SEXP scan_bam_bin_offsets(SEXP bytes) {
SEXP ans;
if (!IS_RAW(bytes))
Rf_error("'bytes' must be a raw vector");
Rbyte *b = RAW(bytes);
if (strncmp(b, "BAI\1", 4))
Rf_error("wrong magic number");
b += 4;
int32_t nref = *(int32_t *)b; b += 4;
PROTECT(ans = NEW_LIST(nref));
for (int i = 0; i < nref; i++)
SET_VECTOR_ELT(ans, i, _scan_bin_offsets_seq(&b));
UNPROTECT(1);
return ans;
}
SEXP digest(SEXP Txt, SEXP Algo, SEXP Length, SEXP Skip, SEXP Leave_raw) {
FILE *fp=0;
char *txt;
int algo = INTEGER_VALUE(Algo);
int length = INTEGER_VALUE(Length);
int skip = INTEGER_VALUE(Skip);
int leaveRaw = INTEGER_VALUE(Leave_raw);
SEXP result = NULL;
char output[128+1], *outputp = output; /* 33 for md5, 41 for sha1, 65 for sha256, 128 for sha512; plus trailing NULL */
int nChar;
int output_length = -1;
if (IS_RAW(Txt)) { /* Txt is either RAW */
txt = (char*) RAW(Txt);
nChar = LENGTH(Txt);
} else { /* or a string */
txt = (char*) STRING_VALUE(Txt);
nChar = strlen(txt);
}
if (skip>0) {
if (skip>=nChar) nChar=0;
else {
nChar -= skip;
txt += skip;
}
}
if (length>=0 && length<nChar) nChar = length;
switch (algo) {
case 1: { /* md5 case */
md5_context ctx;
output_length = 16;
unsigned char md5sum[16];
int j;
md5_starts( &ctx );
md5_update( &ctx, (uint8 *) txt, nChar);
md5_finish( &ctx, md5sum );
memcpy(output, md5sum, 16);
if (!leaveRaw)
for(j = 0; j < 16; j++)
sprintf(output + j * 2, "%02x", md5sum[j]);
break;
}
case 2: { /* sha1 case */
int j;
sha1_context ctx;
output_length = 20;
unsigned char sha1sum[20];
sha1_starts( &ctx );
sha1_update( &ctx, (uint8 *) txt, nChar);
sha1_finish( &ctx, sha1sum );
memcpy(output, sha1sum, 20);
if (!leaveRaw)
for( j = 0; j < 20; j++ )
sprintf( output + j * 2, "%02x", sha1sum[j] );
break;
}
case 3: { /* crc32 case */
unsigned long val, l;
l = nChar;
val = digest_crc32(0L, 0, 0);
val = digest_crc32(val, (unsigned char*) txt, (unsigned) l);
sprintf(output, "%2.2x", (unsigned int) val);
break;
}
case 4: { /* sha256 case */
int j;
sha256_context ctx;
output_length = 32;
unsigned char sha256sum[32];
sha256_starts( &ctx );
sha256_update( &ctx, (uint8 *) txt, nChar);
sha256_finish( &ctx, sha256sum );
memcpy(output, sha256sum, 32);
if(!leaveRaw)
for( j = 0; j < 32; j++ )
sprintf( output + j * 2, "%02x", sha256sum[j] );
break;
}
case 5: { /* sha2-512 case */
int j;
SHA512_CTX ctx;
output_length = SHA512_DIGEST_LENGTH;
uint8_t sha512sum[output_length], *d = sha512sum;
SHA512_Init(&ctx);
SHA512_Update(&ctx, (uint8 *) txt, nChar);
// Calling SHA512_Final, because SHA512_End will already
// convert the hash to a string, and we also want RAW
SHA512_Final(sha512sum, &ctx);
memcpy(output, sha512sum, output_length);
// adapted from SHA512_End
if(!leaveRaw) {
for (j = 0; j < output_length; j++) {
*outputp++ = sha2_hex_digits[(*d & 0xf0) >> 4];
*outputp++ = sha2_hex_digits[*d & 0x0f];
d++;
}
*outputp = (char)0;
}
break;
}
case 101: { /* md5 file case */
int j;
md5_context ctx;
output_length = 16;
unsigned char buf[1024];
unsigned char md5sum[16];
if (!(fp = fopen(txt,"rb"))) {
error("Cannot open input file: %s", txt);
return(NULL);
}
if (skip > 0) fseek(fp, skip, SEEK_SET);
md5_starts( &ctx );
if (length>=0) {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0
&& length>0) {
if (nChar>length) nChar=length;
md5_update( &ctx, buf, nChar );
length -= nChar;
}
} else {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0)
md5_update( &ctx, buf, nChar );
}
fclose(fp);
md5_finish( &ctx, md5sum );
memcpy(output, md5sum, 16);
if (!leaveRaw)
for(j = 0; j < 16; j++)
sprintf(output + j * 2, "%02x", md5sum[j]);
break;
}
case 102: { /* sha1 file case */
int j;
sha1_context ctx;
output_length = 20;
unsigned char buf[1024];
unsigned char sha1sum[20];
if (!(fp = fopen(txt,"rb"))) {
error("Cannot open input file: %s", txt);
return(NULL);
}
if (skip > 0) fseek(fp, skip, SEEK_SET);
sha1_starts ( &ctx );
if (length>=0) {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0
&& length>0) {
if (nChar>length) nChar=length;
sha1_update( &ctx, buf, nChar );
length -= nChar;
}
} else {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0)
sha1_update( &ctx, buf, nChar );
}
fclose(fp);
sha1_finish ( &ctx, sha1sum );
memcpy(output, sha1sum, 20);
if(!leaveRaw)
for( j = 0; j < 20; j++ )
sprintf( output + j * 2, "%02x", sha1sum[j] );
break;
}
case 103: { /* crc32 file case */
unsigned char buf[1024];
unsigned long val;
if (!(fp = fopen(txt,"rb"))) {
error("Cannot open input file: %s", txt);
return(NULL);
}
if (skip > 0) fseek(fp, skip, SEEK_SET);
val = digest_crc32(0L, 0, 0);
if (length>=0) {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0
&& length>0) {
if (nChar>length) nChar=length;
val = digest_crc32(val , buf, (unsigned) nChar);
length -= nChar;
}
} else {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0)
val = digest_crc32(val , buf, (unsigned) nChar);
}
fclose(fp);
sprintf(output, "%2.2x", (unsigned int) val);
break;
}
case 104: { /* sha256 file case */
int j;
sha256_context ctx;
output_length = 32;
unsigned char buf[1024];
unsigned char sha256sum[32];
if (!(fp = fopen(txt,"rb"))) {
error("Cannot open input file: %s", txt);
return(NULL);
}
if (skip > 0) fseek(fp, skip, SEEK_SET);
sha256_starts ( &ctx );
if (length>=0) {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0
&& length>0) {
if (nChar>length) nChar=length;
sha256_update( &ctx, buf, nChar );
length -= nChar;
}
} else {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0)
sha256_update( &ctx, buf, nChar );
}
fclose(fp);
sha256_finish ( &ctx, sha256sum );
memcpy(output, sha256sum, 32);
if(!leaveRaw)
for( j = 0; j < 32; j++ )
sprintf( output + j * 2, "%02x", sha256sum[j] );
break;
}
case 105: { /* sha2-512 file case */
int j;
SHA512_CTX ctx;
output_length = SHA512_DIGEST_LENGTH;
uint8_t sha512sum[output_length], *d = sha512sum;
unsigned char buf[1024];
if (!(fp = fopen(txt,"rb"))) {
error("Cannot open input file: %s", txt);
return(NULL);
}
if (skip > 0) fseek(fp, skip, SEEK_SET);
SHA512_Init(&ctx);
if (length>=0) {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0
&& length>0) {
if (nChar>length) nChar=length;
SHA512_Update( &ctx, buf, nChar );
length -= nChar;
}
} else {
while( ( nChar = fread( buf, 1, sizeof( buf ), fp ) ) > 0)
SHA512_Update( &ctx, buf, nChar );
}
fclose(fp);
// Calling SHA512_Final, because SHA512_End will already
// convert the hash to a string, and we also want RAW
SHA512_Final(sha512sum, &ctx);
memcpy(output, sha512sum, output_length);
// adapted from SHA512_End
if(!leaveRaw) {
for (j = 0; j < output_length; j++) {
*outputp++ = sha2_hex_digits[(*d & 0xf0) >> 4];
*outputp++ = sha2_hex_digits[*d & 0x0f];
d++;
}
*outputp = (char)0;
}
break;
}
default: {
error("Unsupported algorithm code");
return(NULL);
}
}
if (leaveRaw && output_length > 0) {
PROTECT(result=allocVector(RAWSXP, output_length));
memcpy(RAW(result), output, output_length);
} else {
PROTECT(result=allocVector(STRSXP, 1));
SET_STRING_ELT(result, 0, mkChar(output));
}
UNPROTECT(1);
return result;
}
int pluto_loop_is_parallel(const PlutoProg *prog, Ploop *loop)
{
int parallel, i;
fprintf(stderr,"%s\n",__PRETTY_FUNCTION__);
/* All statements under a parallel loop should be of type orig */
for (i=0; i<loop->nstmts; i++) {
if (loop->stmts[i]->type != ORIG) break;
}
if (i<loop->nstmts) {
fprintf(stderr,"%s: is not parallel du to no statements\n",__PRETTY_FUNCTION__);
return 0;
}
if (prog->hProps[loop->depth].dep_prop == PARALLEL) {
fprintf(stderr,"%s: is parallel due to hProps\n",__PRETTY_FUNCTION__);
return 1;
}
parallel = 1;
fprintf(stderr,"ndeps %d\n",prog->ndeps);
PlutoProg* nc_prog = (PlutoProg*)prog;
nc_prog->deps_explanation = (char**)malloc(sizeof(char*)*prog->ndeps);
for( int i = 0 ; i < prog->ndeps ; i++ ) {
nc_prog->deps_explanation[i] = (char*)malloc( sizeof(char) * 256 );
sprintf(nc_prog->deps_explanation[i],"undefined");
}
// or all dependencies that are not rar dependencies
for (i=0; i<prog->ndeps; i++) {
Dep *dep = prog->deps[i];
fprintf(stderr,"dep->src %d dep->dest %d\n",dep->src, dep->dest);
if (IS_RAR(dep->type)) {
fprintf(stderr,"dep %d is rar dep\n",i);
continue;
}
sprintf(nc_prog->deps_explanation[i],"ok");
assert(dep->satvec != NULL);
// are members of the loop
if (pluto_stmt_is_member_of(prog->stmts[dep->src]->id, loop->stmts, loop->nstmts)
&& pluto_stmt_is_member_of(prog->stmts[dep->dest]->id, loop->stmts,
loop->nstmts)) {
fprintf(stderr,"dep %d both are members of this loop\n",i);
// and does not have a satvec that is != 0
if (dep->satvec[loop->depth]) {
fprintf(stderr,"dep %d stavec is != 0 for loop->depth %d\n",i, loop->depth);
parallel *= 0;
char* type = "";
if ( IS_RAR(dep->type) ) {
type = "RAR";
}
if ( IS_RAW(dep->type) ) {
type = "RAW";
}
if ( IS_WAR(dep->type) ) {
type = "WAR";
}
if ( IS_WAW(dep->type) ) {
type = "WAW";
}
sprintf(nc_prog->deps_explanation[i],"from stmt %d to stmt %d type %s: prevents parallelism", dep->src, dep->dest, type);
//break;
}
}
}
if ( parallel ) {
fprintf(stderr,"loop IS parallel\n");
} else {
fprintf(stderr,"loop is NOT parallel \n");
}
return parallel;
}
