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This repository is dedicated to store different workflows that we have done for different scientific communities ( e.g., Seismologists, Astrophysics, etc) .
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internal_extinction
tc_cross_correlation
twitter_sentiment
AstroWorkflow.pdf
BatchVsRealTime.pdf
EasyToUseFrameworks-RosaFilgueira.pdf
EasyToUseFrameworks-RosaFilgueira.pptx
README.md
TweetsWorkflow.pdf
XcorrWorkflow.pdf
dispel4py_MSC.tar

README.md

dispel4py_workflows

This repository is dedicated to store "real" workflows that we have implemented for different scientific communities ( e.g., Seismologists, Astrophysics, etc) . Simpler dispel4py workflows can be found here

The dispel4py workflows stored in this repository have been presented at several conferences:

More information about these workflows can be foud here.

dispel4py

dispel4py is a free and open-source Python library for describing abstract stream-based workflows for distributed data-intensive applications. It enables users to focus on their scientific methods, avoiding distracting details and retaining flexibility over the computing infrastructure they use. It delivers mappings to diverse computing infrastructures, including cloud technologies, HPC architectures and specialised data-intensive machines, to move seamlessly into production with large-scale data loads. The dispel4py system maps workflows dynamically onto multiple enactment systems, such as MPI, STORM and Multiprocessing, without users having to modify their workflows.

Installation

Visit the dispel4py GitHub repository, which contains the instructions for installing dispel4py

Training Material

For learning more about dispel4py, visit the dispel4py training GitHub repository, which contains several tutorial and simple workflows for starting with dispel4py

Seismology: Seismic Noise Cross Correlation Workflow

Earthquakes and volcanic eruptions are sometimes preceded or accompanied by changes in the geophysical properties of the Earth, such as wave velocities or event rates. The development of reliable risk assessment methods for these hazards requires real-time analysis of seismic data and truly prospective forecasting and testing to reduce bias. However, potential techniques, including seismic interferometry and earthquake "repeater" analysis, require a large number of waveform cross-correlations, which is computationally intensive, and is particularly challenging in real-time.

With dispel4py we have developed the Seismic Ambient Noise Cross-Correlation workflow (also called the xcorr workflow) as part of the VERCE project project, which preprocesses and cross-correlates traces from several stations in real-time. The xcorr workflow consists of two main phases:

Figure xcorr workflow

  • Phase 1 -- Preprocess: Each continuous time series from a given seismic station (called a trace), is subject to a series of treatments. The processing of each trace is independent from other traces, making this phase "embarrassingly" parallel (complexity O(n), where n is the number of stations
  • Phase 2 -- Cross-Correlation Pairs all of the stations and calculates the cross-correlation for each pair (complexity O(n2)).

Important! All the codes for tesing the xcorr workflow can be found here repository, which includes the instructions for running it.

In this repostory I have stored the presentation BatchVsRealTime, that I gave in the School of GeoScience (University of Edinburgh) group, 2015, for presenting the different options that we could use for implementing this use case in their computing resources (Terracorrelator machine).

Note: Recently the Pegasus team and the dispel4py team have collaborated to enable to run the xcorr workflow across different computing resources (MPI cluster and Storm cluster) collecting data from IRIS. For this work, we have submitted (and run) the preprocess phase to a MPI cluster, and the cross-correlation phase to a Storm cluster. The streaming and the mapping to different enactment systems, such as MPI or Storm, are managed by dispel4py, while the data movement between different execution computing resources (MPI cluster and Storm cluster), and the coordination of the workflow execution are automatically managed by Pegasus. And we have adopted Docker containers for implementing this work, because they can substantially improve computational research reproducibility.

More information about this work can be found here and pegasus_dispel4py GitHub repository.

Astrophysics: Internal Extinction of Galaxies Workflow

A Virtual Observatory (VO) is a network of tools and services implementing the standards published by the International Virtual Observatory Alliance (IVOA) to provide transparent access to multiple archives of astronomical data. VO services are used in Astronomy for data sharing and serve as the main data access point for astronomical workflows in many cases. This is the case of the workflow presented here, which calculates the Internal Extinction of the Galaxies from the AMIGA catalogue. This property represents the dust extinction within the galaxies and is a correction coefficient needed to calculate the optical luminosity of a galaxy.

Figure Internal Extinction workflow

This workflow first reads an input file (coordinates.txt size 19KB) that contains the right ascension (Ra) and declination (Dec) values for 1051 galaxies. Then queries a VO service for each galaxy in the input file using the Ra and Dec values. The results of these queries are filtered by selecting only the values that correspond to the morphological type (Mtype) and the apparent flattening (logr25) features of the galaxies. Finally, their internal extinction is calculated.

Important! All the codes for tesing the internal extinction workflow can be found at this repository, which includes the instructions for running it.

Social Computing: Twitter Sentiment Analysis Workflow

With over 500 million tweets per day16 and 240 million active users who post opinions about people, events, products or services, Twitter has become an interesting resource for sentiment analysis . In this case study, we investigate the benefits of dispel4py for analysing Twitter data by implementing a basic Sentiment Analysis workflow, called sentiment.

Figure sentiment workflow

The sentiment workflow, first scans the tweets preprocessing the words they contain, and then classifies each tweet based on the total counts for positive and negative words. As the sentiment workflow applies two analyses, different preprocessing and classification tasks need to be performed. To classify each tweet with the AFINN lexicon, the sentimentAFINN PE tokenises each tweet “text” word, and then a very rudimentary sentiment score for the tweet is calculated by adding the score of each word. After determining the sentiments of all tweets, they are sent to the findState PE, which searches the US state from which the tweet originated, and discards tweets which are not sent from the US. The HappyState PE applies a grouping by based on the state and aggregates the sentiment scores of tweets from the same state, which are sent to the top3Happiest PE. This PE applies all-to-one grouping and determines which are the top three happiest states.

The sentiment workflow also calculates tweet sentiment in parallel using the SWN3 lexicon. The tokenizationWD PE is a composite PE, where tweet tokenisation and tagging takes place: the tokenTweet PE splits the tweet text into tokens, the POSTagged PE produces a part-of-speech (POS) tag as an annotation based on the role of each word (e.g. noun, verb, adverb) and the wordnetDef PE determines the meaning of each word by selecting the synset that best represents the word in its context. After pre-processing each tweet, the second phase of the analysis is performed by the sentiment SWN3 composite PE: the SWN3 Interpretation PE searches the sentiment score associated with each synset in the SWN3 lexicon, the sentimentOrientation PE gets the positives, negatives and average scores of each term found in a tweet and the classifySWN3Tweet PE determines the sentiment of the tweet. After the classification, the same procedure as before is applied to each tweet, to know which are the three happiest states.

Important! All the codes for tesing the sentiment workflow can be found here, which includes the instructions for running it.

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