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Refactor main C++ function to avoid use "constant" memory and avoid new/delete #55

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merged 19 commits into from
Feb 9, 2018
Merged

Refactor main C++ function to avoid use "constant" memory and avoid new/delete #55

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f5444a3
Refactor main C++ function to avoid use "constant" memory and avoid n…
Jan 15, 2018
5d5338f
Refactor Dice coefficient calculation.
Feb 1, 2018
88e3625
Temporary fiddling with benchmark code.
Feb 1, 2018
a705de8
Calculate and report popcount speed from native code implementation.
Feb 1, 2018
cff1cb6
Give some values more sensible variable names.
Feb 2, 2018
603b6d4
Remove unused import.
Feb 2, 2018
de33a67
Add documentation.
Feb 2, 2018
a458ed0
Expand reporting of various measurements.
Feb 2, 2018
7d2e66c
Comments.
Feb 5, 2018
9666eae
Update README.
Feb 5, 2018
6fe3663
Bring test suite up-to-date.
Feb 5, 2018
66d9b6e
Refactor main C++ function to avoid use "constant" memory and avoid n…
Jan 15, 2018
05246f2
Merge branch 'hlaw-refactor-cpp' of github.com:n1analytics/anonlink i…
Feb 5, 2018
166f6e9
Address Brian's comments.
Feb 7, 2018
9cbc243
Update tests; also test native code version.
Feb 7, 2018
cf26901
Print popcount throughput; give some variables better names.
Feb 8, 2018
c986021
Merge branch 'hlaw-fix-issue-56' into hlaw-refactor-cpp
Feb 8, 2018
ff3bf51
Merge remote-tracking branch 'origin/develop' into hlaw-refactor-cpp
Feb 9, 2018
c8c11c0
Merge branch 'develop' into hlaw-refactor-cpp
Feb 9, 2018
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31 changes: 10 additions & 21 deletions _cffi_build/dice_one_against_many.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -177,9 +177,6 @@ extern "C"
std::priority_queue<Node, std::vector<Node>, score_cmp> max_k_scores;

uint32_t count_one = builtin_popcnt_unrolled_errata_manual(comp1);

double *all_scores = new double[n];

uint32_t max_popcnt_delta = 1024;
if(threshold > 0) {
max_popcnt_delta = calculate_max_difference(count_one, threshold);
Expand All @@ -188,32 +185,24 @@ extern "C"

for (int j = 0; j < n; j++) {
const uint64_t *current = comp2 + j * KEYWORDS;
const uint32_t counts_many_j = counts_many[j];
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It always suprises me what you have to help the compiler with

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Yeah, this can be more or less important depending on the context. Here it's more about showing intent to fellow programmers than to the compiler.


if(count_one > counts_many[j]){
current_delta = count_one - counts_many[j];
if (count_one > counts_many_j) {
current_delta = count_one - counts_many_j;
} else {
current_delta = counts_many[j] - count_one;
current_delta = counts_many_j - count_one;
}

if(current_delta <= max_popcnt_delta){
all_scores[j] = dice_coeff(comp1, count_one, current, counts_many[j]);
} else {
// Skipping because popcount difference too large
all_scores[j] = -1;
}
}

for (int j = 0; j < n; j++) {

if(all_scores[j] >= threshold) {
max_k_scores.push(Node(j, all_scores[j]));
double score = dice_coeff(comp1, count_one, current, counts_many_j);
if (score >= threshold) {
max_k_scores.push(Node(j, score));
if (max_k_scores.size() > k)
max_k_scores.pop();
}
}

if(max_k_scores.size() > k) max_k_scores.pop();
}

delete[] all_scores;

int i = 0;
while (!max_k_scores.empty()) {

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