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Memory corresponds to the maximum memory usage during the program execution in megabytes.
The maximum memory usage during the assembly reached 800 GB during the super-reads step.
A perl script (memmon) was used to frequently sample the contents of/proc/meminfo to monitor the memory usage during each program execution.
As illustrated in Figure 3(a), several bottom spots in the plot are clearly pointed out to represent the aligners with relatively minor memory usage during short-read datasets aligning process, which were Bowtie, BOAT, SOAP2, BWA, and mrsFAST.
Most of existing methods save memory usage during the computation by using sophisticated algorithms and advanced data structures [bloom filter (Melsted and Pritchard, 2011), lock-free memory-efficient hash table (Marcais and Kingsford, 2011), suffix array (Kurtz et al., 2008)] or relying on disk space to compensate memory space (Rizk et al., 2013).
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Table 2 shows the memory usage comparison during coding.
Figures 7 and 8 show, for each algorithm and for each value of n respectively, the average number of enumerated traces and the average memory usage observed during the executions of each set of 100 permutations.
It can achieve the same compression performance as EZBC but the memory usage was greatly reduced during the coding process.
Bit Length Quadtree was presented to replace the Amplitude Quadtree in the improved algorithm, which was used to complete the coding process and construct the context, so the memory usage was greatly reduced during the coding.
The total length of execution was corrected according to the average CPU usage, and the memory usage corresponds to the maximum reached during program execution, as reported by the Unix "top" command.
Categorization of applications according to the kind of resources required during execution – such as CPU and memory usage – is a sough-after piece of knowledge for the aims of computer system design and management.
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