Operating Systems

• Linux
• Introduction to the Linux Shell (SciNet)

• Advanced Shell Programming (SciNet)

Resource and Project manager

• Slurm
  • GPGPU's on Slurm (documentation and configuration)
• RICAP cloud infrastructure
• Elastic deployment of virtualized resources with Unacloud
• OpenNebula
• GitHub

Programming models, libraries and languages

• GCC Optimization flagships
  • Document
• MPI
  • POP tutorial
    • Part 01
    • Part 02
    • Part 03
    • Lab
  • LNLL tutorial
• OpenMP
  • POP tutorial
    • Part 01
    • Part 02
    • Part 03
    • Lab
    • Getting Performance from OpenMP Programs on NUMA Architectures (POP webinar)
  • LNLL tutorial
• Python
  • RAR file
  • Published by the Python organization
  • Google's class
  • SciNet's class

  • Intro to Scientific Computing with Python (SciNet)

• R

  • Introduction to R (SciNet)

• C
  • Beginners level
• POSIX
  • Threads programming
• OpenCL
  • Tutorial
  • PyOpenCL
• OpenACC
  • Course
  • PGI Accelerator
• MapReduce
  • tutorial
• Spark
  • Pyhton tutorial
  • Examples
• Performance tools
  • Cube (Tutorial, User guide, Metrics)
  • Darshan (I/O webinar, POP)
  • Dimemas (Tutorial)
  • Extrae (Tutorial, User guide)
  • Paraver (Tutorial, User guide)
  • Scalasca (Tutorial, User guide, Patterns)
  • Score-P (Tutorial)
  • How to Improve the Performance of Parallel Codes (POP webinar)

Computer Science

• RICAP solutions for an efficient use ofcomputational infrastructures
  • Deliverable D4
  • Deliverable D8
  • Deliverable D9
  • Management of virtualized environments
  • Deliverable D13
  • Deliverable D15
• Parallel computing
  • Basics of cooking
  • Basics of code optimization
  • Basics of code optimization 2
  • Course (LLNL)
  • Accelerated/Hybrid computing with GPGPU

  • Advanced Parallel Scientific Computing (SciNet)

• Scheduling and management of HPC and HTC resources
  • Oral presentation
  • Updated oral presentation
• Dynamic migration of tasks by means of checkpointing and fault tolerance techniques
  • ECAR 2017
  • Integration of the checkpointing library DMTCP into the Slurm resource manager (video in Spanish - video in English)
• Parallel performance
  • How to Improve the Performance of Parallel Codes (POP webinar)
• Data management
  • Storage and I/O in Large Scale Scientific Projects (SciNet)
  • Relational Database Basics (SciNet)

Artificial Intelligence

• ECAR 2017
• Deep learning (MIT)
• Data Science and Visualization (SciNet)
• Introduction to Data Analysis with R (SciNet)
• Quantitative Applications for Data Analysis (SciNet)
• Neural Network Programming (SciNet)
• Advanced Neural Network (SciNet)

Other Scientific Fields

• Scientific Computing for Physicists (SciNet)
• Introduction to Computational BioStatistics (SciNet)
• Introduction to Clinical BioStatistics (SciNet)
• Examples on HPC & Energy

PhD theses

• Carlos Gómez. Confiabilidad en Sistemas Desktop Cloud.
• Miguel A. Fernández Castellanos. Estudio teórico del efecto del MgSO₄ sobre la peroxidación lipídica en membranas celulares: cálculos multi-escala de las interacciones entre lípidos de membrana, agua, radicales hidroxilo y MgSO4 
• Juan A. Freitez. Estudio teórico de las reacciones de hidrogenación de asfaltenos en presencia de malteno sin catalizador.
• Yenner Bentarcurt. Estudio teórico de la hidrogenación de nitrobenceno en estructuras de γ-Fe2O3, en grafeno N-Dopado usando la Teoría del Funcional de la Densidad (DFT)
• Raamsés Díaz. Integración de los fenómenos de transporte en poro en un lecho empacado fijo sobre un estudio multi-escala del coeficiente de flujo difusional.

MSc theses

• Aurelio Vivas, Límites de la computación  científica en sistemas desktop grids.
• José Gregorio Cisneros. Estudio de las variaciones en las propiedades interfaciales de los sistemas agua-aceite con surfactantes mediante simulaciones de dinámica molecular clásica y cálculos de estructura electrónica.
• Carlos Gómez. Diseño de una arquitectura para el manejo de paquetes en ambientes HPC usando NiX
• Otavio Carvalho. A model for distributed data aggregation in edge and cloud environments
• Jonathan Guedez. Simulación en 2D de la formación de un trombo, en una sección de la arteria coronaria en presencia del campo de elasticidad mediante el método S.P.H.

BSc theses

• Luis Plazas. Opportunistic IaaS platform based on containers
• César Bernal. Implementación de una arquitectura de visualización remota sobre un esquema de Visualización como Servicio
• Miguel Antonio Fernández Castellanos. Estudio teórico del efecto del MgSO₄ sobre la peroxidación lipídica en membranas celulares: cálculos multi-escala de las interacciones entre lípidos de membrana, agua, radicales hidroxilo y MgSO₄. 
• María Remolina. Optimización y paralelización del diseño hidráulico de un sistema de alcantarillado.
• José Tamura. Detección y predicción de fallas a partir de métricas de performance en sistemas Desktop Cloud.
• Noelia Molero Puerto. Determinación de configuraciones de vórtices superconductores con procesos estocásticos con aceleradores gráficos en entornos de supercomputación.
• Andrés Muñoz. Optimización en transferencia de imágenes en la plataforma UnaCloud.
• Juan Molano. Configuración y despliegue automático de aplicaciones en UnaCloud. 

• Network presentations
  • 3rd Workshop on HPC Collaboration Between Europe and LatinAmerica (Sep 2020)
  • TICAL Conference (Aug 2020)
    Foro RENATA (Jul 2020)
  • CYTED Meeting (Oct 2019)
  • SIGESTIC 2019 (Sep 2019)
  • ISUM 2019 (Mar 2019)
  • Latin American Physics Conference (Oct 2018)
  • CYTED Meeting (Sep 2018)
  • TICAL Conference (Sep 2018)
  • Annual meeting 2018 (May, 2018)
  • RedCLARA Virtual Day (April 2018)
  • ISUM 2018 (March, 2018)
  • Supercomputing 2017 (November, 2017)
  • CYTED Meeting (October, 2017)
  • CARLA Conference (September 2017)
  • TICAL Conference (July 2017)
• Report on the accesses to the RICAP website
  • 2018
• Dissemination material
  • Network deliverable template
  • Network poster template
  • Network presentation template
• AUP
  • HPC infrastructure
  • HTC cloud infrastructure
  • Institution application for admission fom

• A. Alberto et al. Impacto de la e-Infraestructura de RICAP para el desarrollo de la e-Ciencia en Iberoamérica. Actas TICAL 2020 y 4º Encuentro Latinoamericano de e-Ciencia, 195-206 (2020)
• R. Mayo-García. La Red Iberoamericana de Computación de Altas Prestaciones (RICAP). Vértices 31, 37-39 (2919)
• A.J. Rubio-Montero et al. La infraestructura de RICAP en la nube para realizar e-Ciencia en Latinoamérica. Actas TICAL 2018 y 2º Encuentro Latinoamericano de e-Ciencia, 131-140 (2018)
• E. Mocskos et al. Boosting the use and development of advanced computational applications and resources in Latin America through collaboration and sharing. Computing Science & Enginnering 20, 39-48 (2018)
• A. de la Ossa Osegueda et al. La Red Iberoamericana de Computación de Altas Prestaciones: una plataforma tecnológica al servicio de la comunidad académica. Actas TICAL 2017, 525-534 (2017)

• G. Aguero-Chapin et al. Graph Theory-Based Sequence Descriptors as Remote Homology Predictors. Biomolecules 10 (1), 2-32 (2020)
• M. Bello et al. Deep neural network to extract high-level features and labels in multi-label classification problems. Neurocomputing 413, 259–270 (2020)
• Y. González-Valle et al. Ensemble K-means for semi-supervised learning in enzymatic activity classification of GH-70 enzymes. MDPI SciForum 6 (1), 2624-5078 (2020)
• E.A. Bea, M.F. Carusela, A. Soba, A.G. Monastra, A.M. Mancardo Viotti. Thermal conductance of structured silicon nanocrystals. Modelling and Simulation in Materials Science and Engineering, Volume 28 (7)
• M.W. Camargo, M.S. Serpa, D. Carastan-Santos, A. Carissimi, P.O.A. Navaux. Accelerating Machine Learning Algorithms with TensorFlow using Thread Mapping Policies. Proc HPC2020-Carla2020, virtual, Quito, Equador (in print)
• M.L. Tovar, M. Sánchez, K. Serny, F. Ruette, La estructuración de una herramienta para la enseñanza de la química de bachillerato (EduQuim)utilizando la plataforma Moodle y la opinión del alumnado y el profesorado, Ikastorratza e-Revista de Didáctica 25, 208-227 (2020).
• R. Díaz, L. Di G. Sigalloti, J. Klapp. Aproximación numérica en un reactor de lecho empacado estructurado sobre la influencia de transferencia de masa en la conversión química. CATÁLISIS (in print)
• K. Paredes. Stacking fault Energy (SFE) of multi-component alloys based in Fe80-X MnXCo10Cr10 (X= 20, 30, 40, 50 at percentage) using a computational approach. Proc. LatinXChem Twitter Conference 2020
• G. del Río, S. Allés. Narrativas digitales de la COVID-19 project
• N.D. Aagaard et al. Mechanistic Framework for the Formation of Different Sulfur Species by Electron Irradiation of n‐Dodecanethiol Self-Assembled Monolayers on Au(111) and Au(100). J. Phys. Chem. C 124 41, 22591–22600 (2020)
• J. Moríñigo, P. García-Muller, A.J. Rubio-Montero, A. Gómez-Iglesias, N. Meyer, R. Mayo-García. Performance drop at executing communication-intensive parallel algorithms. The Journal of Supercomputing 76, 6834-6859 (2020)
• Antonio J. Rubio-Montero et al. Evolución de la sostenibilidad de las infraestructuras HPC en la sede central del CIEMAT. Revista UIS Ingenierías 19 (2), 85-88 (2020)
• A. Lepland et al. Targeting pro-tumoral macrophages in early primary and metastatic breast tumors with CD206-binding mUNO peptide. Molecular Pharmaceutics; ISSN: 1543-8384 (2020)
• J. Peña Rodríguez et al. Design and construction of MuTe: a hybrid Muon Telescope to study Colombian Volcanoes. arXiv preprint arXiv:2004.09364 (2020)
• M. Rodríguez-Pascual, A.J. Rubio-Montero, J.A. Moríñigo, R. Mayo-García. Execution data logs of a supercomputer workload over its extended lifetime. Data in brief 28 (2020) 105006
• A. Vesga-Ramírez et al. Simulated Annealing for Volcano Muography arXiv preprint arXiv: 2005.08295 (2020)
• M. Sánchez, F. Ruette. Calculations of adsorption, coadsorption, diffusion, and reaction barriers of H atoms in the H2 formation on a positively charged coronene. Chemical Physics Letters 738, 136913 (2020)
• J. Marquina et al. Theoretical study of Mn doping effects and O or Zn vacancies on the magnetic properties in wurtzite ZnO. Chinese Journal of Physics 63, 63–69 (2020)
• J.C. Jiménez, J.A. Olmos-Asar, E. Franceschini, M. Mariscal. Electrochemical area of graphene supported metal nanoparticles from an atomistic approach. Journal of Applied Electrochemistry (printed online, 2020)
• D. Domínguez-Pérez et al. The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba. Genomics 111 (6), 1720-1727 (2019)
• A. Vasquez-Ramírez et al. Simulated Response of MuTe, a Hybrid Muon Telescope. arXiv preprint arXiv:1912.10081 (2019)
• J. A. Olmos-Asar, M. Mariscal. Avoiding oxidation with coating: graphene protected magnesium surfaces. Phys. Chem. Chem. Phys. 21, 18660-18666 (2019)
• F.R. Negreiros et. al. Ultrathin WO3 Bilayer on Ag(100): A Model for the Structure of 2D WO3 Nanosheets. J. Phys. Chem. C 123, 27584-27593 (2019)
• F.R. Negreiros et. al. The unexpected effect of vacancies and wrinkling on the electronic properties of MoS2 layers, Phys. Chem. Chem. Phys. 21, 24731-24739 (2019)
• C. Gómez, J. Chavarriaga, H. Castro. Fault Characterization and Mitigation Strategies in Desktop Cloud Systems. Communications in Computer and Information Science, Volume 979, pp 322-335, March 2019
• J. Chavarriaga, C. Gómez, D. Bonilla, H. Castro. Capacity of Desktop Clouds for Running HPC Applications: A Revisited Analysis. lorez H., Leon M., Diaz-Nafria J., Belli S. (eds) Applied Informatics. ICAI 2019, Communications in Computer and Information Science, pp. 257-268, vol 1051. Springer, Cham.
• M. Rodríguez-Pascual, J.A. Moríñigo, R. Mayo-García. Effect of MPI tasks location on cluster throughput using NAS. Cluster Computing 22, 1187–1198 (2019)
• N. Molero-Puerto, R. Mayo-García. Using GPUs for determining the energy configuration of superconducting vortex lattices with stochastic methods. In: Proc. 2019 Winter Simulation Conf, 3277-3284 (2019)
• J. Muraña et al. Characterization, modeling and scheduling of power consumption of scientific computing applications in multicores. Cluster Computing 22 (3), 839-859 (2019)
• M. Alaniz, S. Neschmanow. A semi-automatic approach for parallel problem solving using the Multi-BSP model. Programming and Computer Software 45(8), 517-531 (2019)
• S. Iturriaga et al. Evolutionary Algorithms for Optimizing Cost and QoS on Cloud-based Content Distribution Networks. Programming and Computer Software 45(8), 544-556 (2019)
• R. Díaz et al. Aproximación numérica en un reactor de lecho empacado estructurado sobre la influencia de la transferencia de masa en la conversión química. Proc. XXII Congreso Venezolano de Catálisis 2019. ISBN: 978-980-12-3931-4
• M. Fernández et al. Deslocalización de la densidad de espín del radical hidroxilo sobre el MgSO₄. Un estudio teórico. Proc. XXII Congreso Venezolano de Catálisis 2019. ISBN: 978-980-12-3931-4
• M. Guarecuco et al. Estudio computacional de la adsorción de hidrógeno en átomos de níquel soportado en coroneno funcionalizado con grupos cetona y amino. Proc. XXII Congreso Venezolano de Catálisis 2019. ISBN: 978-980-12-3931-4
• K. Serny et al. Evaluación de la conversión química en un reactor empacado usando modelos heurísticos de flujodinámica. Un acercamiento al comportamiento real. Proc. XXII Congreso Venezolano de Catálisis 2019. ISBN: 978-980-12-3931-4
• J.G. Cisneros et al. Estudio de la modificación de las propiedades interfaciales del sistema agua-decano por distintos tipos de surfactantes mediante cálculos de Dinámica Molecular. Proc. XXII Congreso Venezolano de Catálisis 2019. ISBN: 978-980-12-3931-4
• Y. Bentarcurt et al. Una metodología para calcular energías del sólido (bulk) considerando la partición de la energía por capas. Aplicación en bloques (slabs) estequiométricos asimétricos tipo magnetita en la dirección [001]. Proc. XXII Congreso Venezolano de Catálisis 2019. ISBN: 978-980-12-3931-4
• E.L. Padoin et al. Optimizing Water Cooling Applications on Shared Memory Systems. Proc. CARLA 2019
• M. Rodríguez-Pascual et al. Job migration in HPC clusters by means of checkpoint/restart. The Journal of Supercomputing 75, 6517-6541 (2019)
• A.M.  Maliszewski et al. Minimizing Communication Overheads in Container-based Clouds for HPC Applications. Proc. ISCC 2019
• E. Roloff et al. Exploring Instance Heterogeneity in Public Cloud Providers for HPC Applications. Proc. CLOSER 2019
• O. Carvalho et al. GaruaGeo: Global Scale Data Aggregation in Hybrid Edge and Cloud Computing Environments. Proc. CLOSER 2019
• J.A. Moríñigo et al. Benchmarking LAMMPS: Sensitivity to Task Location Under CPU-Based Weak-Scaling. Communications in Computer and Information Science 979, 224-238 (2019)
• J.A. Moríñigo et al. On the modelling of optimal coordinated checkpoint period in supercomputers. The Journal of Supercomputing (2019) 75:930–954
• M. Sánchez, F. Ruette. Calculations of adsorption energies, coadsorptions, diffusion barriers, and H2 formation on a nanographene surface (coronene), International Journal of Quantum Chemistry. Iin press, https://doi.org/10.1002/qua.25893 (2019)
• C. Gómez, J. Chavarriaga, H Castro, A. Tchernykh. Improving Reliability for Provisioning of Virtual Machines in Desktop Clouds. 12th Workshop on Resiliency in High Performance Computing (Resilience) in Clusters, Clouds, and Grids, Europar, Göttingen, Germany, August 2019
• H. Asorey et al. Preliminary results from the Latin American Giant Observatory space weather simulation chain. Space Weather, 16(5), 461-475 (2018)
• P. Arce, J.I. Lagares. CPU time optimization and precise adjustment of the Geant4 physics parameters for a VARIAN 2100 C/D gamma radiotherapy linear accelerator simulation using GAMOS. Phys. Med. Biol. 63, 035007 (2018)
• D. Rojas, M.C. Alvarez, C. Ulloa, V. Nuñez, MP Delgado, S. Aguilera, H. Castro, C. Jaramillo, A. González. Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains’ pathogenicity level. Computational Biology and Chemistry, Vol 76, pp. 17-22, October 2018
• C. Gómez, J. Chavarriaga, D. Bonilla, H. Castro. Global Snapshot File Tracker. Communications in Computer and Information Science, vol 942, pp 90-104, ICAI 2018, Bogotá, Colombia, November 2018
• M. Fernández, J. Klapp, L. Sigalotti F. Ruette, Hydration study of MgSO₄ using different theoretical and model approaches.Is there a proton transfer?, Chemical Physics Letters, 713 (2018) 39-45.
• Y.L. Bentarcurt, F. Ruette, M. Calatayud, J. Klapp, Periodic density functional theory study of maghemite (001) surface. Structure and electronic properties, Surface Science, 677 (2018) 239-253
• P. Arce, J.I. Lagares. CPU time optimization and precise adjustment of the Geant4 physics parameters for a VARIAN 2100 C/D gamma radiotherapy linear accelerator simulation using GAMOS. Phys Med Biol. 2018 Jan 25, 63(3)
• V. Martínez et al. Performance improvement of stencil computations for multi-core architectures based on machine learning. Procedia Computer Science108, 305-314
• C. Gómez et al. Fault Characterization and Mitigation Strategies in Desktop Cloud Systems. Proc. CARLA 2018
• V. Martínez et al. Performance evaluation of stencil computations based on source-to-source transformations. Proc. CARLA 2018
• P.J. Pavan et al. Improving performance and energy efficiency of geophysics applications on GPU architectures. Proc. CARLA 2018
• J.A. Moríñigo et al. Benchmarking LAMMPS: Sensitivity to Task Location under CPU-based Weak-scaling. Proc. CARLA 2018
• V. Martínez et al. Performance Prediction of Geophysics Numerical Kernels on Accelerator Architectures. Proc. Energy 2018
• M. Rodríguez-Pascual et al. Energy Determination of Superconducting Vortex Lattices with Stochastic Methods Calculated on GPUs. Proc. Energy 2018
• E. Roloff et al. Exploiting Load Imbalance Patterns for Heterogeneous Cloud Computing Platforms. Proc. CLOSER 2018.
• O. Carvalho et al. A Distributed Stream Processing based Architecture for IoT Smart Grids Monitoring. Proc. CloudAM 2017
• E. Roloff et al. Exploiting Price and Performance Tradeoffs in Heterogeneous Clouds. Proc. CloudAM 2017
• C. Gómez, H. Castro, C. Varela. Global snapshot of a distributed system running on virtual machines. Proc of the 29th International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2017, pp. 169-176, Campinas, Brazil, October 2017
• J. Chavarriaga, J. Padilla, C. Forero, A. Martínez, H. Castro. Scaling the deployment of Virtual Machines in UnaCloud. Mocskos E., Nesmachnow S. (eds) High Performance Computing. CARLA 2017, Buenos Aires, Argentina. Communications in Computer and Information Science, vol 796. Springer, Cham, pp 399-413, September 2017
• O. Carvalho et al. IoT Workload Distribution Impact between Edge and Cloud Computing in a Smart Grid Application. Proc. CARLA 2017
• V. Martínez et al. Performance Prediction of Acoustic Wave Numerical Kernel on Intel Xeon Phi Processor. Proc. CARLA 2017
• E. Meneses. Exploring Application-Level Message-Logging in Scalable HPC Programs. Proc. CARLA 2017
• A. Vesga-Ramírez et al. T Muon Tomography sites for Colombian volcanoes. arXiv preprints  arXiv:1705.09884