To follow up on my comments that your benchmark results were peculiar,
here's my benchmark code.

It just computes the hash of all n*(n+1)/2 possible non-empty substrings
of a buffer of n (called "max" below) bytes.  "cpb" is "cycles per byte".

(The average length is (n+2)/3, c.f. https://oeis.org/A000292)

On x86-32, HSipHash is asymptotically twice the speed of SipHash,
rising to 2.5x for short strings:

SipHash/HSipHash benchmark, sizeof(long) = 4
 SipHash: max=   4 cycles=     10495 cpb=524.7500 (sum=47a4f5554869fa97)
HSipHash: max=   4 cycles=      3400 cpb=170.0000 (sum=146a863e)
 SipHash: max=   8 cycles=     24468 cpb=203.9000 (sum=21c41a86355affcc)
HSipHash: max=   8 cycles=      9237 cpb= 76.9750 (sum=d3b5e0cd)
 SipHash: max=  16 cycles=     94622 cpb=115.9583 (sum=26d816b72721e48f)
HSipHash: max=  16 cycles=     34499 cpb= 42.2782 (sum=16bb7475)
 SipHash: max=  32 cycles=    418767 cpb= 69.9811 (sum=dd5a97694b8a832d)
HSipHash: max=  32 cycles=    156695 cpb= 26.1857 (sum=eed00fcb)
 SipHash: max=  64 cycles=   2119152 cpb= 46.3101 (sum=a2a725aecc09ed00)
HSipHash: max=  64 cycles=   1008678 cpb= 22.0428 (sum=99b9f4f)
 SipHash: max= 128 cycles=  12728659 cpb= 35.5788 (sum=420878cd20272817)
HSipHash: max= 128 cycles=   5452931 cpb= 15.2419 (sum=f1f4ad18)
 SipHash: max= 256 cycles=  38931946 cpb= 13.7615 (sum=e05dfb28b90dfd98)
HSipHash: max= 256 cycles=  13807312 cpb=  4.8805 (sum=ceeafcc1)
 SipHash: max= 512 cycles= 205537380 cpb=  9.1346 (sum=7d129d4de145fbea)
HSipHash: max= 512 cycles= 103420960 cpb=  4.5963 (sum=7f15a313)
 SipHash: max=1024 cycles=1540259472 cpb=  8.5817 (sum=cca7cbdc778ca8af)
HSipHash: max=1024 cycles= 796090824 cpb=  4.4355 (sum=d8f3374f)

On x86-64, SipHash is consistently faster, asymptotically approaching 2x
for long strings:

SipHash/HSipHash benchmark, sizeof(long) = 8
 SipHash: max=   4 cycles=      2642 cpb=132.1000 (sum=47a4f5554869fa97)
HSipHash: max=   4 cycles=      2498 cpb=124.9000 (sum=146a863e)
 SipHash: max=   8 cycles=      5270 cpb= 43.9167 (sum=21c41a86355affcc)
HSipHash: max=   8 cycles=      7140 cpb= 59.5000 (sum=d3b5e0cd)
 SipHash: max=  16 cycles=     19950 cpb= 24.4485 (sum=26d816b72721e48f)
HSipHash: max=  16 cycles=     23546 cpb= 28.8554 (sum=16bb7475)
 SipHash: max=  32 cycles=     80188 cpb= 13.4004 (sum=dd5a97694b8a832d)
HSipHash: max=  32 cycles=    101218 cpb= 16.9148 (sum=eed00fcb)
 SipHash: max=  64 cycles=    373286 cpb=  8.1575 (sum=a2a725aecc09ed00)
HSipHash: max=  64 cycles=    535568 cpb= 11.7038 (sum=99b9f4f)
 SipHash: max= 128 cycles=   2075224 cpb=  5.8006 (sum=420878cd20272817)
HSipHash: max= 128 cycles=   3336820 cpb=  9.3270 (sum=f1f4ad18)
 SipHash: max= 256 cycles=  14276278 cpb=  5.0463 (sum=e05dfb28b90dfd98)
HSipHash: max= 256 cycles=  28847880 cpb= 10.1970 (sum=ceeafcc1)
 SipHash: max= 512 cycles=  50135180 cpb=  2.2281 (sum=7d129d4de145fbea)
HSipHash: max= 512 cycles=  86145916 cpb=  3.8286 (sum=7f15a313)
 SipHash: max=1024 cycles= 334111900 cpb=  1.8615 (sum=cca7cbdc778ca8af)
HSipHash: max=1024 cycles= 640432452 cpb=  3.5682 (sum=d8f3374f)


Here's the code; compile with -DSELFTEST.  (The main purpose of
printing the sum is to prevent dead code elimination.)


#if SELFTEST
#include <stdint.h>
#include <stdlib.h>

static inline uint64_t rol64(uint64_t word, unsigned int shift)
{
        return word << shift | word >> (64 - shift);
}

static inline uint32_t rol32(uint32_t word, unsigned int shift)
{
        return word << shift | word >> (32 - shift);
}

static inline uint64_t get_unaligned_le64(void const *p)
{
        return *(uint64_t const *)p;
}

static inline uint32_t get_unaligned_le32(void const *p)
{
        return *(uint32_t const *)p;
}

static inline uint64_t le64_to_cpup(uint64_t const *p)
{
        return *p;
}

static inline uint32_t le32_to_cpup(uint32_t const *p)
{
        return *p;
}


#else
#include <linux/bitops.h>       /* For rol64 */
#include <linux/cryptohash.h>
#include <asm/byteorder.h>
#include <asm/unaligned.h>
#endif

/* The basic ARX mixing function, taken from Skein */
#define SIP_MIX(a, b, s) ((a) += (b), (b) = rol64(b, s), (b) ^= (a))

/*
 * The complete SipRound.  Note that, when unrolled twice like below,
 * the 32-bit rotates drop out on 32-bit machines.
 */
#define SIP_ROUND(a, b, c, d) \
        (SIP_MIX(a, b, 13), SIP_MIX(c, d, 16), (a) = rol64(a, 32), \
         SIP_MIX(c, b, 17), SIP_MIX(a, d, 21), (c) = rol64(c, 32))

/*
 * This is rolled up more than most implementations, resulting in about
 * 55% the code size.  Speed is a few precent slower.  A crude benchmark
 * (for (i=1; i <= max; i++) for (j = 0; j < 4096-i; j++) hash(buf+j, i);)
 * produces the following timings (in usec):
 *
 *              i386    i386    i386    x86_64  x86_64  x86_64  x86_64
 * Length       small   unroll  halfmd4 small   unroll  halfmd4 teahash
 * 1..4            1069    1029    1608     195     160     399     690
 * 1..8            2483    2381    3851     410     360     988    1659
 * 1..12           4303    4152    6207     690     618    1642    2690
 * 1..16           6122    5931    8668     968     876    2363    3786
 * 1..20           8348    8137   11245    1323    1185    3162    5567
 * 1..24          10580   10327   13935    1657    1504    4066    7635
 * 1..28          13211   12956   16803    2069    1871    5028    9759
 * 1..32          15843   15572   19725    2470    2260    6084   11932
 * 1..36          18864   18609   24259    2934    2678    7566   14794
 * 1..1024      5890194 6130242 10264816 881933  881244 3617392 7589036
 *
 * The performance penalty is quite minor, decreasing for long strings,
 * and it's significantly faster than half_md4, so I'm going for the
 * I-cache win.
 */
uint64_t
siphash24(char const *in, size_t len, uint32_t const seed[4])
{
        uint64_t a = 0x736f6d6570736575;        /* somepseu */
        uint64_t b = 0x646f72616e646f6d;        /* dorandom */
        uint64_t c = 0x6c7967656e657261;        /* lygenera */
        uint64_t d = 0x7465646279746573;        /* tedbytes */
        uint64_t m = 0;
        uint8_t padbyte = len;

        m = seed[2] | (uint64_t)seed[3] << 32;
        b ^= m;
        d ^= m;
        m = seed[0] | (uint64_t)seed[1] << 32;
        /* a ^= m; is done in loop below */
        c ^= m;

        /*
         * By using the same SipRound code for all iterations, we
         * save space, at the expense of some branch prediction.  But
         * branch prediction is hard because of variable length anyway.
         */
        len = len/8 + 3;        /* Now number of rounds to perform */
        do {
                a ^= m;

                switch (--len) {
                        unsigned bytes;

                default:        /* Full words */
                        d ^= m = get_unaligned_le64(in);
                        in += 8;
                        break;
                case 2:         /* Final partial word */
                        /*
                         * We'd like to do one 64-bit fetch rather than
                         * mess around with bytes, but reading past the end
                         * might hit a protection boundary.  Fortunately,
                         * we know that protection boundaries are aligned,
                         * so we can consider only three cases:
                         * - The remainder occupies zero words
                         * - The remainder fits into one word
                         * - The remainder straddles two words
                         */
                        bytes = padbyte & 7;

                        if (bytes == 0) {
                                m = 0;
                        } else {
                                unsigned offset = (unsigned)(uintptr_t)in & 7;

                                if (offset + bytes <= 8) {
                                        m = le64_to_cpup((uint64_t const *)
                                                                (in - offset));
                                        m >>= 8*offset;
                                } else {
                                        m = get_unaligned_le64(in);
                                }
                                m &= ((uint64_t)1 << 8*bytes) - 1;
                        }
                        /* Could use | or +, but ^ allows associativity */
                        d ^= m ^= (uint64_t)padbyte << 56;
                        break;
                case 1:         /* Beginning of finalization */
                        m = 0;
                        c ^= 0xff;
                        /*FALLTHROUGH*/
                case 0:         /* Second half of finalization */
                        break;
                }

                SIP_ROUND(a, b, c, d);
                SIP_ROUND(a, b, c, d);
        } while (len);

        return a ^ b ^ c ^ d;
}

#undef SIP_ROUND
#undef SIP_MIX


#define HSIP_MIX(a, b, s) ((a) += (b), (b) = rol32(b, s), (b) ^= (a))

/*
 * These are the PRELIMINARY rotate constants suggested by
 * Jean-Philippe Aumasson.  Update to final when available.
 */
#define HSIP_ROUND(a, b, c, d) \
        (HSIP_MIX(a, b,  5), HSIP_MIX(c, d,  8), (a) = rol32(a, 16), \
         HSIP_MIX(c, b,  7), HSIP_MIX(a, d, 13), (c) = rol32(c, 16))

uint32_t
hsiphash24(char const *in, size_t len, uint32_t const key[2])
{
        uint32_t c = key[0];
        uint32_t d = key[1];
        uint32_t a =     0x6c796765 ^ 0x736f6d65;
        uint32_t b = d ^ 0x74656462 ^ 0x646f7261;
        uint32_t m = c;
        uint8_t padbyte = len;

        /*
         * By using the same SipRound code for all iterations, we
         * save space, at the expense of some branch prediction.  But
         * branch prediction is hard because of variable length anyway.
         */
        len = len/sizeof(m) + 3;        /* Now number of rounds to perform */
        do {
                a ^= m;

                switch (--len) {
                        unsigned bytes;

                default:        /* Full words */
                        d ^= m = get_unaligned_le32(in);
                        in += sizeof(m);
                        break;
                case 2:         /* Final partial word */
                        /*
                         * We'd like to do one 32-bit fetch rather than
                         * mess around with bytes, but reading past the end
                         * might hit a protection boundary.  Fortunately,
                         * we know that protection boundaries are aligned,
                         * so we can consider only three cases:
                         * - The remainder occupies zero words
                         * - The remainder fits into one word
                         * - The remainder straddles two words
                         */
                        bytes = padbyte & 3;

                        if (bytes == 0) {
                                m = 0;
                        } else {
                                unsigned offset = (unsigned)(uintptr_t)in & 3;

                                if (offset + bytes <= 4) {
                                        m = le32_to_cpup((uint32_t const *)
                                                                (in - offset));
                                        m >>= 8*offset;
                                } else {
                                        m = get_unaligned_le32(in);
                                }
                                m &= ((uint32_t)1 << 8*bytes) - 1;
                        }
                        /* Could use | or +, but ^ allows associativity */
                        d ^= m ^= (uint32_t)padbyte << 24;
                        break;
                case 1:         /* Beginning of finalization */
                        m = 0;
                        c ^= 0xff;
                        /*FALLTHROUGH*/
                case 0:         /* Second half of finalization */
                        break;
                }

                HSIP_ROUND(a, b, c, d);
                HSIP_ROUND(a, b, c, d);
        } while (len);

        return a ^ b ^ c ^ d;
        // return c + d;
}

#undef HSIP_ROUND
#undef HSIP_MIX

/*
 * No objection to EXPORT_SYMBOL, but we should probably figure out
 * how the seed[] array should work first.  Homework for the first
 * person to want to call it from a module!
 */

#if SELFTEST

#include <stdio.h>

static uint64_t rdtsc()
{
        uint32_t eax, edx;

        asm volatile ("rdtsc" : "=a" (eax), "=d" (edx));
        return (uint64_t)edx << 32 | eax;
}

int
main(void)
{
        static char const buf[1024] = { 0 };
        unsigned max;
        static const uint32_t key[4] = { 1, 2, 3, 4 };

        printf("SipHash/HSipHash benchmark, sizeof(long) = %u\n",
                (unsigned)sizeof(long));
        for (unsigned max = 4; max <= 1024; max *= 2) {
                uint64_t sum1 = 0;
                uint32_t sum2 = 0;
                uint64_t cycles;
                uint32_t bytes = 0;

                /* A less lazy person could figure out the closed form */
                for (int i = 1; i <= max; i++)
                        bytes += i * (max + 1 - i);

                cycles = rdtsc();
                for (int i = 1; i <= max; i++)
                        for (int j = 0; j <= max-i; j++)
                                sum1 += siphash24(buf+j, i, key);
                cycles = rdtsc() - cycles;

                printf(" SipHash: max=%4u cycles=%10llu cpb=%8.4f (sum=%llx)\n",
                        max, cycles, (double)cycles/bytes, sum1);

                cycles = rdtsc();
                for (int i = 1; i <= max; i++)
                        for (int j = 0; j <= max-i; j++)
                                sum2 += hsiphash24(buf+j, i, key);
                cycles = rdtsc() - cycles;
                printf("HSipHash: max=%4u cycles=%10llu cpb=%8.4f (sum=%lx)\n",
                        max, cycles, (double)cycles/bytes, sum2);
        }
        return 0;
}


#endif
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