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1,902 results for “consumption”
Snail Consumption of Marsh Grasses in Mesocosms, 2018 and 2020
This experiment evaluated the effects of resource availability via nutrient addition and snail herbivory on the plant traits of Spartina alterniflora. Marsh periwinkles (Littoraria irrorata) and smooth cordgrass (Spartina alterniflora) were collected from Cushman's Landing marsh on the Eastern Shore in the summer of 2018 and set up in mesocosm tanks at the Virginia Institute of Marine Science in Gloucester Point, VA. There were four treatments: nutrient addition only, herbivory only, nutrient addition plus herbivory, and a control. At the end of the experiment, plants were analyzed for a series of plant traits. Dried and ground plant tissues were then resuspended in agar and a feeding assay was conducted in the summer of 2020 to evaluate how treatments influenced subsequent snail grazing. Six types of data were collected: 1) Feeding Assay Snail Morphometrics, 2) Final Plant Measurements, 3) Initial Plant Measurements, 4) Mesocosm Snail Morphometrics, 5) Plant Traits and 6) Snail Consumption.
Short-term consumption of sucralose with, but not without, carbohydrate impairs neural and metabolic sensitivity to sugar
Open the record for dataset details and reuse information.
Dataset: The Role of News Consumption on Influencers' Facebook Pages in Threat Perception and Political Conservatism During Times of COVID-19: A Comparative Study between the USA, Spain, and Egypt
<p>Este archivo ofrece los datos en bruto de una encuesta examina el impacto del consumo de noticias en las páginas de Facebook de los influencers en la motivación del conservadurismo político durante amenazas como el terrorismo o las pandemias. Muestra: N=1309, jóvenes de entre 18 y 35 años en Estados Unidos, España y Egipto. Trabajo de campo realizado entre el 10 de agosto de 2021 y el 5 de septiembre de 2021.</p> <p><span>Dataset correspondiente al proyecto El rol de la ciudadanía en la comunicación política digital CI-COMPOL (PID2020-119492GB-I00) financiado por MCIN/AEI/10.13039/501100011033/. IP: Andreu Casero-Ripollés, Departamento de Ciencias de la Comunicación, Universitat Jaume I de Castellón</span></p>
Biomass Domestic Material Consumption by Country and over Time
<p>Biomass domestic material consumption in thousand tons, and tons per capita for European countries.</p> <p>Our dataset has a 10.4% larger congruent dataset (to be used in various supervised or unsupervised learning models, such as machine learning) than the original Eurostat dataset after imputation, backcasting, forecasting. It has overall 18% more observations after processing than the dataset at source. </p>
Survey data on climate policy in three countries (Peru, Ghana, Philippines) within the project "Sustainable Middle Classes in Middle Income Countries: Transforming Carbon Consumption Patterns (SMMICC)"
<p>The unprecedented growth of the new middle classes in middle income developing countries implies a strong growth in both consumption and carbon emissions. The research project Sustainable Middle Classes in Middle Income Countries (SMMICC) investigates the drivers of carbon consumption choices of the new middle classes and policy options to decrease their carbon footprints, including the implementation of carbon taxes</p> <p>The research of the authors generated quantitative data on the acceptability of carbon taxes in three countries (Peru, Ghana, Philippines).</p> <p> </p> <p><strong>The data is provided in the following formats:</strong></p> <p>- 2024-07-26_malerba_10.5281/zenodo.12662722_ghana.csv<br>- 2024-07-26_malerba_10.5281/zenodo.12662722_peru.csv<br>- 2024-07-26_malerba_10.5281/zenodo.12662722_philippines.csv</p> <p>- 2024-07-26_malerba_10.5281/zenodo.12662722_ghana.dta<br>- 2024-07-26_malerba_10.5281/zenodo.12662722_peru.dta<br>- 2024-07-26_malerba_10.5281/zenodo.12662722_philippines.dta</p> <p>Additionally, the codebooks on variables of questionnaire and political parties in each country are attached in a csv format.</p>
Average daily alcohol consumption
<p>Average daily alcohol consumption by sex and age group. Average and standard deviation. Population aged 15 years old and over that consumes alcoholic beverages more than once per month</p>
Working time, energy throughput and value added embodied in production, consumption and trade by subsectors for the US, the EU, China and rest of the world (2011)
<p>This repository contains the data needed to reproduce the results in:</p> <p>Pérez-Sánchez, L., Velasco-Fernández, R., Giampietro, M., The international division of labor and embodied working time in trade for the US, the EU and China, Ecological Economics. <a href="http://doi.org/10.1016/j.ecolecon.2020.106909">https://doi.org/10.1016/j.ecolecon.2020.1069097</a></p> <p>Sources of data are specified in the dataset (under tab "references")</p> <p> </p>
S10 | SWISSPHARMA | Pharmaceutical List with Consumption Data
<p>This is the collection associated with list S10 SWISSPHARMA on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>S10 | SWISSPHARMA | <strong>Pharmaceutical List with Consumption Data</strong></p> <p>Table S2 from Singer <em>et al.</em> 2016. DOI: <a href="http://pubs.acs.org/doi/abs/10.1021/acs.est.5b03332">10.1021/acs.est.5b03332</a></p> <p>2024: added consumption data and mappings file for PubChem. </p>
MSP430FR5969 Basic Block Worst Case Energy Consumption (WCEC) and Worst Case Execution Time (WCET) dataset
<p>This dataset contains around 30 000 basic blocks whose energy consumption and execution time have been measured in isolation on the MSP430FR5969 microcontroller, at 1MHz. Basic blocks were executed in a worst case scenario regarding the MSP430 FRAM cache and CPU pipeline. The dataset creation process is described thoroughly in [1].</p> <h2>Folder structure</h2> <p>This dataset is composed of the following files:</p> <ul> <li><code>basic_blocks.tar.xz</code> contains all basic blocks (BB) used in the dataset, in a custom JSON format,</li> <li><code>data.csv</code>/<code>data.xlsx</code> contains the measured energy consumption and execution time for each basic block</li> </ul> <p>We first details how the <code>basic_blocks.tar.gz</code> archive is organized, and then present the CSV/XSLX spreadsheet format.</p> <h2>Basic Blocks</h2> <p>We extracted the basic blocks from a subset of programs of the <em>AnghaBench</em> benchmark suite [2]. The <code>basic_blocks.tar.gz</code> archive consist of the extracted basic blocks organized as <code>json</code> files. Each <code>json</code> file correspond to a C source file from <em>AnghaBench</em>, and is given a unique identifier. An example json (<code>137.json</code>) is available here:</p> <div> <pre><code>{ "extr_pfctl_altq.c_pfctl_altq_init": [ # Basic block 1 [ # Instruction 1 of BB1 [ "MOV.W", "#queue_map", "R13" ], # Instruction 2 of BB1 [ "MOV.B", "#0", "R14" ], # Instruction 3 of BB1 [ "CALL", "#hcreate_r", null ] ], # Basic block 2 [ .... ] ] }</code></pre> </div> <p>The json contains a dict with only one key pointing to an array of basic blocks. This key is the name of the original C source file in <em>AnghaBench</em> from which the basic blocks were extracted (here <a href="https://github.com/brenocfg/AnghaBench/blob/master/freebsd/sbin/pfctl/extr_pfctl_altq.c_pfctl_altq_init.c">extr_pfctl_altq.c_pfctl_altq_init.c</a>). The array contains severals basic blocks, which are represented as an array of instructions, which are themselves represented as an array <code>[OPCODE, OPERAND1, OPERAND2]</code>.</p> <p>Then, each basic block can be identified uniquely using two ids : its <em>file id</em> and its <em>offset</em> in the file (<code>id=<file id>_<offset></code>). In our example, the basic block 1 can be identified by the json file id (<code>137</code>) and its offset in the file (<code>0</code>). Its ID is <code>137_0</code>. This ID is used to make the mapping between a basic block and its energy consumption/execution time, with the <code>data.csv</code>/<code>data.xlsx</code> spreadsheet.</p> <h2>Energy Consumption and Execution Time</h2> <p>Energy consumption and execution time data are stored in the <code>data.csv</code> file. Here is the extract of the csv file corresponding to the basic block <code>137_0</code>. The spreadsheet format is described below.</p> <pre><code>bb_id;nb_inst;max_energy;max_time;avg_time;avg_energy;energy_per_inst;nb_samples;unroll_factor 137_0;3;8.77;7.08;7.04;8.21;2.92;40;50</code></pre> <p>Spreadsheet format :</p> <ul> <li><code>bb_id</code>: the unique identifier of a basic block (cf. <a>Basic Blocks</a>)</li> <li><code>nb_inst</code>: the number of instructions in the basic block</li> <li><code>max_energy</code>: the maximum energy comsumption (in nJ) measured during the experiment</li> <li><code>max_time</code>: the maximum execution time (in us) measured during the experiment</li> <li><code>avg_time</code>: the average execution time (in us) measured during the experiment</li> <li><code>avg_energy</code>: the average energy comsumption (in nJ) measured during the experiment</li> <li><code>energy_per_inst</code>: the average energy consumption per instruction (correspond to <code>avg_energy</code>/<code>nb_inst</code>)</li> <li><code>nb_samples</code>: how much time the basic block energy consumption/execution time has been measured</li> <li><code>unroll_factor</code>: how much time the basic block was unrolled (cf Basic Block Unrolling)</li> </ul> <h3>Basic Block Unrolling</h3> <p>To measure the energy consumption and execution time of the msp430, we need to be able to handle the scale difference between the measurement tool and the basic block execution time. This is achieved by duplicating the basic block multiple times while making sure to keep the worst-case memory layout as explained in the paper. The number of time the basic block has been duplicated is called the <code>unroll_factor</code>.</p> <p>Values of energy and time are always given per basic block, so they have already been divided by the unroll factor.</p> <p> </p> <h2>Dataset description</h2> <h3>Features</h3> <p>The selected features after PCA analysis for both energy and time model are listed here: <strong> MOV.W_Rn_Rn, MOV.W_X(Rn)_X(Rn), CALL, MOV.B_#N_Rn, ADD.W_Rn_Rn, MOV.W_@Rn_Rn, MOV.W_X(Rn)_Rn, ADD.W_#N_Rn, PUSHM.W_#N_Rn, MOV.W_X(Rn)_ADDR, CMP.W_#N_Rn, MOV.W_&ADDR_X(Rn), MOV.W_Rn_X(Rn), BIS.W_Rn_Rn, RLAM.W_#N_Rn, SUB.W_#N_Rn, MOV.W_&ADDR_Rn, MOV.W_#N_X(Rn), CMP.W_Rn_Rn, BIT.W_ADDR_Rn, MOV.W_@Rn_X(Rn), ADD.W_#N_X(Rn), MOV.W_#N_Rn, AND.W_Rn_Rn, MOV.W_Rn_ADDR, SUB.W_Rn_Rn, MOV.W_ADDR_Rn, MOV.W_X(Rn)_&ADDR, MOV.W_ADDR_ADDR, JMP, ADD_#N_Rn, BIS.W_Rn_X(Rn), SUB_Rn_Rn, MOV.W_ADDR_X(Rn), ADDC_#N_X(Rn), MOV.B_Rn_Rn, CMP.W_X(Rn)_X(Rn), ADD_Rn_Rn, nb_inst, INV.W_Rn_, NOP__, ADD.W_X(Rn)_X(Rn), ADD.W_Rn_X(Rn), MOV.B_@Rn_Rn, BIS.W_X(Rn)_X(Rn), MOV.B_#N_X(Rn), MOV.W_#N_ADDR, AND.W_#N_ADDR, SUBC_X(Rn)_X(Rn), BIS.W_#N_X(Rn), SUB.W_X(Rn)_X(Rn), AND.B_#N_Rn, ADD_X(Rn)_X(Rn), MOV.W_@Rn_ADDR, MOV.W_&ADDR_ADDR, ADDC_Rn_Rn, AND.W_#N_X(Rn), SUB_#N_Rn, RRUM.W_#N_Rn, AND_ADDR_Rn, CMP.W_X(Rn)_ADDR, MOV.B_#N_ADDR, ADD.W_#N_ADDR, CMP.B_#N_Rn, SXT_Rn_, XOR.W_Rn_Rn, CMP.W_@Rn_Rn, ADD.W_@Rn_Rn, ADD.W_X(Rn)_Rn, AND.W_Rn_X(Rn), CMP.B_Rn_Rn, AND.W_X(Rn)_X(Rn), BIC.W_#N_Rn, BIS.W_#N_Rn, AND.B_#N_X(Rn), MOV.B_X(Rn)_X(Rn), AND.W_@Rn_Rn, MOV.W_#N_&ADDR, BIS.W_Rn_ADDR, SUB.W_X(Rn)_Rn, SUB.W_Rn_X(Rn), SUB_X(Rn)_X(Rn), MOV.B_@Rn_X(Rn), CMP.W_@Rn_X(Rn), ADD.W_X(Rn)_ADDR, CMP.W_Rn_X(Rn), BIS.W_@Rn_X(Rn), CMP.B_X(Rn)_X(Rn), RRC.W_Rn_, MOV.W_@Rn_&ADDR, CMP.W_#N_X(Rn), ADDC_X(Rn)_Rn, CMP.W_X(Rn)_Rn, BIS.W_X(Rn)_Rn, SUB_X(Rn)_Rn, MOV.B_X(Rn)_Rn, MOV.W_ADDR_&ADDR, AND.W_#N_Rn, RLA.W_Rn_, INV.W_X(Rn)_, XOR.W_#N_Rn, SUB.W_Rn_ADDR, BIC.W_#N_X(Rn), MOV.B_X(Rn)_ADDR, ADD_#N_X(Rn), SUB_Rn_X(Rn), MOV.B_&ADDR_Rn, MOV.W_Rn_&ADDR, ADD_X(Rn)_Rn, AND.W_X(Rn)_Rn, PUSHM.A_#N_Rn, RRAM.W_#N_Rn, AND.W_@Rn_X(Rn), BIS.B_Rn_X(Rn), SUB.W_@Rn_Rn, CLRC__, CMP.W_#N_ADDR, XOR.W_Rn_X(Rn), MOV.B_Rn_ADDR, CMP.B_X(Rn)_Rn, BIS.B_Rn_Rn, BIS.W_X(Rn)_ADDR, CMP.B_#N_X(Rn), CMP.W_Rn_ADDR, XOR.W_X(Rn)_Rn, MOV.B_Rn_X(Rn), ADD.B_#N_Rn</strong></p> <h3>Code</h3> <p>The trained machine learning model, tests, and local explanation code can be generated and found here: <a href="https://colab.research.google.com/drive/1zaCIkbKDRDtwzhY-r3Iff0OpOSkOUibW?usp=sharing" target="_blank" rel="noopener">WORTEX Machine learning code</a> </p> <h2>Acknowledgment</h2> <p>This work has received a French government support granted to the Labex CominLabs excellence laboratory and managed by the National Research Agency in the “Investing for the Future” program under reference ANR-10-LABX-07-01</p> <h2>Licensing</h2> <p>Copyright 2024 Hector Chabot Copyright 2024 Abderaouf Nassim Amalou Copyright 2024 Hugo Reymond Copyright 2024 Isabelle Puaut</p> <p>Licensed under the Creative Commons Attribution 4.0 International License</p> <h2>References</h2> <p>[1] Reymond, H., Amalou, A. N., Puaut, I. “WORTEX: Worst-Case Execution Time and Energy Estimation in Low-Power Microprocessors using Explainable ML” in 22nd International Workshop on Worst-Case Execution Time Analysis (WCET 2024) </p> <p>[2] Da Silva, Anderson Faustino, et al. “Anghabench: A suite with one million compilable C benchmarks for code-size reduction.” 2021 IEEE/ACM International Symposium on Code Generation and Optimization (CGO). IEEE, 2021.</p>
Statistical analysis and dataset for: Three-dimensional body reconstruction enables quantification of liquid consumption in small invertebrates
<p>Linked to the journal article published in bioRxiv (https://doi.org/10.1101/2024.06.14.599002).</p> <p><em><strong>Abstract</strong></em></p> <p>Quantifying feeding patterns provides valuable insights into animal behaviour. However, small invertebrates often consume incredibly small amounts of food. This renders traditional methods, such as weighing individuals before and after food acquisition, either inaccurate or prohibitively expensive. Here, we present a non-invasive method to quantify food consumption of small invertebrates whose body expands during feeding. Using the markerless pose estimation software DeepLabCut, we three-dimensionally track the body of Argentine ants, <em>Linepithema humile</em>. Using these extracted markers, we developed an algorithm which computationally reconstructs the ant’s body, directly measuring volumetric change over time. Moreover, we provide measures of accuracy and quantify the ant’s feeding response to a range of sucrose concentrations, as well as a gradient of caffeine-laced sucrose solutions. Small invertebrates are often prolific invasive species and disease vectors, causing significant ecological and economical damage. Understanding their feeding behaviour could be an important step towards effective control strategies.</p> <p> </p> <ul> <li><strong>VolEst_C1_volume_calculation_multiprocessing.py</strong>: Takes as input H5 3D DeepLabCut files, calculates the gaster volume at every frame using seven different methods and outputs these as CSV files.</li> <li><strong>VolEst_C2_interactive_GUI.py</strong>: Given a folder with Volume CSV files, interactively plots the volume over time, 3D coordinates tracked by DeepLabCut and the frame of interest for both cameras.</li> <li><strong>VolEst_C3_linear_regression.py</strong>: Applies a linear regression to each feeding event tracked and provides measures of interest such as crop load and consumption rate.</li> <li><strong>VolEst_C4_statistical_analysis</strong>: Complete statistical analysis and code for the manuscript.</li> <li><strong>VolEst_D1_sucrose_density.csv</strong>: Data obtained to quantify the density of sucrose solutions of varying molarity.</li> <li><strong>VolEst_D2_accuracy_weight_metadata.csv</strong>: Manually collected metadata pertaining to experimental conditions, subjects, and treatments for the weight-volume accuracy measurements.</li> <li><strong>VolEst_D3_accuracy_weight.zip</strong>: Folder containing the raw points tracked using DeepLabCut, all relevant data obtained from the algorithms created, and a sample video of the experiment for the weight-volume accuracy measurements.</li> <li><strong>VolEst_D4_accuracy_nanoliter_metadata.csv</strong>: Manually collected metadata pertaining to experimental conditions, subjects, and treatments for the volume-volume accuracy measurements.</li> <li><strong>VolEst_D5_accuracy_nanoliter.zip</strong>: Folder containing the raw points tracked using DeepLabCut, all relevant data obtained from the algorithms created, and a sample video of the experiment for the volume-volume accuracy measurements.</li> <li><strong>VolEst_D6_sucrose_caffeine_consumption_metadata.csv</strong>: Manually collected metadata pertaining to experimental conditions, subjects, and treatments for the sucrose and caffeine dilutions application measurements.</li> <li><strong>VolEst_D7_sucrose_caffeine_consumption.zip</strong>: Folder containing the raw points tracked using DeepLabCut, all relevant data obtained from the algorithms created, and a sample video of the experiment for the sucrose and caffeine dilutions application measurements.</li> <li><strong>VolEst_Camera_A-Henrique-2023-09-20.zip</strong>: DeepLabCut labels and trained network for camera A.</li> <li><strong>VolEst_Camera_B-Henrique-2023-09-20.zip</strong>: DeepLabCut labels and trained network for camera B.</li> <li><strong>VolEst_base.stl</strong>: 3D file for the resin platform used in the experimental validation of the setup.</li> <li><strong>VolEst_platform.stl</strong>: 3D file for the resin platform used in the experimental validation of the setup.</li> </ul>
Proline and β-alanine influence bumblebee nectar consumption without affecting survival
<p>These files (.txt) contain the dataset used for analyses of bumblebee aminoacid consumption and survival in the article "Proline and β-alanine influence bumblebee nectar consumption without affecting survival" by Bogo G. et al., accepted for publication in Apidologie (2024, xx:xxx-xxx, DOI: xxx).</p>
European consumers ́ preference and willingness to pay for food products labelled as obtained by a circular farming system -in relation to environmental attitudes and consumption behaviours
<p>Data was collected with questionnaire-based research carried out in Belgium, Croatia, Hungary, Italy, Poland, and Spain as part of a European project. The survey questions were designed to obtain the Willingness to pay using 2 different methodologies the discrete choice experiment and the open-end choice experiment. The survey also included questions about consumers environmental attitudes, and consumption behavior (purchase, use and recycling), to identify if them have influence on preferences towards more sustainable food products. The 3 analyzed food products were pork meat, milk and bread, all of them obtained through different agricultural production systems (circular, conventional, and organic agriculture). The sample was stratified in terms of gender and age to be representative to the average population in each country. Furthermore, respondents included in this study were those that are mainly, or in part responsible for the household food shopping. The questionnaire was translated to the languages of the countries involved in the data collection and pre-launched using a pilot sample of 50 consumers in each case study country. Finally, a total of 5,362 validated questionnaires were obtained. Data was collected online using the Qualtrics market research company, and Net panel market company for Hungary from June 2021 to January 2022.</p>
Consumption rates of tethered live and dead pinfish and dried squid in mudflat and seagrass habitats in the Upper Laguna Madre in 2018.
These data were recorded during surveys of a tethering experiment conducted on June 7, 2018, during which 180 tethered prey were deployed in two habitat types (seagrass and mudflat) in the Upper Laguna Madre, Texas, USA (27.544006, -97.285912). In each habitat, the following prey types were deployed: squidpops (1 cm2 discs of dried squid (Duffy et al. 2015) attached to 5 cm tethers, n=50), live (n=20) and dead (n=20) pinfish (Lagodon rhomboides, 4 cm fork length, attached to 20 cm tethers) at midday in each habitat. The presence/absence of tethered prey on each stake was observed and recorded after 1 hour and 24 hours. The rate of decay (i.e., disappearance or consumption rate of tethered prey over time) was calculated as the slope of an exponential model fit to discrete observations of the presence/absence of tethered prey over time. Additional environmental variables (temperature, salinity) were also recorded at the site.
Gross methane production and consumption estimated for intact soil cores from agricultural plots including environmental covariates and example raw isotope pool dilution data
This study was performed to determine how different soil moistures, soil sources, and agricultural practices affected the gross CH4 fluxes (i.e., rates of methanogenesis) of soils. We extracted intact soil cores from two agricultural sites in the USA in row crop plots under conventional, no-till, and organic management. We then took them to the lab, manipulated their moisture levels, incubated them at room temperature for 22 weeks, and measured gas fluxes at weeks 6 and 21. We developed and utilized a new form of CH4 isotope pool dilution (IPD) to estimate gross CH4 production and consumption fluxes. This new method can measure IPD in a bag headspace that loses volume over time due to sampling. We fit the IPD model to the data and extracted gross CH4 production (P) and consumption (K) constants. These along with calculated fluxes and covariates measured (e.g., moisture, inorganic N) are reported in the main data table.
Habitat use, consumption, and growth by slimy sculpin (Cottus cognatus) held under different levels of temperature at Toolik Field Station 2019
We tested effects of temperature (12 and 19.3 degrees C; 27 days) on habitat use, consumption, and growth of slimy sculpin (Cottus cognatus). To measure temperature selection by sculpin, we connected two 5.7 L tanks with a PVC pipe that was passable by sculpin (n = 12 tanks). We heated one side of the tank to 12 °C and the other to 19.3 °C using aquarium heaters.
Rates of consumption of marsh periwinkles (Littoraria irrorata) by mud crabs (Eurytium limosum and Panopeus obesus) between August and December in a Georgia salt marsh
Predatory mud crabs (Panopeus obesus and Eurytium limosum) are two of the main resident infaunal predators in southeastern US salt marshes.The relative importance of the two species in the trophic control of marsh periwinkles (snails; Littoraria irrorata) is likley to change across seasons. We therefore manipulated the these predator species (Panopeus obesus and Eurytium limosum) in experimental cages in the field (at Dean Creek, Sapelo Island, GA) and assessed monthly predation rates over four months, between 15th August to 15th December. We included 3 treatments, consisting of two treatments containing each species alone, and one containing both species together; all treatments had the same density. Specifically, 1) 4 x Panopeus individuals; 2) 4 x Eurytium individuals; 3) 2 x Panopeus individuals + 2 Eurytium individuals. Only adult crabs (33-40mm carapace diameter) were used. We maintained the treatments over 4 months (15th Aug - 15th Dec 2009), replacing any missing crabs every two weeks and counting the number of snails killed by predators each month.
SBC LTER: Effect of algal diet on consumption, growth, and gonad weight of the purple sea urchin (Strongylocentrotus pupuratus)
Data are for an experiment evaluating the effects of algal diet on consumption, growth, and gonad weight of an important kelp forest grazer, the purple sea urchin, Strongylocentrotus pupuratus over a 13 week period (November 2010 - February 2011). Four co-occurring species of macroalgae known to be part of its diet were offered: two kelps Macrocystis pyrifera and Pterygophora californica, and the red algae Chondracanthus corymbiferus and Rhodymenia californica. During 9 consectutive trials in a controlled laboratory setting, we measured consumption, test (exoskeleton) growth, jaw growth, change in whole body wet weight and gonad weight of urchins fed one of five experimental diets. The algae chosen represent a large proportion (> 75%) of the algal biomass in Santa Barbara Channel reefs (California, USA). Changes in the availability of these four species of macroalgae could have large implications for the performance of purple sea urchins and consequently, for the structure of subtidal reef communities. These data are presented in a paper describing the effects of five southern California macroalgal diets on the consumption, growth and gonad weight of the purple sea urchin: Matthew C. Foster, M., Byrnes, J. E. K., D. C. Reed. 2015. Effects of five southern California macroalgal diets on consumption, growth and gonad weight in the purple sea urchin, Strongylocentrotus purpuratus. PeerJ. DOI: 10.7717/peerj.719
Brazilian Ministries' Esplanade Power Consumption
<p>Electric and climatic dataset of one building of Ministries' Esplanade (headquarter of the Brazilian Executive Government), from 2018-02-01 to 2019-12-13.</p> <p>There are 84926 samples, each for 10 minutes of electrical and climatic measurements, described by 12 variables.</p>
Investigating dynamics between energy use and socio-demographic characteristics in spatial modeling of residential energy consumption
<p>Files represent datasets (2017 Residential Building Stock Assessment and American Community Survey 2012-2017 5-year estimate) and R-code associated with the analysis. </p>
Block-wise sparse matrix-vector product dataset and convolutional neural nets for estimating the run time and energy consumption of the sparse matrix-vector product
<p><strong>Introduction</strong></p> <p><strong>SpMV-CNN</strong> is a set of Convolutional Neural Networks (CNNs) that provide accurate estimations of the performance and energy consumption of the SpMV kernel. The proposed CNN-based models use a block-wise approach to make the CNN architecture independent of the matrix size. These models cat be trained to estimate run time as well as total, package and DRAM energy consumption at different processor frequencies.</p> <p><strong>Prerequisites</strong></p> <p><strong>SpMV-CNN</strong> requires Python3 with the following packages:</p> <pre><code>keras==2.1.6 tensorflow==1.8.0 h5py==2.7.1 matplotlib==2.1.1 scikit-learn==0.19.1 </code></pre> <p><strong>Obtaining the dataset</strong></p> <p>The execution time and energy consumption data corresponding to the SpMV operation on a set of sparse matrices from the SuiteSparse Matrix Collection have been obtained on an Intel Xeon E5-2630 core running at frequencies 1.2, 1.6, 2.0, 2.4 GHz. The energy consumption measurements are obtained via the Intel RAPL interface and gathered at three different levels (total, package and DRAM, where total = package + DRAM) for this specific processor.</p> <p>The <code>spmv-cnn-dataset.tgz</code> archive contains the whole dataset, including the following HDF5 files:</p> <pre><code>$ tree . |-- test | |-- f_1200000_b250 | | |-- output_2cubes_sphere_1200000.h5 | | |-- output_apache2_1200000.h5 | | |-- output_bcsstk36_1200000.h5 | | |-- output_cfd1_1200000.h5 | | |-- output_cfd2_1200000.h5 | | |-- output_ct20stif_1200000.h5 | | |-- output_denormal_1200000.h5 | | |-- output_Dubcova2_1200000.h5 | | |-- output_Dubcova3_1200000.h5 | | |-- output_ecology2_1200000.h5 | | |-- output_gyro_1200000.h5 | | |-- output_gyro_k_1200000.h5 | | |-- output_msc10848_1200000.h5 | | |-- output_msc23052_1200000.h5 | | |-- output_nasasrb_1200000.h5 | | |-- output_nd3k_1200000.h5 | | |-- output_offshore_1200000.h5 | | |-- output_oilpan_1200000.h5 | | |-- output_olafu_1200000.h5 | | |-- output_parabolic_fem_1200000.h5 | | |-- output_qa8fm_1200000.h5 | | |-- output_raefsky4_1200000.h5 | | |-- output_s3dkq4m2_1200000.h5 | | |-- output_s3dkt3m2_1200000.h5 | | |-- output_ship_001_1200000.h5 | | |-- output_ship_003_1200000.h5 | | |-- output_shipsec1_1200000.h5 | | |-- output_shipsec5_1200000.h5 | | |-- output_shipsec8_1200000.h5 | | |-- output_smt_1200000.h5 | | |-- output_thermomech_dM_1200000.h5 | | |-- output_thread_1200000.h5 | | `-- output_vanbody_1200000.h5 | |-- f_1600000_b250 | | |-- output_2cubes_sphere_1600000.h5 | | |—- ... | | `-- output_vanbody_1600000.h5 | |-- f_2000000_b250 | | |-- output_2cubes_sphere_2000000.h5 | | |—- ... | | `-- output_vanbody_2000000.h5 | `-- f_2400000_b250 | |-- output_2cubes_sphere_2400000.h5 | |—- ... | `-- output_vanbody_2400000.h5 |-- test_pagerank | |-- f_1200000_b250 | | |-- output_adaptive_1200000.h5 | | |-- output_cit-HepPh_1200000.h5 | | |-- output_delaunay_n22_1200000.h5 | | |-- output_email-Enron_1200000.h5 | | |-- output_email-EuAll_1200000.h5 | | |-- output_europe_osm_1200000.h5 | | |-- output_hugebubbles-00020_1200000.h5 | | |-- output_rgg_n_2_24_s0_1200000.h5 | | |-- output_road_usa_1200000.h5 | | |-- output_Stanford_1200000.h5 | | |-- output_wb-edu_1200000.h5 | | |-- output_web-BerkStan_1200000.h5 | | |-- output_web-Google_1200000.h5 | | |-- output_web-NotreDame_1200000.h5 | | |-- output_wiki-Talk_1200000.h5 | | `-- output_wiki-Vote_1200000.h5 | |-- f_1600000_b250 | | |-- output_adaptive_1600000.h5 | | |—- ... | | `-- output_wiki-Vote_1600000.h5 | |-- f_2000000_b250 | | |-- output_adaptive_2000000.h5 | | |—- ... | | `-- output_wiki-Vote_2000000.h5 | `-- f_2400000_b250 | |-- output_adaptive_2400000.h5 | |—- ... | `-- output_wiki-Vote_2400000.h5 `-- train |-- merged_energy_train_shuffle_f1200000_250.h5 |-- merged_energy_train_shuffle_f1600000_250.h5 |-- merged_energy_train_shuffle_f2000000_250.h5 `-- merged_energy_train_shuffle_f2400000_250.h5 </code></pre> <p>The matrices contained in the merged training files (<code>merged_energy_train_shuffle_fXX00000_250.h5</code>) are the following:</p> <pre><code>$ tree . |-- output_af_0_k101_1200000.h5 |-- output_af_1_k101_1200000.h5 |-- output_af_2_k101_1200000.h5 |-- output_af_3_k101_1200000.h5 |-- output_af_4_k101_1200000.h5 |-- output_af_5_k101_1200000.h5 |-- output_af_shell10_1200000.h5 |-- output_af_shell1_1200000.h5 |-- output_af_shell2_1200000.h5 |-- output_af_shell3_1200000.h5 |-- output_af_shell4_1200000.h5 |-- output_af_shell5_1200000.h5 |-- output_af_shell6_1200000.h5 |-- output_af_shell7_1200000.h5 |-- output_af_shell8_1200000.h5 |-- output_af_shell9_1200000.h5 |-- output_atmosmodd_1200000.h5 |-- output_atmosmodj_1200000.h5 |-- output_atmosmodl_1200000.h5 |-- output_audikw_1_1200000.h5 |-- output_BenElechi1_1200000.h5 |-- output_bmw3_2_1200000.h5 |-- output_bmw7st_1_1200000.h5 |-- output_bmwcra_1_1200000.h5 |-- output_bone010_1200000.h5 |-- output_boneS01_1200000.h5 |-- output_boneS10_1200000.h5 |-- output_bundle_adj_1200000.h5 |-- output_cage14_1200000.h5 |-- output_cage15_1200000.h5 |-- output_circuit5M_1200000.h5 |-- output_circuit5M_dc_1200000.h5 |-- output_CO_1200000.h5 |-- output_consph_1200000.h5 |-- output_CoupCons3D_1200000.h5 |-- output_crankseg_1_1200000.h5 |-- output_crankseg_2_1200000.h5 |-- output_CurlCurl_2_1200000.h5 |-- output_CurlCurl_3_1200000.h5 |-- output_CurlCurl_4_1200000.h5 |-- output_dielFilterV2real_1200000.h5 |-- output_dielFilterV3real_1200000.h5 |-- output_Emilia_923_1200000.h5 |-- output_ESOC_1200000.h5 |-- output_F1_1200000.h5 |-- output_F2_1200000.h5 |-- output_Fault_639_1200000.h5 |-- output_Freescale1_1200000.h5 |-- output_Freescale2_1200000.h5 |-- output_FullChip_1200000.h5 |-- output_G3_circuit_1200000.h5 |-- output_Ga10As10H30_1200000.h5 |-- output_Ga19As19H42_1200000.h5 |-- output_Ga3As3H12_1200000.h5 |-- output_Ga41As41H72_1200000.h5 |-- output_Ge87H76_1200000.h5 |-- output_Ge99H100_1200000.h5 |-- output_Geo_1438_1200000.h5 |-- output_gsm_106857_1200000.h5 |-- output_Hardesty3_1200000.h5 |-- output_hood_1200000.h5 |-- output_Hook_1498_1200000.h5 |-- output_human_gene1_1200000.h5 |-- output_human_gene2_1200000.h5 |-- output_inline_1_1200000.h5 |-- output_JP_1200000.h5 |-- output_kkt_power_1200000.h5 |-- output_ldoor_1200000.h5 |-- output_Long_Coup_dt0_1200000.h5 |-- output_Long_Coup_dt6_1200000.h5 |-- output_mat_104_10000_1200000.h5 |-- output_mat_104_1000_1200000.h5 |-- output_mat_104_5000_1200000.h5 |-- output_mat_112_10000_1200000.h5 |-- output_mat_112_1000_1200000.h5 |-- output_mat_112_5000_1200000.h5 |-- output_mat_120_10000_1200000.h5 |-- output_mat_120_1000_1200000.h5 |-- output_mat_120_5000_1200000.h5 |-- output_mat_128_10000_1200000.h5 |-- output_mat_128_1000_1200000.h5 |-- output_mat_128_5000_1200000.h5 |-- output_mat_16_10000_1200000.h5 |-- output_mat_16_1000_1200000.h5 |-- output_mat_16_5000_1200000.h5 |-- output_mat_24_10000_1200000.h5 |-- output_mat_24_1000_1200000.h5 |-- output_mat_24_5000_1200000.h5 |-- output_mat_32_10000_1200000.h5 |-- output_mat_32_1000_1200000.h5 |-- output_mat_32_5000_1200000.h5 |-- output_mat_40_10000_1200000.h5 |-- output_mat_40_1000_1200000.h5 |-- output_mat_40_5000_1200000.h5 |-- output_mat_48_10000_1200000.h5 |-- output_mat_48_1000_1200000.h5 |-- output_mat_48_5000_1200000.h5 |-- output_mat_56_10000_1200000.h5 |-- output_mat_56_1000_1200000.h5 |-- output_mat_56_5000_1200000.h5 |-- output_mat_64_10000_1200000.h5 |-- output_mat_64_1000_1200000.h5 |-- output_mat_64_5000_1200000.h5 |-- output_mat_72_10000_1200000.h5 |-- output_mat_72_1000_1200000.h5 |-- output_mat_72_5000_1200000.h5 |-- output_mat_80_10000_1200000.h5 |-- output_mat_80_1000_1200000.h5 |-- output_mat_80_5000_1200000.h5 |-- output_mat_8_10000_1200000.h5 |-- output_mat_8_1000_1200000.h5 |-- output_mat_8_5000_1200000.h5 |-- output_mat_88_10000_1200000.h5 |-- output_mat_88_1000_1200000.h5 |-- output_mat_88_5000_1200000.h5 |-- output_mat_96_10000_1200000.h5 |-- output_mat_96_1000_1200000.h5 |-- output_mat_96_5000_1200000.h5 |-- output_memchip_1200000.h5 |-- output_ML_Laplace_1200000.h5 |-- output_mouse_gene_1200000.h5 |-- output_msdoor_1200000.h5 |-- output_m_t1_1200000.h5 |-- output_nd12k_1200000.h5 |-- output_nd24k_1200000.h5 |-- output_nd6k_1200000.h5 |-- output_nlpkkt120_1200000.h5 |-- output_nlpkkt80_1200000.h5 |-- output_PFlow_742_1200000.h5 |-- output_pwtk_1200000.h5 |-- output_rajat31_1200000.h5 |-- output_RM07R_1200000.h5 |-- output_Rucci1_1200000.h5 |-- output_Serena_1200000.h5 |-- output_Si34H36_1200000.h5 |-- output_Si41Ge41H72_1200000.h5 |-- output_Si87H76_1200000.h5 |-- output_SiO2_1200000.h5 |-- output_sls_1200000.h5 |-- output_StocF-1465_1200000.h5 |-- output_TEM152078_1200000.h5 |-- output_TEM181302_1200000.h5 |-- output_thermal2_1200000.h5 |-- output_tmt_sym_1200000.h5 |-- output_torso1_1200000.h5 |-- output_Transport_1200000.h5 |-- output_TSOPF_FS_b300_c2_1200000.h5 |-- output_TSOPF_FS_b300_c3_1200000.h5 |-- output_TSOPF_RS_b2383_1200000.h5 |-- output_TSOPF_RS_b2383_c1_1200000.h5 |-- output_TSOPF_RS_b678_c2_1200000.h5 `-- output_x104_1200000.h5 f_1600000_b250 |-- output_af_0_k101_1600000.h5 |—- ... `-- output_x104_1600000.h5 f_2000000_b250 |-- output_af_0_k101_2000000.h5 |—- ... `-- output_x104_2000000.h5 f_2400000_b250 |-- output_af_0_k101_2400000.h5 |—- ... `-- output_x104_2400000.h5 </code></pre> <p><strong>Creating your own dataset</strong></p> <p>If you wish to create your own training/testing dataset on a different target architecture you need to take the following steps:</p> <ol> <li> <p>Build the SpMV driver:</p> <ol> <li> <p>Go to <code>cd SpMV-driver/src</code></p> </li> <li> <p>Edit makefile and set the PAPI and HDF5 install prefixes.</p> </li> <li> <p>Build the driver via <code>make.</code></p> </li> </ol> </li> <li> <p>Run the SpMV driver: </p> <p><code>./driver <arg0> <arg1> ...</code></p> <p>List of driver arguments:</p> <pre><code>matrix = audikw_1.rb # Input matrix in rb format reps = 10000 # Number of repetitions of the operation to avoid overhead block_size_ini = 250 # Minimum block size block_size_end = 1000 # Maximum block size increment = 250 # Increment between block sizes base = 0 # Starting nnz of the matrix freq = [2400000, 2000000, 1600000, 1200000] # Operating frequency sym = 1 # If 1 the matrix is symmetric. If 0 the matrix is no-symmetric.</code></pre> <p>Example:</p> <p><code>numactl --membind 0 taskset -c 0 ./src/driver audikw_1.rb 10000 250 1000 250 0 2400000</code></p> <p>Note that <code>numactl</code> and <code>taskset</code> utilities are used to guarantee both NUMA and process-to-core affinity.</p> </li> <li> <p>Generating the dataset:</p> <ol> <li> <p>Edit the <code>SpMV-driver/run_all.sh</code> and uncomment the line <code>matrices =</code> in order to launch the driver for Train_symmetric / Train_noSymmetric / Test_symmetric / Test_noSymmetric matrices.</p> </li> <li> <p>Edit the 3rd parameter in the command SpMV-driver/run_driver.sh: 1 for symmetric matrices, 2 for unsymmetric matrices.</p> </li> <li> <p>Edit the command in SpMV-driver/run_driver.sh to select the input parameters of the driver as explained before.</p> </li> <li> <p>Run <code>SpMV-driver/run_all.sh</code> to obtain <code>hdf5</code> files that will create the dataset.</p> </li> </ol> </li> <li> <p>Merging the dataset:</p> <p>Run the script</p> <p><code>python3 SpMV-driver/merge_train_matrices.py /path/to/hdf5/matrix/files /output/path</code></p> <p>to obtain a single <code>hdf5</code> file containing all data from individual <code>hdf5</code> files obtained in the previous step. This merged file is the training dataset.</p> </li> </ol> <p><strong>Hyperparameter search</strong></p> <p>The script <code>spmv_cnn_hyperas.py</code> performs the hyperparameter search via the Hyperas tool. This script requires the hdf5 file dataset in the directory <code>dataset/train/</code> and produces both a <code>best_model_*.json</code> and <code>best_run_*.json </code>files in the <code>results/models/</code> directory containing the model structure and hyperparameters of the best performing configuration.</p> <p>This script can be invoked in the following way:</p> <p><code>python3 spmv_cnn_hyper.py 2400000 Time</code></p> <p>where <code>2400000</code> is the operating processor frequency (2.4 GHz) at which the dataset was generated and <code>Time</code> the modeled metric. According to the labels in the dataset, the hyperparameter search can also be performed with the <code>Energy</code>, <code>EPKG</code> and <code>EDRAM</code> metrics, corresponding to the energy measured by the Intel RAPL counters from our Intel Xeon Haswell core. In our case, however, we only search hyperparameters for the <code>Time</code> and <code>Energy</code> metrics at 2.4 GHz. Other metrics and frequencies inherit the best performing model and settings from the previous configuration.</p> <p><strong>Training</strong></p> <p>The script <code>spmv_cnn_train.py</code> performs the training on the best performing models obtained on the previous step. For that, it uses both the <code>best_model_*.json</code> and <code>best_run_*.json</code> files obtained in the hyperparameter search.</p> <p>This script can be invoked in the following way:</p> <p><code>python3 spmv_cnn_train.py 2400000 Time</code></p> <p>where <code>2400000</code> is the operating processor frequency (2.4 GHz) and <code>Time</code> the modeled metric. The training should be performed per metric and frequency. The training produces a file that contains the trained weights, so the model is ready for performing inference (testing).</p> <p><strong>Testing</strong></p> <p>The script <code>spmv_cnn_test.py</code> performs the test on the set of testing matrices involved in the SpMV operation.</p> <p>This script can be invoked in the following way:</p> <p><code>python3 spmv_cnn_test.py 2400000 Time</code></p> <p>where <code>2400000</code> is the operating processor frequency (2.4 GHz) and <code>Time</code> the modeled metric. The test should be performed per metric and frequency. The training produces two files in the <code>results/tests/</code> directory:</p> <ul> <li><code>Pred_*.txt</code>: This file contains the real measurements and the predictions obtained by the CNN for the individual vpos blocks of the testing matrices.</li> <li><code>Test_*.txt</code>: This file summarizes the information of <code>Pred_*.txt</code> file, showing the average relative error among the blocks of each test matrix and the total relative error, which is computed by summing up the real measurements and the predictions for all the blocks of a same matrix and computing the relative error upon those values.</li> </ul> <p><em>Note that this testing step and the two previous steps (hyperparameter search and training) can be performed at once using the <code>run.sh</code> script.</em></p> <p><strong>References</strong></p> <p>Publications describing <strong>SpMV-CNN-Model</strong>:</p> <ul> <li>Barreda, M., Dolz, M.F., Castaño, M.A. et al. Performance modeling of the sparse matrix–vector product via convolutional neural networks. J Supercomputing (2020). <a href="https://doi.org/10.1007/s11227-020-03186-1">https://doi.org/10.1007/s11227-020-03186-1</a></li> </ul> <p><strong>Acknowledgments</strong></p> <p>The <strong>SpMV-CNN-Model</strong> research has been partially supported by:</p> <ul> <li> <p>Project TIN2017-82972-R <strong>“Agorithmic Techniques for Energy-Aware and Error-Resilient High Performance Computing”</strong> funded by the Spanish Ministry of Economy and Competitiveness (2018-2020).</p> </li> <li> <p>Project CDEIGENT/2017/04 <strong>“High Performance Computing for Neural Networks” </strong>funded by the Valencian Government.</p> </li> <li> <p>Project UJI-A2019-11 <strong>“Energy-Aware High Performance Computing for Deep Neural Networks”</strong> funded by the Universitat Jaume I.</p> </li> </ul>
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