... | ... | @@ -18,6 +18,6 @@ For the tests, I used the files in the data-virome directory. |
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My aim was to bench execution time and to see how openCL or another python package could improve things compared to regexp. So, I didnt' bother with Pair-end. I searched for the first 20 characters (default value for seed in phageterm) of each SRR4295172_1_div6.fastq in all the sequences in Contigs_30min.fasta.
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Tests ran on myriad-n403 or on my machine (openCL part).
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| original regexp | tryalgo | openCL on imac|OpenCL on myriad K40|
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| --------------- |:---------:| -------------:|-------------------:|
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| 17min10s | >16 hours | 64s | 4min8s | |
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| original regexp | tryalgo | openCL on imac|OpenCL on myriad K40|OpenCL, tars, K80|OpenCL tars M40|OpenCL tars P100|
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| --------------- |:---------:|:---------:| -------------:|-------------------:|----------------:|----------------:|
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| 17min10s | >16 hours | 64s | 4min8s (cuda 7.5) |4min (cuda 8) |56 s| 32,5s | |