

Boston

Date: 10/15/2019

Register Here

Grafton

Date: 10/15/2019

Register Here

Introduction To Tufts HPC Cluster Workshop

This workshop is a brief introduction of the structure of the Tufts HPC cluster, as well as the basic usage of it’s scheduler “SLURM”.

Medford

Date: 10/25/2019

Register Here

Boston

Date: 10/22/2019

Register Here

Grafton

Date: 10/22/2019

Register Here

Intro to Bioinformatics for NGS Data Using Tufts Compute Cluster

This course will cover some examples of using the Tufts High Performance Compute Cluster (HPC) to manipulate Next Generation Sequencing (NGS) data. Tufts HPC hosts many different tools and datasets to facilitate analysis of sequencing data. Basic knowledge of Linux and an account on Tufts Compute Cluster are required. 

Medford

Date: 12/6/2019

Register Here

Boston

Date: 12/10/2019

Register Here

Upcoming XSEDE Events

PLEASE PUT THESE EVENTS ON YOUR CALENDAR!
Further details and sign-up information will be provided when available.

 

XSEDE Workshop: Multicore programming in C and Fortran using OpenMP

Date: Tuesday 11/5/2019

Time: 11 am - 5 pm

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

 

XSEDE Workshop: Big Data using Python and Spark

Dates: Tuesday 12/3/2019 and Wednesday 12/4/2019

Time: 11 am - 5 pm (both days)

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

LabArchives Use Cases

Click on the links below to learn how other institutions are utilizing LabArchives Digital Notebook:

Are you interested in having your research team use or try LabArchives? To request access, click here

April showers bring May flowers, but this year they are also bringing workshops! We have events in the spring and summer, including two very special week-long workshops on High Performance Computing. Be sure to check them out, sign up, and show up for some excellent training material. As always, let us know of any additional topics you may be interested in!

Announcements

GIS Poster Expo

Please join Data Lab for a university-wide exposition of the GIS research being done at Tufts!

Date: Wednesday, May 08 2019

Time: 3:30 - 5:00 pm

Location: Alumnae Lounge, Aidekman Arts Center

 

Monthly Outage Window Scheduled

Attention Cluster users: Starting in April, a monthly outage window has been set for the 2nd Wednesday of every month. The outage window will go from 6am-6pm with the option to extend if necessary. At this time regular maintenance work will be performed (if needed) on various cluster subsystems such as the login, xfer, compute nodes, Slurm scheduler, storage or the web gateways including OnDemand, FastX, WebMo, etc.

Jobs running or scheduled to run at this time may have to be rescheduled.

This schedule is in keeping with other HPC sites, both local and national. Maintenance has to be done, as this gives us access to the best available vendor support and staffing.

If there are any questions, please email us.

 

OnDemand (OOD) Survey

Open OnDemand Community Members: The team at Ohio Supercomputer Center (OSC) which develops Open Ondemand (OOD) has received a 5 year NSF award to continue with “Phase 2” of the project. This is the software used at Tufts as the web portal to our High Performance Compute (HPC) cluster. A big component of that is to understand the views and needs of our existing community. To that end, we’ve got a very short survey (only 8 questions) we’d really appreciate your participation!

The purpose of the survey is to:

  • Get a feeling of how our users benchmark us today with the idea that we will ask again and hopefully see improvement.

  • Get ideas on what users see as possible improvements in the existing interface.

  • Get ideas for extensions of the interface.

 

$15,000/Year Fellowships in Computational and Data Science

Several years ago, ACM SIGHPC and Intel launched a new international program of graduate fellowships in computational and data science. The goal of this graduate fellowship is to increase the diversity of students pursuing graduate degrees in data science and computational science, including women as well as students from racial/ethnic backgrounds that have not traditionally participated in the computing field. The program supports students pursuing degrees at institutions anywhere in the world.

Submissions are now open! Interested faculty advisors and students can find more information on the fellowships, including a description of the online nomination process, here. Nominations close April 30, 2019.

Please contact fellowships@sighpc.org if you have any questions.

Workshops

XSEDE Workshop: High Performance Compute (HPC) Multicore/Multinode MPI Programming in C and Fortran

This workshop is intended to give C and Fortran programmers a hands-on introduction to MPI programming. Attendees will leave with a working knowledge of how to write codes using MPI, the standard programming tool of scalable parallel computing. It will have a hands-on component using the Bridges computing platform at the Pittsburgh Supercomputing Center but the material is equally applicable on all High Performance Compute (HPC) clusters including Tufts. All faculty, students and staff are welcome! 

We encourage everyone to register for the workshop on the XSEDE website. But we understand the official registration closes early, so WALK-INs are also welcome!

 

Date: Monday 5/06/2019 and Tuesday 5/07/2019

Time: 11 am - 5 pm (both days)

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

Register Here

 

Agenda:

Monday 5/06/2019

11:00 Welcome

11:15 Computing Environment

12:00 Intro to Parallel Computing

1:00 Lunch break

2:00 Introduction to MPI

3:30 Introductory Exercises

4:10 Intro Exercises Review

4:15 Scalable Programming: Laplace code

5:00 Adjourn/Laplace Exercises

Tuesday 5/07/2019

11:00 Advanced MPI

12:30 Lunch break

1:30 Laplace Review

2:00 Outro to Parallel Computing

2:45 Parallel Debugging and Profiling Tools

3:00 Exercises

4:30 Adjourn

Upcoming XSEDE Events

Further details and sign-up information will be provided when available.

 

XSEDE HPC Summer Boot Camp

Dates: Monday 6/03/2019 through Thursday 6/06/2019

Time: 11 am - 5 pm (all days)

Location: Collaborative Learning and Innovation Complex rm 310 (Medford campus)

 

Petascale Computing Institute

Logistics

Dates: Monday 8/19/2019 through Friday 8/23/2019

Time: 11 am - 4 pm (all days)

Location: Collaborative Learning and Innovation Complex rm 310 (Medford campus)

Register Here

 

Overview

The goal of the institute is to enable computational and data-enabled discovery in all fields of study by teaching the participants to scale their computational codes to leadership-class computing systems. The institute will be broadcast to Host Sites (listed on the Registration page to the left) using full-duplex audio/video connections. Participants will receive training accounts, on-site mentoring, and the ability to ask questions of the presenters orally and via on-line chats. Sessions will also be webcast on YouTube live, although participants will not receive training accounts and will only be able to post questions on-line. 

Participants must REGISTER to attend one of the Host Sites (listed on the Registration page to the left) or to watch the sessions on YouTube. Recordings of the presentations will be made publicly available after the institute is completed.

 

Audience

The institute is free and open to everyone. The content is targeted to individuals conducting research and scholarship in all disciplines, including graduate and undergraduate students, postdocs, faculty, researchers, scholars, educators, and practitioners in academia, industry and government agencies.

The institute will be beneficial to research teams who are preparing to scale their codes to petascale-class resources, people who are working on parallel codes, or have a need to scale up computational codes and/or data analysis programs. Individuals who are current or pending users of large-scale HPC systems will benefit the most from this institute. People who do not have access to research codes, such as those using commercial packages, are not likely to benefit from the institute.

 

Computing Resources

The institute will provide training accounts to participants who register to attend at one of the Host Sites. The training accounts will be provided on multiple HPC systems which are described in the Resources tab in the left menu bar.

Participants watching the YouTube live webcast will not be provided with training accounts, due to security policies and procedures for setting up training accounts.

 

Participant Prerequisites 

Participants are expected to have the following background, knowledge and experience:

  • Familiarity with programming in Fortran, C, C++, Python or a comparable language
  • Familiarity with Linux
  • Familiarity with use of clusters and/or HPC systems

Announcements

Open Science Grid User School 2019

Applications for the 2019 Open Science Grid User School are open! This week-long opportunity is especially helpful for research CI professionals who help researchers at their institution to use large-scale computing. The application process is very simple, and the school covers all participant costs.

The OSG School will give you the skills to identify, facilitate, and/or execute research computing tasks that could be scaled by orders of magnitude with execution strategies and infrastructure for high-throughput computing (HTC), including the Open Science Grid. Using lectures, discussions, role-play, and lots of hands-on work with OSG experts in HTC, participants will learn how HTC systems work, how to run and manage work across many computing jobs and large datasets, how to implement a realistic scientific computing workflow, and where to turn for help and more info.

Ideal candidates are graduate students doing research and staff supporting research that involves or could involve large-scale computing – work that cannot be done on one laptop or a handful of computers. The school also accepts post-doctoral students, faculty, research staff, and advanced undergraduates.

The school covers all basic travel, hotel, and food costs for applicants who are selected to attend.

 

Important Dates

Application Deadline: April 12 2019

OSG User School Dates: July 15 2019 - July 19 2019

 

More Information

OSG User School Facebook

OSG User School Twitter

If you have any questions, don't hesitate to send an email to user-school@opensciencegrid.org.

 

SigmaPlot v14 is Available!

The latest version of SigmaPlot v14 is now available to Tufts faculty, staff, student and research computers. Please call 617-627-3376 or email it@tufts.edu for assistance with the installation of the software.

SigmaPlot v14 is also installed on the TTS Virtual Lab. If you prefer to use the application on a virtual desktop or would like to tryout the application before having it installed on your computer, please follow the steps below:

  1. Open a web-browser (i.e. Firefox, Chrome, Safari or Microsoft Edge)
  2. Go to https://vdi.it.tufts.edu
  3. Click on VMWare Horizon HTML Access
  4. Login with your Tufts username (i.e. JDOE01) and password
  5. Click on TTS Virtual Lab
  6. Once preparing windows is complete, double click SigmaPlot 14.0 icon on the desktop

For more information on new features of SigmaPlot v14, click here.

NOTE: The license for SigmaPlot v13 has expired after Sunday, 3/24/2019.

Events

Bioinformatics for RNA-Seq

Taught by Rebecca Batorsky, Senior Bioinformatics Specialist, TTS High throughput RNA sequencing allows genome-wide investigation of gene expression and regulation. However, designing an experiment and choosing the right tools for analysis can be challenging. This two-day course aims to teach the basics of obtaining and analyzing RNA-seq data: Experiment design, quality control, alignment and visualization of reads and differential expression analysis. Analysis will be done with tools available on the Tufts High Performance Compute Cluster and example code and tutorials will be available at Tutorials.

Dates: Monday 4/08/2019 and Tuesday 4/09/2019

Time: 9 am - 12 pm

Location: Sackler rm 514 (Boston campus)

Register Here

 

Introduction to Basic Linux

If you are new to Linux environment and Tufts HPC cluster, this is a great place to start! This is designed to be an introductory level workshop on Basic Linux (the command line environment and some useful commands).

This is a hands-on workshop and an account on the Tufts HPC cluster (created at least one week prior to the workshop) is required.

No previous Linux experience is required. Please bring your own laptop.

Date: Thursday 4/11/2019

Time: 1:30 p.m. – 3:00 p.m

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

Register Here

Please email us if you have any questions!

 

Introduction to Tufts HPC Cluster

If you are new to Tufts HPC cluster, this is a great place to start! This workshop is a brief introduction of the structure of the Tufts HPC cluster (different nodes, different partitions, storage options, and available software,.etc), as well as the basic usage of its scheduler “SLURM”.

This is a hands-on workshop and an account on the Tufts HPC cluster (created at least one week prior to the workshop) is required.

Basic Linux knowledge is required. If you are not familiar with Linux, please check out our “Introduction to Basic Linux Workshop”. Please bring your own laptop.

Please email us if you have any questions!

Date: Thursday 4/04/2019

Time: 1:30 p.m. – 3:00 p.m.

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

Register Here

Date: Thursday 4/18/2019

Time: 1:30 p.m. – 3:00 p.m.

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

Register Here

Upcoming XSEDE Events

Further details and sign-up information will be provided when available.

High Performance Compute (HPC) Multicore/Multinode MPI Programming in C and Fortran

Dates: Monday 5/06/2019 and Tuesday 5/07/2019

Time: 11 am - 5 pm

Location: Collaborative Learning and Innovation Complex rm 114 (Medford campus)

 

XSEDE HPC Summer Boot Camp

Dates: Monday 6/03/2019 through Thursday 5/06/2019

Time: 11 am - 5 pm

Location: Collaborative Learning and Innovation Complex rm 310 (Medford campus)

 

Petascale Computing Institute

Overview

The goal of the institute is to enable computational and data-enabled discovery in all fields of study by teaching the participants to scale their computational codes to leadership-class computing systems. The institute will be broadcast to Host Sites (listed on the Registration page to the left) using full-duplex audio/video connections. Participants will receive training accounts, on-site mentoring, and the ability to ask questions of the presenters orally and via on-line chats. Sessions will also be webcast on YouTube live, although participants will not receive training accounts and will only be able to post questions on-line.

Participants must REGISTER to attend one of the Host Sites (listed on the Registration page to the left) or to watch the sessions on YouTube. Recordings of the presentations will be made publicly available after the institute is completed.

Audience

The institute is free and open to everyone. The content is targeted to individuals conducting research and scholarship in all disciplines, including graduate and undergraduate students, postdocs, faculty, researchers, scholars, educators, and practitioners in academia, industry and government agencies.

The institute will be beneficial to research teams who are preparing to scale their codes to petascale-class resources, people who are working on parallel codes, or have a need to scale up computational codes and/or data analysis programs. Individuals who are current or pending users of large-scale HPC systems will benefit the most from this institute. People who do not have access to research codes, such as those using commercial packages, are not likely to benefit from the institute.

Computing Resources

The institute will provide training accounts to participants who register to attend at one of the Host Sites. The training accounts will be provided on multiple HPC systems which are described in the Resources tab in the left menu bar.

Participants watching the YouTube live webcast will not be provided with training accounts, due to security policies and procedures for setting up training accounts.

Participant Prerequisites

Participants are expected to have the following background, knowledge and experience:

  • Familiarity with programming in Fortran, C, C++, Python or a comparable language
  • Familiarity with Linux
  • Familiarity with use of clusters and/or HPC systems
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