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• W1528203611 abstract "As high performance computing centers (HPCC) continue to grow in popularity, issues of resource management and reliability are becoming limiting factors in scheduling long-running jobs. One of the factors is time. Efficacy of Avida, the platform of research for digital evolution, is limited by the allocated time available on HPCC. Saving the state of the software at a point and restarting the execution from the paused state will allow for better resource utilization, as well as help reduce restrictions that constrain the potential of the software. This research examines whether or not Berkeley Lab Checkpoint/Restart (BLCR) can be integrated with the run script that is used for Avida. Adding checkpoint/restart functionality to Avida will have multiple impacts on, effectiveness of the software and future research. Introduction Increasingly, scientists use computer experiments and simulations to study real-world models and systems. Computer simulation software has significantly altered the way research is being conducted. Often, in science, technology, engineering, and mathematics fields, scientists use computer modeling when the real-world system is not feasible to study. For example, when studying evolution, scientists need to overcome the obstacle that evolution happens extremely slow [3]. Considering this fact, related experiments are conducted only with organisms that can undergo many generations in a short amount of time [4]. At the Bio-Computational Evolution in Action Consortium (BEACON) Center, researchers utilize Avida software, an artificial life platform, to study evolutionary biology. The digital Avida organisms, Avidians, are capable of evolving and replicating very quickly. In a computer, it is easy to measure any number of generations one might be interested in studying with arbitrary precision. However, the number of generations and the time it takes to propagate organisms for several thousand generations is limited by the processing power available [4]. At Michigan State University the High Performance Computer Center (HPCC) only provides, at most, one week of continuous computational power for a job running on the cluster. In other words, if an experiment requires a time frame of more than one week or 168 hours of wall-time, HPCC will not be able to provide the resources necessary. When one week of computational time is not sufficient it, it seems obvious that researchers would want to save the state of the software and restart from the same point for another period of time, repeating the process as necessary. However, Avida software cannot save its state. In other words, the application does not have comprehensive checkpoint/restart feature implemented. The goal of this research project is to improve computational tools that scientists and researchers use to study evolutionary biology models by adding checkpoint/restart functionality to Avida software." @default.
• W1528203611 created "2016-06-24" @default.
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• W1528203611 date "2014-01-01" @default.
• W1528203611 modified "2023-09-26" @default.
• W1528203611 title "Avida Checkpoint/Restart Implementation" @default.
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