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[Users] NERSC Weekly Email, Week of January 20, 2020

Author: Rebecca Hartman-Baker <rjhartmanbaker_at_lbl.gov>
Date: 2020-01-20 13:17:55

# NERSC Weekly Email, Week of January 20, 2020 # ## Contents ## - [Summary of Upcoming Events and Key Dates](#dates) - [Martin Luther King, Jr. Day Holiday Today; No Consulting or Account Support](#mlkday) - [New Community File System Now Available](#cfs) - [Interested in High-Performance Python? Submit to SciPy2020 Conference!](#scipy2020) - [Argonne Training Program on Extreme-Scale Computing Now Accepting Applications!](#atpesc) - [Need Help Switching to Cori KNL Nodes? KNL Office Hours on Fridays All Month!](#knlofficehrs) - [CUDA Training Series Resumes February 19](#cudatrain) - [Women in HPC Summit Call for Submissions; Poster Submissions Deadline January 31!](#whpc) - [Dynamic Linking Is Now Default on Cori](#dynamic) - [User Dotfile Changes Planned for February 2020](#dotfiles) - [Performance, Portability, and Productivity in HPC Forum (P3HPC) Submissions Close Next Friday](#p3hpc) - [NERSC Now Supports Only Python3](#python2) - [No New "NERSC User News" Podcast this Week](#nopodcast) - [Come Work for NERSC!](#careers) - [Upcoming Outages](#outages) - [About this Email](#about) ## Summary of Upcoming Events and Key Dates <a name="dates"/></a> ## January 2020 Su Mo Tu We Th Fr Sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 *20* 21 22 23 *24* 25 20 Jan MLK Holiday [1] 24 Jan P3HPC Submissions due [2] 25 Jan KNL Office Hours [3] 26 27 28 29 30 *31* 31 Jan WHPC Poster Submissions due [4] 31 Jan KNL Office Hours [3] February 2020 Su Mo Tu We Th Fr Sa 1 2 *3* 4 5 6 7 8 3 Feb ALCC Due Date [5] 9 10 *11* 12 13 14 15 11 Feb SciPy2020 Submissions Due [6] 16 *17* 18 *19* 20 21 22 17 Feb Presidents Day Holiday [7] 19 Feb CUDA Shared Mem Training [8] 23 24 25 26 27 28 29 March 2020 Su Mo Tu We Th Fr Sa 1 *2* 3 4 5 6 7 2 Mar ATPESC Applications Due [9] 8 9 10 11 12 13 14 15 16 17 *18* 19 20 21 18 Mar CUDA Optimization Training [8] 22 23 24 25 26 27 28 29 30 31 Notes: 1. **January 20, 2020**: Martin Luther King Jr. Day Holiday (No Consulting or Account Support) 2. **January 24, 2020**: [P3HPC Submissions due](#p3hpc) 3. **January 25 and 31, 2020**: [KNL Office Hours](#knlofficehrs) 4. **January 31, 2020**: [Women in HPC Summit poster submissions due](#whpc) 5. **February 3, 2020**: [ALCC Proposals due](#alcc) 6. **February 11, 2020**: [SciPy2020 submissions due](#scipy2020) 7. **February 17, 2020**: Presidents Day Holiday (No Consulting or Account Support) 8. **February 19 & March 18, 2020**: [NVIDIA CUDA Training Series](#cudatrain) 9. **March 2, 2020**: [ATPESC applications due](#atpesc) 10. All times are **Pacific Time zone** ### Other Significant Dates ### - **April 7-9, 2020**: [Performance, Portability, and Productivity in HPC Forum](https://p3hpcforum2020.alcf.anl.gov/) - **April 16 & May 13, 2020**: Additional CUDA Training dates - **April 29-May 1, 2020**: [Women in HPC Summit](https://womeninhpc.org/events/summit-2020) - **May 25, 2020**: Memorial Day Holiday (No Consulting or Account Support) - **July 4, 2020**: Independence Day Holiday (No Consulting or Account Support) - **July 6-12, 2020**: [SciPy2020](https://www.scipy2020.scipy.org/) Conference - **September 7, 2020**: Labor Day Holiday (No Consulting or Account Support) - **November 26-27, 2020**: Thanksgiving Holiday (No Consulting or Account Support) - **December 24, 2020-January 1, 2021**: Christmas/New Year Holiday (Limited Consulting or Account Support) ## Martin Luther King, Jr. Day Holiday Today; No Consulting or Account Support <a name="mlkday"/></a> ## Consulting and account support will be unavailable today, January 20, due to the Berkeley Lab-observed Martin Luther King, Jr. Day holiday. Regular consulting and account support services will resume tomorrow. Operations staff are available for urgent queries via 1-800-66-NERSC, Option 1, at all times. ## New Community File System Now Available <a name="cfs"/></a> ## The new "Community" File System (CFS) has replaced the Project file system in the new allocation year (AY). It was made available via a rolling reboot that started this past Friday, January 17. Each active project has a directory on CFS with the path structure `/global/cfs/cdirs/<repo_name>`, but existing `/global/project/projectdirs/<repo_name>` paths will redirect to the corresponding CFS path until mid-2020. ## Interested in High-Performance Python? Submit to SciPy2020 Conference! <a name="scipy2020"/></a> ## Are you running large Python jobs at NERSC? Have you worked hard to make your Python code run fast? Are you exploring options for running your Python code on Perlmutter's GPUs? If so, we invite you and your colleagues to consider submitting to the new [High-Performance Python track](https://www.scipy2020.scipy.org/talk-poster-presentations) at [SciPy2020](https://www.scipy2020.scipy.org/), which will be held July 6-12 in Austin, Texas. Submissions for talks and posters are being accepted through **February 11, 2020.** Sucessful talk submissions are eligible to submit a paper to be published in the conference proceedings. We hope to see you in Austin! ## Argonne Training Program on Extreme-Scale Computing Now Accepting Applications! <a name="atpesc"/></a> ## Are you a doctoral student, postdoc, or computational scientist looking for advanced training on the key skills, approaches, and tools to design, implement, and execute computational science and engineering applications on current high-end computing systems and the leadership-class computing systems of the future? If so, consider applying for the Argonne Training Program on Extreme-Scale Computing (ATPESC) program. The core of the two-week program focuses on programming methodologies that are effective across a variety of supercomputers and applicable to exascale systems. Additional topics to be covered include computer architectures, mathematical models and numerical algorithms, approaches to building community codes for HPC systems, and methodologies and tools relevant for Big Data applications. There is no cost to attend. For more information and to apply, please see <https://extremecomputingtraining.anl.gov/>. The application deadline is March 2, 2020. ## Need Help Switching to Cori KNL Nodes? KNL Office Hours on Fridays All Month! <a name="knlofficehrs"/></a> ## NERSC will hold virtual office hours over Zoom from 9:00 am to 3:00 pm Pacific Time for every Friday in January, including this Friday (January 24), to help users get their codes running efficiently on the Cori KNL nodes. For many users, running efficiently on the KNL nodes is as simple as making sure that their job script is set to request the proper thread affinity on the node, and their executable is compiled correctly to exploit the KNL architecture. We have seen a performance gap shrink by a factor of 7 just with these two simple steps. Other user codes may require some relatively straightforward code changes (for example, a loop reordering to exploit vectorization). Profiling the code is the first step towards finding these hot spots or bottlenecks. During the KNL Office Hours, NERSC experts will be on hand to help you take these steps. Please (virtually) drop by for help with - Setting up your job script for proper thread affinity - Compiling your code with the best optimization flags - Getting started with profiling your code - Interpreting the results of profiling, and advice on how to proceed A [podcast](https://anchor.fm/nersc-news/episodes/KNL-Office-Hours-Jack-Deslippe-Interview-e3uk9f/a-aee631) from May provides additional information about the office hours. Join online at <https://lbnl.zoom.us/j/943079374> or view the event on the [NERSC Public Events calendar](https://calendar.google.com/calendar/embed?src=lbl.gov_ls0gdtgi7b93jredles0ibl0u4%40group.calendar.google.com&ctz=America%2FLos_Angeles) for full connection information. ## CUDA Training Series Resumes February 19 <a name="cudatrain"/></a> ## NVIDIA is presenting a 9-part CUDA training series intended to help new and existing GPU programmers understand the main concepts of the CUDA platform and its programming model. Each part will include a 1-hour presentation and example exercises. The exercises are meant to reinforce the material from the presentation and can be completed during a 1-hour hands-on session following each lecture (for in-person participants) or on your own (for remote participants). OLCF and NERSC will both be holding in-person events for each part of the series. The second training in the series, on CUDA shared memory, will take place on Wednesday, February 19, 2020, from 10 am to 12 pm (Pacific time). This training will introduce users to CUDA shared memory, and how to use it to manage data caches, speed up high-performance cooperative parallel algorithms, and facilitate global memory coalescing in cases where it would otherwise not be possible. Following the presentation will be a hands-on session where in-person participants can complete example exercises meant to reinforce the presented concepts. For more information (including registration information) please see <https://www.nersc.gov/users/training/events/cuda-shared-memory-part-2-of-9-cuda-training-series/> Other scheduled dates in the series: - March 18: [3. Fundamental CUDA Optimization (Part 1)](https://www.nersc.gov/users/training/events/fundamental-cuda-optimization-part-1-part-3-of-9-cuda-training-series/) - April 16: [4. Fundamental CUDA Optimization (Part 2)](https://www.nersc.gov/users/training/events/fundamental-cuda-optimization-part-2-part-4-of-9-cuda-training-series/) - May 13: [5. CUDA Atomics, Reductions, and Warp Shuffle](https://www.nersc.gov/users/training/events/cuda-atomics-reductions-and-warp-shuffle-part-5-of-9-cuda-training-series/) ## Women in HPC Summit Call for Submissions; Poster Submissions Deadline January 31! <a name="whpc"/></a> ## Submissions for posters are now being accepted for the first Women in HPC Summit, to be held April 29-May 1, 2020 in Vancouver, British Columbia, Canada. Posters are solicited on a diverse range of technical and diversity, inclusion, and leadership topics, including but not limited to: - Programming models and applications for HPC, Big Data, and AI; - Architectures and accelerators on high-performance platforms; - Computational models and algorithms for HPC, Big Data, and AI; - Using machine learning to analyze large-scale systems; - Performance modeling, analysis, and benchmarking of HPC, Big Data, and AI applications/architectures; - Methods and techniques to create a diverse workforce; - Inclusive leadership and retention strategies; - Building diversity advocates and allies; - Dealing with unconscious bias and sexism in the workplace; - Fostering creativity through diversity. The tutorial and paper submission deadlines have passed, but poster submissions are due next Friday, January 31, 2020, AOE. For more information and to submit, please see <https://womeninhpc.org/events/summit-2020>. ## Dynamic Linking Is Now Default on Cori <a name="dynamic"/></a> ## When the new CDT/19.11 is set as default at the time of the Allocation Year transition tomorrow, the default linking mode on Cori will change from static to dynamic. With the change in default software environment for the new allocation year, the default linking mode on Cori is now dynamic. For best performance with dynamically linked executables running on the compute nodes, we recommend storing your executable on `/global/common/software/<your_proj>` instead of the community file system. Note that i`/global/common` is mounted as read-write on login nodes, and read-only on compute nodes. If you prefer to use static linking as default (e.g., for workflow or performance reasons), you can set: ``` % export CRAYPE_LINK_TYPE=static ``` or add the `-static` flag in your compile and link lines to retain static linking. If you need to use the previous default CDT/19.03 version (which has static linking as default), you can do so with: ``` % module load cdt/19.03 % export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH ``` (this second line is needed only for dynamically linked executables.) ## User Dotfile Changes Planned for February 2020 <a name="dotfiles"/></a> ## Currently, by default, `.bashrc`/`.bash_profile`/`.cshrc`/`.login` files are symlinks in your `$HOME` to read-only NERSC-supplied startup files. You may have made changes to your starting environment by adding `.bashrc.ext`/`.bash_profile.ext`/`.cshrc.ext`/`.login.ext` files. To reduce some shell startup overhead, and to bring NERSC in line with most other HPC centers, we will migrate away from this arrangement during the scheduled maintenance in **February 2020**. After the change is made, you will be able to edit `.bashrc` (etc.) directly. During the change, your `.bashrc` (etc.), which is currently a symlink, will be replaced by a template `.bashrc` (etc.) that simply sources your `.bashrc.ext` (etc.). For most users this should have no other impact. But some non-default environments and workflows might experience some changes to their environment. You can test the changes now, by using the `dotmgr` command and logging in to cori12 or dtn12, which now have the new configuration: `dotmgr -l` # list my current dotfiles `dotmgr -s` # save my current dotfiles, and print the location `dotmgr -e` # replace my existing dotfiles with the new arrangement You can then login to cori12 and/or dtn12 to check whether this affected your environment. Check that things still look the same and your aliases still work. `ssh cori12` You can then return your dotfiles to the current configuration with: `dotmgr -r <directory-that-the-save-step-returned>` Note that `dotmgr -e` and `dotmgr -r` **don't affect your current environment** -- they affect the contents of your dotfiles. For the changes to take effect, you must log out and log back in. For detailed help, please see <https://docs.nersc.gov/environment/>. Please let us know of any problems you encounter, by filing a ticket at <https://help.nersc.gov>. ## Performance, Portability, and Productivity in HPC Forum (P3HPC) Submissions Close Next Friday <a name="p3hpc"/></a> ## The call for papers for the Performance, Portability, and Productivity in HPC Forum (P3HPC) is now open. This workshop is an opportunity for researchers to share ideas, practical experiences, and methodologies for tackling the compelling problems that lie at the intersection of performance, portability and productivity. We are particularly interested in research that addresses the complexities of real-life applications and/or realistic workloads, the composability challenges arising from the use of bespoke solutions, and the desire to "future-proof" applications in the long term. Submissions close this Friday, January 24, 2020. For more information and to submit a paper, please see <https://p3hpcforum2020.alcf.anl.gov/>. ## NERSC Now Supports Only Python3 <a name="python2"/></a> ## Python 2 has reached its end of life ([January 1, 2020](https://devguide.python.org/#status-of-python-branches)), so there will be no more development, bug fixes, patches, etc. Therefore, NERSC now supports only Python 3. - At the AY rollover, the default Python module changed to python/3.7-anaconda-2019.10, a module based on a Python 3 distribution. - The old Python 2 module is still available for use but users must specify the version suffix. - No new installations of Python 2 packages or modules will be performed. - During the next Cori operating system upgrade, which could occur sometime in 2020, the Python 2 modules will be retired. NERSC will actively support only Python 3 (or future Python versions should Python 3 become deprecated) on Perlmutter and future systems. Please let us know your questions via a ticket to <https://help.nersc.gov>. ## No New "NERSC User News" Podcast this Week <a name="nopodcast"/></a> ## There will be no new episode of the "NERSC User News" podcast this week. We encourage you to instead enjoy some of our most recent episodes and greatest hits: - [NERSC 2019 in Review and Looking Forward](https://anchor.fm/nersc-news/episodes/NERSC-2019-in-Review-and-Looking-Forward--Sudip-Dosanjh-Interview-ea5d5t/a-a1a6cpd) NERSC director Sudip Dosanjh reflects upon the accomplishments of NERSC and its users in 2019, and what he's looking forward to in 2020 at NERSC. - [Community File System](https://anchor.fm/nersc-news/episodes/Community-File-System-Kristy-Kallback-Rose--Greg-Butler--and-Ravi-Cheema-Interview-e9d88q/a-a149hf5) NERSC Storage System Group staff Kristy Kallback-Rose, Greg Butler, and Ravi Cheema talk about the new Community File System and the migration timeline. - [May Quarterly Maintenance & James Botts Interview](https://anchor.fm/nersc-news/episodes/May-Quarterly-Maintenance--James-Botts-Interview-e1ec2g/a-a3cfi7) The first-ever NERSC User News podcast, in which James Botts from NERSC's Computational Systems Group describes the process of rebooting Cori after an outage. - [Monitoring System Performance](https://anchor.fm/nersc-news/episodes/Monitoring-System-Performance-Eric-Roman-Interview-e5g20m/a-aobd6p) NERSC Computational Systems Group's Eric Roman discusses how NERSC monitors system performance, what we're doing with the data right now, and how we plan to use it in the future. - [The Superfacility Concept](https://anchor.fm/nersc-news/episodes/The-Superfacility-Concept-Debbie-Bard-Interview-e5a5th/a-amoglk): Join NERSC Data Science Engagement Group Lead Debbie Bard in a discussion about the concept of the superfacility: what it means, how facilities interact, and what NERSC and partner experimental facilities are doing to prepare for the future of data-intensive science. - [Optimizing I/O in Applications](https://anchor.fm/nersc-news/episodes/Optimizing-IO-in-Applications-Jialin-Liu-Interview-e50nvm): Listen to an I/O optimization success story in this interview with NERSC Data and Analytics Services Group's Jialin Liu. - [ERCAP Allocation Requests](https://anchor.fm/nersc-news/episodes/ERCAP-Allocation-Requests-Clayton-Bagwell-Interview-e4u09l): Learn how to get compute and storage allocations on NERSC resources for next year in this interview with NERSC User Engagement Group's Clayton Bagwell. - [Roofline Model for Application Performance](https://anchor.fm/nersc-news/episodes/Roofline-Model-for-Application-Performance-Charlene-Yang-Interview-e4osl1): NERSC Application Performance Specialist Charlene Yang discusses the roofline model for application performance: what it is and how it works, how to use it to improve your application's performance, and future directions in roofline model research. - [Parallelware Trainer; Manuel Arenaz Interview](https://anchor.fm/nersc-news/episodes/Parallelware-Trainer-Manuel-Arenaz-Interview-e4g46r): Learn about the Appentra Parallelware Trainer tool: how it can help you learn to code with OpenMP and OpenACC, the features of the tool, and how to use it on Cori. - [Profiling Codes with Cray Performance Tools](https://anchor.fm/nersc-news/episodes/Profiling-Codes-with-Cray-Performance-Tools-Heidi-Poxon-Interview-e42veg): Learn about why you would want to profile your codes and the tools for profiling provided by Cray from Cray senior principal engineer and senior manager Heidi Poxon. - [Energy Efficiency and Environmental Consciousness at NERSC](https://anchor.fm/nersc-news/episodes/Energy-Efficiency-and-Environmental-Consciousness-at-NERSC--Norm-Bourassa-Interview-e35tfp): Learn about all the energy efficiency work going on at NERSC from building energy efficiency expert Norm Bourassa. - [Getting a Machine from Contract to Reality](https://anchor.fm/nersc-news/episodes/Getting-a-Machine-from-Contract-to-Reality--Tina-Declerck-Interview-e307eg/a-a9521c): Listen to Systems Department Head Tina Declerck describe the complex process of going from a contract with a vendor to a supercomputer on the floor in production for users. - [A Day in the Control Room](https://anchor.fm/nersc-news/episodes/A-Day-in-the-Control-Room--Interview-with-Owen-James-e2uh9v/a-a8rppe): In this interview, NERSC Site Reliability Engineer Owen James talks about what it's like in the NERSC control room and how they ensure that the systems stay up for you. - [NESAP Postdocs](https://anchor.fm/nersc-news/episodes/NESAP-Postdocs--Laurie-Stephey-Interview-e2lsg0): Learn from NESAP postdoc Laurie Stephey what it's like working as a postdoc in the NESAP program at NERSC. The NERSC User News podcast, produced by the NERSC User Engagement Group, is available at <https://anchor.fm/nersc-news> and syndicated through iTunes, Google Play, Spotify, and more. Please give it a listen and let us know what you think, via a ticket at <https://help.nersc.gov>. ## Come Work for NERSC! <a name="careers"/></a> ## NERSC currently has several openings for postdocs, system administrators, and more! If you are looking for new opportunities, please consider the following openings: - **NEW** [NESAP Engineer](https://jobs.lbl.gov/jobs/nesap-engineer-2476): Work as part of a multidisciplinary team composed of computational and domain scientists working together to produce mission-relevant science that pushes the limits of HPC in simulation, data, or learning. - [HPC Architecture and Performance Engineer](https://jobs.lbl.gov/jobs/hpc-architecture-and-performance-engineer-2427): Evaluate global technology trends and combine them with the needs of NERSC users with the goal of architecting the supercomputing ecosystem of the future. - [Application Performance Specialist](https://jobs.lbl.gov/jobs/application-performance-specialist-1010): Help prepare large-scale scientific codes for next-generation high performance computing (HPC) systems as part of the ECP project. - [High Performance Computing Security Developer](https://jobs.lbl.gov/jobs/high-performance-computing-security-developer-2295): Protect Exascale class systems in an open science environment and enhance network and host intrusion prevention as we migrate from 100G to Terabit networks. - [Software Engineer (Storage and I/O)](https://jobs.lbl.gov/jobs/software-engineer-storage-and-i-o-2275): Enable DOE researchers and the broader science community to benefit from improvements to HDF5 and other leading high-performance computing (HPC) storage and I/O software. - [NESAP for Simulations Postdoctoral Fellow](https://jobs.lbl.gov/jobs/nesap-for-simulations-postdoctoral-fellow-2004): work in multidisciplinary teams to transition simulation codes to NERSC's new Perlmutter supercomputer and produce mission-relevant science that truly pushes the limits of high-end computing. - [NESAP for Data Postdoctoral Fellow](https://jobs.lbl.gov/jobs/nesap-for-data-postdoctoral-fellow-2412) work in multidisciplinary teams to transition data-analysis codes to NERSC's new Perlmutter supercomputer and produce mission-relevant science that truly pushes the limits of high-end computing. - [NESAP for Learning Postdoctoral Fellow](https://jobs.lbl.gov/jobs/nesap-for-learning-postdoctoral-fellow-1964): work in multidisciplinary teams to develop and implement cutting-edge machine learning/deep learning solutions in codes that will run on NERSC's new Perlmutter supercomputer and produce mission-relevant science that truly pushes the limits of high-end computing. - [HPC Storage Systems Analyst](https://jobs.lbl.gov/jobs/hpc-storage-systems-analyst-1851): Help architect, deploy, and manage NERSC's storage hierarchy (including Burst Buffer, Lustre, and Spectrum Scale filesystems, and HPSS archives). (**Note:** We have received reports that the URLs for the jobs change without notice, so if you encounter a page indicating that a job is closed or not found, please check by navigating to <https://https://jobs.lbl.gov/>, scrolling down to the 9th picture that says "All Jobs" and clicking on that. Then, under "Business," select "View More" and scroll down until you find the checkbox for "NE-NERSC" and select it.) We know that NERSC users can make great NERSC employees! We look forward to seeing your application. ## Upcoming Outages <a name="outages"/></a> ## - **HPSS Archive (User)** - 01/22/20 9:00-13:00 PST, Scheduled Maintenance Visit <http://www.nersc.gov/users/live-status/> for latest status and outage information. ## About this Email <a name="about"/></a> ## You are receiving this email because you are the owner of an active account at NERSC. This mailing list is automatically populated with the email addresses associated with active NERSC accounts. In order to remove yourself from this mailing list, you must close your account, which can be done by emailing <accounts@nersc.gov> with your request. _______________________________________________ Users mailing list Users@nersc.gov

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