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Commit 7670a84f authored by Uwe Jandt (DESY, HIFIS)'s avatar Uwe Jandt (DESY, HIFIS)
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Merge branch 'spotlights_draft' into 'master' 

Helmholtz Software Spotlights

See merge request !309
parents e11b89df 6fd8fc28
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_config.yml
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......@@ -36,24 +36,30 @@ defaults:
type: "events"
values:
author: "HIFIS"
-
scope:
path: ""
type: "spotlights"
values:
author: "HIFIS"
-
scope:
path: ""
type: "posts"
values:
author: "HIFIS"
-
-
scope:
path: ""
values:
lang: "en"
-
-
scope:
path: "de/"
values:
lang: "de"
hidden: true
gitlab:
project_url: https://gitlab.hzdr.de/hifis/hifis.net
......@@ -100,6 +106,10 @@ collections:
output: true
permalink: /:collection/:slug
spotlights:
output: true
permalink: /:collection/:slug
events:
output: true
permalink: /:collection/:year/:month/:day/:title
......
_layouts/spotlight-list.html 0 → 100644
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{% include top.html %}
<body>
{% include header.html %}
<main>
{% include title_image.html %}
<section class="events-container">
{% assign spotlights = site.spotlights %}
<div class="alert alert-success">
This is a preliminary list of software spotlights and more will be added soon. Stay tuned!
</div>
{% for spotlight in spotlights %}
<article class="list-entry">
<div class="image-block">
<a href="{{ spotlight.url | relative_url}}">
<img
class="help-image left"
alt="Logo of {{ spotlight.name }}"
src="{{ site.directory.images | relative_url }}spotlights/{{spotlight.preview_image}}"
style="max-height:7rem;"
/>
</a>
<div>
<h3>
<a href="{{ spotlight.url | relative_url }}">
{{ spotlight.name }}
</a>
</h3>
<p>
{{ spotlight.excerpt }}
</p>
<a href="{{ spotlight.url | relative_url }}" >
<span>&nbsp;more…&nbsp;</span>
</a>
</div>
</div>
</article>
{% endfor %}
</section>
</main>
{% include footer.html %}
</body>
</html>
_layouts/spotlight.html 0 → 100644
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{% include top.html %}
<body>
<link rel="stylesheet" href="{{ site.baseurl }}/assets/css/spotlights.css">
{% include header.html %}
<main>
{% capture title-content%}
<h1>{{ page.title }}</h1>
{% endcapture %}
{% include title_image.html content=title-content %}
<section>
<article>
<div class="alert alert-success spotlight-info">
<h3>Centres</h3>
{% for center in page.hgf_centers %}
<span>{{ center }}</span>
{% endfor %}
{% if page.contributing_organisations %}
<h3>Contributing organisations</h3>
{% for org in page.contributing_organisations %}
<span>{{ org }}</span>
{% endfor %}
{% endif %}
<h3><i class="fas fa-tags"></i> Keywords</h3>
{% for keyword in page.keywords %}
<span class="badge badge-pill badge-secondary"><i class="fas fa-tag"></i> {{ keyword }}</span>
{% endfor %}
<h3>Research field</h3>
<span>{{ page.hgf_research_field }}</span>
{% if page.scientific_community %}
<h3>Scientific community</h3>
{% for obj in page.scientific_community %}
<span>{{ obj }}</span>
{% endfor %}
{% endif %}
{% if page.funding %}
<h3><i class="fas fa-coins"></i> Funding</h3>
{% if page.funding.link_as %}
<span><a href="{{ page.funding.link_as }}">{{ page.funding.name}}</a></span>
{% else %}
<span>{{ page.funding.name }}</span>
{% endif %}
{% endif %}
{% if page.programming_languages %}
<h3><i class="fas fa-code"></i> Programming Languages</h3>
{% for obj in page.programming_languages %}
<span>{{ obj }}</span>
{% endfor %}
{% endif %}
{% if page.license %}
<h3><i class="fas fa-balance-scale"></i> License</h3>
<span>{{ page.license }}</span>
{% endif %}
{% if page.costs %}
<h3><i class="fas fa-credit-card"></i> Costs</h3>
<span>{{ page.costs }}</span>
{% endif %}
{% if page.doi %}
<h3><i class="fas fa-quote-right"></i> Cite</h3>
<a href="https://doi.org/{{ page.doi }}">{{ page.doi }}</a>
{% endif %}
<h3>Contact</h3>
<span><i class="fas fa-envelope"></i> <a href="mailto:{{ page.contact }}">{{ page.contact }}</a></span>
{% if page.platforms %}
<h3>Resources</h3>
{% for platform in page.platforms %}
{% if platform.type == "webpage" %}
{% assign fa_icon = "fas fa-globe" %}
{% assign hint = "Official wepage" %}
{% elsif platform.type == "telegram" %}
{% assign fa_icon = "fab fa-telegram" %}
{% assign hint = "Telegram channel"%}
{% elsif platform.type == "mailing-list" %}
{% assign fa_icon = "fas fa-envelope-open-text" %}
{% assign hint = "Mailing list"%}
{% elsif platform.type == "twitter" %}
{% assign fa_icon = "fab fa-twitter" %}
{% assign hint = "Twitter" %}
{% elsif platform.type == "gitlab" %}
{% assign fa_icon = "fab fa-gitlab" %}
{% assign hint = "Gitlab" %}
{% elsif platform.type == "github" %}
{% assign fa_icon = "fab fa-github" %}
{% assign hint = "GitHub" %}
{% else %}
{% continue %}
{% endif %}
<span>
<a href="{{ platform.link_as }}" title="{{ hint }}">
<i class="{{ fa_icon }} fa-2x"></i>
</a>
</span>
{% endfor %}
{% endif %}
</div>
{{ content }}
</article>
</section>
</main>
{% include footer.html %}
</body>
</html>
_spotlights/_picongpu.md 0 → 100644
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---
layout: spotlight
# Spotlight list attributes
name: PIConGPU
preview_image: picongpu/picongpu-logo.png
excerpt: PIConGPU is a relativistic Particle-in-Cell code running on graphic processing units. It is Open Source und is freely available for download. PIConGPU is developed and maintained by the Junior Group Computational Radiation Physics at the Institute for Radiation Physics at HZDR in close collaboration with the Center for Information Services and High Performance Computing (ZIH) of the Technical University Dresden.
# Title for individual page
title_image:
title: PIConGPU - A Many-GPGPU Particle-in-Cell Code
keywords:
- GPU
- Particle-in-Cell
- Simulation
hgf_research_field: Matter
hgf_centers:
- HZDR
contributing_organisations:
- TU Dresden
scientific_community:
- Matter / Photon Science
impact_on_community:
contact: m.bussmann@hzdr.de
platforms:
- type: github
link_as: https://github.com/ComputationalRadiationPhysics/picongpu
- type: webpage
link_as: https://picongpu.readthedocs.io/
license: GPL-3.0-only
costs:
software_type:
- Simulation
application_type:
- Desktop
programming_languages:
- C++
doi: 10.1109/TPS.2010.2064310
funding:
---
# PIConGPU Features
* A variable, Yee-like grid, on which electric and magnetic fields are approximated.
* Particle-Pushers following the works of Boris and Vay
* Maxwell-Solvers as proposed by Yee and Lehe
* Current-Deposition schemes published by Esirkepov and Villasenor-Buneman
* Macro-Particle Form Factors: NGP, CIC, TSC, PSQ
* Computation of far field radiation due to electron motion
* Parallel HDF5 Output
* Online-Visualization (2D/3D)
* The Particle-in-Cell algorithm is a central tool in plasma physics. It describes the dynamics of a plasma by computing the motion of electrons and ions in the plasma based on Maxwell's equations.
## How does the Particle-in-Cell Algorithm work?
The PIC algorithm solves the so-called Maxwell-Vlasov equation. To solve this equation, electric and magnetic fields are interpolated on a physical grid dividing the simulated volume into cells.
Charged particles like electrons and ions are modeled by macro-particles. These can describe the motion of up to several hundred particles by the motion of a single spread-out particle distribution. The macro-particles' motion is influenced by the electric and magnetic fields on the grid.
The particle motion in turn creates currents. Following Ampère's law these currents create magnetic fields. These magnetic fields in turn create electric fields as described by Faraday's law.
These new fields then act back on the particles.
## What is so new about PIConGPU?
GPUs show very high computational performance, because many processors work in parallel. In order to make the most out of this performance, the processors should work independently of each other. In case of the PIC-Algorithm this is hard to achieve, since in the current deposition step, currents which are fixed to the cells have to be computed from the velocity of particles moving freely between grid cells. This motion leads to memory access patterns in which current data and particle data are located at different places in the memory and parallel processes can disturb each others execution when accessing the same part of the memory.
Recently, this problem was solved in our group using a new data model for particle and grid-based data and asynchronous data transfer.
## All that with a single GPU?
No, because GPUs do not have enough memory to simulate large physical systems. This makes it necesarry to use more than one GPU and distribute the simulated volume between the GPUs.
The problem with this approach is the data transfer between GPUs. For this, data has to be transferred from the GPU to the main memory of the computer housing the GPU. The data has then to be sent via network to the other computers housing the other GPUs
This process normally takes a long time and GPUs have to wait for the end of the data transfer before continuing their computations.
We were able to solve this problem by interleaving the data transfer between GPUs and the computation on a single GPU, so that the GPUs can execute the algorithmic steps continuously without interruption [3,4]. This was only possible because we got help from ZIH, TU Dresden, which provided an efficient library for data transfer between GPUs and tools to measure the performance of our code.
## What does this mean for simulations?
We want to speed up the time of the simulation to reduce the time between the start of the simulation and the reception of the final result. With GPUs this speed up can mean that a simulation that normally takes a week to finish can finish within a few hours.
_spotlights/_template.md 0 → 100644
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---
layout: spotlight
###############################################################################
# Template for Software spotlights
###############################################################################
# Templates starting with a _, e.g. "_template.md" will not be integrated into
# the spotlights.
#
# Optional settings can be left empty.
# -----------------------------------------------------------------------------
# Properties for spotlights list page
# -----------------------------------------------------------------------------
# The name of the software
name:
# Small preview image shown at the spotlights list page.
# Note: the path is relative to /assets/img/spotlights/
preview_image:
# One or two sentences describing the software
excerpt:
# -----------------------------------------------------------------------------
# Properties for individual spotlights page
# -----------------------------------------------------------------------------
# Entries here will be shown in the green box on the right of the screen.
# Jumbotron (optional)
# The path is relative to /assets/img/jumbotrons/
title_image:
# Title at the top, inside the title-content-container
title:
# Add at least one keyword
keywords:
-
# The Helmholtz research field
hgf_research_field:
# At least one responsible centre
hgf_centers:
-
# List of other contributing organisations (optional)
contributing_organisations:
# List of scientific communities
scientific_community:
-
# Impact on community (optional, not implemented yet)
impact_on_community:
# An e-mail address
contact:
# Platforms (optional)
# Provide platforms in this format
# - type: TYPE
# link_as: LINK
# Valid TYPES are: webpage, telegram, mailing-list, twitter, gitlab, github
# Mailing lists should be added as "mailto:mailinglist@url.de"
# More types can be implemented by modifying /_layouts/spotlight.html
platforms:
- type:
link_as:
# The software license (optional)
license:
# Is the software pricey or free? (optional)
costs:
# What is this software used for in general (e.g. modelling)? (optional, not implemented yet)
software_type:
-
# The applicaiton type (Desktop, Mobile, Web) (optional, not implemented yet)
application_type:
-
# List of programming languages (optional)
programming_languages:
-
# DOI (without URL, just 10.1000/1.0000000 ) (optional)
doi:
# Funding of the software (optional)
funding:
name: # Name
link_as: # Link (optional)
---
# Markdown
Here is space for some custom markdown.
Please provide images always with a footnote like this:
<div class="spotlights-text-image">
<img src="{{ site.directory.images | relative_url}}spotlights/PATH_TO_IMAGE">
<span>Descriptive sentence.</span>
</div>
_spotlights/enpt.md 0 → 100644
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---
layout: spotlight
###############################################################################
# Template for Software spotlights
###############################################################################
# Templates starting with a _, e.g. "_template.md" will not be integrated into
# the spotlights.
#
# Optional settings can be left empty.
# -----------------------------------------------------------------------------
# Properties for spotlights list page
# -----------------------------------------------------------------------------
# The name of the software
name: EnPT
# Small preview image shown at the spotlights list page.
# Note: the path is relative to /assets/img/spotlights/
preview_image: enpt/logo.svg
# One or two sentences describing the software
excerpt: The Environmental Mapping and Analysis Program (EnMAP) is a German hyperspectral satellite mission that aims at monitoring and characterising Earth’s environment on a global scale. EnMAP measures and models key dynamic processes of Earth’s ecosystems by extracting geochemical, biochemical and biophysical parameters that provide information on the status and evolution of various terrestrial and aquatic ecosystems.
# -----------------------------------------------------------------------------
# Properties for individual spotlights page
# -----------------------------------------------------------------------------
# Entries here will be shown in the green box on the right of the screen.
# Jumbotron (optional)
# The path is relative to /assets/img/jumbotrons/
title_image:
# Title at the top, inside the title-content-container
title: EnPT - EnMAP Processing Tool
# Add at least one keyword
keywords:
- Remote sensing
- Hyperspectral
- Satellite data
- EnMAP
# The Helmholtz research field
hgf_research_field: Earth and Environment
# At least one responsible centre
hgf_centers:
- "GFZ, AWI, DLR"
# Other contributing organisations (optional)
contributing_organisations:
# List of scientific communities
scientific_community:
- Remote sensing
# Impact on community (optional, not implemented yet)
impact_on_community:
# An e-mail address
contact: daniel.scheffler@gfz-potsdam.de
# Platforms (optional)
# Provide platforms in this format
# - type: TYPE
# link_as: LINK
# Valid TYPES are: webpage, telegram, mailing-list, twitter, gitlab, github
# Mailing lists should be added as "mailto:mailinglist@url.de"
# More types can be implemented by modifying /_layouts/spotlight.html
platforms:
- type: gitlab
link_as: https://git.gfz-potsdam.de/EnMAP/GFZ_Tools_EnMAP_BOX/EnPT
- type: github
link_as: https://github.com/GFZ/enpt
- type: webpage
link_as: https://www.gfz-potsdam.de/en/scientific-infrastructure/research-software/enmap-processing-tool-enpt/
# The software license (optional)
license: GPL-3.0-or-later
# Is the software pricey or free? (optional)
costs:
# What is this software used for in general (e.g. modelling)? (optional, not implemented yet)
software_type:
-
# The applicaiton type (Desktop, Mobile, Web) (optional, not implemented yet)
application_type:
-
# List of programming languages (optional)
programming_languages:
- Python
# DOI (without URL, just 10.1000/1.0000000 ) (optional)
doi: 10.5281/zenodo.3742344
# Funding of the software (optional)
funding:
name: German Federal Ministry of Economic Affairs and Energy (50 EE 0850)
link_as: # Link (optional)
---
# EnPT - EnMAP Processing Tool
The Environmental Mapping and Analysis Program ([EnMAP](https://www.enmap.org/)) is a German hyperspectral satellite mission that aims at monitoring and characterising the Earth’s environment on a global scale. The EnPT Python package is an automated pre-processing pipeline for the new EnMAP hyperspectral satellite data. It provides free and open-source features to transform EnMAP Level-1B data to Level-2A. The package has been developed at the German Research Centre for Geosciences Potsdam (GFZ) as an alternative to the processing chain of the EnMAP Ground Segment.
<div class="spotlights-text-image">
<img src="{{ site.directory.images | relative_url}}spotlights/enpt/screenshot.png" alt="The graphical user interface of EnPT">
<span>The screenshot shows an exemplary EnMAP level 2A output image of EnPT (Arcachon test dataset), visualized within the EnMAP-Box.</span>
</div>
This software was developed within the context of the EnMAP project supported by the DLR Space Administration with funds of the German Federal Ministry of Economic Affairs and Energy and contributions from DLR, GFZ and OHB System AG.
EnPT is especially designed for the needs of the hyperspectral data community who want to have extensive control about the processes and algorithms included in the EnMAP level 2 processing chain. The package is freely available from the [Python package index](https://pypi.org/project/enpt/) or [conda-forge](https://anaconda.org/conda-forge/enpt).
_spotlights/igmas.md 0 → 100644
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---
layout: spotlight
# Spotlight list attributes
name: IGMAS+
preview_image: igmas_logo.png
excerpt: Modern geophysical interpretation requires an interdisciplinary approach and software capable of handling multiple inhomogeneous data like seismic, FTG gravity, magnetic and magnetotelluric in complex geological environments.
# Title for individual page
title_image: igmas_timeline.png
title: IGMAS+ Interactive Gravity and Magnetic Application System
keywords:
- Gravity
- Magnetic
- Modelling
hgf_research_field: Earth and Environment
hgf_centers:
- GFZ Potsdam
contributing_organisations:
scientific_community:
- Structural Modelling
impact_on_community:
contact: igmas@gfz-potsdam.de
platforms:
- type: webpage
link_as: https://www.gfz-potsdam.de/igmas
- type: telegram
link_as: https://t.me/igmas
- type: mailing-list
link_as: mailto:igmas-users-subscribe@gfz-potsdam.de?subject=Subscribe&body=Please%20subscribe%20me%20to%20the%20IGMAS+%20Users%20mailing%20list.
license: Proprietary
costs: Free
software_type:
- Modelling
application_type:
- Desktop
programming_languages:
- Java
doi: 10.1190/1.1442546
funding:
name: GFZ
link_as: https://gfz-potsdam.de # Optional
---
# IGMAS+ in a nutshell
Modern geophysical interpretation requires an interdisciplinary approach and software capable of handling multiple inhomogeneous data like seismic, FTG gravity, magnetic and magnetotelluric in complex geological environments.
<div class="spotlights-text-image">
<img src="{{ site.directory.images | relative_url}}spotlights/igmas/western_south_american_margin.png" alt="3D flat model of the central Western South American margin, modelled gravity, and modelling constraings">
<span>3D flat model of the central Western South American margin, modelled gravity, and modelling constraings.</span>
</div>
IGMAS+ (Interactive Gravity and Magnetic Application System) is a geo-modelling software for three-dimensional joint inversion of potential fields and its derivatives under the condition of constraining data and independent information.
Three-dimensional gravity and magnetic modelling appreciably improves the results of distinct depth imaging projects. This regards especially to areas of strong lateral seismic velocity and density contrasts and corresponding imaging problems. Typical areas where grav/mag modelling has been successfully used are sub-salt and sub-basalt settings.
What makes IGMAS+ highly efficient and user-friendly is that it allows adjusting the geometries and physical properties of modelled subsurface bodies interactively, i.e. while the corresponding calculated and measured potential field components are visualized together with independent observations.
See our [main publication list](https://igmas.git-pages.gfz-potsdam.de/igmas-pages/about/#main), as well as [related publications](https://igmas.git-pages.gfz-potsdam.de/igmas-pages/about/#related) and [citing instructions](https://igmas.git-pages.gfz-potsdam.de/igmas-pages/citing).
## Functionality
A brief summary of recent functionality
* Fully featured graphical user interface
* Algorithm kernel
* Polyhedron formula for triangulation, mass points and FFT for voxel cubes
* Borehole gravity
* Gravity field components Gx, Gy and Gz
* Full tensor gravity gradient
* Geoid
* Invariants
* Magnetic field components Bx, By and Bz
* Remanent and induced rock magnetisation
* Full tensor of magnetic gradients
* Model input
* Import regular or irregular horizon data
* Voxel cubes / Voxet
* Simultaneous use of triangulated and gridded (voxel) data
* Geometry and parameter editor
* Interactive modification of vertices and physical parameters with instant field updates
* Optimisation (inversion) of physical parameters, including grouped voxel cell effects
* Interactive geometry changes automatically affect the voxel cube
* Visualisation
* Multiple undockable views (cross sections, maps)
* Object browser including property editor for all model elements
* Multicore processing
* Multi language support
* Extensive User Manual
_spotlights/rce.md 0 → 100644
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---
layout: spotlight
# Spotlight list attributes
name: RCE
preview_image: rce/rce-logo.png
excerpt: RCE is a distributed integration environment for scientists and engineers to analyze, optimize, and design complex systems like aircraft, ships, or satellites.