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Execution times and main memory requirements are notably higher in BLUR3 than in the other degradation cases in our method.
An efficient design of an algorithm is an optimal balance between its speed and its main memory requirements.
Also note that if we set M = 1, the HTMQ reduces to its naïve version and its main memory requirements are then O(L T ).
Our approach based on local implementations of network-based algorithms and on novel secondary memory-based technologies provides a solution to the large main memory requirements induced by large multi-species protein networks, thus making possible the analysis of big networks using off-the-shelf machines.
A possible solution to this problem might consist in the construction of big networks including multiple species, but this in turn poses challenging computational problems, due to the scalability limitations of existing algorithms and the main memory requirements induced by the construction of big networks.
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The largest published ML-based phylogenomic study in terms of CPU hours and memory requirements already required 2.25 million CPU hours and 15 GB of main memory on an IBM BlueGene/L supercomputer (Hejnol et al., 2009).
This significant reduction in computational cost and memory requirements represents the main advantage of ITKrMM over wKSVD.
The total memory requirements are then dominated by the memory required for the unknowns.
The main advantage offered by this technique is a reduction in memory requirements.
However, we cannot increase the number of MPI processes exceed the memory capacity of computer, because each MPI process occupies the main memory during its computation process, resulting in an increase in the overall memory requirement.
Memory requirements and runtime are given separately for the two main programs within the GemSIM workflow, GemErr and GemReads.
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