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RUN PDB Size forward backward Others Total Total(200) Speedup GPU
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01 py aev fd small.pdb 264 1.8 ms 0.0 ms 0.0 ms 1.8 ms 368.1 ms - 757.1MB
02 cu aev fd small.pdb 264 0.5 ms 0.0 ms 0.0 ms 0.5 ms 106.9 ms 3.44 751.1MB
03 py aev fd 1hz5.pdb 973 2.7 ms 0.0 ms 0.0 ms 2.7 ms 535.9 ms - 809.1MB
04 cu aev fd 1hz5.pdb 973 1.0 ms 0.0 ms 0.0 ms 1.0 ms 209.3 ms 2.56 771.1MB
05 py aev fd 6W8H.pdb 3410 7.0 ms 0.0 ms 0.0 ms 7.0 ms 1.394 sec - 1121.1MB
06 cu aev fd 6W8H.pdb 3410 4.8 ms 0.0 ms 0.0 ms 4.8 ms 958.4 ms 1.45 1065.1MB
07 py aev fd 1C17.pdb 6000 24.5 ms 0.0 ms 0.0 ms 24.6 ms 4.912 sec - 2113.1MB
08 cu aev fd 1C17.pdb 6000 15.5 ms 0.0 ms 0.0 ms 15.5 ms 3.108 sec 1.58 1761.1MB
09 py aev fd 1C17.pdb 10000 56.4 ms 0.0 ms 0.0 ms 56.4 ms 11.277 sec - 3983.1MB
10 cu aev fd 1C17.pdb 10000 39.4 ms 0.0 ms 0.0 ms 39.4 ms 7.879 sec 1.43 3597.1MB
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11 py aev fd+bd small.pdb 264 3.8 ms 3.5 ms 0.0 ms 7.3 ms 1.457 sec - 811.1MB
12 cu aev fd+bd small.pdb 264 0.6 ms 0.8 ms 0.0 ms 1.4 ms 282.6 ms 5.16 811.1MB
13 py aev fd+bd 1hz5.pdb 973 3.9 ms 4.3 ms 0.0 ms 8.2 ms 1.648 sec - 1047.1MB
14 cu aev fd+bd 1hz5.pdb 973 1.1 ms 1.3 ms 0.0 ms 2.4 ms 489.2 ms 3.37 1023.1MB
15 py aev fd+bd 6W8H.pdb 3410 8.0 ms 4.2 ms 0.0 ms 12.2 ms 2.440 sec - 1365.1MB
16 cu aev fd+bd 6W8H.pdb 3410 4.9 ms 1.3 ms 0.0 ms 6.2 ms 1.241 sec 1.97 1631.1MB
17 py aev fd+bd 1C17.pdb 6000 24.8 ms 21.3 ms 0.0 ms 46.1 ms 9.225 sec - 3869.1MB
18 cu aev fd+bd 1C17.pdb 6000 15.7 ms 6.9 ms 0.0 ms 22.6 ms 4.521 sec 2.04 4667.1MB
19 py aev fd+bd 1C17.pdb 10000 - - - - - - -
20 cu aev fd+bd 1C17.pdb 10000 39.9 ms 11.1 ms 0.0 ms 51.0 ms 10.199 sec - 5415.1MB
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new benchmark result:
new way of construct neighbor list for single big molecule
shared memory
atom j counter
remove thrust::fill
Radial neighbor list:
replace deviceSelect with cutoffSelect by maintaining a list of atom j counters that are within cutoff for each atom i
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RUN PDB Size forward backward Others Total Total(200) Speedup GPU
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01 py aev fd small.pdb 264 1.9 ms 0.0 ms 0.0 ms 2.0 ms 394.9 ms - 757.1MB
02 cu aev fd small.pdb 264 0.6 ms 0.0 ms 0.0 ms 0.6 ms 122.9 ms 3.21 749.1MB
03 py aev fd 1hz5.pdb 973 2.8 ms 0.0 ms 0.0 ms 2.8 ms 555.3 ms - 809.1MB
04 cu aev fd 1hz5.pdb 973 0.8 ms 0.0 ms 0.0 ms 0.8 ms 161.7 ms 3.43 763.1MB
05 py aev fd 6W8H.pdb 3410 7.1 ms 0.0 ms 0.0 ms 7.1 ms 1.415 sec - 1121.1MB
06 cu aev fd 6W8H.pdb 3410 1.1 ms 0.0 ms 0.0 ms 1.1 ms 215.4 ms 6.57 975.1MB
07 py aev fd 1C17.pdb 6000 24.8 ms 0.0 ms 0.0 ms 24.8 ms 4.956 sec - 2113.1MB
08 cu aev fd 1C17.pdb 6000 3.6 ms 0.0 ms 0.0 ms 3.6 ms 721.2 ms 6.87 1487.1MB
09 py aev fd 1C17.pdb 10000 56.7 ms 0.0 ms 0.0 ms 56.7 ms 11.346 sec - 3983.1MB
10 cu aev fd 1C17.pdb 10000 6.1 ms 0.0 ms 0.0 ms 6.1 ms 1.216 sec 9.33 2831.1MB
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11 py aev fd+bd small.pdb 264 3.8 ms 3.6 ms 0.0 ms 7.4 ms 1.480 sec - 811.1MB
12 cu aev fd+bd small.pdb 264 0.6 ms 0.9 ms 0.0 ms 1.5 ms 301.5 ms 4.91 807.1MB
13 py aev fd+bd 1hz5.pdb 973 4.1 ms 4.4 ms 0.0 ms 8.5 ms 1.698 sec - 1047.1MB
14 cu aev fd+bd 1hz5.pdb 973 0.9 ms 1.3 ms 0.0 ms 2.2 ms 442.1 ms 3.84 1015.1MB
15 py aev fd+bd 6W8H.pdb 3410 8.2 ms 4.3 ms 0.0 ms 12.6 ms 2.513 sec - 1365.1MB
16 cu aev fd+bd 6W8H.pdb 3410 1.1 ms 1.3 ms 0.0 ms 2.5 ms 500.3 ms 5.02 1251.1MB
17 py aev fd+bd 1C17.pdb 6000 25.0 ms 21.3 ms 0.0 ms 46.4 ms 9.277 sec - 3869.1MB
18 cu aev fd+bd 1C17.pdb 6000 3.7 ms 6.7 ms 0.0 ms 10.4 ms 2.075 sec 4.47 3797.1MB
19 py aev fd+bd 1C17.pdb 10000 - - - - - - -
20 cu aev fd+bd 1C17.pdb 10000 6.2 ms 10.8 ms 0.0 ms 17.0 ms 3.397 sec - 3843.1MB
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original benchmark result:
new benchmark result:
thrust::fill
deviceSelect
withcutoffSelect
by maintaining a list of atom j counters that are within cutoff for each atom i