Submission information
Submission Number: 101
Submission ID: 152
Submission UUID: e51a24de-a6ae-4723-9657-350b021b3643
Submission URI: /form/project
Created: Tue, 05/18/2021 - 18:32
Completed: Tue, 05/18/2021 - 18:32
Changed: Mon, 10/25/2021 - 10:25
Remote IP address: 69.5.117.142
Submitted by: David Matthews
Language: English
Is draft: No
Webform: Project
| Project Title | AMD GPU-accelerated design tools for creating novel lifeforms |
|---|---|
| Program | Northeast |
| Project Leader | Josh Bongard |
| jbongard@uvm.edu | |
| Mobile Phone | |
| Work Phone | |
| Mentor(s) | Keri Toksu |
| Student-facilitator(s) | David Matthews |
| Mentee(s) | |
| Project Description | While automatically designing machines in silico and manufacturing them as robots using 3D printers is now well established, automatically designing and instantiating living systems was only recently demonstrated to be possible (Kriegman et al., PNAS 117: 4, 2020). Novel lifeforms were assembled according to a computer-generated blueprint which tells a microsurgeon or 3D bioprinter, at some resolution of detail, precisely where all the tissues should go in relation to each other to achieve some desired behavior. The software used to design this artificial life simulates living tissues and cells as collections of elastic voxels, the dynamics of which can be calculated concurrently on GPUs. This allows for orders of magnitude greater resolution of biological detail than the original CPU-based simulation used by Kriegman et al. However, the GPU based simulation is currently limited to Nvidia’s CUDA platform and therefore confined to Nvidia GPUs. Thus, this project aims to expand the number and kind of computers in which artificial life can be designed. |
| Project Deliverables | Existing tools will be incorporated into the software so that any new code will be cross-compatible with NVIDIA and AMD. Specifically, the AMD ROCm Platform and the hipify tool will be used. If unsuccessful, new code in the HIP language will be developed so that the software can run on both AMD and Nvidia clusters with minimal effort. Basic performance benchmarks will be implemented to test memory speed, memory latency, etc. on the AMD / HIP system and the original CUDA system. |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Can work with any level |
| Mentee Programming Skill Level | |
| Project Institution | University of Vermont |
| Project Address | Vermont |
| Anchor Institution | NE-University of Vermont |
| Preferred Start Date | 06/01/2021 |
| Start as soon as possible. | Yes |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | 2 |
| Launch Presentation | |
| Launch Presentation Date | 08/25/2021 |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
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| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | The results of this work may be included as a part of a future paper on phototaxis in Xenobots. |
| What will the student learn? | How to develop GPU accelerated software that is platform agnostic and capable of utilizing both AMD and NVIDIA GPUs. |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | How to create cross-platform software. |
| HPC resources needed to complete this project? | A cluster that runs using CUDA and another cluster that runs using ROCm. |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |