https://snicdocs.nsc.liu.se/w/api.php?action=feedcontributions&user=Birgitte+Brydsoe+%28HPC2N%29&feedformat=atomSNIC Documentation - User contributions [en]2024-03-29T15:22:37ZUser contributionsMediaWiki 1.31.10https://snicdocs.nsc.liu.se/w/index.php?title=Using_Python_in_an_HPC_environment,_May_2023,_UPPMAX/HPC2N&diff=8032Using Python in an HPC environment, May 2023, UPPMAX/HPC2N2023-04-27T08:50:38Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Using Python in an HPC environment |fields=Python; High performance computing |event type=Workshop |location=Umeå, Uppsala (ONLINE) |start..."</p>
<hr />
<div>{{training event info<br />
|description=Using Python in an HPC environment<br />
|fields=Python; High performance computing<br />
|event type=Workshop<br />
|location=Umeå, Uppsala (ONLINE)<br />
|start date=2023-05-23<br />
|end date=2023-05-23<br />
}}<br />
<br />
== Course overview ==<br />
This course aims to give a brief, but comprehensive introduction to using Python in an HPC environment. You will learn how to use modules to load Python, how to find site installed Python packages, as well as how to install packages yourself. In addition, you will learn how to use virtual environments, write a batch script for running Python, use Python in parallel, and how to use Python for ML and on GPUs. <br />
<br />
The course is a cooperation between UPPMAX and HPC2N. The instructors will use UPPMAX's systems for demos and there will be hands-on exercises for the participants.<br />
<br />
This course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned.<br />
<br />
The goal for the course is that you will be able to:<br />
<br />
* Load Python modules and site-installed Python packages<br />
* Create a virtual environment<br />
* Install Python packages with pip and/or conda<br />
* Write batch scripts for running Python<br />
* Use Python in parallel<br />
* Use Python for ML<br />
* Use GPUs with Python<br />
<br />
'''NOTE''': The course is online, using Zoom. <br />
<br />
'''Prerequisites''': familiarity with the Linux command line, basic Python, and batch jobs.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to either of these <br />
* [https://www.uppmax.uu.se/support/courses-and-workshops/HPC-python UPPMAX course page] <br />
* [https://www.hpc2n.umu.se/events/courses/2023/python-in-hpc HPC2N course page]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=The_future_of_HPC_programming_-_a_Modern_Fortran_workshop,_Ume%C3%A5,_2022-11-(24-25)&diff=7923The future of HPC programming - a Modern Fortran workshop, Umeå, 2022-11-(24-25)2022-11-02T12:59:01Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=The future of HPC programming - a Modern Fortran workshop |fields=applications, fortran, programming, hpc |event type=Workshop |location=Ume..."</p>
<hr />
<div>{{training event info<br />
|description=The future of HPC programming - a Modern Fortran workshop<br />
|fields=applications, fortran, programming, hpc<br />
|event type=Workshop<br />
|location=Umeå University, Online<br />
|start date=2022-11-24<br />
|end date=2022-11-25<br />
}}<br />
<br />
== Course overview ==<br />
The workshop will be hybrid (on-site at Umeå University and also streamed over Zoom). <br />
<br />
Fortran is the primordial HPC language. Its handling of multidimensional arrays have ensured that compilers can produce highly efficient code, and inclusion of coarrays in the 2008 standard made it the first major programming language with builtin support for parallelism. The 2008 inclusion of object-oriented modernised the language, bringing it on par with many of its contenders. In 2019 the Fortran standards committee started work on generics (templates). Templates are planned for the 202y release of Fortran, the one after the upcoming 2023 release.<br />
<br />
Unlike C++ templates, Fortran templates are type-safe (strong concepts) and does not support meta-programming. This enables some very powerful programming techniques not matched by other high performance languages.<br />
<br />
In this workshop we will give a hands-on preview of such techniques. This includes defining your own Fortran integrated domain specific programming languages (IDSLs) while benefitting from Fortran's efficient code generation. We also look at the dichotomy between well-structured code and efficient code, and show some systematic transformations between these. Lastly, we suggest just-in-time compilation and interpreters for user defined Fortran IDSLs, achieving much of the same flexibility as the current integration of Fortran and Python.<br />
<br />
It is a cooperation between HPC2N and LUNARC. <br />
<br />
== Pre-requisites ==<br />
Participants should have at least basic programming experience <br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [ https://www.hpc2n.umu.se/events/courses/2022/modern-fortran course webpage].</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=R_in_an_HPC_environment,_Ume%C3%A5,_2022-12-(14-15)&diff=7918R in an HPC environment, Umeå, 2022-12-(14-15)2022-10-12T13:25:00Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=R in an HPC environment |fields=applications, R, hpc, parallelization |event type=Course |location=Online |start date=2022-12-14 |end date=2..."</p>
<hr />
<div>{{training event info<br />
|description=R in an HPC environment<br />
|fields=applications, R, hpc, parallelization<br />
|event type=Course<br />
|location=Online<br />
|start date=2022-12-14<br />
|end date=2022-12-15<br />
}}<br />
<br />
== Course overview ==<br />
In this online course you will learn several strategies to write faster and more efficient code in R. This will be done in several steps starting from a serial code and then using existing packages to parallelize code so that it can take advantage of the many core architecture of Kebnekaise. An HPC cluster such as Kebnekaise is useful for R users because it can provide both more CPU power and memory than what a personal computer can offer but one needs to make code aware of these resources. We will explore ways to achieve the latter and when parallel algorithms are suitable and possible. <br />
<br />
It is a cooperation between HPC2N and PDC, and it is also a part of the PRACE Training Courses. <br />
<br />
== Pre-requisites ==<br />
Participants should have at least a basic knowledge of using the command line. <br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2022/R-in-HPC course webpage].</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Git,_Ume%C3%A5,_2022-11-(14-18)&diff=7917Introduction to Git, Umeå, 2022-11-(14-18)2022-10-12T13:19:12Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to Git |fields=applications, git, hpc |event type=Course |location=Online |start date=2022-11-14 |end date=2022-11-18 }} == Co..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to Git<br />
|fields=applications, git, hpc<br />
|event type=Course<br />
|location=Online<br />
|start date=2022-11-14<br />
|end date=2022-11-18<br />
}}<br />
<br />
== Course overview ==<br />
The course will be an introduction to version control, with a strong focus on Git.<br />
<br />
This online course covers some of the main concepts, like repositories, commits, trees, branches, and merges will be covered, as will many of the basic commands, like clone, add, push, pull, commit, and fork. We will also go one step beyond the basic concepts and explain the fundamentals of how commits and branches can be manually created by using so-called "plumbing" (low-level) subcommands.<br />
<br />
It is a cooperation between HPC2N and UPPMAX, and it is also a part of the PRACE Training Courses. <br />
<br />
== Pre-requisites ==<br />
Participants should have at least a basic knowledge of using the command line. <br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2022/introduction-to-git course webpage].</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Using_Python_in_an_HPC_environment,_September_2022,_UPPMAX/HPC2N&diff=7880Using Python in an HPC environment, September 2022, UPPMAX/HPC2N2022-05-24T12:59:18Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{training event info<br />
|description=Using Python in an HPC environment<br />
|fields=Python; High performance computing<br />
|event type=Workshop<br />
|location=Umeå, Uppsala (ONLINE)<br />
|start date=2022-09-09<br />
|end date=2022-09-09<br />
}}<br />
<br />
== Course overview ==<br />
UPPMAX and HPC2N are organising a joint workshop on how to run Python codes and install additional Python packages on the computer resources provided by these two HPC centres. Participants are encouraged to bring their particular software request for discussion as well.<br />
<br />
The goal for the course is that you will be able to:<br />
<br />
* Load Python modules and site-installed Python packages<br />
* Create a virtual environment<br />
* Install Python packages with pip (Kebnekaise, Rackham, Snowy)<br />
* Install Python packages with conda (Bianca)<br />
* Write batch scripts for running Python<br />
* Use Python in parallel<br />
* Use Python for ML<br />
* Use GPUs with Python<br />
<br />
'''NOTE''': The course is online, using Zoom. <br />
<br />
'''Prerequisites''': familiarity with the Linux command line, basic Python, and batch jobs.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to either of these <br />
* [https://www.uppmax.uu.se/support/courses-and-workshops/HPC-python UPPMAX course page] <br />
* [https://www.hpc2n.umu.se/events/courses/2022/python-in-hpc HPC2N course page]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Using_Python_in_an_HPC_environment,_September_2022,_UPPMAX/HPC2N&diff=7879Using Python in an HPC environment, September 2022, UPPMAX/HPC2N2022-05-24T12:58:29Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Using Python in an HPC environment |fields=Python; High performance computing |event type=Workshop |location=Umeå, Uppsala |start date=2022..."</p>
<hr />
<div>{{training event info<br />
|description=Using Python in an HPC environment<br />
|fields=Python; High performance computing<br />
|event type=Workshop<br />
|location=Umeå, Uppsala<br />
|start date=2022-09-09<br />
|end date=2022-09-09<br />
}}<br />
<br />
== Course overview ==<br />
UPPMAX and HPC2N are organising a joint workshop on how to run Python codes and install additional Python packages on the computer resources provided by these two HPC centres. Participants are encouraged to bring their particular software request for discussion as well.<br />
<br />
The goal for the course is that you will be able to:<br />
<br />
* Load Python modules and site-installed Python packages<br />
* Create a virtual environment<br />
* Install Python packages with pip (Kebnekaise, Rackham, Snowy)<br />
* Install Python packages with conda (Bianca)<br />
* Write batch scripts for running Python<br />
* Use Python in parallel<br />
* Use Python for ML<br />
* Use GPUs with Python<br />
<br />
'''Prerequisites''': familiarity with the Linux command line, basic Python, and batch jobs.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to either of these <br />
* [https://www.uppmax.uu.se/support/courses-and-workshops/HPC-python UPPMAX course page] <br />
* [https://www.hpc2n.umu.se/events/courses/2022/python-in-hpc HPC2N course page]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Kebnekaise,_2022-09-15,_HPC2N/UmU&diff=7878Introduction to Kebnekaise, 2022-09-15, HPC2N/UmU2022-05-24T11:14:41Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{training event info<br />
|description=Introduction to Kebnekaise<br />
|fields=Linux; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2022-09-15<br />
|end date=2022-09-15<br />
}}<br />
<br />
== Course overview ==<br />
We begin with a short (optional) introduction to the Linux operating system that is used on HPC2N's compute clusters. Then, we continue with a walk-through of the Kebnekaise system, including the GPUs and KNLs. After lunch, we go through the module system and take a brief look at how to submit jobs. During the hands-on you will get the opportunity to try loading modules, compile a program, and submit a job to the Kebnekaise cluster.<br />
<br />
The course will be completely online and we will use Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Introduction to HPC2N, Kebnekaise and High Performance Computing<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2022/intro-fall course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Kebnekaise,_2022-09-15,_HPC2N/UmU&diff=7877Introduction to Kebnekaise, 2022-09-15, HPC2N/UmU2022-05-24T11:13:55Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to Kebnekaise |fields=Linux; High performance computing |event type=Course |location=Umeå |start date=2022-09-15 |end date=202..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to Kebnekaise<br />
|fields=Linux; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2022-09-15<br />
|end date=2022-09-15<br />
}}<br />
<br />
== Course overview ==<br />
We begin with a short (optional) introduction to the Linux operating system that is used on HPC2N's compute clusters. Then, we continue with a walk-through of the Kebnekaise system, including the GPUs and KNLs. After lunch, we go through the module system and take a brief look at how to submit jobs. During the hands-on you will get the opportunity to try loading modules, compile a program, and submit a job to the Kebnekaise cluster.<br />
<br />
The course will be completely online and we will use Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Introduction to HPC2N, Kebnekaise and High Performance Computing<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2022/intro-fall<br />
course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=MD_simulations_with_a_focus_on_NAMD_(HPC2N,_UmU),_2022-04-(07-08)&diff=7851MD simulations with a focus on NAMD (HPC2N, UmU), 2022-04-(07-08)2022-02-28T13:38:40Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=MD simulations with a focus on NAMD |fields=MD; High performance computing; NAMD |event type=Course |location=Umeå |start date=2022-04-07 |..."</p>
<hr />
<div>{{training event info<br />
|description=MD simulations with a focus on NAMD<br />
|fields=MD; High performance computing; NAMD<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2022-04-07<br />
|end date=2022-04-08<br />
}}<br />
<br />
== Course overview ==<br />
The aim of the course is to let participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files.<br />
<br />
We will start from scratch by setting a MD Biomolecular (protein+water) simulation, in the first day of the course. During the second day, we will learn how to setup a steered molecular dynamics simulation (Na-Cl system) and use the results to compute the free energies of separation. Regarding the software, we will use software already installed at HPC2N, i.e. VMD, and NAMD for the full protocol. We will also provide users with a set of best practices to improve the performance of their simulations.<br />
<br />
This course will be two half-days. It will have lectures interspersed with live-demo sessions where you get to try out what the instructor shows.<br />
<br />
The course will be completely online. We will use Zoom.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2022/namd-spring course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Kebnekaise_(HPC2N),_2022-01-19&diff=7835Introduction to Kebnekaise (HPC2N), 2022-01-192021-12-13T12:38:34Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to Kebnekaise |fields=Linux; High performance computing |event type=Course |location=Umeå |start date=2022-01-19 |end date=202..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to Kebnekaise<br />
|fields=Linux; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2022-01-19<br />
|end date=2022-01-19<br />
}}<br />
<br />
== Course overview ==<br />
HPC2N is offering an ONLINE introduction course to HPC2N and Kebnekaise.<br />
<br />
We begin with a short (optional) introduction to Linux, then continue with an introduction to HPC, HPC2N, and a walkthrough of Kebnekaise, including the GPUs and the KNLs. We then look at the module system and loading the software you need, and how to submit jobs through the batch system.<br />
<br />
There will be hands-ons as a part of the course, where the participants get the opportunity to load modules, compile programs, and submit jobs to the Kebnekaise system.<br />
<br />
Remote/online participation: The course will be completely online. We will use Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Introduction to HPC2N, Kebnekaise and High Performance Computing<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2022/intro-spring course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=QM/MM_best_practices,_HPC2N,_2021-12-9&diff=7831QM/MM best practices, HPC2N, 2021-12-92021-11-09T14:56:16Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=QM/MM best practices |fields=QM/MM; MD; High performance computing |event type=Course |location=Umeå |start date=2021-12-09 |end date=2021-..."</p>
<hr />
<div>{{training event info<br />
|description=QM/MM best practices<br />
|fields=QM/MM; MD; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-12-09<br />
|end date=2021-12-09<br />
}}<br />
<br />
== Course overview ==<br />
The aim of the course is to give an intro to classical Molecular Dynamics (MD) simulations and the combined Quantum Mechanical and Molecular Mechanics (QM/MM) simulations. We will start from scratch by setting a MD simulation, in the first half-day of the course, and then use this system to setup a QM/MM simulation. Regarding the software, we will use VMD, NAMD, ORCA, and GAUSSIAN for the full QM/MM protocol. We will also provide users with a set of best practices to improve the performance of their simulations.<br />
<br />
This course will be one-day. It will have lectures interspersed with live-demo sessions where you get to try out what the instructor shows.<br />
<br />
NOTE: The course will be online!<br />
<br />
Time and date: 9 December 2021, 09:00-16:00.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/qm-mm course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Git,_HPC2N,_2021-11-(9-12)&diff=7821Introduction to Git, HPC2N, 2021-11-(9-12)2021-09-30T09:47:06Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{training event info<br />
|description=Introduction to Git<br />
|fields=Git; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-11-09<br />
|end date=2021-11-12<br />
}}<br />
<br />
== Course overview ==<br />
HPC2N is offering an ONLINE (Zoom) introduction course to Git.<br />
<br />
The course will be an introduction to version control, with a focus on Git.<br />
<br />
Some of the main concepts, like repositories, commits, trees, branches, and merges will be covered, as will many of the basic commands, like clone, add, push, pull, commit, and fork.<br />
<br />
The lectures will be complemented by hands-on, during which the participants will learn both how to do simple Git commands as well as more complex cases. The hands-ons will mainly be done using GitHub.<br />
<br />
This HPC2N/SNIC course is also part of the PRACE Training courses. It is thus open for academics and people who work in industry in the PRACE member countries.<br />
<br />
'''Date''': 2021-11-(9-12)<br />
<br />
'''Time''': 8:30-12:00 on the first day (the first half-hour is an optional Git installation/Kebnekaise login-session for those that need it), 9:00-12:00 on the rest of the days.<br />
<br />
'''Deadline for registration''': 2021-11-01<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/git course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Git,_HPC2N,_2021-11-(9-12)&diff=7820Introduction to Git, HPC2N, 2021-11-(9-12)2021-09-30T09:45:40Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to Git |fields=Git; High performance computing |event type=Course |location=Umeå |start date=2021-11-09 |end date=2021-11-12 }..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to Git<br />
|fields=Git; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-11-09<br />
|end date=2021-11-12<br />
}}<br />
<br />
== Course overview ==<br />
HPC2N is offering an ONLINE (Zoom) introduction course to Git.<br />
<br />
The course will be an introduction to version control, with a focus on Git.<br />
<br />
Some of the main concepts, like repositories, commits, trees, branches, and merges will be covered, as will many of the basic commands, like clone, add, push, pull, commit, and fork.<br />
<br />
The lectures will be complemented by hands-on, during which the participants will learn both how to do simple Git commands as well as more complex cases. The hands-ons will mainly be done using GitHub.<br />
<br />
This HPC2N/SNIC course is also part of the PRACE Training courses. It is thus open for academics and people who work in industry in the PRACE member countries.<br />
<br />
Date: 2021-11-(9-12)<br />
Time: 8:30-12:00 on the first day (the first half-hour is an optional Git installation/Kebnekaise login-session for those that need it), 9:00-12:00 on the rest of the days.<br />
Deadline for registration: 2021-11-01<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/git course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Kebnekaise_(HPC2N),_2021-09-08&diff=7812Introduction to Kebnekaise (HPC2N), 2021-09-082021-06-14T13:59:19Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to Kebnekaise |fields=Linux; High performance computing |event type=Course |location=Umeå |start date=2021-09-08 |end date=202..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to Kebnekaise<br />
|fields=Linux; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-09-08<br />
|end date=2021-09-08<br />
}}<br />
<br />
== Course overview ==<br />
HPC2N is offering an ONLINE introduction course to HPC2N and Kebnekaise.<br />
<br />
We begin with a short (optional) introduction to Linux, then continue with an introduction to HPC, HPC2N, and a walkthrough of Kebnekaise, including the GPUs and the KNLs. We then look at the module system and loading the software you need, and how to submit jobs through the batch system.<br />
<br />
There will be hands-ons as a part of the course, where the participants get the opportunity to load modules, compile programs, and submit jobs to the Kebnekaise system.<br />
<br />
Remote/online participation: The course will be streamed. We will use Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Introduction to HPC2N, Kebnekaise and High Performance Computing<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/intro-fall course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Task-based_parallelism_in_scientific_computing_(HPC2N/PRACE,_May_2021)&diff=7798Task-based parallelism in scientific computing (HPC2N/PRACE, May 2021)2021-04-14T17:05:23Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{training event info<br />
|description=Task-based parallelism in scientific computing<br />
|fields=High performance computing; parallel programming; GPU computing; OpenMP; Task-based parallelism<br />
|event type=Course<br />
|location=Online, organized from Umeå<br />
|start date=2021-05-10<br />
|end date=2021-05-12<br />
}}<br />
<br />
== Course overview ==<br />
The purpose of the course is to learn when a code could benefit from task-based parallelism, and how to apply it. A task-based algorithm does not call the associated computation kernels directly, instead it is the role of a runtime system to schedule the task to various computational resources, such as CPUs and GPUs. The main benefit is that the underlying parallelism is exposed automatically. The course mainly focuses on the task-pragmas implemented in the newer incarnations of OpenMP. Other task-based runtime systems, e.g., StarPU, and GPU offloading are briefly discussed.<br />
<br />
This course will be three half-days. It will have lectures as well as some hands-on sessions where you get to try out what you have just learned.<br />
<br />
NOTE: Due to the COVID-19 situation, the course will be fully online, through Zoom.<br />
<br />
This HPC2N/SNIC course is part of the PRACE Training courses. It is open for participants from PRACE member countries.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/task-based-parallelism-spring-2021 course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Task-based_parallelism_in_scientific_computing_(HPC2N/PRACE,_May_2021)&diff=7789Task-based parallelism in scientific computing (HPC2N/PRACE, May 2021)2021-04-06T08:42:39Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{training event info<br />
|description=Task-based parallelism in scientific computing<br />
|fields=High performance computing; parallel programming; GPU computing; OpenMP; Task-based parallelism<br />
|event type=Course<br />
|location=Online, organized from Umeå<br />
|start date=2021-05-10<br />
|end date=2021-05-12<br />
}}<br />
<br />
== Course overview ==<br />
The purpose of the course is to learn when a code could benefit from task-based parallelism, and how to apply it. A task-based algorithm comprises of a set of self-contained tasks that have well-defined inputs and outputs. This differs from the common practice of organizing an implementation into subroutines in that a task-based implementation does not call the associated computation kernels directly, instead it is the role of a runtime system to schedule the task to various computational resources, such as CPU cores and GPUs. One of the main benefits of this approach is that the underlying parallelism is exposed automatically as the runtime system gradually traverses the resulting task graph.<br />
<br />
This course will be three half-days. It will have lectures as well as some hands-on sessions where you get to try out what you have just learned.<br />
<br />
NOTE: Due to the COVID-19 situation, the course will be fully online, through Zoom.<br />
<br />
This HPC2N/SNIC course is part of the PRACE Training courses. It is open for participants from PRACE member countries.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/task-based-parallelism-spring-2021 course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Task-based_parallelism_in_scientific_computing_(HPC2N/PRACE,_May_2021)&diff=7788Task-based parallelism in scientific computing (HPC2N/PRACE, May 2021)2021-04-06T08:40:16Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Task-based parallelism in scientific computing |fields=High performance computing; parallel programming; GPU computing; OpenMP; Task-based p..."</p>
<hr />
<div>{{training event info<br />
|description=Task-based parallelism in scientific computing<br />
|fields=High performance computing; parallel programming; GPU computing; OpenMP; Task-based parallelism<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-05-10<br />
|end date=2021-05-12<br />
}}<br />
<br />
== Course overview ==<br />
The purpose of the course is to learn when a code could benefit from task-based parallelism, and how to apply it. A task-based algorithm comprises of a set of self-contained tasks that have well-defined inputs and outputs. This differs from the common practice of organizing an implementation into subroutines in that a task-based implementation does not call the associated computation kernels directly, instead it is the role of a runtime system to schedule the task to various computational resources, such as CPU cores and GPUs. One of the main benefits of this approach is that the underlying parallelism is exposed automatically as the runtime system gradually traverses the resulting task graph.<br />
<br />
This course will be three half-days. It will have lectures as well as some hands-on sessions where you get to try out what you have just learned.<br />
<br />
NOTE: Due to the COVID-19 situation, the course will be fully online, through Zoom.<br />
<br />
This HPC2N/SNIC course is part of the PRACE Training courses. It is open for participants from PRACE member countries.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/task-based-parallelism-spring-2021 course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Running_MD_applications_efficiently_in_HPC,_HPC2N,_26-27_April_2021&diff=7722Running MD applications efficiently in HPC, HPC2N, 26-27 April 20212021-02-23T13:55:21Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{training event info<br />
|description=Running MD applications efficiently in HPC<br />
|fields=MD; High performance computing; SLURM<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-04-26<br />
|end date=2021-04-27<br />
}}<br />
<br />
== Course overview ==<br />
The aim of this HPC2N course is to provide MD users with a set of best practices to improve the performance of their simulations. This will mainly be accomplished by tuning the appropriate SLURM switches and flags proper to the MD packages.<br />
<br />
This course will be two half-days. It will have lectures as well as some hands-on sessions where you get to try out what you have just learned.<br />
<br />
There will also be time for user's to discuss, test, and get help with their own scripts.<br />
<br />
NOTE: Due to the COVID-19 situation, the course will be fully online, through Zoom.<br />
<br />
The course if free to anyone in Swedish academia.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/md-in-hpc course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Running_MD_applications_efficiently_in_HPC,_HPC2N,_26-27_April_2021&diff=7721Running MD applications efficiently in HPC, HPC2N, 26-27 April 20212021-02-23T13:54:36Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Running MD applications efficiently in HPC |fields=MD; High performance computing; SLURM |event type=Course |location=Umeå |start date=2021-04..."</p>
<hr />
<div>{{training event info<br />
|description=Running MD applications efficiently in HPC<br />
|fields=MD; High performance computing; SLURM<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-04-26<br />
|end date=2021-04-27<br />
}}<br />
<br />
== Course overview ==<br />
The aim of this HPC2N course is to provide MD users with a set of best practices to improve the performance of their simulations. This will mainly be accomplished by tuning the appropriate SLURM switches and flags proper to the MD packages.<br />
<br />
This course will be two half-days. It will have lectures as well as some hands-on sessions where you get to try out what you have just learned.<br />
<br />
There will also be time for user's to discuss, test, and get help with their own scripts.<br />
NOTE: Due to the COVID-19 situation, the course will be fully online, through Zoom.<br />
<br />
The course if free to anyone in Swedish academia.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/md-in-hpc course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Using_R_in_an_HPC_environment,_HPC2N,_2021-02-(25-26)&diff=7686Using R in an HPC environment, HPC2N, 2021-02-(25-26)2021-01-12T13:26:39Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Using R in an HPC environment |fields=R; High performance computing |event type=Course |location=Umeå |start date=2021-02-25 |end date=2021-02..."</p>
<hr />
<div>{{training event info<br />
|description=Using R in an HPC environment<br />
|fields=R; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-02-25<br />
|end date=2021-02-26<br />
}}<br />
<br />
== Course overview ==<br />
HPC2N is offering an ONLINE course; "Using R in an HPC environment". This course will be two half-days. <br />
<br />
There is interest among R users to get started in High Performance Computing (HPC) as they need more CPU power, memory or both. Because most of the Machine Learning (ML) models in R are computationally demanding, they are a good starting point to introduce HPC concepts. In the present course, you will learn how to improve your code so that it could run more efficiently on a Desktop and also in an HPC environment. As realistic ML models are computationally expensive when running on a Desktop, we will also teach you how to run these models on Kebnekaise, a HPC cluster at our center. The focus of the course will not be about ML though.<br />
<br />
There will be both lectures and hands-on parts of the course. <br />
<br />
The course will be done through Zoom. <br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Profiling code<br />
* Optimizing code<br />
* Large arrays<br />
* Using R at HPC2N<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/r-in-hpc-spring-2021 course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_HPC_and_Kebnekaise,_HPC2N,_2021-01-21&diff=7683Introduction to HPC and Kebnekaise, HPC2N, 2021-01-212020-12-15T12:00:11Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to HPC and Kebnekaise |fields=Linux; High performance computing |event type=Course |location=Umeå |start date=2021-01-21 |end dat..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to HPC and Kebnekaise<br />
|fields=Linux; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2021-01-21<br />
|end date=2021-01-21<br />
}}<br />
<br />
== Course overview ==<br />
HPC2N is offering an ONLINE introduction course to HPC and our systems.<br />
<br />
We begin with a short (optional) introduction to Linux, then continue with an introduction to HPC and a walkthrough of Kebnekaise, including the GPUs and the KNLs. In the afternoon we look at the module system and loading the software you need, and how to submit jobs through the batch system.<br />
<br />
There will be a hands-on part of the course, where the participants get the opportunity to load modules, compile programs, and submit jobs to the Kebnekaise system.<br />
<br />
Remote/online participation: The course will be streamed. We will use Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Introduction to HPC2N, Kebnekaise and High Performance Computing<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the [https://www.hpc2n.umu.se/events/courses/2021/intro-spring course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Heterogeneous_computing_with_performance_modelling,_Ume%C3%A5,_2020-11-(4-5)&diff=7610Heterogeneous computing with performance modelling, Umeå, 2020-11-(4-5)2020-09-14T14:57:26Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Heterogeneous computing with performance modelling |fields=Linux; High performance computing; GPU computing; Performance optimisation; Parallel..."</p>
<hr />
<div>{{training event info<br />
|description=Heterogeneous computing with performance modelling<br />
|fields=Linux; High performance computing; GPU computing; Performance optimisation; Parallel programming <br />
|event type=Course<br />
|location=Umeå<br />
|start date=2020-11-04<br />
|end date=2020-11-05<br />
}}<br />
<br />
== Course overview ==<br />
Modern high core count CPUs and accelerators, such as GPUs, have been shown to provide significant performance benefits in many different applications. However, for a novice, or even for a moderately experienced scientist or programmer, it is not always clear which applications could potentially benefit from these resources and which do not. For example, a Nvidia V100 GPU can perform artificial intelligence (AI) related computations in a fraction of the time it takes a regular CPU to perform the same computations but ill-informed OpenACC compiler pragmas can actually make a code run slower. Why is this? When should one invest time in parallelization and/or GPU-acceleration? How much speedup can be expected with a given application?<br />
<br />
The main goal of this two-day ONLINE course is to start answering these questions. The course also covers the basics of GPU programming and aims to provide the necessary information for avoiding the most common pitfalls.<br />
<br />
There will be a hands-on part of the course, where the participants get the opportunity to try and run some examples on the Kebnekaise system. <br />
<br />
Remote/online participation: The course will be streamed. We will use Zoom. <br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to <br />
[https://www.hpc2n.umu.se/events/courses/2020/heterogeneous-computing-fall https://www.hpc2n.umu.se/events/courses/2020/heterogeneous-computing-fall]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_Git,_Ume%C3%A5_(2020-09-30)&diff=7594Introduction to Git, Umeå (2020-09-30)2020-06-18T18:42:43Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to Git |fields=Linux; High performance computing; Version control |event type=Course |location=Umeå |start date=2020-09-30 |end d..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to Git<br />
|fields=Linux; High performance computing; Version control<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2020-09-30<br />
|end date=2020-09-30<br />
}}<br />
<br />
== Course overview ==<br />
The course will be an introduction to version control, with a focus on Git.<br />
Some of the main concepts, like repositories, commits, trees, branches, and merges will be covered, as will many of the basic commands, like clone, add, push, pull, commit, and fork.<br />
<br />
The lectures will be complemented by hands-on, during which the participants will learn both how to do simple Git commands as well as more complex cases. The hands-ons will mainly be done using GitHub.<br />
<br />
Remote/online participation: The course will be streamed. We will use Zoom. The participants who have expressed a wish to participate remotely will receive an email the day before the course, containing the connection info.<br />
<br />
NOTE: depending on the developing situation with COVID-19, the course may become completely online. If that happens, participants will be given information about any changes to the course as well as how to connect, using Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to <br />
[https://www.hpc2n.umu.se/events/courses/git-fall-2020 https://www.hpc2n.umu.se/events/courses/git-fall-2020]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_HPC2N_(September_2020)&diff=7593Introduction to HPC2N (September 2020)2020-06-18T18:32:33Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to HPC2N |fields=Linux; High performance computing |event type=Course |location=Umeå |start date=2020-09-09 |end date=2020-09-09 ..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to HPC2N<br />
|fields=Linux; High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2020-09-09<br />
|end date=2020-09-09<br />
}}<br />
<br />
== Course overview ==<br />
This whole day course will begin with a short (optional) introduction to Linux. We then continue with an introduction to HPC and HPC2N, followed by a walkthrough of the Kebnekaise system, including the GPUs and KNLs. In the afternoon we go through the module system and take a brief look at how to submit jobs. During the hands-on you will get the opportunity to try loading modules, compile a program, and submit a job to the Kebnekaise cluster. For those who are interested, there will be a guided tour of the machine rooms (only if the course does not become online-only). <br />
<br />
Remote/online participation: The course will be streamed. We will use Zoom. The participants who have expressed a wish to participate remotely will receive an email the day before the course, containing the connection info.<br />
<br />
NOTE: depending on the developing situation with COVID-19, the course may become completely online. If that happens, participants will be given information about any changes to the course as well as how to connect, using Zoom.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Short presentation of HPC2N<br />
* HPC<br />
* HPC2N – Kebnekaise<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the <br />
[https://www.hpc2n.umu.se/events/courses/intro-fall-2020]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mikael_R%C3%A4nnar_(HPC2N)&diff=7591User:Mikael Rännar (HPC2N)2020-06-10T15:10:54Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div><!--{{application expert info<br />
|first name=Mikael<br />
|last name=Rännar<br />
|centre=HPC2N<br />
|fields=Computational science<br />
|fte=50<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=PRACE<br />
|general activities=PRACE activities<br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Room E447 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ--><br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
<!--}}--><br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mikael_R%C3%A4nnar_(HPC2N)&diff=7590User:Mikael Rännar (HPC2N)2020-06-10T15:09:27Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div><!--{{application expert info<br />
|first name=Mikael<br />
|last name=Rännar<br />
|centre=HPC2N<br />
|fields=Computational science<br />
|fte=50<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=PRACE<br />
|general activities=PRACE activities<br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Room E447 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}--><br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mikael_R%C3%A4nnar_(HPC2N)&diff=7586User:Mikael Rännar (HPC2N)2020-06-10T15:07:34Z<p>Birgitte Brydsoe (HPC2N): moved DELETEDUser:Mikael Rännar (HPC2N) to User:Mikael Rännar (HPC2N) over redirect</p>
<hr />
<div>{{application expert info<br />
|first name=Mikael<br />
|last name=Rännar<br />
|centre=HPC2N<br />
|fields=Computational science<br />
|fte=50<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=PRACE<br />
|general activities=PRACE activities<br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Room E447 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User_talk:Mikael_R%C3%A4nnar_(HPC2N)&diff=7588User talk:Mikael Rännar (HPC2N)2020-06-10T15:07:34Z<p>Birgitte Brydsoe (HPC2N): moved Talk:DELETEDUser:Mikael Rännar (HPC2N) to User talk:Mikael Rännar (HPC2N) over redirect</p>
<hr />
<div>This page is intended for informal discussion. Please feel free to use this page to contact me for anything related to my research area or expertises! This page uses the [[Help:Editing|mediawiki text format]], just like all other pages on this wiki. Order and structure are not really that important on this page, but please try to keep your additions constructive and readable. It is however recommended to start a new heading for every new topic, and to mark your additions with your signature (there is a button for that just on top of the editing area). <br />
<br />
This page will be moderated from time to time, and topics of general interest may be moved to any of the relevant articles. <br />
<br />
Please click any of the Edit links to start talking! <br />
<br />
== Talk ==<br />
<br />
--[[User:Mikael Rännar (HPC2N)|Mikael Rännar (HPC2N)]]: Comments, suggestions and ideas are all welcome!</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=DELETEDUser:Mikael_R%C3%A4nnar_(HPC2N)&diff=7587DELETEDUser:Mikael Rännar (HPC2N)2020-06-10T15:07:34Z<p>Birgitte Brydsoe (HPC2N): moved DELETEDUser:Mikael Rännar (HPC2N) to User:Mikael Rännar (HPC2N) over redirect</p>
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<div>#REDIRECT [[User:Mikael Rännar (HPC2N)]]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Talk:DELETEDUser:Mikael_R%C3%A4nnar_(HPC2N)&diff=7589Talk:DELETEDUser:Mikael Rännar (HPC2N)2020-06-10T15:07:34Z<p>Birgitte Brydsoe (HPC2N): moved Talk:DELETEDUser:Mikael Rännar (HPC2N) to User talk:Mikael Rännar (HPC2N) over redirect</p>
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<div>#REDIRECT [[User talk:Mikael Rännar (HPC2N)]]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User_talk:Mikael_R%C3%A4nnar_(HPC2N)&diff=7584User talk:Mikael Rännar (HPC2N)2020-06-10T15:06:49Z<p>Birgitte Brydsoe (HPC2N): moved User talk:Mikael Rännar (HPC2N) to Talk:DELETEDUser:Mikael Rännar (HPC2N)</p>
<hr />
<div>This page is intended for informal discussion. Please feel free to use this page to contact me for anything related to my research area or expertises! This page uses the [[Help:Editing|mediawiki text format]], just like all other pages on this wiki. Order and structure are not really that important on this page, but please try to keep your additions constructive and readable. It is however recommended to start a new heading for every new topic, and to mark your additions with your signature (there is a button for that just on top of the editing area). <br />
<br />
This page will be moderated from time to time, and topics of general interest may be moved to any of the relevant articles. <br />
<br />
Please click any of the Edit links to start talking! <br />
<br />
== Talk ==<br />
<br />
--[[User:Mikael Rännar (HPC2N)|Mikael Rännar (HPC2N)]]: Comments, suggestions and ideas are all welcome!</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mikael_R%C3%A4nnar_(HPC2N)&diff=7582User:Mikael Rännar (HPC2N)2020-06-10T15:06:47Z<p>Birgitte Brydsoe (HPC2N): moved User:Mikael Rännar (HPC2N) to DELETEDUser:Mikael Rännar (HPC2N)</p>
<hr />
<div>{{application expert info<br />
|first name=Mikael<br />
|last name=Rännar<br />
|centre=HPC2N<br />
|fields=Computational science<br />
|fte=50<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=PRACE<br />
|general activities=PRACE activities<br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Room E447 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Lars_Viklund_(HPC2N)&diff=7581User:Lars Viklund (HPC2N)2020-06-10T15:04:58Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{application expert info |first name=Lars |last name=Viklund |centre=HPC2N |fields=HPC; General programming |fte= |snic ae financing= |other ae financing= |financing= |general ..."</p>
<hr />
<div>{{application expert info<br />
|first name=Lars<br />
|last name=Viklund<br />
|centre=HPC2N<br />
|fields=HPC; General programming<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing= <br />
|financing=<br />
|general activities=HPC, General programming, installation of software, support, containers <br />
|other activities=<br />
|image=Lars-viklund.jpg<br />
|office=Room C245 MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=File:Lars-viklund.jpg&diff=7580File:Lars-viklund.jpg2020-06-10T15:04:44Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Jerry_Eriksson_(HPC2N)&diff=7579User:Jerry Eriksson (HPC2N)2020-06-10T14:58:24Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{application expert info |first name=Jerry |last name=Eriksson |centre=HPC2N |fields=HPC; Parallel programming |fte= |snic ae financing= |other ae financing=PRACE |financing= |g..."</p>
<hr />
<div>{{application expert info<br />
|first name=Jerry<br />
|last name=Eriksson<br />
|centre=HPC2N<br />
|fields=HPC; Parallel programming<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=<br />
|general activities=HPC, Parallel programming <br />
|other activities=<br />
|image=Jerry-eriksson.jpg<br />
|office=Room E427 MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=File:Jerry-eriksson.jpg&diff=7578File:Jerry-eriksson.jpg2020-06-10T14:58:05Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Pedro_Ojeda-May_(HPC2N)&diff=7577User:Pedro Ojeda-May (HPC2N)2020-06-10T14:53:21Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{application expert info<br />
|first name=Pedro<br />
|last name=Ojeda-May<br />
|centre=HPC2N<br />
|fields=Molecular dynamics; Machine learning<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=<br />
|general activities=HPC, Molecular dynamics, advanced support <br />
|other activities=<br />
|image=Pedro-ojeda-may.jpg<br />
|office=MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Pedro_Ojeda-May_(HPC2N)&diff=7576User:Pedro Ojeda-May (HPC2N)2020-06-10T14:53:05Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{application expert info |first name=Pedro |last name=Ojeda-May |centre=HPC2N |fields=Molecular dynamics, Machine learning |fte= |snic ae financing= |other ae financing=PRACE |f..."</p>
<hr />
<div>{{application expert info<br />
|first name=Pedro<br />
|last name=Ojeda-May<br />
|centre=HPC2N<br />
|fields=Molecular dynamics, Machine learning<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=<br />
|general activities=HPC, Molecular dynamics, advanced support <br />
|other activities=<br />
|image=Pedro-ojeda-may.jpg<br />
|office=MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=File:Pedro-ojeda-may.jpg&diff=7575File:Pedro-ojeda-may.jpg2020-06-10T14:52:39Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mirko_Myllykoski_(HPC2N)&diff=7574User:Mirko Myllykoski (HPC2N)2020-06-10T14:07:59Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{application expert info<br />
|first name=Mirko<br />
|last name=Myllykoski<br />
|centre=HPC2N<br />
|fields=Parallel programming; GPU computing<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=<br />
|general activities=Parallel programming, HPC, GPU programming, advanced support <br />
|other activities=<br />
|image=Mirko-myllykoski.jpg<br />
|office=Room D451 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=File:Mirko-myllykoski.jpg&diff=7573File:Mirko-myllykoski.jpg2020-06-10T14:07:36Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mirko_Myllykoski_(HPC2N)&diff=7572User:Mirko Myllykoski (HPC2N)2020-06-10T12:55:34Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{application expert info<br />
|first name=Mirko<br />
|last name=Myllykoski<br />
|centre=HPC2N<br />
|fields=Parallel programming; GPU computing<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=<br />
|general activities=Parallel programming, HPC, GPU programming, advanced support <br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Room D451 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mirko_Myllykoski_(HPC2N)&diff=7571User:Mirko Myllykoski (HPC2N)2020-06-10T12:55:24Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{application expert info |first name=Mirko |last name=Myllyoski |centre=HPC2N |fields=Parallel programming; GPU computing |fte= |snic ae financing= |other ae financing=PRACE |fi..."</p>
<hr />
<div>{{application expert info<br />
|first name=Mirko<br />
|last name=Myllyoski<br />
|centre=HPC2N<br />
|fields=Parallel programming; GPU computing<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=PRACE<br />
|financing=<br />
|general activities=Parallel programming, HPC, GPU programming, advanced support <br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Room D451 MIT building;<br />
Dept. of Computing Science;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Birgitte_Bryds%C3%B6_(HPC2N)&diff=7570User:Birgitte Brydsö (HPC2N)2020-06-10T12:49:11Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{application expert info<br />
|first name=Birgitte<br />
|last name=Brydsö<br />
|centre=HPC2N<br />
|fields=HPC; Parallel programming<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=<br />
|financing=<br />
|general activities=Training, general support<br />
|other activities=<br />
|image=Birgitte-Brydso.jpg<br />
|office=Room C244 MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Birgitte_Bryds%C3%B6_(HPC2N)&diff=7569User:Birgitte Brydsö (HPC2N)2020-06-10T12:46:42Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div>{{application expert info<br />
|first name=Birgitte<br />
|last name=Brydsö<br />
|centre=HPC2N<br />
|fields=HPC, Parallel programming<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=<br />
|financing=<br />
|general activities=Training, general support<br />
|other activities=<br />
|image=Birgitte-Brydso.jpg<br />
|office=Room C244 MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=User:Birgitte_Bryds%C3%B6_(HPC2N)&diff=7568User:Birgitte Brydsö (HPC2N)2020-06-10T12:42:04Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{application expert info |first name=Birgitte |last name=Brydsö |centre=HPC2N |fields=HPC, parallel programming |fte= |snic ae financing= |other ae financing= |financing= |gene..."</p>
<hr />
<div>{{application expert info<br />
|first name=Birgitte<br />
|last name=Brydsö<br />
|centre=HPC2N<br />
|fields=HPC, parallel programming<br />
|fte=<br />
|snic ae financing=<br />
|other ae financing=<br />
|financing=<br />
|general activities=Training, general support<br />
|other activities=<br />
|image=Birgitte-Brydso.jpg<br />
|office=Room C244 MIT building;<br />
HPC2N;<br />
Umeå University;<br />
SE-90187 UMEÅ<br />
<!--<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
--><br />
}}<br />
<!--<br />
== Quick facts ==<br />
* Or any other heading. <br />
* This part is clear text and very much up to you.<br />
* Bullet lists are good <br />
* for the lazy<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::mass spectrometry]]<br />
* [[expertise::flux capacitor calibration]]<br />
--></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=File:Birgitte-Brydso.jpg&diff=7567File:Birgitte-Brydso.jpg2020-06-10T12:40:15Z<p>Birgitte Brydsoe (HPC2N): </p>
<hr />
<div></div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Task-based_parallelism_in_scientific_computing_(March_2020)&diff=7384Task-based parallelism in scientific computing (March 2020)2020-02-28T16:22:01Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Task-based parallelism in scientific computing |fields=High performance computing; parallel programming; GPU computing; OpenMP; Task-based para..."</p>
<hr />
<div>{{training event info<br />
|description=Task-based parallelism in scientific computing<br />
|fields=High performance computing; parallel programming; GPU computing; OpenMP; Task-based parallelism<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2020-03-30<br />
|end date=2020-03-30<br />
}}<br />
<br />
== Course overview ==<br />
The purpose of the course is to learn when a code could benefit from task-based parallelism, and how to apply it. Some codes can be simplified by the use of tasks and some codes can benefit performance-wise from the use of tasks. <br />
<br />
The course mainly focuses on the task-pragmas implemented in the newer incarnations of OpenMP, but other task-based runtime systems are briefly mentioned. <br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the <br />
[https://www.hpc2n.umu.se/events/courses/task-based-parallelism-spring-2020 Course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Course:_Efficient_MD_simulations_at_HPC2N_(February_2020)&diff=7240Course: Efficient MD simulations at HPC2N (February 2020)2020-02-10T16:34:21Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Efficient MD simulations at HPC2N |fields=High performance computing, Molecular Dynamics |event type=Course |location=Umeå |start date=2020-0..."</p>
<hr />
<div>{{training event info<br />
|description=Efficient MD simulations at HPC2N <br />
|fields=High performance computing, Molecular Dynamics<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2020-02-28<br />
|end date=2020-02-28 <br />
}}<br />
<br />
== Course overview ==<br />
The aim of the course is to provide MD users with a set of best practices to improve the performance of their simulations. This will be accomplished by tuning the appropriate SLURM switches and flags proper to the MD packages.<br />
<br />
Topics to be covered are:<br />
<br />
* Performance analysis of different versions of the packages (AMBER, NAMD, GROMACS, LAMMPS)<br />
* Performance analysis on different architectures (CPU, GPU, KNL)<br />
* General recommendations when using plugins. <br />
<br />
Participation is free and open to all existing and prospective users of HPC from Swedish institutions. Coffee and lunch will be provided.<br />
<br />
Please bring your laptop for the hands-on. <br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the <br />
[https://www.hpc2n.umu.se/events/courses/md-course-spring-2020 Course webpage]</div>Birgitte Brydsoe (HPC2N)https://snicdocs.nsc.liu.se/w/index.php?title=Introduction_to_HPC2N_(January_2020)&diff=7210Introduction to HPC2N (January 2020)2019-12-05T10:42:05Z<p>Birgitte Brydsoe (HPC2N): Created page with "{{training event info |description=Introduction to HPC2N |fields=Linux, High performance computing |event type=Course |location=Umeå |start date=2020-01-22 |end date=2020-01-22 ..."</p>
<hr />
<div>{{training event info<br />
|description=Introduction to HPC2N<br />
|fields=Linux, High performance computing<br />
|event type=Course<br />
|location=Umeå<br />
|start date=2020-01-22<br />
|end date=2020-01-22<br />
}}<br />
<br />
== Course overview ==<br />
This whole day course will begin with a short (optional) introduction to Linux. We then continue with an introduction to HPC and HPC2N, followed by a walkthrough of the Kebnekaise system, including the GPUs and KNLs. In the afternoon we go through the module system and take a brief look at how to submit jobs. During the hands-on you will get the opportunity to try loading modules, compile a program, and submit a job to the Kebnekaise cluster. For those who are interested, there will be a guided tour of the machine rooms.<br />
<br />
Participation is open to all existing and prospective users of HPC from Swedish institutions.<br />
<br />
== Topics ==<br />
* Introduction to Linux for beginners<br />
* Short presentation of HPC2N<br />
* HPC<br />
* HPC2N – Kebnekaise<br />
* How to use our systems<br />
* File Systems<br />
* The Module System, including Compiler Tool Chains<br />
* The Batch System (SLURM)<br />
* Examples and hands-on<br />
<br />
== Course web page and registration ==<br />
For more information and registration refer to the <br />
[https://www.hpc2n.umu.se/events/courses/intro-spring-2020 Course webpage]</div>Birgitte Brydsoe (HPC2N)