int main(){
// In production code, of course, we won't hardcode this
struct Link * link = load("data.txt");
printf("Print as ordered by genome A\n");
recursive_print(link, 0);
printf("\nPrint as ordered by genome B\n");
recursive_print(link, 1);
printf("\nLowest position on genome A\n");
print_link(get_minimum(link, 0));
printf("\nLowest position on genome B\n");
print_link(get_minimum(link, 1));
printf("\nAll links with scores above 50\n");
recursive_print(winnow(link, 50), 0);
return EXIT_SUCCESS;
}
static void cb_hop(void* args, usb_pkt_rx *rx, int bank)
{
char syms[BANK_LEN * NUM_BANKS];
int i, j, k;
access_code r;
uint8_t channel;
uint32_t time; /* in 100 nanosecond units */
uint8_t clkn_high;
packet pkt;
piconet* pn = (piconet *)args;
uint8_t uap = pn->UAP;
channel = rx->channel;
time = letoh32(rx->clk100ns); /* wire format is le32 */
clkn_high = rx->clkn_high;
unpack_symbols(rx->data, symbols[bank]);
/*
fprintf(stderr, "rx block timestamp %u * 100 nanoseconds\n", time);
*/
/* awfully repetitious */
k = 0;
for (i = 0; i < 2; i++)
for (j = 0; j < BANK_LEN; j++)
syms[k++] = symbols[(i + 1 + bank) % NUM_BANKS][j];
r = find_ac(syms, BANK_LEN, pn->LAP);
if (r.offset > -1) {
for (i = 2; i < NUM_BANKS; i++)
for (j = 0; j < BANK_LEN; j++)
syms[k++] = symbols[(i + 1 + bank) % NUM_BANKS][j];
init_packet(&pkt, &syms[r.offset], BANK_LEN * NUM_BANKS - r.offset);
pkt.LAP = r.LAP;
pkt.clkn = (clkn_high << 19) | ((time + r.offset * 10) / 6250);
pkt.channel = channel;
if ((pkt.LAP == pn->LAP) && header_present(&pkt)) {
printf("\nGOT PACKET on channel %d, LAP = %06x at time stamp %u, clkn %u\n",
channel, pkt.LAP, time + r.offset * 10, pkt.clkn);
if (pn->have_clk6) {
UAP_from_header(&pkt, pn);
if (!pn->have_clk6) {
printf("CLK1-27 discovery failed\n");
exit(1); /* FIXME */
winnow(pn);
}
if (pn->have_clk27) {
printf("got CLK1-27\n");
exit(0);
}
} else {
if (UAP_from_header(&pkt, pn)) {
if (uap == pn->UAP) {
printf("got CLK1-6\n");
init_hop_reversal(0, pn);
winnow(pn);
} else {
printf("failed to confirm UAP\n");
exit(1);
}
}
}
}
}
}
int
main(
int argc, /* arg count */
char * argv[] /* arg vector */
){
static char * context = "main(chain)";
char * stem = NULL; /* dump filename stem */
char * suffix = NULL; /* dump filename suffix */
char * suff2 = NULL; /* last half of suffix */
int nr, nc; /* integer matrix sizes */
int n; /* square matrix/vector size */
real base_x, base_y; /* base of Mandelbrot */
real ext_x, ext_y; /* extent of Mandelbrot */
int limit, seed; /* randmat controls */
real fraction; /* invperc/thresh filling */
int itersLife; /* life iterations */
int itersElastic, relax; /* elastic controls */
int2D i2D; /* integer matrix */
bool2D b2D; /* boolean matrix */
pt1D cities; /* cities point vector */
int n_cities; /* number of cities */
pt1D net; /* net point vector */
int n_net; /* number of net points */
real2D r2D_gauss; /* real matrix for Gaussian */
real2D r2D_sor; /* real matrix for SOR */
real1D r1D_gauss_v; /* real vector input for Gaussian */
real1D r1D_sor_v; /* real vector input for SOR */
real1D r1D_gauss_a; /* real vector answer for Gaussian */
real1D r1D_sor_a; /* real vector answer for SOR */
real1D r1D_gauss_c; /* real vector check for Gaussian */
real1D r1D_sor_c; /* real vector check for SOR */
real tol; /* SOR tolerance */
real realDiff; /* vector difference */
bool choicesSet = FALSE; /* path choices set? */
bool doMandel = TRUE; /* mandel vs. randmat */
bool doInvperc = TRUE; /* invperc vs. thresholding */
bool doDump = FALSE; /* dump intermediate results? */
int argd = 1; /* argument index */
/* arguments */
#if NUMA
MAIN_INITENV(,32000000)
#endif
while (argd < argc){
CHECK(argv[argd][0] == '-',
fail(context, "bad argument", "index", "%d", argd, NULL));
switch(argv[argd][1]){
case 'E' : /* elastic */
itersElastic = arg_int(context, argc, argv, argd+1, argv[argd]);
relax = arg_int(context, argc, argv, argd+2, argv[argd]);
argd += 3;
break;
case 'F' : /* fraction (invperc/thresh) */
fraction = arg_real(context, argc, argv, argd+1, argv[argd]);
argd += 2;
break;
case 'L' : /* life */
itersLife = arg_int(context, argc, argv, argd+1, argv[argd]);
argd += 2;
break;
case 'M' : /* mandel */
base_x = arg_real(context, argc, argv, argd+1, argv[argd]);
base_y = arg_real(context, argc, argv, argd+2, argv[argd]);
ext_x = arg_real(context, argc, argv, argd+3, argv[argd]);
ext_y = arg_real(context, argc, argv, argd+4, argv[argd]);
argd += 5;
break;
case 'N' : /* winnow */
n_cities = arg_int(context, argc, argv, argd+1, argv[argd]);
argd += 2;
break;
case 'R' : /* randmat */
limit = arg_int(context, argc, argv, argd+1, argv[argd]);
seed = arg_int(context, argc, argv, argd+2, argv[argd]);
argd += 3;
break;
case 'S' : /* matrix size */
nr = arg_int(context, argc, argv, argd+1, argv[argd]);
nc = arg_int(context, argc, argv, argd+2, argv[argd]);
argd += 3;
break;
case 'T' : /* SOR tolerance */
tol = arg_real(context, argc, argv, argd+1, argv[argd]);
argd += 2;
break;
case 'c' : /* choice */
CHECK(!choicesSet,
fail(context, "choices already set", NULL));
suffix = arg_str(context, argc, argv, argd+1, argv[argd]);
argd += 2;
switch(suffix[0]){
case 'i' : doInvperc = TRUE; break;
case 't' : doInvperc = FALSE; break;
default :
fail(context, "unknown choice(s)", "choice", "%s", suffix, NULL);
}
switch(suffix[1]){
case 'm' : doMandel = TRUE; break;
case 'r' : doMandel = FALSE; break;
default :
fail(context, "unknown choice(s)", "choice", "%s", suffix, NULL);
}
suff2 = suffix+1;
choicesSet = TRUE;
break;
case 'd' : /* dump */
doDump = TRUE;
argd += 1;
if ((argd < argc) && (argv[argd][0] != '-')){
stem = arg_str(context, argc, argv, argd, argv[argd-1]);
argd += 1;
}
break;
#if GRAPHICS
case 'g' :
gfx_open(app_chain, arg_gfxCtrl(context, argc, argv, argd+1, argv[argd]));
argd += 2;
break;
#endif
#if MIMD
case 'p' :
DataDist = arg_dataDist(context, argc, argv, argd+1, argv[argd]);
ParWidth = arg_int(context, argc, argv, argd+2, argv[argd]);
argd += 3;
break;
#endif
case 'u' :
io_init(FALSE);
argd += 1;
break;
default :
fail(context, "unknown flag", "flag", "%s", argv[argd], NULL);
break;
}
}
CHECK(choicesSet,
fail("context", "choices not set using -c flag", NULL));
/* initialize */
#if MIMD
sch_init(DataDist);
#endif
/* mandel vs. randmat */
if (doMandel){
mandel(i2D, nr, nc, base_x, base_y, ext_x, ext_y);
if (doDump) io_wrInt2D(context, mkfname(stem, NULL, suff2, "i2"), i2D, nr, nc);
} else {
randmat(i2D, nr, nc, limit, seed);
if (doDump) io_wrInt2D(context, mkfname(stem, NULL, suff2, "i2"), i2D, nr, nc);
}
/* half */
half(i2D, nr, nc);
if (doDump) io_wrInt2D(context, mkfname(stem, "h", suff2, "i2"), i2D, nr, nc);
/* invperc vs. thresh */
if (doInvperc){
invperc(i2D, b2D, nr, nc, fraction);
if (doDump) io_wrBool2D(context, mkfname(stem, NULL, suffix, "b2"), b2D, nr, nc);
} else {
thresh(i2D, b2D, nr, nc, fraction);
if (doDump) io_wrBool2D(context, mkfname(stem, NULL, suffix, "b2"), b2D, nr, nc);
}
/* life */
life(b2D, nr, nc, itersLife);
if (doDump) io_wrBool2D(context, mkfname(stem, "l", suffix, "b2"), b2D, nr, nc);
/* winnow */
winnow(i2D, b2D, nr, nc, cities, n_cities);
if (doDump) io_wrPt1D(context, mkfname(stem, "w", suffix, "p1"), cities, n_cities);
/* norm */
norm(cities, n_cities);
if (doDump) io_wrPt1D(context, mkfname(stem, "n", suffix, "p1"), cities, n_cities);
/* elastic */
n_net = (int)(ELASTIC_RATIO * n_cities);
CHECK(n_net <= MAXEXT,
fail(context, "too many net points required",
"number of net points", "%d", n_net, NULL));
elastic(cities, n_cities, net, n_net, itersElastic, relax);
if (doDump) io_wrPt1D(context, mkfname(stem, "e", suffix, "p1"), net, n_net);
/* outer */
n = n_net;
outer(net, r2D_gauss, r1D_gauss_v, n);
if (doDump){
io_wrReal2D(context, mkfname(stem, "o", suffix, "r2"), r2D_gauss, n, n);
io_wrReal1D(context, mkfname(stem, "o", suffix, "r1"), r1D_gauss_v, n);
}
cpReal2D(r2D_gauss, r2D_sor, n, n);
cpReal1D(r1D_gauss_v, r1D_sor_v, n);
/* gauss */
gauss(r2D_gauss, r1D_gauss_v, r1D_gauss_a, n);
if (doDump) io_wrReal1D(context, mkfname(stem, "g", suffix, "r1"), r1D_gauss_a, n);
/* product (gauss) */
product(r2D_gauss, r1D_gauss_a, r1D_gauss_c, n, n);
if (doDump) io_wrReal1D(context, mkfname(stem, "pg", suffix, "r1"), r1D_gauss_c, n);
/* sor */
sor(r2D_sor, r1D_sor_v, r1D_sor_a, n, tol);
if (doDump) io_wrReal1D(context, mkfname(stem, "s", suffix, "r1"), r1D_gauss_a, n);
/* product (sor) */
product(r2D_sor, r1D_sor_a, r1D_sor_c, n, n);
if (doDump) io_wrReal1D(context, mkfname(stem, "ps", suffix, "r1"), r1D_gauss_c, n);
/* difference */
vecdiff(r1D_gauss_a, r1D_sor_a, n, &realDiff);
if (doDump) io_wrReal0D(context, mkfname(stem, "v", suffix, "r0"), realDiff);
#if IEEE
ieee_retrospective(stderr);
#endif
#if NUMA
MAIN_END;
#endif
return 0;
}
MAIN_ENV
#endif
#include "specific.h"
int
main(
int argc, /* arg count */
char * argv[] /* arg vector */
){
static char * context = "main(winnow)";
int2D matrix; /* matrix of values */
bool2D mask; /* mask on values */
int nr, nc, nrM, ncM; /* sizes */
pt1D pt; /* resulting point vector */
int npt; /* number of points to keep */
char * infnMat = NULL; /* input matrix file name */
char * infnMask = NULL; /* input mask file name */
char * outfn = NULL; /* output file name */
int argd = 1; /* argument index */
/* arguments */
#if NUMA
MAIN_INITENV(,32000000)
#endif
while (argd < argc){
CHECK(argv[argd][0] == '-',
fail(context, "bad argument", "index", "%d", argd, NULL));
switch(argv[argd][1]){
case 'N' :
npt = arg_int(context, argc, argv, argd+1, argv[argd]);
argd += 2;
break;
#if GRAPHICS
case 'g' :
gfx_open(app_winnow, arg_gfxCtrl(context, argc, argv, argd+1, argv[argd]));
argd += 2;
break;
#endif
#if MIMD
case 'p' :
DataDist = arg_dataDist(context, argc, argv, argd+1, argv[argd]);
ParWidth = arg_int(context, argc, argv, argd+2, argv[argd]);
argd += 3;
break;
#endif
case 'i' :
infnMat = arg_str(context, argc, argv, argd+1, argv[argd]);
infnMask = arg_str(context, argc, argv, argd+2, argv[argd]);
argd += 3;
break;
case 'o' :
outfn = arg_str(context, argc, argv, argd+1, argv[argd]);
argd += 2;
break;
case 'u' :
io_init(FALSE);
argd += 1;
break;
default :
fail(context, "unknown flag", "flag", "%s", argv[argd], NULL);
break;
}
}
/* setup */
#if MIMD
sch_init(DataDist);
#endif
CHECK(npt > 0,
fail(context, "non-positive number of points requested",
"number of points", "%d", npt, NULL));
io_rdInt2D(context, infnMat, matrix, &nr, &nc);
io_rdBool2D(context, infnMask, mask, &nrM, &ncM);
CHECK((nr == nrM) && (nc == ncM),
fail(context, "matrix/mask size mismatch",
"matrix file", "%s", infnMat,
"mask file", "%s", infnMask, NULL));
/* run */
winnow(matrix, mask, nr, nc, pt, npt);
/* takedown */
io_wrPt1D(context, outfn, pt, npt);
#if GRAPHICS
gfx_close();
#endif
#if IEEE
ieee_retrospective(stderr);
#endif
#if NUMA
MAIN_END;
#endif
return 0;
}
