knucleotide: add parallelized zig version (#473)

Author: PanSashko

bench/algorithm/knucleotide/1-m.zig

@@ -0,0 +1,194 @@
+const std = @import("std");
+
+const gpa = std.heap.c_allocator;
+const stdout = std.io.getStdOut().writer();
+
+const Code = struct {
+    data: u64,
+
+    pub inline fn encodeByte(c: u8) u2 {
+        return @intCast((c >> 1) & 0b11);
+    }
+
+    pub inline fn makeMask(frame: usize) u64 {
+        return (@as(u64, 1) << @as(u6, @intCast(2 * frame))) - 1;
+    }
+
+    pub inline fn push(self: *Code, c: u8, mask: u64) void {
+        self.data = ((self.data << 2) | c) & mask;
+    }
+
+    pub fn fromStr(s: []const u8) Code {
+        const mask = Code.makeMask(s.len);
+        var res = Code{ .data = 0 };
+        for (s) |c| {
+            res.push(Code.encodeByte(c), mask);
+        }
+        return res;
+    }
+
+    pub fn toString(self: Code, frame: usize) ![]const u8 {
+        var result = std.ArrayList(u8).init(gpa);
+        var code = self.data;
+        for (0..frame) |_| {
+            const c: u8 = switch (@as(u2, @truncate(code))) {
+                Code.encodeByte('A') => 'A',
+                Code.encodeByte('T') => 'T',
+                Code.encodeByte('G') => 'G',
+                Code.encodeByte('C') => 'C',
+            };
+            try result.append(c);
+            code >>= 2;
+        }
+        std.mem.reverse(u8, result.items);
+        return result.toOwnedSlice();
+    }
+};
+
+pub fn readInput() ![]const u8 {
+    const args = try std.process.argsAlloc(gpa);
+    defer std.process.argsFree(gpa, args);
+    const file_name = if (args.len > 1) args[1] else "25000_in";
+    const file = try std.fs.cwd().openFile(file_name, .{});
+    var buffered_reader = std.io.bufferedReader(file.reader());
+    const reader = buffered_reader.reader();
+    { // skip past first lines starting with '>'
+        var i: u8 = 0;
+        while (i < 3) : (i += 1) {
+            while (true) {
+                const c = try reader.readByte();
+                if (c == '>') break;
+            }
+        }
+        while (true) {
+            const c = try reader.readByte();
+            if (c == '\n') break;
+        }
+    }
+
+    var buf = try reader.readAllAlloc(gpa, std.math.maxInt(u32));
+    // In place, remove all newlines from buf and encode nucleotides
+    // using only the last 2 bits in each byte.
+    {
+        var i: usize = 0;
+        for (buf) |c| {
+            if (c != '\n') {
+                // Gives a -> 0x00, c -> 0x01, g -> 0x03, t -> 0x02
+                buf[i] = (c >> 1) & 0x03;
+                i += 1;
+            }
+        }
+        buf.len = i;
+    }
+    return buf;
+}
+
+const CodeContext = struct {
+    pub fn eql(_: CodeContext, a: Code, b: Code) bool { return a.data == b.data; }
+    pub fn hash(_: CodeContext, c: Code) u64 { return c.data ^ (c.data >> 7); }
+};
+
+const Map = std.HashMapUnmanaged(Code, u32, CodeContext, 45);
+
+fn genMap(taskIndex: usize, from: usize, to: usize, seq: []const u8, frame: usize, maps: []Map) !void {
+    const map = &maps[taskIndex];
+    const mask = Code.makeMask(frame);
+    var code: Code = .{ .data = 0 };
+    for (seq[from..][0..frame - 1]) |e| code.push(e, mask);
+    for (seq[frame - 1..][from .. to]) |e| {
+        code.push(e, mask);
+        const kv = try map.getOrPutValue(gpa, code, 0);
+        kv.value_ptr.* += 1;
+    }
+}
+
+const CountCode = struct {
+    count: u32,
+    code: Code,
+
+    pub fn dsc(_: void, a: CountCode, b: CountCode) bool {
+        const order = std.math.order(a.count, b.count);
+        return order == .gt or (order == .eq and b.code.data > a.code.data);
+    }
+};
+
+fn printMap(frame: usize, maps: []const Map) !void {
+    const code_limit = 16;
+    var counts: [code_limit]u32 = @splat(0);
+    var total: u64 = 0;
+    for (maps) |map| {
+        var iter = map.iterator();
+        while (iter.next()) |it| {
+            const code = it.key_ptr.*;
+            const count = it.value_ptr.*;
+            total += count;
+            counts[code.data] += count;
+        }
+    }
+
+    var cc: std.BoundedArray(CountCode, code_limit) = .{};
+    for (counts, 0..) |count, code_data| if (count > 0) {
+        cc.appendAssumeCapacity(.{ .count = count, .code = .{ .data = @intCast(code_data) } });
+    };
+    std.mem.sort(CountCode, cc.slice(), {}, CountCode.dsc);
+
+    for (cc.slice()) |c| {
+        try stdout.print("{!s} {d:.3}\n", .{
+            c.code.toString(frame),
+            @as(f32, @floatFromInt(c.count)) / @as(f32, @floatFromInt(total)) * 100.0,
+        });
+    }
+    try stdout.print("\n", .{});
+}
+
+fn printOcc(occ: []const u8, maps: []const Map) !void {
+    const code = Code.fromStr(occ);
+    var total: u32 = 0;
+    for (maps) |m| {
+        if (m.get(code)) |count| total += count;
+    }
+    try stdout.print("{}\t{s}\n", .{ total, occ });
+}
+
+fn runInParallel(task_count: usize, len: usize, comptime f: anytype, args: anytype) !void {
+    const tasks = try gpa.alloc(std.Thread, task_count - 1);
+    defer gpa.free(tasks);
+    const len_per_task = @divTrunc(len, task_count);
+    for (tasks, 0..) |*task, i| {
+        const first = len_per_task * i;
+        const last = first + len_per_task;
+        task.* = try std.Thread.spawn(.{}, f, .{ i, first, last } ++ args);
+    }
+    try @call(.auto, f, .{ tasks.len, tasks.len * len_per_task, len } ++ args);
+    for (tasks) |*task| task.join();
+}
+
+fn genMaps(seq: []const u8, frame: usize, maps: []Map) !void {
+    for (maps) |*m| m.clearAndFree(gpa);
+    try runInParallel(maps.len, seq.len - (frame - 1), genMap, .{seq, frame, maps});
+}
+
+pub fn main() !void {
+    const seq = try readInput();
+    const task_count = try std.Thread.getCpuCount();
+    const maps = try gpa.alloc(Map, task_count);
+    defer gpa.free(maps);
+    @memset(maps, .empty);
+
+    try genMaps(seq, 1, maps);
+    try printMap(1, maps);
+    try genMaps(seq, 2, maps);
+    try printMap(2, maps);
+
+    const occs = [_][]const u8{
+        "GGT",
+        "GGTA",
+        "GGTATT",
+        "GGTATTTTAATT",
+        "GGTATTTTAATTTATAGT",
+    };
+    for (occs) |occ| {
+        try genMaps(seq, occ.len, maps);
+        try printOcc(occ, maps);
+    }
+}

bench/bench_zig.yaml

@@ -53,6 +53,7 @@ problems:
   - name: knucleotide
     source:
       - 1.zig
+      - 1-m.zig
 compiler_version_command: zig version
 compiler_version_regex:
 runtime_version_parameter: