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esl_dsqdata.c
1810 lines (1599 loc) · 81 KB
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esl_dsqdata.c
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/* esl_dsqdata : faster sequence input
*
* Implements a predigitized binary file format for biological
* sequences. Sequence data are packed bitwise into 32-bit packets,
* where each packet contains either six 5-bit residues or fifteen
* 2-bit residues, plus two control bits. Input is asynchronous,
* using POSIX threads, with a "loader" thread doing disk reads and
* "unpacker" thread(s) preparing chunks of sequences for
* analysis. Sequence data and metadata are stored in separate files,
* which may allow further input acceleration by deferring
* metadata accesses until they're actually needed.
*
* All thread synchronization is handled internally. A caller does not
* need to worry about the internal parallelism; it just calls
* <esl_dsqdata_Read()>. Caller can create multiple threads, each
* calling <esl_dsqdata_Read()>.
*
* A DSQDATA database <basename> is stored in four files:
* - basename : a human-readable stub
* - basename.dsqi : index file, enabling random access & parallel chunking
* - basename.dsqm : metadata including names, accessions, descs, taxonomy
* - basename.dsqs : sequences, in a packed binary format
*
* Contents:
* 1. ESL_DSQDATA: reading dsqdata format
* 2. Creating dsqdata format from a sequence file
* 3. ESL_DSQDATA_CHUNK, a chunk of input sequence data
* 4. Loader and unpacker, the input threads
* 5. Packing sequences and unpacking chunks
* 6. Notes and references
* 7. Unit tests
* 8. Test driver
* 9. Examples
*/
#include <esl_config.h>
#include <stdio.h>
#include <string.h>
#include <stdint.h>
#include <pthread.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_random.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_dsqdata.h"
static ESL_DSQDATA_CHUNK *dsqdata_chunk_Create (ESL_DSQDATA *dd);
static void dsqdata_chunk_Destroy(ESL_DSQDATA_CHUNK *chu);
static void *dsqdata_loader_thread (void *p);
static void *dsqdata_unpacker_thread(void *p);
static int dsqdata_unpack_chunk(ESL_DSQDATA_CHUNK *chu, int do_pack5);
static int dsqdata_unpack5(uint32_t *psq, ESL_DSQ *dsq, int *ret_L, int *ret_P);
static int dsqdata_unpack2(uint32_t *psq, ESL_DSQ *dsq, int *ret_L, int *ret_P);
static int dsqdata_pack5 (ESL_DSQ *dsq, int L, uint32_t *psq, int *ret_P);
static int dsqdata_pack2 (ESL_DSQ *dsq, int L, uint32_t *psq, int *ret_P);
/* Embedded magic numbers allow us to validate the correct binary
* format, with version (if needed in the future), and to detect
* byteswapping.
*/
static uint32_t eslDSQDATA_MAGIC_V1 = 0xc4d3d1b1; // "dsq1" + 0x80808080
static uint32_t eslDSQDATA_MAGIC_V1SWAP = 0xb1d1d3c4; // ... as above, but byteswapped.
/*****************************************************************
*# 1. <ESL_DSQDATA>: reading dsqdata format
*****************************************************************/
/* Function: esl_dsqdata_Open()
* Synopsis: Open a digital sequence database for reading
* Incept: SRE, Wed Jan 20 09:50:00 2016 [Amtrak 2150, NYP-BOS]
*
* Purpose: Open dsqdata database <basename> for reading. The file
* <basename> is a stub describing the database. The bulk
* of the data are in three accompanying binary files: the
* index file <basename>.dsqi, the metadata file
* <basename>.dsqm, and the sequence file <basename>.dsqs.
*
* <nconsumers> is an upper bound on the number of threads
* in which the caller plans to be calling
* <esl_dsqdata_Read()> -- or, more precisely, the maximum
* number of data chunks that the caller could be working
* on at any given instant. This is a hint, not a
* commitment. The dsqdata loader uses it to determine the
* maximum number of data chunks that can be in play at
* once (including chunks it is juggling internally, plus
* if all the caller's reader threads are busy on
* theirs). If <nconsumers> is set too small, the loader
* may stall waiting for chunks to come back for recycling.
*
* Reading digital sequence data requires a digital
* alphabet. You can either provide one (in which case we
* validate that it matches the alphabet used by the
* dsqdata) or, as a convenience, <esl_dsqdata_Open()> can
* create one for you. Either way, you pass a pointer to an
* <ESL_ALPHABET> structure <abc>, in <byp_abc>. <byp_abc>
* uses a partial Easel "bypass" idiom: if <*byp_abc> is
* NULL, we allocate and return a new alphabet; if
* <*byp_abc> is a ptr to an existing alphabet, we use it
* for validation. That is, you have two choices:
*
* ```
* ESL_ALPHABET *abc = NULL;
* esl_dsqdata_Open(&abc, basename...)
* // <abc> is now the alphabet of <basename>;
* // now you're responsible for Destroy'ing it
* ```
*
* or:
*
* ```
* ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
* status = esl_dsqdata_Open(&abc, basename);
* // if status == eslEINCOMPAT, alphabet in basename
* // doesn't match caller's expectation
* ```
*
* Args: byp_abc : expected or created alphabet; pass &abc, abc=NULL or abc=expected alphabet
* basename : data are in files <basename> and <basename.dsq[ism]>
* nconsumers : upper bound on number of consumer threads caller is going to Read() with
* ret_dd : RETURN : the new ESL_DSQDATA object.
*
* Returns: <eslOK> on success.
*
* <eslENOTFOUND> if one or more of the expected datafiles
* aren't there or can't be opened.
*
* <eslEFORMAT> if something looks wrong in parsing file
* formats. Includes problems in headers, and also the
* case where caller provides a digital alphabet in
* <*byp_abc> and it doesn't match the database's alphabet.
*
* On any normal error, <*ret_dd> is still returned, but in
* an error state, and <dd->errbuf> is a user-directed
* error message that the caller can relay to the user. Other
* than the <errbuf>, the rest of the contents are undefined.
*
* Caller is responsible for destroying <*byp_abc>.
*
* Throws: <eslEMEM> on allocation error.
* <eslESYS> on system call failure.
* <eslEUNIMPLEMENTED> if data are byteswapped
* TODO: handle byteswapping
*
* On any thrown exception, <*ret_dd> is returned NULL.
*
* On <eslESYS> exceptions, some thread resources may
* not be fully freed, leading to some memory leakage.
*/
int
esl_dsqdata_Open(ESL_ALPHABET **byp_abc, char *basename, int nconsumers, ESL_DSQDATA **ret_dd)
{
ESL_DSQDATA *dd = NULL;
int bufsize = 4096;
uint32_t magic = 0;
uint32_t tag = 0;
uint32_t alphatype = eslUNKNOWN;
int ndd;
char *p; // used for strtok() parsing of fields on a line
char buf[4096];
int u;
int status;
ESL_DASSERT1(( nconsumers > 0 ));
ESL_DASSERT1(( byp_abc != NULL )); // either *byp_abc == NULL or *byp_abc = the caller's expected alphabet.
ESL_ALLOC(dd, sizeof(ESL_DSQDATA));
dd->stubfp = NULL;
dd->ifp = NULL;
dd->sfp = NULL;
dd->mfp = NULL;
dd->abc_r = *byp_abc; // This may be NULL; if so, we create it later.
dd->magic = 0;
dd->uniquetag = 0;
dd->flags = 0;
dd->max_namelen = 0;
dd->max_acclen = 0;
dd->max_desclen = 0;
dd->max_seqlen = 0;
dd->nseq = 0;
dd->nres = 0;
dd->chunk_maxseq = eslDSQDATA_CHUNK_MAXSEQ; // someday we may want to allow tuning these
dd->chunk_maxpacket = eslDSQDATA_CHUNK_MAXPACKET;
dd->do_byteswap = FALSE;
dd->pack5 = FALSE;
dd->nconsumers = nconsumers;
dd->n_unpackers = eslDSQDATA_UNPACKERS; // we'll want to allow tuning this too
dd->errbuf[0] = '\0';
/* Open the four files.
*/
ndd = strlen(basename) + 6; // +5 for .dsqx; +1 for \0
ESL_ALLOC( dd->basename, ndd);
if ( snprintf(dd->basename, ndd, "%s.dsqi", basename) <= 0) ESL_XEXCEPTION_SYS(eslESYS, "sprintf() failure");
if (( dd->ifp = fopen(dd->basename, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open index file %s\n", dd->basename);
if ( snprintf(dd->basename, ndd, "%s.dsqm", basename) <= 0) ESL_XEXCEPTION_SYS(eslESYS, "sprintf() failure");
if (( dd->mfp = fopen(dd->basename, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open metadata file %s\n", dd->basename);
if ( snprintf(dd->basename, ndd, "%s.dsqs", basename) <= 0) ESL_XEXCEPTION_SYS(eslESYS, "sprintf() failure");
if (( dd->sfp = fopen(dd->basename, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open sequence file %s\n", dd->basename);
strcpy(dd->basename, basename);
if (( dd->stubfp = fopen(dd->basename, "r")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open stub file %s\n", dd->basename);
/* The stub file is unparsed, intended to be human readable, with one exception:
* The first line contains the unique tag that we use to validate linkage of the 4 files.
* The format of that first line is:
* Easel dsqdata v123 x0000000000
*/
if ( fgets(buf, bufsize, dd->stubfp) == NULL) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file is empty - no tag line found");
if (( p = strtok(buf, " \t\n\r")) == NULL) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format: tag line has no data");
if ( strcmp(p, "Easel") != 0) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format in tag line");
if (( p = strtok(NULL, " \t\n\r")) == NULL) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format in tag line");
if ( strcmp(p, "dsqdata") != 0) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format in tag line");
if (( p = strtok(NULL, " \t\n\r")) == NULL) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format in tag line");
if ( *p != 'v') ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format: no v on version");
if ( ! esl_str_IsInteger(p+1)) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file had bad format: no version number");
// version number is currently unused: there's only 1
if (( p = strtok(NULL, " \t\n\r")) == NULL) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format in tag line");
if ( *p != 'x') ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file has bad format: no x on tag");
if ( ! esl_str_IsInteger(p+1)) ESL_XFAIL(eslEFORMAT, dd->errbuf, "stub file had bad format: no integer tag");
dd->uniquetag = strtoul(p+1, NULL, 10);
/* Index file has a header of 7 uint32's, 3 uint64's */
if ( fread(&(dd->magic), sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file has no header - is empty?");
if ( fread(&tag, sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no tag");
if ( fread(&alphatype, sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no alphatype");
if ( fread(&(dd->flags), sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no flags");
if ( fread(&(dd->max_namelen), sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no max name len");
if ( fread(&(dd->max_acclen), sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no max accession len");
if ( fread(&(dd->max_desclen), sizeof(uint32_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no max description len");
if ( fread(&(dd->max_seqlen), sizeof(uint64_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no max seq len");
if ( fread(&(dd->nseq), sizeof(uint64_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no nseq");
if ( fread(&(dd->nres), sizeof(uint64_t), 1, dd->ifp) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file header truncated, no nres");
/* Check the magic and the tag */
if (tag != dd->uniquetag) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file has bad tag, doesn't go with stub file");
// Eventually we would set dd->do_byteswap = TRUE; below.
if (dd->magic == eslDSQDATA_MAGIC_V1SWAP) ESL_XEXCEPTION(eslEUNIMPLEMENTED, "dsqdata cannot yet read data in different byte orders");
else if (dd->magic != eslDSQDATA_MAGIC_V1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file has bad magic");
/* Either validate, or create the alphabet */
if (dd->abc_r)
{
if (alphatype != dd->abc_r->type)
ESL_XFAIL(eslEFORMAT, dd->errbuf, "data files use %s alphabet; expected %s alphabet",
esl_abc_DecodeType(alphatype),
esl_abc_DecodeType(dd->abc_r->type));
}
else
{
if ( esl_abc_ValidateType(alphatype) != eslOK) ESL_XFAIL(eslEFORMAT, dd->errbuf, "index file has invalid alphabet type %d", alphatype);
if (( dd->abc_r = esl_alphabet_Create(alphatype)) == NULL) ESL_XEXCEPTION(eslEMEM, "alphabet creation failed");
}
/* If it's protein, flip the switch to expect all 5-bit packing */
if (dd->abc_r->type == eslAMINO) dd->pack5 = TRUE;
/* Metadata file has a header of 2 uint32's, magic and uniquetag */
if (( fread(&magic, sizeof(uint32_t), 1, dd->mfp)) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "metadata file has no header - is empty?");
if (( fread(&tag, sizeof(uint32_t), 1, dd->mfp)) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "metadata file header truncated - no tag?");
if ( magic != dd->magic) ESL_XFAIL(eslEFORMAT, dd->errbuf, "metadata file has bad magic");
if ( tag != dd->uniquetag) ESL_XFAIL(eslEFORMAT, dd->errbuf, "metadata file has bad tag, doesn't match stub");
/* Sequence file also has a header of 2 uint32's, magic and uniquetag */
if (( fread(&magic, sizeof(uint32_t), 1, dd->sfp)) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "sequence file has no header - is empty?");
if (( fread(&tag, sizeof(uint32_t), 1, dd->sfp)) != 1) ESL_XFAIL(eslEFORMAT, dd->errbuf, "sequence file header truncated - no tag?");
if ( magic != dd->magic) ESL_XFAIL(eslEFORMAT, dd->errbuf, "sequence file has bad magic");
if ( tag != dd->uniquetag) ESL_XFAIL(eslEFORMAT, dd->errbuf, "sequence file has bad tag, doesn't match stub");
/* unpacker inboxes and outboxes */
for (u = 0; u < dd->n_unpackers; u++)
{
dd->inbox[u] = NULL;
if ( pthread_mutex_init(&(dd->inbox_mutex[u]), NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_init() failed");
if ( pthread_cond_init (&(dd->inbox_cv[u]), NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_cond_init() failed");
dd->inbox_eod[u] = FALSE;
dd->outbox[u] = NULL;
if ( pthread_mutex_init(&(dd->outbox_mutex[u]), NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_init() failed");
if ( pthread_cond_init (&(dd->outbox_cv[u]), NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_cond_init() failed");
dd->outbox_eod[u] = FALSE;
}
/* consumers share access to <nchunk> counter */
dd->nchunk = 0;
if ( pthread_mutex_init(&dd->nchunk_mutex, NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_init() failed");
/* chunk recycling stack */
dd->recycling = NULL;
if ( pthread_mutex_init(&dd->recycling_mutex, NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_init() failed");
if ( pthread_cond_init(&dd->recycling_cv, NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_cond_init() failed");
/* Create the "initialization is complete" signaling mechanism
* before creating any threads, and lock the initialization mutex
* while we're creating them. The issue here is that unpackers
* identify their [u] index by comparing their self thread id to the
* master list of thread ids, so make sure that master list actually
* exists.
*/
dd->go = FALSE;
if ( pthread_mutex_init(&dd->go_mutex, NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_init() failed on go_mutex");
if ( pthread_cond_init( &dd->go_cv, NULL) != 0) ESL_XEXCEPTION(eslESYS, "pthread_cond_init() failed on go_cv");
if ( pthread_mutex_lock(&dd->go_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_lock() failed on go_mutex");
/* Create the loader and the unpackers.
* They will wait to start until we signal through go->cv.
*/
if ( pthread_create(&dd->loader_t, NULL, dsqdata_loader_thread, dd) != 0) ESL_XEXCEPTION(eslESYS, "pthread_create() failed");
for (u = 0; u < dd->n_unpackers; u++)
if ( pthread_create(&(dd->unpacker_t[u]), NULL, dsqdata_unpacker_thread, dd) != 0) ESL_XEXCEPTION(eslESYS, "pthread_create() failed");
/* All threads started, initialization complete - broadcast "go" signal to all threads */
dd->go = TRUE;
if ( pthread_mutex_unlock(&dd->go_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_unlock() failed on go_mutex");
if ( pthread_cond_broadcast(&dd->go_cv) != 0) ESL_XEXCEPTION(eslESYS, "pthread_cond_broadcast() failed on go_cv");
*ret_dd = dd;
*byp_abc = dd->abc_r; // If caller provided <*byp_abc> this is a no-op, because we set abc_r = *byp_abc.
return eslOK; // .. otherwise we're passing the created <abc> back to caller, caller's
// responsibility, we just keep the reference to it.
ERROR:
if (status == eslENOTFOUND || status == eslEFORMAT || status == eslEINCOMPAT)
{ /* on normal errors, we return <dd> with its <errbuf>, don't change *byp_abc */
*ret_dd = dd;
if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r);
return status;
}
else if (status != eslESYS)
{ /* on most exceptions, we free <dd>, return it NULL, don't change *byp_abc */
esl_dsqdata_Close(dd);
*ret_dd = NULL;
if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r);
return status;
}
else
{ /* on eslESYS exceptions - pthread initializations failing - we can't assume we can _Close() correctly. */
*ret_dd = NULL;
if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r);
return status;
}
}
/* Function: esl_dsqdata_Read()
* Synopsis: Read next chunk of sequence data.
* Incept: SRE, Thu Jan 21 11:21:38 2016 [Harvard]
*
* Purpose: Read the next chunk from <dd>, return a pointer to it in
* <*ret_chu>, and return <eslOK>. When data are exhausted,
* return <eslEOF>, and <*ret_chu> is <NULL>.
*
* Threadsafe. All thread operations in the dsqdata reader
* are handled internally. Caller does not have to worry
* about wrapping this in a mutex. Multiple caller threads
* can call <esl_dsqdata_Read()>.
*
* All chunk allocation and deallocation is handled
* internally. After using a chunk, caller gives it back to
* the reader using <esl_dsqdata_Recycle()>.
*
* Args: dd : open dsqdata object to read from
* ret_chu : RETURN : next chunk of seq data
*
* Returns: <eslOK> on success. <*ret_chu> is a chunk of seq data.
* Caller must call <esl_dsqdata_Recycle()> on each chunk
* that it Read()'s.
*
* <eslEOF> if we've reached the end of the input file;
* <*ret_chu> is NULL.
*
* Throws: <eslESYS> if a pthread call fails.
* Caller should treat this as disastrous. Without correctly
* working pthread calls, we cannot read, and we may not be able
* to correctly clean up and close the reader. Caller should
* treat <dd> as toxic, clean up whatever else it may need to,
* and exit.
*/
int
esl_dsqdata_Read(ESL_DSQDATA *dd, ESL_DSQDATA_CHUNK **ret_chu)
{
ESL_DSQDATA_CHUNK *chu = NULL;
int u;
/* First, determine which slot the next chunk is in, using the consumer-shared <nchunk> counter */
if ( pthread_mutex_lock(&dd->nchunk_mutex) != 0) ESL_EXCEPTION(eslESYS, "failed to lock reader mutex");
u = (int) (dd->nchunk % dd->n_unpackers);
/* Acquire a lock that outbox, wait for it to be in full or EOD state */
if ( pthread_mutex_lock(&(dd->outbox_mutex[u])) != 0) ESL_EXCEPTION(eslESYS, "failed to lock outbox[u] mutex");
while (! dd->outbox_eod[u] && dd->outbox[u] == NULL) {
if ( pthread_cond_wait(&(dd->outbox_cv[u]), &(dd->outbox_mutex[u])) != 0) ESL_EXCEPTION(eslESYS, "failed to wait on outbox[u] signal");
}
/* Get the chunk from outbox. */
chu = dd->outbox[u];
dd->outbox[u] = NULL;
if (chu) dd->nchunk++; // chu==NULL if we're EOD. (and eod flag is up too, but we already know that by getting here)
/* Release the outbox lock and signal back to unpacker (skip signalling if we're EOD; unpacker[u] is done) */
if ( pthread_mutex_unlock(&(dd->outbox_mutex[u])) != 0) ESL_EXCEPTION(eslESYS, "failed to unlock outbox[u] mutex");
if ( chu && pthread_cond_signal (&(dd->outbox_cv[u])) != 0) ESL_EXCEPTION(eslESYS, "failed to signal outbox[u] is empty");
/* Release the reader lock that protects dd->nchunk counter */
if ( pthread_mutex_unlock(&dd->nchunk_mutex) != 0) ESL_EXCEPTION(eslESYS, "failed to unlock reader mutex");
*ret_chu = chu;
return (chu ? eslOK : eslEOF);
}
/* Function: esl_dsqdata_Recycle()
* Synopsis: Give a chunk back to the reader.
* Incept: SRE, Thu Feb 11 19:24:33 2016
*
* Purpose: Recycle chunk <chu> back to the reader <dd>. The reader
* is responsible for all allocation and deallocation of
* chunks. The reader will either reuse the chunk's memory
* if more chunks remain to be read, or it will free it.
*
* Args: dd : dsqdata reader
* chu : chunk to recycle
*
* Returns: <eslOK> on success.
*
* Throws: <eslESYS> on a pthread call failure. Caller should regard
* such an error as disastrous; if pthread calls are
* failing, you cannot depend on the reader to be working
* at all, and you should treat <dd> as toxic. Do whatever
* desperate things you need to do and exit.
*/
int
esl_dsqdata_Recycle(ESL_DSQDATA *dd, ESL_DSQDATA_CHUNK *chu)
{
if (chu)
{
if ( pthread_mutex_lock(&dd->recycling_mutex) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex lock failed");
chu->nxt = dd->recycling; // Push chunk onto head of recycling stack
dd->recycling = chu;
if ( pthread_mutex_unlock(&dd->recycling_mutex) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex unlock failed");
if ( pthread_cond_signal(&dd->recycling_cv) != 0) ESL_EXCEPTION(eslESYS, "pthread cond signal failed"); // loader may wait for this signal
}
return eslOK;
}
/* Function: esl_dsqdata_Close()
* Synopsis: Close a dsqdata reader.
* Incept: SRE, Thu Feb 11 19:32:54 2016
*
* Purpose: Close a dsqdata reader.
*
* Returns: <eslOK> on success.
* Throws: <eslESYS> on a system call failure, including pthread
* calls and fclose(). Caller should regard such a failure
* as disastrous: treat <dd> as toxic and exit as soon as
* possible without making any other system calls, if possible.
*
* Note: Normally Easel would call _Close() not only on a correctly
* opened object (after the Open returns) but also from
* within the Open call to clean up on failure. This relies
* on being able to tell which parts of an incomplete
* object have been initialized; this is why Easel sets
* ptrs to NULL before allocating them, for example. POSIX
* threads doesn't seem to give us a way to check whether a
* mutex, condition variable, or thread has been
* initialized; and destroying an uninitialized mutex or CV
* results in undefined behavior. We could include a
* boolean flag for each pthreads component -- or one for
* all of them -- but instead, we simply say that a failure
* of pthreads initialization in the Open function is so
* catastrophic and unexpected that we exit that function
* without cleaning up the incomplete ESL_DSQDATA
* structure. We expect that the caller is simply going to
* have to quit anyway, so we don't need to worry about
* memory leakage.
*/
int
esl_dsqdata_Close(ESL_DSQDATA *dd)
{
int u;
if (dd)
{
/* out of abundance of caution - wait for threads to join before breaking down <dd> */
if ( pthread_join(dd->loader_t, NULL) != 0) ESL_EXCEPTION(eslESYS, "pthread join failed");
for (u = 0; u < dd->n_unpackers; u++)
if ( pthread_join(dd->unpacker_t[u], NULL) != 0) ESL_EXCEPTION(eslESYS, "pthread join failed");
if (dd->basename) free(dd->basename);
if (dd->stubfp) { if ( fclose(dd->stubfp) != 0) ESL_EXCEPTION(eslESYS, "fclose failed"); }
if (dd->ifp) { if ( fclose(dd->ifp) != 0) ESL_EXCEPTION(eslESYS, "fclose failed"); }
if (dd->sfp) { if ( fclose(dd->sfp) != 0) ESL_EXCEPTION(eslESYS, "fclose failed"); }
if (dd->mfp) { if ( fclose(dd->mfp) != 0) ESL_EXCEPTION(eslESYS, "fclose failed"); }
for (u = 0; u < dd->n_unpackers; u++)
{
if ( pthread_mutex_destroy(&(dd->inbox_mutex[u])) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex destroy failed");
if ( pthread_cond_destroy(&(dd->inbox_cv[u])) != 0) ESL_EXCEPTION(eslESYS, "pthread cond destroy failed");
if ( pthread_mutex_destroy(&(dd->outbox_mutex[u])) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex destroy failed");
if ( pthread_cond_destroy(&(dd->outbox_cv[u])) != 0) ESL_EXCEPTION(eslESYS, "pthread cond destroy failed");
}
if ( pthread_mutex_destroy(&dd->nchunk_mutex) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex destroy failed");
if ( pthread_mutex_destroy(&dd->recycling_mutex) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex destroy failed");
if ( pthread_cond_destroy(&dd->recycling_cv) != 0) ESL_EXCEPTION(eslESYS, "pthread cond destroy failed");
if ( pthread_mutex_destroy(&dd->go_mutex) != 0) ESL_EXCEPTION(eslESYS, "pthread mutex destroy failed");
if ( pthread_cond_destroy(&dd->go_cv) != 0) ESL_EXCEPTION(eslESYS, "pthread cond destroy failed");
/* Loader thread is responsible for freeing all chunks it created, even on error. */
#if (eslDEBUGLEVEL >= 1)
for (u = 0; u < dd->n_unpackers; u++) {
assert( dd->inbox[u] == NULL );
assert( dd->outbox[u] == NULL );
}
assert(dd->recycling == NULL );
#endif
free(dd);
}
return eslOK;
}
/*****************************************************************
*# 2. Creating dsqdata format from a sequence file
*****************************************************************/
/* Function: esl_dsqdata_Write()
* Synopsis: Create a dsqdata database
* Incept: SRE, Sat Feb 13 07:33:30 2016 [AGBT 2016, Orlando]
*
* Purpose: Caller has just opened <sqfp>, in digital mode.
* Create a dsqdata database <basename> from the sequence
* data in <sqfp>.
*
* <sqfp> must be protein, DNA, or RNA sequence data. It
* must be rewindable (i.e. a file), because we have to
* read it twice. It must be newly opened (i.e. positioned
* at the start).
*
* Args: sqfp - newly opened sequence data file
* basename - base name of dsqdata files to create
* errbuf - user-directed error message on normal errors
*
* Returns: <eslOK> on success.
*
* <eslEWRITE> if an output file can't be opened. <errbuf>
* contains user-directed error message.
*
* <eslEFORMAT> if a parse error is encountered while
* reading <sqfp>.
*
*
* Throws: <eslESYS> A system call failed, such as fwrite().
* <eslEINVAL> Sequence handle <sqfp> isn't digital and rewindable.
* <eslEMEM> Allocation failure
* <eslEUNIMPLEMENTED> Sequence is too long to be encoded.
* (TODO: chromosome-scale DNA sequences)
*/
int
esl_dsqdata_Write(ESL_SQFILE *sqfp, char *basename, char *errbuf)
{
ESL_RANDOMNESS *rng = NULL;
ESL_SQ *sq = NULL;
FILE *stubfp = NULL;
FILE *ifp = NULL;
FILE *mfp = NULL;
FILE *sfp = NULL;
char *outfile = NULL;
uint32_t magic = eslDSQDATA_MAGIC_V1;
uint32_t uniquetag;
uint32_t alphatype;
uint32_t flags = 0;
uint32_t max_namelen = 0;
uint32_t max_acclen = 0;
uint32_t max_desclen = 0;
uint64_t max_seqlen = 0;
uint64_t nseq = 0;
uint64_t nres = 0;
int do_pack5 = FALSE;
uint32_t *psq;
ESL_DSQDATA_RECORD idx; // one index record to write
int plen;
int64_t spos = 0;
int64_t mpos = 0;
int n;
int na;
int status;
if (! esl_sqfile_IsRewindable(sqfp)) ESL_EXCEPTION(eslEINVAL, "sqfp must be rewindable (e.g. an open file)");
if (! sqfp->abc) ESL_EXCEPTION(eslEINVAL, "sqfp must be digital");
// Could also check that it's positioned at the start.
if ( (sq = esl_sq_CreateDigital(sqfp->abc)) == NULL) { status = eslEMEM; goto ERROR; }
/* First pass over the sequence file, to get statistics.
* Read it now, before opening any files, in case we find any parse errors.
*/
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
if (sq->n >= 6 * eslDSQDATA_CHUNK_MAXPACKET) // guaranteed limit
ESL_EXCEPTION(eslEUNIMPLEMENTED, "dsqdata cannot currently deal with large sequences");
nseq++;
nres += sq->n;
if (sq->n > max_seqlen) max_seqlen = sq->n;
n = strlen(sq->name); if (n > max_namelen) max_namelen = n;
n = strlen(sq->acc); if (n > max_acclen) max_acclen = n;
n = strlen(sq->desc); if (n > max_desclen) max_desclen = n;
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) ESL_XFAIL(eslEFORMAT, errbuf, sqfp->get_error(sqfp));
else if (status != eslEOF) return status;
if ((status = esl_sqfile_Position(sqfp, 0)) != eslOK) return status;
if (( rng = esl_randomness_Create(0) ) == NULL) { status = eslEMEM; goto ERROR; }
uniquetag = esl_random_uint32(rng);
alphatype = sqfp->abc->type;
if (alphatype == eslAMINO) do_pack5 = TRUE;
else if (alphatype != eslDNA && alphatype != eslRNA) ESL_EXCEPTION(eslEINVAL, "alphabet must be protein or nucleic");
na = strlen(basename) + 6; // '.dsq?' + '\0'
ESL_ALLOC(outfile, na);
if ( snprintf(outfile, na, "%s.dsqi", basename) < 0) ESL_EXCEPTION(eslESYS, "sprintf failed");
if (( ifp = fopen(outfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata index file %s for writing", outfile);
if ( snprintf(outfile, na, "%s.dsqm", basename) < 0) ESL_EXCEPTION(eslESYS, "sprintf failed");
if (( mfp = fopen(outfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata metadata file %s for writing", outfile);
if ( snprintf(outfile, na, "%s.dsqs", basename) < 0) ESL_EXCEPTION(eslESYS, "sprintf failed");
if (( sfp = fopen(outfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata sequence file %s for writing", outfile);
if (( stubfp = fopen(basename, "w")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata stub file %s for writing", basename);
/* Header: index file */
if (fwrite(&magic, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&uniquetag, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&alphatype, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&flags, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&max_namelen, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&max_acclen, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&max_desclen, sizeof(uint32_t), 1, ifp) != 1 ||
fwrite(&max_seqlen, sizeof(uint64_t), 1, ifp) != 1 ||
fwrite(&nseq, sizeof(uint64_t), 1, ifp) != 1 ||
fwrite(&nres, sizeof(uint64_t), 1, ifp) != 1)
ESL_XEXCEPTION_SYS(eslESYS, "fwrite() failed, index file header");
/* Header: metadata file */
if (fwrite(&magic, sizeof(uint32_t), 1, mfp) != 1 ||
fwrite(&uniquetag, sizeof(uint32_t), 1, mfp) != 1)
ESL_XEXCEPTION_SYS(eslESYS, "fwrite() failed, metadata file header");
/* Header: sequence file */
if (fwrite(&magic, sizeof(uint32_t), 1, sfp) != 1 ||
fwrite(&uniquetag, sizeof(uint32_t), 1, sfp) != 1)
ESL_XEXCEPTION_SYS(eslESYS, "fwrite() failed, metadata file header");
/* Second pass: index, metadata, and sequence files */
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
/* Packed sequence */
psq = (uint32_t *) sq->dsq; // pack-in-place
ESL_DASSERT1(( sq->salloc >= 4 )); // required min space for pack-in-place
if (do_pack5) dsqdata_pack5(sq->dsq, sq->n, psq, &plen);
else dsqdata_pack2(sq->dsq, sq->n, psq, &plen);
if ( fwrite(psq, sizeof(uint32_t), plen, sfp) != plen)
ESL_XEXCEPTION(eslESYS, "fwrite() failed, packed seq");
spos += plen;
/* Metadata */
n = strlen(sq->name);
if ( fwrite(sq->name, sizeof(char), n+1, mfp) != n+1)
ESL_XEXCEPTION(eslESYS, "fwrite () failed, metadata, name");
mpos += n+1;
n = strlen(sq->acc);
if ( fwrite(sq->acc, sizeof(char), n+1, mfp) != n+1)
ESL_XEXCEPTION(eslESYS, "fwrite () failed, metadata, accession");
mpos += n+1;
n = strlen(sq->desc);
if ( fwrite(sq->desc, sizeof(char), n+1, mfp) != n+1)
ESL_XEXCEPTION(eslESYS, "fwrite () failed, metadata, description");
mpos += n+1;
if ( fwrite( &(sq->tax_id), sizeof(int32_t), 1, mfp) != 1)
ESL_XEXCEPTION(eslESYS, "fwrite () failed, metadata, taxonomy id");
mpos += sizeof(int32_t);
/* Index file */
idx.psq_end = spos-1; // could be -1, on 1st seq, if 1st seq L=0.
idx.metadata_end = mpos-1;
if ( fwrite(&idx, sizeof(ESL_DSQDATA_RECORD), 1, ifp) != 1)
ESL_XEXCEPTION(eslESYS, "fwrite () failed, index file");
esl_sq_Reuse(sq);
}
/* Stub file */
fprintf(stubfp, "Easel dsqdata v1 x%" PRIu32 "\n", uniquetag);
fprintf(stubfp, "\n");
fprintf(stubfp, "Original file: %s\n", sqfp->filename);
fprintf(stubfp, "Original format: %s\n", esl_sqio_DecodeFormat(sqfp->format));
fprintf(stubfp, "Type: %s\n", esl_abc_DecodeType(sqfp->abc->type));
fprintf(stubfp, "Sequences: %" PRIu64 "\n", nseq);
fprintf(stubfp, "Residues: %" PRIu64 "\n", nres);
esl_sq_Destroy(sq);
esl_randomness_Destroy(rng);
free(outfile);
fclose(stubfp);
fclose(ifp);
fclose(mfp);
fclose(sfp);
return eslOK;
ERROR:
if (sq) esl_sq_Destroy(sq);
if (rng) esl_randomness_Destroy(rng);
if (outfile) free(outfile);
if (stubfp) fclose(stubfp);
if (ifp) fclose(ifp);
if (mfp) fclose(mfp);
if (sfp) fclose(sfp);
return status;
}
/*****************************************************************
* 3. ESL_DSQDATA_CHUNK: a chunk of input sequence data
*****************************************************************/
static ESL_DSQDATA_CHUNK *
dsqdata_chunk_Create(ESL_DSQDATA *dd)
{
ESL_DSQDATA_CHUNK *chu = NULL;
int U; // max size of unpacked seq data, in bytes (smem allocation)
int status;
ESL_ALLOC(chu, sizeof(ESL_DSQDATA_CHUNK));
chu->i0 = 0;
chu->N = 0;
chu->pn = 0;
chu->dsq = NULL;
chu->name = NULL;
chu->acc = NULL;
chu->desc = NULL;
chu->taxid = NULL;
chu->L = NULL;
chu->metadata = NULL;
chu->smem = NULL;
chu->nxt = NULL;
/* dsq, name, acc, desc are arrays of pointers into smem, metadata.
* taxid is cast to int, from the metadata.
* L is figured out by the unpacker.
* All of these are set by the unpacker.
*/
ESL_ALLOC(chu->dsq, dd->chunk_maxseq * sizeof(ESL_DSQ *));
ESL_ALLOC(chu->name, dd->chunk_maxseq * sizeof(char *));
ESL_ALLOC(chu->acc, dd->chunk_maxseq * sizeof(char *));
ESL_ALLOC(chu->desc, dd->chunk_maxseq * sizeof(char *));
ESL_ALLOC(chu->taxid, dd->chunk_maxseq * sizeof(int));
ESL_ALLOC(chu->L, dd->chunk_maxseq * sizeof(int64_t));
/* On the <smem> allocation, and the <dsq> and <psq> pointers into it:
*
* <maxpacket> (in uint32's) sets the maximum single fread() size:
* one load of a new chunk of packed sequence, up to maxpacket*4
* bytes. <smem> needs to be able to hold both that and the fully
* unpacked sequence, because we unpack in place. Each packet
* unpacks to at most 6 or 15 residues (5-bit or 2-bit packing) We
* don't pack sentinels, so the maximum unpacked size includes
* <maxseq>+1 sentinels... because we concat the digital seqs so
* that the trailing sentinel of seq i is the leading sentinel of
* seq i+1.
*
* The packed seq (max of P bytes) loads overlap with the unpacked
* data (max of U bytes):
* psq
* v[ P bytes ]
* smem: 0........0........0..........0
* ^[ U bytes ]
* ^dsq[0] ^dsq[1] ^dsq[2]
*
* and as long as we unpack psq left to right -- and as long as we
* read the last packet before we write the last unpacked residues
* to smem - we're guaranteed that the unpacking works without
* overwriting any unpacked data.
*/
U = (dd->pack5 ? 6 * dd->chunk_maxpacket : 15 * dd->chunk_maxpacket);
U += dd->chunk_maxseq + 1;
ESL_ALLOC(chu->smem, sizeof(ESL_DSQ) * U);
chu->psq = (uint32_t *) (chu->smem + U - 4*dd->chunk_maxpacket);
/* We don't have any guarantees about the amount of metadata
* associated with the N sequences, so <metadata> has to be a
* reallocatable space. We make a lowball guess for the initial
* alloc, on the off chance that the metadata size is small (names
* only, no acc/desc): minimally, say 12 bytes of name, 3 \0's, and
* 4 bytes for the taxid integer: call it 20.
*/
chu->mdalloc = 20 * dd->chunk_maxseq;
ESL_ALLOC(chu->metadata, sizeof(char) * chu->mdalloc);
return chu;
ERROR:
dsqdata_chunk_Destroy(chu);
return NULL;
}
static void
dsqdata_chunk_Destroy(ESL_DSQDATA_CHUNK *chu)
{
if (chu)
{
if (chu->metadata) free(chu->metadata);
if (chu->smem) free(chu->smem);
if (chu->L) free(chu->L);
if (chu->taxid) free(chu->taxid);
if (chu->desc) free(chu->desc);
if (chu->acc) free(chu->acc);
if (chu->name) free(chu->name);
if (chu->dsq) free(chu->dsq);
free(chu);
}
}
/*****************************************************************
* 4. Loader and unpacker, the input threads
*****************************************************************/
static void *
dsqdata_loader_thread(void *p)
{
ESL_DSQDATA *dd = (ESL_DSQDATA *) p;
ESL_DSQDATA_RECORD *idx = NULL;
ESL_DSQDATA_CHUNK *chu = NULL;
int64_t nchunk = 0; // total number of chunks loaded (including empty EOF)
int nalloc = 0; // number of chunks we create, and need to destroy.
int nidx = 0; // how many records in <idx>: usually MAXSEQ, until end
int nload = 0; // how many sequences we load: >=1, <=nidx
int ncarried = 0; // how many records carry over to next iteration: nidx-nload
int nread = 0; // fread()'s return value
int nmeta = 0; // how many bytes of metadata we want to read for this chunk
int i0 = 0; // absolute index of first record in <idx>, 0-offset
int64_t psq_last = -1; // psq_end for record i0-1
int64_t meta_last = -1; // metadata_end for record i0-1
int u; // which unpacker outbox we put this chunk in
int status;
/* Don't use <dd> until we get the structure-is-ready signal */
if ( pthread_mutex_lock(&dd->go_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_lock failed on go_mutex");
while (! dd->go) {
if ( pthread_cond_wait(&dd->go_cv, &dd->go_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread_cond_wait failed on go_cv");
}
if ( pthread_mutex_unlock(&dd->go_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread_mutex_lock failed on go_mutex");
/* We can begin. */
ESL_ALLOC(idx, sizeof(ESL_DSQDATA_RECORD) * dd->chunk_maxseq);
while (1)
{
//printf("loader: working on chunk %d\n", (int) nchunk+1);
/* Get a chunk structure we can use - either by creating it, or recycling it.
* We probably don't benefit from having more than <nconsumers> + 3*<n_unpackers> + 2,
* which is enough to have all threads working, all in/outboxes full, and at least 1
* waiting in recycling.
* SRE TODO: test, how many is optimal, does it matter?
* the two limits below perform comparably in `esl_dsqdata_example -n`, but that
* doesn't have high-cpu reader threads.
*/
//if (nalloc < dd->nconsumers + dd->n_unpackers + 1)
if (nalloc < dd->nconsumers + 3 * dd->n_unpackers + 2)
{
//printf("loader: creating a new chunk\n");
if ( (chu = dsqdata_chunk_Create(dd)) == NULL) { status = eslEMEM; goto ERROR; }
nalloc++;
}
else
{
//printf("loader: getting a new chunk from recycling...\n");
if ( pthread_mutex_lock(&dd->recycling_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread mutex lock failed");
while (dd->recycling == NULL) {
if ( pthread_cond_wait(&dd->recycling_cv, &dd->recycling_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread cond wait failed");
}
chu = dd->recycling; // pop one off recycling stack
dd->recycling = chu->nxt;
if ( pthread_mutex_unlock(&dd->recycling_mutex) != 0) ESL_XEXCEPTION(eslESYS, "pthread mutex unlock failed");
if ( pthread_cond_signal(&dd->recycling_cv) != 0) ESL_XEXCEPTION(eslESYS, "pthread cond signal failed"); // signal *after* unlocking mutex
//printf("loader: ... done, have new chunk from recycling.\n");
}
/* Refill index. (The memmove is avoidable. Alt strategy: we could load in 2 frames)
* The previous loop loaded packed sequence for <nload'> of the <nidx'> entries,
* where the 's indicate the variable has carried over from prev iteration:
* |----- nload' ----||--- (ncarried) ---|
* |-------------- nidx' ----------------|
* Now we're going to shift the remainder ncarried = nidx-nload to the left, then refill:
* |---- ncarried ----||--- (MAXSEQ-ncarried) ---|
* |-------------- MAXSEQ -----------------------|
* while watching out for the terminal case where we run out of
* data, loading less than (MAXSEQ-ncarried) records:
* |---- ncarried ----||--- nidx* ---|
* |------------- nidx --------------|
* where the <nidx*> is what fread() returns to us.
*/
i0 += nload; // this chunk starts with seq #<i0>
ncarried = (nidx - nload);
memmove(idx, idx + nload, sizeof(ESL_DSQDATA_RECORD) * ncarried);
nidx = fread(idx + ncarried, sizeof(ESL_DSQDATA_RECORD), dd->chunk_maxseq - ncarried, dd->ifp);
nidx += ncarried; // usually, this'll be MAXSEQ, unless we're near EOF.
if (nidx == 0) // then we're EOD.
{
//printf("loader: reached EOD.\n");
dsqdata_chunk_Destroy(chu);
nalloc--; // we'd counted that chunk towards <nalloc>.
break; // this is the only way out of loader's main loop
}
/* Figure out how many sequences we're going to load: <nload>
* nload = max i : i <= MAXSEQ && idx[i].psq_end - psq_last <= CHUNK_MAX
*/
ESL_DASSERT1(( idx[0].psq_end - psq_last <= dd->chunk_maxpacket ));
if (idx[nidx-1].psq_end - psq_last <= dd->chunk_maxpacket)
nload = nidx;
else
{ // Binary search for nload = max_i idx[i-1].psq_end - lastend <= MAX
int righti = nidx;
int mid;
nload = 1;
while (righti - nload > 1)
{
mid = nload + (righti - nload) / 2;
if (idx[mid-1].psq_end - psq_last <= dd->chunk_maxpacket) nload = mid;
else righti = mid;
}
}
/* Read packed sequence. */
//printf("loader: loading chunk %d from disk.\n", (int) nchunk+1);
chu->pn = idx[nload-1].psq_end - psq_last;
nread = fread(chu->psq, sizeof(uint32_t), chu->pn, dd->sfp);
//printf("Read %d packed ints from seq file\n", nread);
if ( nread != chu->pn ) ESL_XEXCEPTION(eslEOD, "dsqdata packet loader: expected %d, got %d", chu->pn, nread);
/* Read metadata, reallocating if needed */
nmeta = idx[nload-1].metadata_end - meta_last;
if (nmeta > chu->mdalloc) {
ESL_REALLOC(chu->metadata, sizeof(char) * nmeta); // should be realloc by doubling instead?
chu->mdalloc = nmeta;
}
nread = fread(chu->metadata, sizeof(char), nmeta, dd->mfp);
if ( nread != nmeta ) ESL_XEXCEPTION(eslEOD, "dsqdata metadata loader: expected %d, got %d", nmeta, nread);
chu->i0 = i0;
chu->N = nload;
psq_last = idx[nload-1].psq_end;
meta_last = idx[nload-1].metadata_end;
/* Put chunk in appropriate outbox.
*/
u = nchunk % dd->n_unpackers; // note this is the loader's own private <nchunk> counter, not the consumer-shared one in <dd>
//printf("loader: about to put chunk %d into inbox %d\n", (int) nchunk+1, u);
if ( pthread_mutex_lock(&(dd->inbox_mutex[u])) != 0) ESL_XEXCEPTION(eslESYS, "pthread mutex lock failed");
while (dd->inbox[u] != NULL) {
if (pthread_cond_wait(&(dd->inbox_cv[u]), &(dd->inbox_mutex[u])) != 0) ESL_XEXCEPTION(eslESYS, "pthread cond wait failed");
}
dd->inbox[u] = chu;
if ( pthread_mutex_unlock(&(dd->inbox_mutex[u])) != 0) ESL_XEXCEPTION(eslESYS, "pthread mutex unlock failed");
if ( pthread_cond_signal(&(dd->inbox_cv[u])) != 0) ESL_XEXCEPTION(eslESYS, "pthread cond signal failed");
//printf("loader: finished putting chunk %d into inbox %d\n", (int) nchunk+1, u);
nchunk++;
}
/* Cleanup time. First, set all unpacker inboxes to EOD state. (We overwrite <u> here.)
*/