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bwt_cuda_occ4.cuh
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bwt_cuda_occ4.cuh
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/*
Barracuda - A Short Sequence Aligner for NVIDIA Graphics Cards
Module: barracuda.cu - CUDA alignment and samse kernels
Copyright (C) 2012, University of Cambridge Metabolic Research Labs.
Contributers: Petr Klus, Dag Lyberg, Simon Lam and Brian Lam
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
This program is based on a modified version of BWA
File Creation date: 2012.6.8
*/
/* (0.7.0) beta: $Revision: 1.3 $
1 Mar 2015 WBL bugfix direct_global_bwt reading global_bwt
27 Feb 2015 WBL mycache4 but not direct_global_bwt __ldg to access global_bwt
12 Feb 2015 WBL taken from cuda.cuh r1.1 for cuda2.cuh
4 Dec 2014 WBL Extract aln device code to new separate file cuda.cuh
*/
#define __occ_cuda_aux4(b) (bwt_cuda.cnt_table[(b)&0xff]+bwt_cuda.cnt_table[(b)>>8&0xff]+bwt_cuda.cnt_table[(b)>>16&0xff]+bwt_cuda.cnt_table[(b)>>24])
__device__ inline uint32_t
helper(const int i4, uint4* mycache, const uint32_t * global_bwt4) {
const int i = (i4 & 0x3);
if(i==0) {
#ifdef direct_global_bwt
*mycache = *(uint4*)global_bwt4;
#else
*mycache = __ldg((uint4*)global_bwt4);
#endif /*direct_global_bwt*/
}
return ((uint32_t *)mycache)[i];
}
__device__ inline uint32_t
occ_cuda_aux4(const int i4, uint4* mycache, const uint32_t * global_bwt4) {
return __occ_cuda_aux4(helper(i4,mycache,global_bwt4));}
__device__ inline uint32_t
occ_cuda_aux4(const int i4, uint4* mycache, const uint32_t * global_bwt4, const uint32_t mask) {
return __occ_cuda_aux4(helper(i4,mycache,global_bwt4) & mask);}
__device__ ulong4 bwt_cuda_occ4(uint32_t *global_bwt, bwtint_t k)
// return occurrence of c in bwt with k smallest suffix by reading it from texture memory
{
// total number of character c in the up to the interval of k
ulong4 n = {0,0,0,0};
uint32_t i = 0;
// printf("bwtcudaocc4: k:%u\n",k);
if (k == bwt_cuda.seq_len)
{
//printf("route 1 - lookup at seqence length\n");
n.x = bwt_cuda.L2[1]-bwt_cuda.L2[0];
n.y = bwt_cuda.L2[2]-bwt_cuda.L2[1];
n.z = bwt_cuda.L2[3]-bwt_cuda.L2[2];
n.w = bwt_cuda.L2[4]-bwt_cuda.L2[3];
return n;
}
//if (k == (bwtint_t)(-1)) return n;
if (k >= bwt_cuda.primary){
// printf("k >= primary, %i\n",int(bwt_cuda.primary));
--k; // because $ is not in bwt
}
// printf("route 3\n");
//based on #define bwt_occ_intv(b, k) ((b)->bwt + (k)/OCC_INTERVAL*12) where OCC_INTERVAL = 0x80, i.e. 128
i = k >>7<<4;
// printf("occ_i = %u\n",i);
#define USE_SIMON_OCC4 0
#if USE_SIMON_OCC4 == 0
//shifting the array to the right position
uint32_t * p = global_bwt + i;
// printf("p: %p\n", p);
//effectively assumes mycache4, ie ldg_t is uint4
//assert(sizeof(ulong4)==2*sizeof(uint4));
#ifdef direct_global_bwt
((uint4*)(&n))[0] = *((uint4*)p); //n.x,n.y
((uint4*)(&n))[1] = *((uint4*)&p[4]); //n.z,n.w
#else
((uint4*)(&n))[0] = __ldg((uint4*)p); //n.x,n.y
((uint4*)(&n))[1] = __ldg((uint4*)&p[4]); //n.z,n.w
#endif /*direct_global_bwt*/
/*casting bwtint_t to uint32_t??
n.x = ((bwtint_t *)(p))[0];
n.y = ((bwtint_t *)(p))[1];
n.z = ((bwtint_t *)(p))[2];
n.w = ((bwtint_t *)(p))[3];
*/
// printf("n using occ(i)) tmp.x: %lu, tmp.y: %lu, tmp.z: %lu, tmp.w: %lu\n",n.x,n.y,n.z,n.w);
p += 8 ; //not sizeof(bwtint_t) coz it equals to 7 not 8;
bwtint_t j, l, x ;
j = k >> 4 << 4;
int ii=0; uint4 b;
for (l = k / OCC_INTERVAL * OCC_INTERVAL, x = 0; l < j; l += 16, ++p,++ii)
{
x += occ_cuda_aux4(ii,&b,p);
}
x += occ_cuda_aux4(ii,&b,p, ~((1U<<((~k&15)<<1)) - 1)) - (~k&15);
//Return final counts (n)
n.x += x&0xff;
n.y += x>>8&0xff;
n.z += x>>16&0xff;
n.w += x>>24;
#else
//TODO: Simon's BWTOCC4 is not working yet!
bwtint_t m = 0;
ulong4 tmp;
// remarks: uint4 in CUDA is 4 x integer ( a.x,a.y,a.z,a.w )
// tmp variables
unsigned int tmp1,tmp2;//, tmp3;
//shifting the array to the right position
uint32_t * p = global_bwt + i;
printf("p: %u\n", p);
uint32_t * p1 = p + 1;
printf("p1: %u\n", p1);
//casting bwtint_t to uint32_t??
tmp.x = ((bwtint_t *)(p1))[0];
tmp.y = ((bwtint_t *)(p1))[1];
tmp.z = ((bwtint_t *)(p1))[2];
tmp.w = ((bwtint_t *)(p1))[3];
printf("tmp using occ(p1)) tmp.x: %lu, tmp.y: %lu, tmp.z: %lu, tmp.w: %lu\n",tmp.x,tmp.y,tmp.z,tmp.w);
if (k&0x40)
{
uint32_t *p2 = p + 2;
printf("k&0x40 true: p1: %u\n", p2);
m = __occ_cuda_aux4(tmp.x);
m += __occ_cuda_aux4(tmp.y);
m += __occ_cuda_aux4(tmp.z);
m += __occ_cuda_aux4(tmp.w);
printf("m: %lu\n", m);
tmp.x = ((bwtint_t *)(p2))[0];
tmp.y = ((bwtint_t *)(p2))[1];
tmp.z = ((bwtint_t *)(p2))[2];
tmp.w = ((bwtint_t *)(p2))[3];
printf("k&0x40 is true: occ(p2) tmp.x: %lu, tmp.y: %lu, tmp.z: %lu, tmp.w: %lu\n",tmp.x,tmp.y,tmp.z,tmp.w);
}
if (k&0x20)
{
m += __occ_cuda_aux4(tmp.x);
m += __occ_cuda_aux4(tmp.y);
printf("k&020 is true: m: %lu\n", m);
tmp1=tmp.z;
tmp2=tmp.w;
} else {
tmp1=tmp.x;
tmp2=tmp.y;
}
if (k&0x10)
{
m += __occ_cuda_aux4(tmp1);
printf("k&010 is true: m: %lu\n", m);
tmp1=tmp2;
}
// just shift away the unwanted character, no need to shift back
// number of c in tmp1 will still be correct
m += __occ_cuda_aux4(tmp1>>(((~k)&15)<<1));
printf("none of the ks is true: m: %lu\n", m);
n.x = m&0xff; n.y = m>>8&0xff; n.z = m>>16&0xff; n.w = m>>24; //look into this
printf ("m numbers: %lu, %lu, %lu, %lu\n", n.x, n.y, n.z, n.w);
// retrieve the total count from index the number of character C in the up k/128bits interval
tmp.x = ((bwtint_t *)(p))[0];
tmp.y = ((bwtint_t *)(p))[1];
tmp.z = ((bwtint_t *)(p))[2];
tmp.w = ((bwtint_t *)(p))[3];
printf("final occ(p) tmp.x: %lu, tmp.y: %lu, tmp.z: %lu, tmp.w: %lu\n",tmp.x,tmp.y,tmp.z,tmp.w);
n.x += tmp.x; n.x -= ~k&15; n.y += tmp.y; n.z += tmp.z; n.w += tmp.w;
#endif
// printf("calculated n.0 = %u\n",n.x);
// printf("calculated n.1 = %u\n",n.y);
// printf("calculated n.2 = %u\n",n.z);
// printf("calculated n.3 = %u\n",n.w);
return n;
}