speeding-updataanalysis:divand ... · divand.jl package v2.6.0 (april 27, 2020) ddoi oi...
TRANSCRIPT
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Speeding-up data analysis: DIVAndinterpolation tool in the Virtual Research
Environment
C. Troupin, A. Barth, M. Buurman, S. Mieruch,L. Bruvry Lagadec, T. Zamani & P. Thijsse
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A few definitions before we start
DIVA: software tool designed for spatial interpolation https://github.com/gher-ulg/DIVA
DIVAnd: n-dimensional version of DIVA https://github.com/gher-ulg/divand.jl
Julia: high-level, high-performance dynamic programming languagefor numerical computing https://julialang.org/
Notebook: documents that contain live code, equations, visualizations andnarrative text
Jupyter: open-source web application to create and share notebook http://jupyter.org/
Jupyterhub: multi-user server for Jupyter notebooks https://jupyterhub.readthedocs.io/en/latest/
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Virtual Research Environment (VRE)
Definition: a VRE is made up of software tools, datasets andother resources that several users can access and usein a cooperative way.
Advantages:• Availability of tools – no need to install anything• Availability of data – no download needed• Availability of computing power
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1Context forDIVAnd inthe VRE
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Installing DIVA was sometimes…painful
Back in 2007
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Installing DIVA was sometimes…painful
or in 2013
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What have we improved since then?
1 New mathematical formulation Barth et al. 20142 Julia language instead of Fortran3 Only 2 (!!!) input files data & bathymetry4 Applications as Jupyter notebooks all in one
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What have we improved since then?
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What have we improved since then?
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Jupyter notebooks as guidelines
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Jupyter notebooks as guidelines
Explenatory text
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Jupyter notebooks as guidelines
Explenatory text
Code fragment
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Jupyter notebooks as guidelines
Explenatory text
Code fragment
Results or figure
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Jupyter notebooks as guidelines
Explenatory text
Code fragment
Results or figure
Kernel (language)
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What should we improve?
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What should we improve?
+ Access to computing power+ Data availability+ Documentation
= Virtual Research Environment!
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What should we improve?
+ Access to computing power+ Data availability+ Documentation
= Virtual Research Environment!
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2DIVAndin a fewclicks
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DIVAnd in a few clicks
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DIVAnd in a few clicks
Dashboard
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DIVAnd in a few clicks
Work directory
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DIVAnd in a few clicks
nextcloud_sync allows users to access their private workspace
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DIVAnd in a few clicks
directory where webODV gave me the data files
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DIVAnd in a few clicks
sub-directory where webODV gave me the data files
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DIVAnd in a few clicks
data file to use in the notebooks
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DIVAnd in a few clicks
DIVAnd-Workshop = repository cloned into the VRE
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DIVAnd in a few clicks
Notebooks divided into subdirectories
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DIVAnd in a few clicks
Full-analysis using the extracted data file
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Jupyter notebooks to produce climatologies
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DIVAnd outputs
1 A netCDF file storing the analysis fields and the observationID’s
2 A XML file that can be used for the Sextant catalog3 Figures (here Autumn salinity at 5 m depth)
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3ImprovingDIVAnd inthe VRE
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DIVAnd in 2020
1 Updated mathematical formulation Barth et al. 20142 Julia language3 Only 2 input files data & bathymetry4 User guides = Jupyter notebooks all in one
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Providing users access to notebooks
≡ ×
2017 | 1st deployment at CINECA2019 | Deployment transferred to DKRZ
for the first training workshop2020 | Multiple machines at
DKRZGRNETSTFC
Multiple copies of a Docker container are run(https://hub.docker.com/r/abarth/divand-jupyterhub)
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What’s shipped inside the container?
https://github.com/gher-ulg/DIVAnd-jupyterhub
✓ Libraries: netCDF, unzip, git, …
✓ Julia language (V1.4.1, released on April 14, 2020))✓ Julia packages: PyPlot, NCDatasets, DataStructures, …✓ DIVAnd.jl (#master)✓ DIVAnd workshop notebooks (#master)
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What’s shipped inside the container?
https://github.com/gher-ulg/DIVAnd-jupyterhub
✓ Libraries: netCDF, unzip, git, …✓ Julia language (V1.4.1, released on April 14, 2020))
✓ Julia packages: PyPlot, NCDatasets, DataStructures, …✓ DIVAnd.jl (#master)✓ DIVAnd workshop notebooks (#master)
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What’s shipped inside the container?
https://github.com/gher-ulg/DIVAnd-jupyterhub
✓ Libraries: netCDF, unzip, git, …✓ Julia language (V1.4.1, released on April 14, 2020))✓ Julia packages: PyPlot, NCDatasets, DataStructures, …
✓ DIVAnd.jl (#master)✓ DIVAnd workshop notebooks (#master)
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What’s shipped inside the container?
https://github.com/gher-ulg/DIVAnd-jupyterhub
✓ Libraries: netCDF, unzip, git, …✓ Julia language (V1.4.1, released on April 14, 2020))✓ Julia packages: PyPlot, NCDatasets, DataStructures, …✓ DIVAnd.jl (#master)
✓ DIVAnd workshop notebooks (#master)
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What’s shipped inside the container?
https://github.com/gher-ulg/DIVAnd-jupyterhub
✓ Libraries: netCDF, unzip, git, …✓ Julia language (V1.4.1, released on April 14, 2020))✓ Julia packages: PyPlot, NCDatasets, DataStructures, …✓ DIVAnd.jl (#master)✓ DIVAnd workshop notebooks (#master)
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4 components for improvement
1 Julia language
2 DIVAnd package3 Training notebooks (Diva-Workshop)4 Docker container in the VRE
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4 components for improvement
1 Julia language2 DIVAnd package
3 Training notebooks (Diva-Workshop)4 Docker container in the VRE
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4 components for improvement
1 Julia language2 DIVAnd package3 Training notebooks (Diva-Workshop)
4 Docker container in the VRE
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4 components for improvement
1 Julia language2 DIVAnd package3 Training notebooks (Diva-Workshop)4 Docker container in the VRE
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Julia languagev1.4.1 (April 14, 2020)New features: changes in language features, multi-threading, build
systems, library functions, …PackageCompiler.jl : allows to pre-compile the modules
Reduce the famous ”time-to-first-plot”:when you first load and run a package in a session,Julia needs to compile it first
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DIVAnd.jl package
v2.6.0 (April 27, 2020)DOIDOI 10.5281/zenodo.376866310.5281/zenodo.3768663
New feature: heatmap generationClosed issues: • DIVAnd_qc doesn’t work with advection
constrain• Missing surfextend documentation• Wrong long name for lat• netCDF scalefactore is NaN resulting in an
empty output variable
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Example of heatmaps
Data points are locations acquired by GPS deviceduring running activities
Figure 1: Left: heatmap before the confinement; Right: after the confinement
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Training notebooks (Diva-Workshop)
v1.2 (April 27, 2020)DOIDOI 10.5281/zenodo.376903710.5281/zenodo.3769037
• Compatibility with Julia 1.4• CI (Travis)• Cleaned notebooks• Sub-directories with notebooks arranged by topics.• Minor bugs
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Docker container (DIVAnd-jupyterhub)
Precompiled DIVAnd with PackageCompiler
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Conclusions
1 DIVAnd is deployed in the SeaDataCloud VRE2 Continuous improvements in:
Julia, DIVAnd, Training notebooks and in the Docker3 Making available data, tools and computing power is essential
to speed up research
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Thanksfor your attention
CharlesTroupin
#shareEGU20