static const char *done_handshake(struct Worker *w)
{
int res;
size_t outlen = 0;
const char *emsg;
emsg = check_fp(w, "sha1", w->peer_fingerprint_sha1, 20);
if (emsg)
return emsg;
emsg = check_fp(w, "sha256", w->peer_fingerprint_sha256, 32);
if (emsg)
return emsg;
if (w->show) {
if (strcmp(w->show, "ciphers") == 0) {
tls_get_connection_info(w->ctx, w->showbuf, sizeof w->showbuf);
} else if (strcmp(w->show, "peer-cert") == 0) {
struct tls_cert *cert = NULL;
tls_get_peer_cert(w->ctx, &cert, NULL);
show_cert(cert, w->showbuf, sizeof w->showbuf);
tls_cert_free(cert);
} else {
snprintf(w->showbuf, sizeof w->showbuf, "bad kw: show=%s", w->show);
}
}
if (!w->is_server) {
res = tls_write(w->ctx, "PKT", 3, &outlen);
if (res != 0 && outlen != 3)
return "write!=3";
}
return wait_for_event(w, EV_READ);
}
nt main(int argc, char *argv[]) {
FILE *genome_f;
int read_size=0; //the size of the reads
int table_factor; //arbitrary
int num_of_reads;
int bf_table_size = table_factor*num_of_reads;
int num_of_hash_func;
BloomFilter* bf_unique; //BF for the unique tries
// char* output_label=(char *)malloc(50); //label name for the output files
hattrie_t* trie_unique; //hattrie that holds the unique reads
hattrie_t* trie_repeat; //hattrie that holds the repetetive reads, and the one that has N inside of them.
hattrie_t* trie_genome_unique; //put 'accepts' (everything that uniqe BF says yes that it's in genome) into a trie
hattrie_t* trie_fp; //triw that holds false negatives set
hattrie_t* trie_fn;//trie that holds false positives set
// f = fopen(argv[1], "r");
trie_repeat = hattrie_create();
trie_unique = hattrie_create();
make_repeat_and_unique_tries((argv[1], "r"), trie_unique, trie_repeat);
table_factor = 10; //arbitrary
num_of_reads = line_number/2;
bf_table_size = table_factor*num_of_reads;
num_of_hash_func = (int) ceil(table_factor*0.69314);
//print the keys of the uniqe and repaet tries
hattrie_iteration(trie_unique, "unique", argv[3]);
hattrie_iteration(trie_repeat, "repeat", argv[3]);
//hashing uniqe reads trie using bloom filter
bf_unique = bloom_filter_new(bf_table_size, string_hash, num_of_hash_func);
hash_trie_into_bf(trie_unique, bf_unique);
check_if_trie_in_bf(trie_unique, bf_unique);
//create trie for all of the sliding windows in the genome reference which are in the unique reads according to the bf_unique
read_size = size-2;
trie_genome_unique = hattrie_create();
query_bf_with_genome(bf_unique, genome_f ,trie_genome_unique, read_size);
check_if_trie_in_bf(trie_unique, bf_unique);
fclose(genome_f);
hattrie_iteration(trie_genome_unique, "genome_unique", argv[3]);
trie_fp = hattrie_create();
trie_fn = hattrie_create();
printf("start checking for false positive \n");
check_fp(trie_unique,trie_genome_unique, trie_fp);
hattrie_iteration(trie_fp, "fp_unique", argv[3]);
printf("start checking for false negative \n");
check_fn(trie_unique,trie_genome_unique, trie_fn);
hattrie_iteration(trie_fn, "fn_unique", argv[3]);
bloom_filter_free(bf_unique);
free(buffer);
hattrie_free(trie_unique);
hattrie_free(trie_repeat);
hattrie_free(trie_genome_unique);
hattrie_free(trie_fn);
hattrie_free(trie_fp);
return 0;
}
static const char *done_handshake(struct Worker *w)
{
int res;
const char *emsg;
emsg = check_fp(w, "sha1", w->peer_fingerprint_sha1, 20);
if (emsg)
return emsg;
emsg = check_fp(w, "sha256", w->peer_fingerprint_sha256, 32);
if (emsg)
return emsg;
if (w->show) {
if (strcmp(w->show, "ciphers") == 0) {
tls_get_connection_info(w->ctx, w->showbuf, sizeof w->showbuf);
} else if (strcmp(w->show, "peer-cert") == 0) {
struct tls_cert *cert = NULL;
tls_get_peer_cert(w->ctx, &cert, NULL);
show_cert(cert, w->showbuf, sizeof w->showbuf);
tls_cert_free(cert);
} else {
snprintf(w->showbuf, sizeof w->showbuf, "bad kw: show=%s", w->show);
}
}
if (w->aggressive_close) {
close(w->socket);
tls_close(w->ctx);
w->wstate = CLOSED;
return "OK";
}
if (!w->is_server) {
res = tls_write(w->ctx, "PKT", 3);
if (res < 0) {
return tls_error(w->ctx);
} else if (res == 0) {
return "write==0";
} else if (res != 3) {
return "write!=3";
}
}
return wait_for_event(w, EV_READ);
}
int main() {
int i;
int d;
int *p;
int (*fp)();
chk_p = &d;
chk_fp = &f;
for( i = 0; i < 16; ++i ) {
p = ( i & 0x01 ) ? &d : 0;
check_p( p, __LINE__ );
p = ( i & 0x01 ) ? 0 : &d;
check_p( p, __LINE__ );
fp = ( i & 0x01 ) ? &f : 0;
check_fp( fp, __LINE__ );
fp = ( i & 0x01 ) ? 0 : &f;
check_fp( fp, __LINE__ );
}
_PASS;
}
bool
__check_arg_fp (FILE *fp, const char *file, const char *func, size_t line)
{
if (!check_fp (fp))
{
rc_errno_set (EBADF);
debug_message (file, func, line, "Invalid file descriptor passed!\n");
return false;
}
return true;
}
int main(int argc, char **argv) {
meta_mpi_init(&argc, &argv);
#ifdef __DEBUG__
int breakMe = 0;
while (breakMe);
#endif
/*{
int i = 0;
char hostname[256];
gethostname(hostname, sizeof(hostname));
printf("PID %d on %s ready for attach\n", getpid(), hostname);
fflush(stdout);
while (0 == i)
sleep(5);
}*/
int comm_sz;
int rank;
MPI_Comm_size(MPI_COMM_WORLD, &comm_sz);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
printf("Hello from rank %d!\n", rank);
int i = argc;
int ni, nj, nk, tx, ty, tz, face_id, l_type;
a_bool async, autoconfig;
meta_face * face_spec;
a_dim3 dimgrid_red, dimblock_red, dimgrid_tr_red, dimarray_3d, arr_start,
arr_end, dim_array2d, start_2d, end_2d, trans_dim, rtrans_dim;
if (i < 11) {
printf(
"<ni> <nj> <nk> <tblockx> <tblocky> <tblockz> <face> <data_type> <async> <autoconfig>\n");
return (1);
}
ni = atoi(argv[1]);
nj = atoi(argv[2]);
nk = atoi(argv[3]);
tx = atoi(argv[4]);
ty = atoi(argv[5]);
tz = atoi(argv[6]);
face_id = atoi(argv[7]);
l_type = atoi(argv[8]);
set_type((meta_type_id) l_type);
async = (a_bool) atoi(argv[9]);
autoconfig = (a_bool) atoi(argv[10]);
dimblock_red[0] = tx, dimblock_red[1] = ty, dimblock_red[2] = tz;
dimgrid_red[0] = ni / tx + ((ni % tx) ? 1 : 0);
dimgrid_red[1] = nj / ty + ((nj % ty) ? 1 : 0);
dimgrid_red[2] = nk / tz + ((nk % tz) ? 1 : 0);
dimarray_3d[0] = ni, dimarray_3d[1] = nj, dimarray_3d[2] = nk;
//These are for the library reduction, which we use for sums
void * sum_gpu, *zero;
sum_gpu = malloc(g_typesize);
zero = malloc(g_typesize);
switch (g_type) {
case a_db:
*(double*) zero = 0;
break;
case a_fl:
*(float*) zero = 0;
break;
case a_ul:
*(unsigned long*) zero = 0;
break;
case a_in:
*(int *) zero = 0;
break;
case a_ui:
*(unsigned int *) zero = 0;
break;
}
#ifdef WITH_TIMERS
metaTimersInit();
#endif
gpu_initialize(rank);
data_allocate(ni, nj, nk);
data_initialize(ni, nj, nk);
MPI_Request request;
MPI_Status status;
for (i = 0; i < 1; i++) {
if (rank == 0) {
//Only process 0 actually needs to initialize data
// proc1 is just a relay that tests things on the receiving
// end and mirror's the data back
//copy the unmodified prism to device
meta_copy_h2d(dev_data3, data3, ni * nj * nk * g_typesize, async);
//check_buffer(data3, dev_data3, ni*nj*nk);
//Validate grid and block sizes (if too big, shrink the z-dim and add iterations)
for (;
meta_validate_worksize(&dimgrid_red, &dimblock_red) != 0
&& dimblock_red[2] > 1;
dimgrid_red[2] <<= 1, dimblock_red[2] >>= 1)
;
//zero out the reduction sum
meta_copy_h2d(reduction, zero, g_typesize, async);
//reduce the face to check that the transfer was correct
//accurately sets start and end indices to sum each face
arr_start[0] = ((face_id == 3) ? ni - 1 : 0);
arr_end[0] = ((face_id == 2) ? 0 : ni - 1);
arr_start[1] = ((face_id == 5) ? nj - 1 : 0);
arr_end[1] = ((face_id == 4) ? 0 : nj - 1);
arr_start[2] = ((face_id == 1) ? nk - 1 : 0);
arr_end[2] = ((face_id == 0) ? 0 : nk - 1);
//check_dims(dimarray_3d, arr_start, arr_end);
// printf("Integrity check dim(%d, %d, %d) start(%d, %d, %d) end(%d, %d, %d)\n", dimarray_3d[0], dimarray_3d[1], dimarray_3d[2], arr_start[0], arr_start[1], arr_start[2], arr_end[0], arr_end[1], arr_end[2]);
a_err ret = meta_reduce(autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red, dev_data3, &dimarray_3d,
&arr_start, &arr_end, reduction, g_type, async);
//a_dim3 testgrid, testblock;
//testgrid[0] = testgrid[1] = testgrid[2] = 1;
//testblock[0] = 16;
//testblock[1] = 8;
//testblock[2] = 1;
//a_err ret = meta_reduce(&testgrid, &testblock, dev_data3, &dimarray_3d, &arr_start, &arr_end, reduction, g_type, async);
printf("Reduce Error: %d\n", ret);
//pull the sum back
meta_copy_d2h(sum_gpu, reduction, g_typesize, async);
//The 4 ternaries ensure the right args are passed to match the face
// so this one call will work for any face
printf("Initial Face Integrity Check: %s\n",
check_face_sum(sum_gpu, (face_id < 4 ? nj : nk),
(face_id < 2 || face_id > 3 ? ni : nk),
(face_id & 1 ?
(face_id < 2 ?
nk - 1 :
(face_id < 4 ? ni - 1 : nj - 1)) :
0)) ? "FAILED" : "PASSED");
//pack the face
//TODO set a_dim3 structs once the internal implementation respects them
face_spec = make_face(face_id, ni, nj, nk);
ret = meta_pack_face(NULL, NULL, dev_face[face_id], dev_data3,
face_spec, g_type, async);
printf("Pack Return Val: %d\n", ret);
//check_buffer(face[face_id], dev_face[face_id], face_spec->size[0]*face_spec->size[1]*face_spec->size[2]);
//reduce the packed face to check that packing was correct
meta_copy_h2d(reduction, zero, g_typesize, async);
dim_array2d[0] = face_spec->size[2], dim_array2d[1] =
face_spec->size[1], dim_array2d[2] = face_spec->size[0];
start_2d[0] = start_2d[1] = start_2d[2] = 0;
end_2d[0] = (dim_array2d[0] == 1 ? 0 : ni - 1);
end_2d[1] = (dim_array2d[1] == 1 ? 0 : nj - 1);
end_2d[2] = (dim_array2d[2] == 1 ? 0 : nk - 1);
//check_dims(dim_array2d, start_2d, end_2d);
ret = meta_reduce(autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red, dev_face[face_id],
&dim_array2d, &start_2d, &end_2d, reduction, g_type, async);
meta_copy_d2h(sum_gpu, reduction, g_typesize, async);
//The 4 ternaries ensure the right args are passed to match the face
// so this one call will work for any face
printf("Packed Face Integrity Check: %s\n",
check_face_sum(sum_gpu, (face_id < 4 ? nj : nk),
(face_id < 2 || face_id > 3 ? ni : nk),
(face_id & 1 ?
(face_id < 2 ?
nk - 1 :
(face_id < 4 ? ni - 1 : nj - 1)) :
0)) ? "FAILED" : "PASSED");
//transpose the packed face (into the companion face's unoccupied buffer)
trans_dim[0] = (
face_spec->size[2] == 1 ?
face_spec->size[1] : face_spec->size[2]);
trans_dim[1] = (
face_spec->size[0] == 1 ?
face_spec->size[1] : face_spec->size[0]);
trans_dim[2] = 1;
rtrans_dim[0] = trans_dim[1];
rtrans_dim[1] = trans_dim[0];
rtrans_dim[2] = 1;
void * stuff = calloc(
face_spec->size[0] * face_spec->size[1]
* face_spec->size[2], g_typesize);
meta_copy_h2d(dev_face[(face_id & 1) ? face_id - 1 : face_id + 1],
stuff,
g_typesize * face_spec->size[0] * face_spec->size[1]
* face_spec->size[2], async);
//printf("**BEFORE**\n");
//check_buffer(face[face_id], dev_face[(face_id & 1) ? face_id-1 : face_id+1], face_spec->size[0]*face_spec->size[1]*face_spec->size[2]);
//printf("**********\n");
//check_dims(dimgrid_red, dimblock_red, trans_dim);
//TODO Figure out what's wrong with transpose and re-enable
ret = meta_transpose_face(NULL, NULL, dev_face[face_id],
dev_face[(face_id & 1) ? face_id - 1 : face_id + 1],
&trans_dim, &trans_dim, g_type, async);
printf("Transpose error: %d\n", ret);
//printf("**AFTER***\n");
//check_buffer(face[face_id], dev_face[(face_id & 1) ? face_id-1 : face_id+1], face_spec->size[0]*face_spec->size[1]*face_spec->size[2]);
//printf("**********\n");
//reduce the specific sums needed to check that transpose was correct
meta_copy_h2d(reduction, zero, g_typesize, async);
//shuffle the (local) X/Y dimension
rtrans_dim[0] = trans_dim[1];
rtrans_dim[1] = trans_dim[0];
rtrans_dim[2] = 1;
start_2d[0] = start_2d[1] = start_2d[2] = 0;
end_2d[0] = trans_dim[0] - 1, end_2d[1] = trans_dim[1] - 1, end_2d[2] =
0;
//check_dims(rtrans_dim, start_2d, end_2d);
ret = meta_reduce(autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red,
dev_face[(face_id & 1) ? face_id - 1 : face_id + 1],
&trans_dim, &start_2d, &end_2d, reduction, g_type, async);
//ret = meta_reduce(NULL, NULL, dev_face[(face_id & 1)? face_id-1 : face_id+1], &trans_dim, &start_2d, &end_2d, reduction, g_type, async);
meta_copy_d2h(sum_gpu, reduction, g_typesize, async);
//The 4 ternaries ensure the right args are passed to match the face
// so this one call will work for any face
printf("Transposed Face Integrity Check: %s\n",
check_face_sum(sum_gpu, (face_id < 4 ? nj : nk),
(face_id < 2 || face_id > 3 ? ni : nk),
(face_id & 1 ?
(face_id < 2 ?
nk - 1 :
(face_id < 4 ? ni - 1 : nj - 1)) :
0)) ? "FAILED" : "PASSED");
//transpose the face back
//TODO figure out what's wrong with transpose and re-enable
ret = meta_transpose_face(autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red,
dev_face[(face_id & 1) ? face_id - 1 : face_id + 1],
dev_face[face_id], &rtrans_dim, &rtrans_dim, g_type, async);
//check_buffer(face[face_id], dev_face[face_id], face_spec->size[0]*face_spec->size[1]*face_spec->size[2]);
//reduce the specified sums to ensure the reverse transpose worked too
meta_copy_h2d(reduction, zero, g_typesize, async);
start_2d[0] = start_2d[1] = start_2d[2] = 0;
end_2d[0] = rtrans_dim[0] - 1, end_2d[1] = rtrans_dim[1] - 1, end_2d[2] =
0;
dimgrid_tr_red[0] = dimgrid_red[1];
dimgrid_tr_red[1] = dimgrid_red[0];
dimgrid_tr_red[2] = dimgrid_red[2];
ret = meta_reduce(autoconfig ? NULL : &dimgrid_tr_red,
autoconfig ? NULL : &dimblock_red,
dev_face[(face_id & 1) ? face_id - 1 : face_id + 1],
&rtrans_dim, &start_2d, &end_2d, reduction, g_type, async);
meta_copy_d2h(sum_gpu, reduction, g_typesize, async);
//The 4 ternaries ensure the right args are passed to match the face
// so this one call will work for any face
printf("Retransposed Face Integrity Check: %s\n",
check_face_sum(sum_gpu, (face_id < 4 ? nj : nk),
(face_id < 2 || face_id > 3 ? ni : nk),
(face_id & 1 ?
(face_id < 2 ?
nk - 1 :
(face_id < 4 ? ni - 1 : nj - 1)) :
0)) ? "FAILED" : "PASSED");
;
//send the packed face to proc1
ret = meta_mpi_packed_face_send(1, dev_face[face_id],
trans_dim[0] * trans_dim[1], i, &request, g_type, async);
//Force the recv and unpack to finish
meta_flush();
//At this point the send should be forced to complete
// which means there's either a failure in the SP helper or the RP helper
//receive and unpack the face
//TODO set a_dim3 structs - i believe these are fine
//TODO set the face_spec - believe these are fine
ret = meta_mpi_recv_and_unpack_face(
autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red, 1, face_spec, dev_data3,
dev_face[face_id], i, &request, g_type, async);
//Force the recv and unpack to finish
meta_flush();
meta_copy_h2d(reduction, zero, g_typesize, async);
arr_start[0] = ((face_id == 3) ? ni - 1 : 0);
arr_end[0] = ((face_id == 2) ? 0 : ni - 1);
arr_start[1] = ((face_id == 5) ? nj - 1 : 0);
arr_end[1] = ((face_id == 4) ? 0 : nj - 1);
arr_start[2] = ((face_id == 1) ? nk - 1 : 0);
arr_end[2] = ((face_id == 0) ? 0 : nk - 1);
//check_dims(dimarray_3d, arr_start, arr_end);
ret = meta_reduce(autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red, dev_data3, &dimarray_3d,
&arr_start, &arr_end, reduction, g_type, async);
meta_copy_d2h(sum_gpu, reduction, g_typesize, async);
//The 4 ternaries ensure the right args are passed to match the face
// so this one call will work for any face
printf("RecvAndUnpacked ZeroFace Integrity Check: %s\n",
(check_fp(0.0, *((double*) sum_gpu), 0.000001)) ?
"PASSED" : "FAILED");
if (!check_fp(0.0, *((double*) sum_gpu), 0.000001))
printf("\tExpected [0.0], returned [%f]!\n", sum_gpu);
ret = meta_mpi_recv_and_unpack_face(
autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red, 1, face_spec, dev_data3,
dev_face[face_id], i, &request, g_type, async);
//Force the recv and unpack to finish
meta_flush();
meta_copy_h2d(reduction, zero, g_typesize, async);
arr_start[0] = ((face_id == 3) ? ni - 1 : 0);
arr_end[0] = ((face_id == 2) ? 0 : ni - 1);
arr_start[1] = ((face_id == 5) ? nj - 1 : 0);
arr_end[1] = ((face_id == 4) ? 0 : nj - 1);
arr_start[2] = ((face_id == 1) ? nk - 1 : 0);
arr_end[2] = ((face_id == 0) ? 0 : nk - 1);
//check_dims(dimarray_3d, arr_start, arr_end);
ret = meta_reduce(autoconfig ? NULL : &dimgrid_red,
autoconfig ? NULL : &dimblock_red, dev_data3, &dimarray_3d,
&arr_start, &arr_end, reduction, g_type, async);
meta_copy_d2h(sum_gpu, reduction, g_typesize, async);
//The 4 ternaries ensure the right args are passed to match the face
// so this one call will work for any face
printf("RecvAndUnpacked Face Integrity Check: %s\n",
check_face_sum(sum_gpu, (face_id < 4 ? nj : nk),
(face_id < 2 || face_id > 3 ? ni : nk),
(face_id & 1 ?
(face_id < 2 ?
nk - 1 :
(face_id < 4 ? ni - 1 : nj - 1)) :
0)) ? "FAILED" : "PASSED");
//TODO reduce the specified sub-sums on the face to further check accuracy of placement
} else {
