int
maingen(int argc, char** argv)
{
uint8_t logs[256];
uint8_t exps[255];
unsigned int x;
unsigned int i;
x = 1;
for( i = 0; i < 255; ++i ) {
exps[i] = x;
logs[x] = i;
x <<= 1;
if( x & 0x100 )
x ^= 0x11d; /* Unset the 8th bit and mix in 0x1d */
}
logs[0] = 0; /* can't log(0) so just set it neatly to 0 */
/* The above generation algorithm clearly demonstrates that
* logs[exps[i]] == i for 0 <= i <= 254
* exps[logs[i]] == i for 1 <= i <= 255
*/
/* Spew out the tables */
fprintf(stdout, "\
/*\n\
* This file is autogenerated by gfshare_maketable.\n\
*/\n\
\n\
static uint8_t logs[256] = {\n ");
for( i = 0; i < 256; ++i ) {
fprintf(stdout, "0x%02x", logs[i]);
if( i == 255 )
fprintf(stdout, " };\n");
else if( (i % 8) == 7 )
fprintf(stdout, ",\n ");
else
fprintf(stdout, ", ");
}
/* The exp table we output from 0 to 509 because that way when we
* do the lagrange interpolation we don't have to be quite so strict
* with staying inside the field which makes it quicker
*/
fprintf(stdout, "\
\n\
static uint8_t exps[510] = {\n ");
for( i = 0; i < 510; ++i ) {
fprintf(stdout, "0x%02x", exps[i % 255]); /* exps[255]==exps[0] */
if( i == 509 )
fprintf(stdout, " };\n");
else if( (i % 8) == 7)
fprintf(stdout, ",\n ");
else
fprintf(stdout, ", ");
}
return 0;
}
void iguana_main(void *arg)
{
int32_t usessl = 0, ismainnet = 1;
struct supernet_info *myinfo; char *tmpstr,*helperargs,*coinargs,helperstr[512]; int32_t i;
mycalloc(0,0,0);
myinfo = SuperNET_MYINFO(0);
FILE *fp; int32_t iter; void ztest(); ztest();
strcpy(myinfo->NXTAPIURL,"http://127.0.0.1:7876/nxt");
for (iter=0; iter<2; iter++)
{
if ( (fp= fopen(iter == 0 ? "nxtpasswords" : "fimpasswords","rb")) != 0 )
{
char line[4096],NXTaddr[64]; int32_t j; uint8_t pubkey[32];
while ( fgets(line,sizeof(line),fp) > 0 )
{
j = (int32_t)strlen(line) - 1;
line[j] = 0;
calc_NXTaddr(NXTaddr,pubkey,(uint8_t *)line,j);
printf("FORGING %s (%s)\n",NXTaddr,issue_startForging(myinfo,line));
}
fclose(fp);
}
strcpy(myinfo->NXTAPIURL,"http://127.0.0.1:7886/nxt");
}
if ( usessl == 0 )
strcpy(myinfo->NXTAPIURL,"http://127.0.0.1:");
else strcpy(myinfo->NXTAPIURL,"https://127.0.0.1:");
if ( ismainnet != 0 )
strcat(myinfo->NXTAPIURL,"7876/nxt");
else strcat(myinfo->NXTAPIURL,"6876/nxt");
if ( 0 )
{
#ifndef _WIN32
signal(SIGINT,sigint_func);
signal(SIGILL,sigillegal_func);
signal(SIGHUP,sighangup_func);
//signal(SIGKILL,sigkill_func);
signal(SIGABRT,sigabort_func);
signal(SIGQUIT,sigquit_func);
signal(SIGCHLD,sigchild_func);
signal(SIGALRM,sigalarm_func);
signal(SIGCONT,sigcontinue_func);
#endif
}
//iguana_chaingenesis(1,1403138561,0x1e0fffff,8359109,bits256_conv("fd1751cc6963d88feca94c0d01da8883852647a37a0a67ce254d62dd8c9d5b2b")); // BTCD
//iguana_chaingenesis(1,1409839200,0x1e0fffff,64881664,bits256_conv("698a93a1cacd495a7a4fb3864ad8d06ed4421dedbc57f9aaad733ea53b1b5828")); // VPN
iguana_chaingenesis(1,1317972665,0x1e0ffff0,2084524493,bits256_conv("97ddfbbae6be97fd6cdf3e7ca13232a3afff2353e29badfab7f73011edd4ced9")); // LTC
iguana_initQ(&helperQ,"helperQ");
OS_ensure_directory("help");
OS_ensure_directory("confs");
OS_ensure_directory("DB"), OS_ensure_directory("DB/ECB");
OS_ensure_directory("tmp");
if ( (tmpstr= SuperNET_JSON(myinfo,cJSON_Parse("{\"agent\":\"SuperNET\",\"method\":\"help\"}"),0)) != 0 )
{
if ( (API_json= cJSON_Parse(tmpstr)) != 0 && (API_json= jobj(API_json,"result")) != 0 )
API_json = jobj(API_json,"API");
free(tmpstr);
}
if ( IGUANA_NUMHELPERS == 0 )
IGUANA_NUMHELPERS = 1;
for (i=0; i<IGUANA_NUMHELPERS; i++)
{
sprintf(helperstr,"{\"name\":\"helper.%d\"}",i);
helperargs = clonestr(helperstr);
iguana_launch(iguana_coinadd("BTCD"),"iguana_helper",iguana_helper,helperargs,IGUANA_PERMTHREAD);
}
iguana_launch(iguana_coinadd("BTCD"),"rpcloop",iguana_rpcloop,SuperNET_MYINFO(0),IGUANA_PERMTHREAD);
category_init(&MYINFO);
if ( (coinargs= SuperNET_keysinit(&MYINFO,arg)) != 0 )
iguana_launch(iguana_coinadd("BTCD"),"iguana_coins",iguana_coins,coinargs,IGUANA_PERMTHREAD);
else if ( 1 )
{
#ifdef __APPLE__
sleep(1);
char *str;
strcpy(MYINFO.rpcsymbol,"BTC");
iguana_launchcoin(MYINFO.rpcsymbol,cJSON_Parse("{}"));
if ( 1 && (str= SuperNET_JSON(&MYINFO,cJSON_Parse("{\"agent\":\"iguana\",\"method\":\"addcoin\",\"services\":128,\"maxpeers\":3,\"newcoin\":\"BTC\",\"active\":0}"),0)) != 0 )
{
free(str);
if ( 1 && (str= SuperNET_JSON(&MYINFO,cJSON_Parse("{\"agent\":\"iguana\",\"method\":\"addcoin\",\"services\":128,\"maxpeers\":3,\"newcoin\":\"BTCD\",\"active\":0}"),0)) != 0 )
{
free(str);
if ( 0 && (str= SuperNET_JSON(&MYINFO,cJSON_Parse("{\"agent\":\"SuperNET\",\"method\":\"login\",\"handle\":\"alice\",\"password\":\"alice\",\"passphrase\":\"alice\"}"),0)) != 0 )
{
free(str);
if ( (str= SuperNET_JSON(&MYINFO,cJSON_Parse("{\"agent\":\"SuperNET\",\"method\":\"login\",\"handle\":\"bob\",\"password\":\"bob\",\"passphrase\":\"bob\"}"),0)) != 0 )
free(str);
}
}
}
sleep(1);
#endif
}
if ( arg != 0 )
SuperNET_JSON(&MYINFO,cJSON_Parse(arg),0);
mainloop(&MYINFO);
}
int
main(int argc, char *argv[])
{
static const int ex_under = FE_UNDERFLOW | FE_INEXACT; /* shorthand */
static const int ex_over = FE_OVERFLOW | FE_INEXACT;
long double ldbl_small, ldbl_eps, ldbl_max;
printf("1..5\n");
#ifdef __i386__
fpsetprec(FP_PE);
#endif
/*
* We can't use a compile-time constant here because gcc on
* FreeBSD/i386 assumes long doubles are truncated to the
* double format.
*/
ldbl_small = ldexpl(1.0, LDBL_MIN_EXP - LDBL_MANT_DIG);
ldbl_eps = LDBL_EPSILON;
ldbl_max = ldexpl(1.0 - ldbl_eps / 2, LDBL_MAX_EXP);
/*
* Special cases involving zeroes.
*/
#define ztest(prec) \
test##prec(copysign##prec(1.0, nextafter##prec(0.0, -0.0)), -1.0, 0); \
test##prec(copysign##prec(1.0, nextafter##prec(-0.0, 0.0)), 1.0, 0); \
test##prec(copysign##prec(1.0, nexttoward##prec(0.0, -0.0)), -1.0, 0);\
test##prec(copysign##prec(1.0, nexttoward##prec(-0.0, 0.0)), 1.0, 0)
ztest();
ztest(f);
ztest(l);
#undef ztest
#define stest(next, eps, prec) \
test##prec(next(-0.0, 42.0), eps, ex_under); \
test##prec(next(0.0, -42.0), -eps, ex_under); \
test##prec(next(0.0, INFINITY), eps, ex_under); \
test##prec(next(-0.0, -INFINITY), -eps, ex_under)
stest(nextafter, 0x1p-1074, );
stest(nextafterf, 0x1p-149f, f);
stest(nextafterl, ldbl_small, l);
stest(nexttoward, 0x1p-1074, );
stest(nexttowardf, 0x1p-149f, f);
stest(nexttowardl, ldbl_small, l);
#undef stest
printf("ok 1 - next\n");
/*
* `x == y' and NaN tests
*/
testall(42.0, 42.0, 42.0, 0);
testall(-42.0, -42.0, -42.0, 0);
testall(INFINITY, INFINITY, INFINITY, 0);
testall(-INFINITY, -INFINITY, -INFINITY, 0);
testall(NAN, 42.0, NAN, 0);
testall(42.0, NAN, NAN, 0);
testall(NAN, NAN, NAN, 0);
printf("ok 2 - next\n");
/*
* Tests where x is an ordinary normalized number
*/
testboth(1.0, 2.0, 1.0 + DBL_EPSILON, 0, );
testboth(1.0, -INFINITY, 1.0 - DBL_EPSILON/2, 0, );
testboth(1.0, 2.0, 1.0 + FLT_EPSILON, 0, f);
testboth(1.0, -INFINITY, 1.0 - FLT_EPSILON/2, 0, f);
testboth(1.0, 2.0, 1.0 + ldbl_eps, 0, l);
testboth(1.0, -INFINITY, 1.0 - ldbl_eps/2, 0, l);
testboth(-1.0, 2.0, -1.0 + DBL_EPSILON/2, 0, );
testboth(-1.0, -INFINITY, -1.0 - DBL_EPSILON, 0, );
testboth(-1.0, 2.0, -1.0 + FLT_EPSILON/2, 0, f);
testboth(-1.0, -INFINITY, -1.0 - FLT_EPSILON, 0, f);
testboth(-1.0, 2.0, -1.0 + ldbl_eps/2, 0, l);
testboth(-1.0, -INFINITY, -1.0 - ldbl_eps, 0, l);
/* Cases where nextafter(...) != nexttoward(...) */
test(nexttoward(1.0, 1.0 + ldbl_eps), 1.0 + DBL_EPSILON, 0);
testf(nexttowardf(1.0, 1.0 + ldbl_eps), 1.0 + FLT_EPSILON, 0);
testl(nexttowardl(1.0, 1.0 + ldbl_eps), 1.0 + ldbl_eps, 0);
printf("ok 3 - next\n");
/*
* Tests at word boundaries, normalization boundaries, etc.
*/
testboth(0x1.87654ffffffffp+0, INFINITY, 0x1.87655p+0, 0, );
testboth(0x1.87655p+0, -INFINITY, 0x1.87654ffffffffp+0, 0, );
testboth(0x1.fffffffffffffp+0, INFINITY, 0x1p1, 0, );
testboth(0x1p1, -INFINITY, 0x1.fffffffffffffp+0, 0, );
testboth(0x0.fffffffffffffp-1022, INFINITY, 0x1p-1022, 0, );
testboth(0x1p-1022, -INFINITY, 0x0.fffffffffffffp-1022, ex_under, );
testboth(0x1.fffffep0f, INFINITY, 0x1p1, 0, f);
testboth(0x1p1, -INFINITY, 0x1.fffffep0f, 0, f);
testboth(0x0.fffffep-126f, INFINITY, 0x1p-126f, 0, f);
testboth(0x1p-126f, -INFINITY, 0x0.fffffep-126f, ex_under, f);
#if LDBL_MANT_DIG == 53
testboth(0x1.87654ffffffffp+0L, INFINITY, 0x1.87655p+0L, 0, l);
testboth(0x1.87655p+0L, -INFINITY, 0x1.87654ffffffffp+0L, 0, l);
testboth(0x1.fffffffffffffp+0L, INFINITY, 0x1p1L, 0, l);
testboth(0x1p1L, -INFINITY, 0x1.fffffffffffffp+0L, 0, l);
testboth(0x0.fffffffffffffp-1022L, INFINITY, 0x1p-1022L, 0, l);
testboth(0x1p-1022L, -INFINITY, 0x0.fffffffffffffp-1022L, ex_under, l);
#elif LDBL_MANT_DIG == 64 && !defined(__i386)
testboth(0x1.87654321fffffffep+0L, INFINITY, 0x1.87654322p+0L, 0, l);
testboth(0x1.87654322p+0L, -INFINITY, 0x1.87654321fffffffep+0L, 0, l);
testboth(0x1.fffffffffffffffep0L, INFINITY, 0x1p1L, 0, l);
testboth(0x1p1L, -INFINITY, 0x1.fffffffffffffffep0L, 0, l);
testboth(0x0.fffffffffffffffep-16382L, INFINITY, 0x1p-16382L, 0, l);
testboth(0x1p-16382L, -INFINITY,
0x0.fffffffffffffffep-16382L, ex_under, l);
#elif LDBL_MANT_DIG == 113
testboth(0x1.876543210987ffffffffffffffffp+0L, INFINITY,
0x1.876543210988p+0, 0, l);
testboth(0x1.876543210988p+0L, -INFINITY,
0x1.876543210987ffffffffffffffffp+0L, 0, l);
testboth(0x1.ffffffffffffffffffffffffffffp0L, INFINITY, 0x1p1L, 0, l);
testboth(0x1p1L, -INFINITY, 0x1.ffffffffffffffffffffffffffffp0L, 0, l);
testboth(0x0.ffffffffffffffffffffffffffffp-16382L, INFINITY,
0x1p-16382L, 0, l);
testboth(0x1p-16382L, -INFINITY,
0x0.ffffffffffffffffffffffffffffp-16382L, ex_under, l);
#endif
printf("ok 4 - next\n");
/*
* Overflow tests
*/
test(idd(nextafter(DBL_MAX, INFINITY)), INFINITY, ex_over);
test(idd(nextafter(INFINITY, 0.0)), DBL_MAX, 0);
test(idd(nexttoward(DBL_MAX, DBL_MAX * 2.0L)), INFINITY, ex_over);
#if LDBL_MANT_DIG > 53
test(idd(nexttoward(INFINITY, DBL_MAX * 2.0L)), DBL_MAX, 0);
#endif
testf(idf(nextafterf(FLT_MAX, INFINITY)), INFINITY, ex_over);
testf(idf(nextafterf(INFINITY, 0.0)), FLT_MAX, 0);
testf(idf(nexttowardf(FLT_MAX, FLT_MAX * 2.0)), INFINITY, ex_over);
testf(idf(nexttowardf(INFINITY, FLT_MAX * 2.0)), FLT_MAX, 0);
testboth(ldbl_max, INFINITY, INFINITY, ex_over, l);
testboth(INFINITY, 0.0, ldbl_max, 0, l);
printf("ok 5 - next\n");
return (0);
}
ATF_TC_BODY(Zone, tc)
{
ztest("%z");
}
int main(int argc, char** argv) {
ros::init(argc, argv, "eigen_test");
ros::NodeHandle nh_jntPub; // node handle for joint command publisher
// ros::Publisher pub_joint_commands; //
// pub_joint_commands = nh_jntPub.advertise<atlas_msgs::AtlasCommand>("/atlas/atlas_command", 1, true);
ROS_INFO("test eigen program");
Eigen::Matrix3f A;
Eigen::Vector3f b;
A << 1,2,3, 4,5,6, 7,8,10;
A(1,2)=0; // how to access one element of matrix; start from 0; no warning out of range...
b << 3,3,4;
std::cout <<"b = "<<b <<std::endl;
// column operaton: replace first column of A with vector b:
A.col(0)= b; // could copy columns of matrices w/ A.col(0) = B.col(0);
std::cout <<"A = "<<A <<std::endl;
Eigen::MatrixXd mat1 = Eigen::MatrixXd::Zero(6, 6); //6x6 matrix full of zeros
Eigen::MatrixXd mat2 = Eigen::MatrixXd::Identity(6, 6); //6x6 identity matrix
std::cout<<mat1<<std::endl;
std::cout<<mat2<<std::endl;
Eigen::Vector3f xtest = A.colPivHouseholderQr().solve(b);
std::cout<<"soln xtest = "<<xtest<<std::endl;
Eigen::Vector3f x = A.partialPivLu().solve(b); //dec.solve(b); //A.colPivHouseholderQr().solve(b);
std::cout<<"soln x = "<<x<<std::endl;
Eigen::Vector3f btest = A*x;
std::cout<<"test soln: A*x = " <<btest<<std::endl;
//extend to 6x6 test: v = M*z, find z using 2 methods
// use double-precision matrices/vectors
Eigen::MatrixXd M = Eigen::MatrixXd::Random(6,6);
std::cout<<"test 6x6: M = "<<M<<std::endl;
Eigen::VectorXd v(6);
v << 1,2,3,4,5,6;
std::cout<<"v = "<<v<<std::endl;
Eigen::VectorXd z(6);
Eigen::VectorXd ztest(6);
ztest = M.colPivHouseholderQr().solve(v);
std::cout<<"soln ztest = "<<ztest<<std::endl;
z = M.partialPivLu().solve(v);
std::cout<<"soln 6x6: z = "<<z<<std::endl;
Eigen::VectorXd vtest(6);
vtest = M*z;
std::cout<<"test soln: M*z = "<<vtest<<std::endl;
// .norm() operator...
double relative_error = (M*z - v).norm() / v.norm(); // norm() is L2 norm
std::cout << "The relative error is:\n" << relative_error << std::endl;
std::cout<<"dot prod, v, z: "<< v.dot(z)<<std::endl;
std::cout<<"cross prod, b-cross-x: " << b.cross(x)<<std::endl;
return 0;
}
int
main(int argc, char **argv)
{
double starttime, endtime;
int ntasks, myrank;
char name[128];
int namelen;
MPI_Status status;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
MPI_Comm_size(MPI_COMM_WORLD, &ntasks);
MPI_Get_processor_name(name,&namelen);
/* Get a few OpenMP parameters. */
int O_P = omp_get_num_procs(); /* get number of OpenMP processors */
int O_T = omp_get_num_threads(); /* get number of OpenMP threads */
int O_ID = omp_get_thread_num(); /* get OpenMP thread ID */
//printf("name:%s M_ID:%d O_ID:%d O_P:%d O_T:%d\n", name,myrank,O_ID,O_P,O_T);
FILE *f;
char line[LINE_SIZE];
int numlines = 0;
exprinfo *exprannot = NULL;
char **glines = NULL;
f = fopen("gene_list.txt", "r");
while(fgets(line, LINE_SIZE, f)) {
glines = (char**)realloc(glines, sizeof(char*)*(numlines+1));
glines[numlines] = strdup(line);
char *pch = strtok (line,",");
char * gene = pch;
pch = strtok (NULL, ",");
int chr = atoi(trimwhitespace(pch));
exprannot = (exprinfo*)realloc(exprannot,sizeof(exprinfo)*(numlines+1));
exprannot[numlines].gene = strdup(gene);
exprannot[numlines].chr = chr;
if (!exprannot) printf("not allcoated\n");
numlines++;
}
fclose(f);
f = fopen("probe_id_mapping.txt", "r");
numlines = 0;
free(glines[0]);
free(glines);
probeinfo *records = NULL;
char **lines = NULL;
while(fgets(line, LINE_SIZE, f)) {
lines = (char**)realloc(lines, sizeof(char*)*(numlines+1));
lines[numlines] = strdup(line);
char *pch = strtok (line,",");
int probeid = atoi(pch);
pch = strtok (NULL, ",");
char * gene = pch;
pch = strtok (NULL, ",");
int chr = atoi(trimwhitespace(pch));
records = (probeinfo*)realloc(records,sizeof(probeinfo)*(numlines+1));
records[numlines].probeid = probeid;
records[numlines].chr = chr;
records[numlines].gene = strdup(gene);
if (!records) printf("not allcoated\n");
numlines++;
}
free(lines[0]);
free(lines);
fclose(f);
int NUM_GENES = numlines;
unsigned long x_nr, x_nc, y_nr, y_nc;
double **X = h5_read("x.h5", 1, "/X", &x_nr, &x_nc);
double **Y = h5_read("filtered_probes.h5", 1, "/FilteredProbes", &y_nr, &y_nc);
//printf("loaded X, num rows = %d, num cols = %d\n", x_nr, x_nc);
//printf("loaded Y, num rows = %d, num cols = %d\n", y_nr, y_nc);
unsigned long total_mem = (x_nr * y_nc);
double **RHO = create2dArray(x_nr, y_nc);
int gene, probe, tid, work_completed;
work_completed = 0;
int BLOCK_SIZE = NUM_ROWS/ntasks;
int offset = myrank*BLOCK_SIZE;
int STOP_IDX = offset+BLOCK_SIZE;
if (NUM_ROWS - STOP_IDX < BLOCK_SIZE)
STOP_IDX = NUM_ROWS;
// printf("offset = %d, for rank %d, with ntasks = %d, and BLOCK_SIZE = %d, STOP_IDX = %d\n",
// offset, myrank, ntasks, BLOCK_SIZE, STOP_IDX);
int num_sig_found = 0;
starttime = MPI_Wtime();
#pragma omp parallel \
for shared(X, Y, RHO, BLOCK_SIZE, offset, work_completed) \
private(probe,gene, tid)
for (gene = offset; gene < STOP_IDX; gene++) {
for (probe = 0; probe < NUM_COLS; probe++) {
double *x = getrowvec(X, gene, BUFFER_SIZE);
double *y = getcolvec(Y, probe, BUFFER_SIZE);
double avgx = mean(x, BUFFER_SIZE);
double * xcentered = sub(x, avgx, BUFFER_SIZE);
double avgy = mean(y, BUFFER_SIZE);
double * ycentered = sub(y, avgy, BUFFER_SIZE);
double * prod_result = prod(xcentered, ycentered, BUFFER_SIZE);
double sum_prod = sum(prod_result, BUFFER_SIZE);
double stdX = stddev(x, avgx, BUFFER_SIZE);
double stdY = stddev(y, avgy, BUFFER_SIZE);
double rho = sum_prod/((BUFFER_SIZE-1)*(stdX*stdY));
RHO[gene][probe] = rho;
if (work_completed % 10000 == 0) {
tid = omp_get_thread_num();
printf("rank = %d, work = %d, result[%d,%d] from %d = %f\n", myrank, work_completed,
gene, probe, tid, rho);
}
work_completed++;
free(x);
free(y);
free(xcentered);
free(ycentered);
free(prod_result);
}
}
//printf("********* %d FINISHED **********\n", myrank);
//f = fopen("significant.txt", "a");
#pragma omp parallel for shared(RHO,exprannot, records)
for (int i = 0; i < NUM_ROWS; i++) {
for (int j = 0; j < NUM_COLS; j++) {
double zscore = ztest(RHO[i][j],BUFFER_SIZE);
/*
if (zscore > 5.0) {
fprintf(f, "%d,%d,%f,%f,%d,%s,%d,%s\n",
i, j, zscore, RHO[i][j], records[j].chr, records[j].gene, exprannot[i].chr,exprannot[i].gene);
if (i*j%1000 == 0)
printf("%d,%d,%f,%f,%d,%s,%d,%s\n",
i, j, zscore, RHO[i][j], records[j].chr, records[j].gene, exprannot[i].chr,exprannot[i].gene);
}
*/
}
}
//fclose(f);
endtime = MPI_Wtime();
free(X[0]);
free(X);
free(Y[0]);
free(Y);
printf("rank %d - elapse time - %f\n",myrank, endtime-starttime);
//for (int i = 0; i < NUM_ROWS; i++) {
//printf("%s,%d\n", exprannot[i].gene, exprannot[i].chr);
//}
//printf("rank %d FINISHED\n",myrank);
//h5_write(RHO, NUM_ROWS, NUM_COLS, "rho_omp.h5", "/rho");
free(RHO[0]);
free(exprannot);
free(records);
free(RHO);
MPI_Finalize();
return 0;
}
