# NERSC Weekly Email, Week of April 26, 2021 <a name="top"></a> # ## Contents ## - [Summary of Upcoming Events and Key Dates](#dates) ## [NERSC Status](#section1) ## - [NERSC Operations Continue, with Minimal Shelter-in-Place Impacts](#curtailment) ## [This Week's Events and Deadlines](#section2) ## - [Nominations for ACM SIGHPC Graduate Fellowships in Computational and Data Science Close on Friday!](#sighpc) - [First Allocation Reductions Begin Next Week](#allocred) ## [Updates at NERSC ](#section3) ## - [(NEW) Codecov Users Must Expire/Reset Tokens or Keys Used by Codecov](#codecov) - [(NEW) New Format for Ticket-Generated Emails](#snemail) - [Flex QOS Now Available on Cori Haswell Nodes](#hwflex) - [Large Jobs on Cori Haswell Now Require Reservation](#hwres) - [JupyterLab 3 Comes to NERSC May 19](#jupyterlab) - [Creating a Script to Run Your Job? Use the NERSC Job Script Generator!](#jobscript) ## [Calls for Participation](#section4) ## - [Call for Papers: Parallel Applications Workshop, Alternatives to MPI+X](#pawatm) ## [Upcoming Training Events ](#section5) ## - [Learn to Use MANA Transparent Checkpointing Tool on May 7](#manatrain) - [IDEAS-ECP Webinar on Automated Fortran-C++ Bindings for Large-Scale Scientific Applications, May 12](#ecpwebinar2) ## [NERSC News ](#section6) ## - [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> ## April 2021 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 26 27 28 29 *30* 30 Apr SIGHPC Fellow Noms Due [1] May 2021 Su Mo Tu We Th Fr Sa 1 2 3 *4* 5 6 *7* 8 4 May First Allocation Reduction [2] 7 May MANA Ckpt Tool Training [3] 9 10 11 *12* 13 14 15 12 May IDEAS-ECP Webinar [4] 16 17 18 *19* 20 21 22 19 May Cori Monthly Maint Window [5] 19 May JupyterLab 3 Available [6] 23 24 25 26 27 28 29 30 *31* 31 May Memorial Day Holiday [7] June 2021 Su Mo Tu We Th Fr Sa 1 2 3 4 5 6 7 8 9 *10* 11 12 10 Jun SpinUp Workshop [8] 13 14 15 *16* 17 18 19 16 Jun Cori Monthly Maint Window [5] 20 21 22 23 24 25 26 27 28 29 30 31 1. **April 30, 2021**: [ACM SIGHPC Graduate Fellowship Nominations Due](#sighpc) 2. **May 4, 2021**: [First Allocation Reduction Date](#allocred) 3. **May 7, 2021**: [MANA Transparent Checkpointing Tool Training](#manatrain) 4. **May 12, 2021**: [IDEAS-ECP Monthly Webinar](#ecpwebinar2) 5. **May 19 & June 16, 2021**: [Cori Monthly Maintenance](#monthlymaint) Window 6. **May 19, 2021**: [JupyterLab 3 Available](#jupyterlab) 7. **May 31, 2021**: Memorial Day Holiday (No Consulting or Account Support) 8. **June 10, 2021**: SpinUp Workshop 9. All times are **Pacific Time zone** - **Upcoming Planned Outage Dates** (see [Outages section](#outages) for more details) - None planned until May 19 - **Other Significant Dates** - **June 25, 2021**: [PERMAVOST Workshop](https://permavost.github.io/) - **July 5, 2021**: Independence Day Holiday (No Consulting or Account Support) - **July 10, 2021**: One-day NERSC building power maintenance (tentative) - **July 21, August 18, & September 15, 2021**: Cori Monthly Maintenance Window - **July 23, 2021**: [PAW-ATM Workshop](#pawatm) Submissions close - **August 1-13, 2021**: Argonne Training Program on Extreme-Scale Computing - **August 19, October 14, & December 9, 2021**: SpinUp Workshops - **September 6, 2021**: Labor Day Holiday (No Consulting or Account Support) - **September 7, 2021**: Second Allocation Reduction Date - **October 20, November 17, & December 15, 2021**: Cori Monthly Maintenance Window - **November 25-26, 2021**: Thanksgiving Holiday (No Consulting or Account Support) - **December 24, 2021 - January 3, 2022**: Winter Shutdown (Limited Consulting and Account Support) ([back to top](#top)) --- ## NERSC Status <a name="section1"/></a> ## ### NERSC Operations Continue, with Minimal Shelter-in-Place Impacts <a name="curtailment"/></a> Alameda County, California, where NERSC is located, remains under public health order restrictions. NERSC continues to remain open while following site-specific protection plans. We remain in operation as before, with the majority of NERSC staff working remotely for the foreseeable future, and only staff essential to operations onsite. You can continue to expect regular online consulting and account support but no telephone support. Trainings will continue to be held online, or postponed if online is infeasible. Regular maintenances on the systems will continue to be performed while minimizing onsite staff presence, which could result in longer downtimes than would occur under normal circumstances. Because onsite staffing is so minimal, we request that you continue to refrain from calling NERSC Operations except to report urgent system issues. For **current NERSC systems status**, please see the online [MOTD](https://www.nersc.gov/live-status/motd/) and [current known issues](https://docs.nersc.gov/current/) webpages. ([back to top](#top)) --- ## This Week's Events and Deadlines <a name="section2"/></a> ## ### Nominations for ACM SIGHPC Graduate Fellowships in Computational and Data Science Close on Friday! <a name="sighpc"/></a> Are you a currently enrolled graduate student focusing on computational or data science (or will you be one no later than October 15)? Are you a woman or a member of a racial or ethnic group that is currently underrepresented in the computing field in the country where you are studying? If so, you may be eligible to apply for the ACM SIGHPC Graduate Fellowship in Computational and Data Science. Each fellowship recipient will receive a stipend of US$15,000 annually for up to 2 years as long as they are progressing in their degree program. In the case of non-US universities, the stipend will be adjusted depending on World Bank national price level ratio for the country where the degree will be earned. In addition, new fellowship recipients will be supported to travel to the annual SC conference, where they will be honored at the awards session. The submissions close **this Friday, April 30, 2021**. For more information please see <https://www.sighpc.org/for-your-career/fellowships>. ### First Allocation Reductions Begin Next Week <a name="allocred"/></a> The first allocation reductions will occur **next Tuesday, May 4.** The allocation reduction process takes unused allocation from projects not using them and allows DOE program managers to redistribute that time to other projects. PIs and PI proxies may request exemptions, at least one week before the reduction date. **If you wish to request an exemption, please do so by tomorrow.** Additional allocation reductions will occur on September 7, 2021. For more information, including how much allocation will be removed, please see <https://www.nersc.gov/users/accounts/allocations/allocation-reductions>. ([back to top](#top)) --- ## Updates at NERSC <a name="section3"/></a> ## ### (NEW) Codecov Users Must Expire/Reset Tokens or Keys Used by Codecov <a name="codecov"/></a> The Codecov software testing tool was recently compromised in a cyber attack. This tool is typically used for continuous integration, and there are some NERSC users who may be using this tool to test their codes. If you have used this tool, **you should immediately expire/reset any tokens or keys used by Codecov, contained in your CI environment or git repository, or located in local source code.** This includes tokens and keys used during CI from GitLab, GitHub, BitBucket, AWS, or any other service, as well as any credentials used as part of your continuous integration pipeline (e.g., database logins). If you have any questions about actions you should take to protect your NERSC account and projects, please submit a ticket at <https://help.nersc.gov>. ### (NEW) New Format for Ticket-Generated Emails <a name="snemail"/></a> You may have already noticed the improved look for emails auto-generated by NERSC's ticketing system (ServiceNow). NERSC has been hard at work improving the user helpdesk experience, first with the web portal and improvements to request forms, and now with better email responses to user tickets. Please let us know what you think, or if you have any ideas that can make it even easier for us to help you, by opening a [ticket](https://help.nersc.gov). ### Flex QOS Now Available on Cori Haswell Nodes <a name="hwflex"/></a> A "flex" QOS is now available on the Cori Haswell partition. This QOS is aimed at users whose jobs are capabile of running for a relatively short amount of time before terminating. For example, if you are running a code that is capable of checkpointing and restarting where it left off, then you may be able to use the flex QOS. Benefits to using the flex QOS include - The ability to improve your throughput by submitting jobs that can fit into the cracks in the job schedule; - A 50% discount in charging for your job. To use the flex QOS, you must add the `-q flex` directive into your job script, plus your job must satisfy the following constraints: - It must request a minimum time (using the `--time-min` directive) of at most 2 hours (e.g., `--time-min=1:30:00` for a request of 1.5 hours); - The number of nodes requested must not exceed 64. For more information, please see - https://docs.nersc.gov/jobs/policy/#flex for information about the QOS, and - https://docs.nersc.gov/jobs/examples/#variable-time-jobs for information about running variable-time jobs. ### Large Jobs on Cori Haswell Now Require Reservation <a name="hwres"/></a> Jobs submitted to the Cori Haswell partition requesting more than 512 nodes will need to be submitted through a [compute reservation](https://nersc.servicenowservices.com/sp/?id=sc_cat_item&sys_id=1c2ac48f6f8cd2008ca9d15eae3ee4a5&sysparm_category=e15706fc0a0a0aa7007fc21e1ab70c2f). This will better enable users submitting large jobs to rapidly debug any issues. ### JupyterLab 3 Comes to NERSC May 19 <a name="jupyterlab"/></a> NERSC currently supports JupyterLab 2 in production. JupyterLab 3 was released several months ago and we have been watching its development closely. We have had a parallel JupyterLab 3 deployment in testing for several months now, with staff and early users kicking the tires. We have been keeping tabs on and actively helping with migration of relevant JupyterLab extensions to JupyterLab 3. We have also been working on understanding JupyterLab 3's new extension installation system and what role it can play in our deployment. For more info on JupyterLab 3 and what's changed from JupyterLab 2, see this [blog post](https://blog.jupyter.org/jupyterlab-3-0-is-out-4f58385e25bb) and the more detailed [changelog](https://jupyterlab.readthedocs.io/en/stable/getting_started/changelog.html). Progress is such that we believe we can upgrade to JupyterLab 3 soon. We are currently planning the upgrade for a short scheduled maintenance on Wednesday, May 19. If all goes well after that maintenance, JupyterLab 3 will replace JupyterLab 2 at NERSC. ### Creating a Script to Run Your Job? Use the NERSC Job Script Generator! <a name="jobscript"/></a> Do you need to create a script to run your job on Cori? Do you find it challenging to get all the details right? If so, consider using NERSC's [Job Script Generator](https://my.nersc.gov/script_generator.php) to generate a batch script for you. The tool generates a bare-bones script that includes the correct process and thread-binding configurations, so you don't have to worry about the details. ([back to top](#top)) --- ## Calls for Participation <a name="section4"/></a> ## ### Call for Papers: Parallel Applications Workshop, Alternatives to MPI+X <a name="pawatm"/></a> The Parallel Applications Workshop, Alternatives to MPI+X (PAW-ATM) is seeking full-length papers and extended abstracts for the workshop to be held in conjunction with SC21 in St. Louis, Missouri in mid-November. PAW-ATM is a forum for discussing HPC applications written in alternatives to MPI+X. These alternatives include new languages (e.g., Chapel, Regent, XcalableMP), frameworks for large-scale data science (e.g., Arkouda, Dask, Spark), and extensions to existing languages (e.g., Charm++, COMPSs, Fortran, Legion, UPC++). Topics of interest include, but are not limited to: - Novel application development using high-level parallel programming languages and frameworks. - Examples that demonstrate performance, compiler optimization, error checking, and reduced software complexity. - Applications from artificial intelligence, data analytics, bioinformatics, and other novel areas. - Performance evaluation of applications developed using alternatives to MPI+X and comparisons to standard programming models. - Novel algorithms enabled by high-level parallel abstractions. - Experience with the use of new compilers and runtime environments. - Libraries using or supporting alternatives to MPI+X. - Benefits of hardware abstraction and data locality on algorithm implementation. Submissions close **July 23, 2021**. For more information and to submit a paper, please visit: <https://sourceryinstitute.github.io/PAW/>. ([back to top](#top)) --- ## Upcoming Training Events <a name="section5"/></a> ## ### Learn to Use MANA Transparent Checkpointing Tool on May 7 <a name="manatrain"/></a> NERSC will host an online, hands-on user training on [MANA](https://github.com/mpickpt/mana), a transparent checkpointing tool, on Friday, May 7, 2021 from 10-11:30 am (Pacific). MANA is an MPI-Agnostic, Network-Agnostic transparent checkpointing tool, **requiring no modifications to user codes.** Benefits of using MANA include the capability of running a job of any length on Cori with checkpoint/restart, the potential for improved job throughput, and the ability to realize a 75% charging discount by running in the Flex queue. The training will begin with a 30-minute presentation, followed by a one-hour hands-on session. For more information and to register, please see <https://www.nersc.gov/users/training/events/user-training-on-mana-a-transparent-checkpointing-tool-on-may-7-2021/>. ### IDEAS-ECP Webinar on Automated Fortran-C++ Bindings for Large-Scale Scientific Applications, May 12 <a name="ecpwebinar2"/></a> The May webinar in the [Best Practices for HPC Software Developers](http://ideas-productivity.org/events/hpc-best-practices-webinars/) series is entitled "Automated Fortran-C++ Bindings for Large-Scale Scientific Applications", and will take place Wednesday, May 12, 2021, at 10:00 am Pacific time. This webinar, presented by Seth Johnson (Oak Ridge National Laboratory), will present a solution to the challenge of connecting existing Fortran code to new internal C++ kernels or external C++ libraries, a challenge many developers interested in performance portability models and other rapidly developing, dynamic programming paradigms. SWIG-Fortran provides a flexible solution that includes support for performant data transfers, MPI support, and direct translation of C++ features to Fortran interfaces. There is no cost to attend, but registration is required. Please register [here](https://www.exascaleproject.org/event/fortran-cpp-bindings/). ([back to top](#top)) --- ## NERSC News <a name="section6"/></a> ## ### 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 2020 in Review & Looking Forward](https://anchor.fm/nersc-news/episodes/NERSC-2020-in-Review-and-Looking-Forward-Sudip-Dosanjh-Interview-ep44l0) NERSC director Sudip Dosanjh discusses the highlights of 2020 at NERSC, as well as what to look forward to in 2021 and beyond. - [Software Support Policy](https://anchor.fm/nersc-news/episodes/NERSC-Software-Support-Policy-Steve-Leak-Interview-ehu6bg) In this interview with NERSC HPC Consultant Steve Leak, learn about the new NERSC software support policy: what it is, how it works, and its benefits for users and NERSC staff alike. - [NERSC Power Upgrade](https://anchor.fm/nersc-news/episodes/NERSC-Power-Upgrade-David-Topete-Interview-egc35v) In this interview with Berkeley Lab Infrastructure Modernization Division's David Topete, learn about the power upgrade happening this weekend, the work that has to be done, and the steps taken to ensure the safety of the workers involved in the effort. - [Dynamic fan](https://anchor.fm/nersc-news/episodes/Dynamic-Fan-Norm-Bourassa-Interview-ef4bkp) NERSC Energy Efficiency Engineer Norm Bourassa talks about how NERSC is saving energy with the dynamic fan settings on the Cori supercomputing cabinets, and what NERSC is doing to make the cabinets even more energy efficient. - [RAPIDS](https://anchor.fm/nersc-news/episodes/The-RAPIDS-Library-Nick-Becker-Interview-eb0h5a) In this interview with NVIDIA RAPIDS senior engineer Nick Becker, learn about the RAPIDS library, how it can accelerate your data science, and how to use it. - [IO Middleware](https://anchor.fm/nersc-news/episodes/IO-Middleware-Quincey-Koziol-Interview-eaf5r3/a-a1c7plt) NERSC Principal Data Architect Quincey Koziol talks about IO Middleware: what it is, how you can benefit from using it in your code, and how it is evolving to support data-intensive computing and future supercomputing architectures. - [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. - [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. - [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: - [Linux Systems Administrator/Dev Ops Engineer](http://m.rfer.us/LBLA3-3fx): Help build and manage systems that complement the NERSC HPC environment, including web services, databases, container and virtual machine platforms, and more. - [Storage Systems Group Lead](http://m.rfer.us/LBLcze3fw): Lead the team that manages, supports, and monitors NERSC's large-scale storage systems. - [HPC Storage Infrastructure Engineer](http://m.rfer.us/LBLGNw3fv): Join the team that architects, deploys, and supports high-performance parallel storage systems at NERSC. - [HPC Performance Engineer](http://m.rfer.us/LBLjuG3fu): Enable new scientific advancements by enabling scientists to exploit cutting-edge computational science techniques in machine learning, data analysis, and/or simulation on NERSC's next supercomputer. - [HPC Architecture and Performance Engineer](http://m.rfer.us/LBLBDS3ft): Help NERSC develop a complete understanding of architecture/performance to improve application and computer-system performance on extreme-scale advanced architectures. - [Machine Learning Engineer](http://m.rfer.us/LBLviN3fs): Enable new scientific advancements by enabling scientists to exploit cutting-edge computational science techniques in machine learning and deep learning on NERSC's future supercomputers. - [NESAP for Data Postdoctoral Fellow](http://m.rfer.us/LBLyHh3fF): 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 Simulations Postdoctoral Fellow](http://m.rfer.us/LBL6vJ3fr): Work in multidisciplinary teams to develop and optimize codes for the Perlmutter system and produce mission-relevant science that pushes the limits of high-performance computing. - [NESAP for Learning Postdoctoral Fellow](http://m.rfer.us/LBL13A3fq): 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 pushes the limits of AI on high-performance computing. (**Note:** You can browse all our job openings by first navigating to <https://jobs.lbl.gov/jobs/search/>. Under "Business," select "View More" and scroll down to find and select the checkbox for "NE-NERSC".) We know that NERSC users can make great NERSC employees! We look forward to seeing your application. ### Upcoming Outages <a name="outages"/></a> - **Cori** - 05/19/21 07:00-20:00 PDT, Scheduled Maintenance Visit <http://my.nersc.gov/> 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