On Sat, 27 Nov 2010 22:08:29 -0500, bearophile <[email protected]>
wrote:
I have done another test:
Timings, dmd compiler, best of 4, seconds:
D #1: 5.72
D #4: 1.84
D #5: 1.73
Psy: 1.59
D #2: 0.55
D #6: 0.47
D #3: 0.34
import std.file: read;
import std.c.stdio: printf;
int test(char[] data) {
int count;
foreach (i; 0 .. data.length - 3) {
char[] codon = data[i .. i + 3];
if ((codon.length == 3 && codon[0] == 'T' && codon[1] == 'A' &&
codon[2] == 'G') ||
(codon.length == 3 && codon[0] == 'T' && codon[1] == 'G' &&
codon[2] == 'A') ||
(codon.length == 3 && codon[0] == 'T' && codon[1] == 'A' &&
codon[2] == 'A'))
count++;
}
return count;
}
void main() {
char[] data0 = cast(char[])read("data.txt");
int n = 300;
char[] data = new char[data0.length * n];
for (size_t pos; pos < data.length; pos += data0.length)
data[pos .. pos+data0.length] = data0;
printf("%d\n", test(data));
}
So when there is to compare among strings known at compile-time to be
small (like < 6 char), the comparison shall be replaced with inlined
single char comparisons. This makes the code longer so it increases code
cache pressure, but seeing how much slow the alternative is, I think
it's an improvement.
(A smart compiler is even able to remove the codon.length==3 test
because the slice data[i..i+3] is always of length 3 (here mysteriously
if you remove those three length tests the program compiled with dmd
gets slower)).
Bye,
bearophile
Hi bearophile,
I've spent some time having fun this afternoon optimizing array-equals
using vectorization techniques. I found that vectorizing using ulongs
worked best on my system except with the shortest strings, where a simple
Duff's device edged it out. If you'd like to try it out on your data set:
bool arrayComp3(bool useBitCompare = true,T)(const T[] a, const T[] b)
pure nothrow {
if(a.length != b.length) return false;
static if(useBitCompare) {
auto pab = cast(ubyte*)a.ptr;
auto pbb = cast(ubyte*)b.ptr;
if(pab is pbb) return true;
auto byte_length = a.length*T.sizeof;
auto pa_end = cast(ulong*)(pab+byte_length);
final switch (byte_length % ulong.sizeof) {
case 7: if(*pab++ != *pbb++ ) return false;
case 6: if(*pab++ != *pbb++ ) return false;
case 5: if(*pab++ != *pbb++ ) return false;
case 4: if(*pab++ != *pbb++ ) return false;
case 3: if(*pab++ != *pbb++ ) return false;
case 2: if(*pab++ != *pbb++ ) return false;
case 1: if(*pab++ != *pbb++ ) return false;
case 0:
}
auto pa = cast(ulong*)pab;
auto pb = cast(ulong*)pbb;
while (pa < pa_end) {
if(*pa++ != *pb++ ) return false;
}
} else { // default to a
short duff's device
auto pa = a.ptr;
auto pb = b.ptr;
if(pa is pb) return true;
auto n = (a.length + 3) / 4;
final switch (a.length % 4) {
case 0: do { if(*pa++ != *pb++ ) return false;
case 3: if(*pa++ != *pb++ ) return false;
case 2: if(*pa++ != *pb++ ) return false;
case 1: if(*pa++ != *pb++ ) return false;
} while (--n > 0);
} }
return true;
}
