Alya Sample Clauses

Alya. Alya, developed by the team of Xxxxxxx Xxxxxxx and Xxxxxxxxx Xxxxxxxx at the Barcelona Supercomputing Centre, performs multi-scale, multi-physics biomechanical simulations. The specialties of Alya regarding biomedical sciences include cardiac electro-mechanic-flow simulations, from ion-channel kinetics up to organ level; and simulations of the respiratory system, particularly focusing on particle deposition. The simulations involve the solution of mathematical models at different scales using a FEM-based approach. Alya has been specifically optimised for the efficient use of supercomputing resources and does not employ external libraries. Within CompBioMed, our work is to collaborate with other partners (notably Oxford, UCL and SURF) setting up cardiovascular simulation scenarios on large-scale systems and supercomputers. BSC’s role is not only to research improving the accuracy and reach of our simulation platform, but also to make it more efficient in heterogeneous supercomputers, always with the exascale era in mind. Additionally, due to its versality, Alya is a paradigm of the three patterns: monlothic single physics applications, coupled multiphyscis (either Xxxx-Xxxx or Alya with other codes) and ensemble runs for, for instance, massive in-silico clinical trials. We consider that the only way of achieving these two objectives is by knowing deeply the architectures, porting the algorithms to them to get the best performance possible and optimizing all possible levels: core, chip, node and supercomputer (see D2.3). Thanks to this knowledge, we have a very beneficial collateral effect: the expertise obtained allows CompBioMed to establish co-design discussions with computer architecture stakeholders.
Sample 1
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Alya. Alya, developed by the team of Xxxxxxx Xxxxxxx and Xxxxxxxxx Xxxxxxxx at the Barcelona Supercomputing Centre, performs multi-scale, multi-physics biomechanical simulations. The specialties of Alya regarding biomedical sciences include cardiac electro-mechanic-flow simulations, from ion-channel kinetics up to organ level; and simulations of the respiratory system, particularly focusing on particle deposition. The simulations involve the solution of mathematical models at different scales using a FEM-based approach. Alya has been specifically optimised for the efficient use of supercomputing resources and does not employ external libraries. Alya is available for use by research scientists on MareNostrum, XXXXXX, and Xxxxxxxxx; for clinical and industrial users, BSC recommends users access it as a service, due to the complexity involved with setting up simulations. To this purpose BSC has launched a spin- off (ELEM Biotech [5]) that will provide commercial software-as-a-service to medical device, pharmaceutical and biomedical industries using Alya.
Sample 1
Alya. The purpose of Alya is to perform Cardiac Computational Mechanics simulations, from tissue to organ level. FEM-based fluid-electro-mechanical coupling solver, specifically designed for the efficient use of supercomputing resources. End-user solution type Please tick one or more Non-clinical research ✔ Clinical research ✔ Clinical decision support ✔ Drug discovery Design & optimisation ✔ In silico preclinical trials In silico clinical trials ✔ Personal health forecasting Provider: BSC Contact email: xxxxxxx.xxxxxxx@xxx.xx Number of user organisations (list the top 5): University of Oxford, Universitat Xxxxxx Xxxxx, Universitat xx Xxxxxxxx, Xxxxxx Xxxxx University, ELEM Biotech, Medtronic Estimated users at M0: 30 internal and 20 external Estimated users at M24: 35 internal and 30 external Estimated users at M36: 40 internal and 40 external (IMPORTANT NOTE: as Alya is used in different domains, the number of users is the grand total) Access mode: Direct URL: xxxxx://xxx.xxx.xx/research-and-development/software-and-apps/software-list/alya User manual: xxxxxxx.xxxxxxx@xxx.xx HPC Systems: MareNostrum (BSC), XXXXXX (EPCC), Cartesius (SURFsara), Blue Waters (NCSA), SuperMUC (LRZ) HPC motivation: Solve unreducible model; Multiscale model; Strongly coupled multiphysics model. Additional user information: End user name Xxxxxx Xxxxxxxxx’x group Xxxxx Xxxxxx’x group JR Cebral’s group ELEM Biotech Dr. Xxxxxxx Xxxxxxxx's group Affiliation UOXF Universitat Xxxxxx Xxxxx Xxxxxx Xxxxx University - University of Strathclyde Application area Cardiac modelling Cardiac modelling Vascular simulations (aneurisms) Cardiovascular modelling, respiratory system, cerebro-spinal fluid Cardiovascular modelling of the right side of the heart No. of associated users 6 5 2 3 1 Target use Research Research / educational Research Commercial, research Research Improvements implemented New models, efficiency, etc. N/A Efficiency Efficiency, models, deployment, etc. N/A Impact Papers Papers Papers Product design, media release, papers N/A yet Use of any e- infrastructure available via CompBioMed BSC and EPCC BSC BSC BSC BSC
Sample 1
Alya. Application description Alya aims to simulate complex multi-physics / multi-scale coupled problems at tissue, organ, and system level. The idea is that of a "Virtual Patient", in which we can model the patient in health, in disease and under treatment. In the context of CompBioMed2, we are focused on the cardiovascular system. So far, the code is being used by colleagues from academia. In its raw version and without any kind of graphical user interface, the code is not friendly and due to the complexity of the problems we are dealing with, only an expert user can setup, run, and analyse the simulations. In 2018 we created the spinoff ELEM Biotech (an Associate Partner of CompBioMed) to speed up the technology transfer to biomedical stakeholders and one of its missions is making the code more usable by non-expert users, including a cloud deployment and an ad-hoc biomedical user interface. Thanks to ELEM action, we are extending the access to Alya to users with biomedical knowledge, such as engineers from device manufacturing or pharmaceutical companies. The code has different types of licences, depending on the case: • Non-commercial available source • Non-commercial cloud SaaS • Open source for a limited version (only fluid mechanics) Technical specifications The code is written in modern Fortran language, with some user tools in Python and Perl. The memory is dynamically allocated and strongly depends on the problem solved. The code has no external third-party high-level library dependency, the only dependencies are of low-level type, such as MPI. The code has been compiled in several platforms such as ARM, Intel, NVIDIA or IBM Power processors. The parallelization strategy is a hybrid one, MPI+OpenMP. Part of the code has been ported to GPUs to offload solvers or matrix assembly. The code has examples of use as monolithic, coupled and in ensembles and for replica computing. Being portable and efficient in both large and small architectures, it has records on different running scenarios. The code relies mostly on internal developed tools. There is no need for containers or workflow managers. Several pre-processing tools have been used in combination with Alya: Ansa, IcemCFD, GMesh or GiD. As post-processing tools, typical used applications include ParaView, VisIt, Ensight or GiD. HPC usage and parallel performance The code is used in complex very large, coupled problems and it is designed and continuously improved to run efficiently in parallel for couple...
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Alya 
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  • Mitsui Iron Ore Corporation Pty Ltd. to vary the Iron Ore (Marillana Creek) Agreement;

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