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fast-bwa/yarn.c

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/* yarn.c -- generic thread operations implemented using pthread functions
* Copyright (C) 2008, 2011, 2012, 2015, 2018, 2019, 2020 Mark Adler
* Version 1.7 12 Apr 2020 Mark Adler
* For conditions of distribution and use, see copyright notice in yarn.h
*/
/* Basic thread operations implemented using the POSIX pthread library. All
pthread references are isolated within this module to allow alternate
implementations with other thread libraries. See yarn.h for the description
of these operations. */
/* Version history:
1.0 19 Oct 2008 First version
1.1 26 Oct 2008 No need to set the stack size -- remove
Add yarn_abort() function for clean-up on error exit
1.2 19 Dec 2011 (changes reversed in 1.3)
1.3 13 Jan 2012 Add large file #define for consistency with pigz.c
Update thread portability #defines per IEEE 1003.1-2008
Fix documentation in yarn.h for yarn_prefix
1.4 19 Jan 2015 Allow yarn_abort() to avoid error message to stderr
Accept and do nothing for NULL argument to free_lock()
1.5 8 May 2018 Remove destruct() to avoid use of pthread_cancel()
Normalize the code style
1.6 3 Apr 2019 Add debugging information to fail() error messages
1.7 12 Apr 2020 Fix use after free bug in ignition()
*/
// For thread portability.
#define _XOPEN_SOURCE 700
#define _POSIX_C_SOURCE 200809L
#define _THREAD_SAFE
// Use large file functions if available.
#define _FILE_OFFSET_BITS 64
// External libraries and entities referenced.
#include <stdio.h> // fprintf(), stderr
#include <stdlib.h> // exit(), malloc(), free(), NULL
#include <pthread.h> // pthread_t, pthread_create(), pthread_join(),
// pthread_attr_t, pthread_attr_init(), pthread_attr_destroy(),
// PTHREAD_CREATE_JOINABLE, pthread_attr_setdetachstate(),
// pthread_self(), pthread_equal(),
// pthread_mutex_t, PTHREAD_MUTEX_INITIALIZER, pthread_mutex_init(),
// pthread_mutex_lock(), pthread_mutex_unlock(), pthread_mutex_destroy(),
// pthread_cond_t, PTHREAD_COND_INITIALIZER, pthread_cond_init(),
// pthread_cond_broadcast(), pthread_cond_wait(), pthread_cond_destroy()
#include <errno.h> // EPERM, ESRCH, EDEADLK, ENOMEM, EBUSY, EINVAL, EAGAIN
// Interface definition.
#include "yarn.h"
// Constants.
#define local static // for non-exported functions and globals
// Error handling external globals, resettable by application.
char *yarn_prefix = (char*)"yarn";
void (*yarn_abort)(int) = NULL;
// Immediately exit -- use for errors that shouldn't ever happen.
local void fail(int err, char const *file, long line, char const *func) {
fprintf(stderr, "%s: ", yarn_prefix);
switch (err) {
case EPERM:
fputs("already unlocked", stderr);
break;
case ESRCH:
fputs("no such thread", stderr);
break;
case EDEADLK:
fputs("resource deadlock", stderr);
break;
case ENOMEM:
fputs("out of memory", stderr);
break;
case EBUSY:
fputs("can't destroy locked resource", stderr);
break;
case EINVAL:
fputs("invalid request", stderr);
break;
case EAGAIN:
fputs("resource unavailable", stderr);
break;
default:
fprintf(stderr, "internal error %d", err);
}
fprintf(stderr, " (%s:%ld:%s)\n", file, line, func);
if (yarn_abort != NULL)
yarn_abort(err);
exit(err);
}
// Memory handling routines provided by user. If none are provided, malloc()
// and free() are used, which are therefore assumed to be thread-safe.
typedef void *(*malloc_t)(size_t);
typedef void (*free_t)(void *);
local malloc_t my_malloc_f = malloc;
local free_t my_free = free;
// Use user-supplied allocation routines instead of malloc() and free().
void yarn_mem(malloc_t lease, free_t vacate) {
my_malloc_f = lease;
my_free = vacate;
}
// Memory allocation that cannot fail (from the point of view of the caller).
local void *my_malloc(size_t size, char const *file, long line) {
void *block;
if ((block = my_malloc_f(size)) == NULL)
fail(ENOMEM, file, line, "malloc");
return block;
}
// -- Lock functions --
struct lock_s {
pthread_mutex_t mutex;
pthread_cond_t cond;
long value;
};
lock_t *new_lock_(long initial, char const *file, long line) {
lock_t *bolt = (lock_t *)my_malloc(sizeof(struct lock_s), file, line);
int ret = pthread_mutex_init(&(bolt->mutex), NULL);
if (ret)
fail(ret, file, line, "mutex_init");
ret = pthread_cond_init(&(bolt->cond), NULL);
if (ret)
fail(ret, file, line, "cond_init");
bolt->value = initial;
return bolt;
}
void possess_(lock_t *bolt, char const *file, long line) {
int ret = pthread_mutex_lock(&(bolt->mutex));
if (ret)
fail(ret, file, line, "mutex_lock");
}
void release_(lock_t *bolt, char const *file, long line) {
int ret = pthread_mutex_unlock(&(bolt->mutex));
if (ret)
fail(ret, file, line, "mutex_unlock");
}
void twist_(lock_t *bolt, enum twist_op op, long val,
char const *file, long line) {
if (op == TO)
bolt->value = val;
else if (op == BY)
bolt->value += val;
int ret = pthread_cond_broadcast(&(bolt->cond));
if (ret)
fail(ret, file, line, "cond_broadcast");
ret = pthread_mutex_unlock(&(bolt->mutex));
if (ret)
fail(ret, file, line, "mutex_unlock");
}
#define until(a) while(!(a))
void wait_for_(lock_t *bolt, enum wait_op op, long val,
char const *file, long line) {
switch (op) {
case TO_BE:
until (bolt->value == val) {
int ret = pthread_cond_wait(&(bolt->cond), &(bolt->mutex));
if (ret)
fail(ret, file, line, "cond_wait");
}
break;
case NOT_TO_BE:
until (bolt->value != val) {
int ret = pthread_cond_wait(&(bolt->cond), &(bolt->mutex));
if (ret)
fail(ret, file, line, "cond_wait");
}
break;
case TO_BE_MORE_THAN:
until (bolt->value > val) {
int ret = pthread_cond_wait(&(bolt->cond), &(bolt->mutex));
if (ret)
fail(ret, file, line, "cond_wait");
}
break;
case TO_BE_LESS_THAN:
until (bolt->value < val) {
int ret = pthread_cond_wait(&(bolt->cond), &(bolt->mutex));
if (ret)
fail(ret, file, line, "cond_wait");
}
}
}
long peek_lock(lock_t *bolt) {
return bolt->value;
}
void free_lock_(lock_t *bolt, char const *file, long line) {
if (bolt == NULL)
return;
int ret = pthread_cond_destroy(&(bolt->cond));
if (ret)
fail(ret, file, line, "cond_destroy");
ret = pthread_mutex_destroy(&(bolt->mutex));
if (ret)
fail(ret, file, line, "mutex_destroy");
my_free(bolt);
}
// -- Thread functions (uses the lock_t functions above) --
struct thread_s {
pthread_t id;
int done; // true if this thread has exited
thread *next; // for list of all launched threads
};
// List of threads launched but not joined, count of threads exited but not
// joined (incremented by ignition() just before exiting).
local lock_t threads_lock = {
PTHREAD_MUTEX_INITIALIZER,
PTHREAD_COND_INITIALIZER,
0 // number of threads exited but not joined
};
local thread *threads = NULL; // list of extant threads
// Structure in which to pass the probe and its payload to ignition().
struct capsule {
void (*probe)(void *);
void *payload;
char const *file;
long line;
};
// Mark the calling thread as done and alert join_all().
local void reenter(void *arg) {
struct capsule *capsule = (struct capsule *)arg;
// find this thread in the threads list by matching the thread id
pthread_t me = pthread_self();
possess_(&(threads_lock), capsule->file, capsule->line);
thread **prior = &(threads);
thread *match;
while ((match = *prior) != NULL) {
if (pthread_equal(match->id, me))
break;
prior = &(match->next);
}
if (match == NULL)
fail(ESRCH, capsule->file, capsule->line, "reenter lost");
// mark this thread as done and move it to the head of the list
match->done = 1;
if (threads != match) {
*prior = match->next;
match->next = threads;
threads = match;
}
// update the count of threads to be joined and alert join_all()
twist_(&(threads_lock), BY, +1, capsule->file, capsule->line);
// free the capsule resource, even if the thread is cancelled (though yarn
// doesn't use pthread_cancel() -- you never know)
my_free(capsule);
}
// All threads go through this routine. Just before a thread exits, it marks
// itself as done in the threads list and alerts join_all() so that the thread
// resources can be released. Use a cleanup stack so that the marking occurs
// even if the thread is cancelled.
local void *ignition(void *arg) {
struct capsule *capsule = (struct capsule *)arg;
// run reenter() before leaving
pthread_cleanup_push(reenter, arg);
// execute the requested function with argument
capsule->probe(capsule->payload);
// mark this thread as done, letting join_all() know, and free capsule
pthread_cleanup_pop(1);
// exit thread
return NULL;
}
// Not all POSIX implementations create threads as joinable by default, so that
// is made explicit here.
thread *launch_(void (*probe)(void *), void *payload,
char const *file, long line) {
// construct the requested call and argument for the ignition() routine
// (allocated instead of automatic so that we're sure this will still be
// there when ignition() actually starts up -- ignition() will free this
// allocation)
struct capsule *capsule = (struct capsule *)my_malloc(sizeof(struct capsule), file, line);
capsule->probe = probe;
capsule->payload = payload;
capsule->file = file;
capsule->line = line;
// assure this thread is in the list before join_all() or ignition() looks
// for it
possess_(&(threads_lock), file, line);
// create the thread and call ignition() from that thread
thread *th = (thread *)my_malloc(sizeof(struct thread_s), file, line);
pthread_attr_t attr;
int ret = pthread_attr_init(&attr);
if (ret)
fail(ret, file, line, "attr_init");
ret = pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
if (ret)
fail(ret, file, line, "attr_setdetachstate");
ret = pthread_create(&(th->id), &attr, ignition, capsule);
if (ret)
fail(ret, file, line, "create");
ret = pthread_attr_destroy(&attr);
if (ret)
fail(ret, file, line, "attr_destroy");
// put the thread in the threads list for join_all()
th->done = 0;
th->next = threads;
threads = th;
release_(&(threads_lock), file, line);
return th;
}
void join_(thread *ally, char const *file, long line) {
// wait for thread to exit and return its resources
int ret = pthread_join(ally->id, NULL);
if (ret)
fail(ret, file, line, "join");
// find the thread in the threads list
possess_(&(threads_lock), file, line);
thread **prior = &(threads);
thread *match;
while ((match = *prior) != NULL) {
if (match == ally)
break;
prior = &(match->next);
}
if (match == NULL)
fail(ESRCH, file, line, "join lost");
// remove thread from list and update exited count, free thread
if (match->done)
threads_lock.value--;
*prior = match->next;
release_(&(threads_lock), file, line);
my_free(ally);
}
// This implementation of join_all() only attempts to join threads that have
// announced that they have exited (see ignition()). When there are many
// threads, this is faster than waiting for some random thread to exit while a
// bunch of other threads have already exited.
int join_all_(char const *file, long line) {
// grab the threads list and initialize the joined count
int count = 0;
possess_(&(threads_lock), file, line);
// do until threads list is empty
while (threads != NULL) {
// wait until at least one thread has reentered
wait_for_(&(threads_lock), NOT_TO_BE, 0, file, line);
// find the first thread marked done (should be at or near the top)
thread **prior = &(threads);
thread *match;
while ((match = *prior) != NULL) {
if (match->done)
break;
prior = &(match->next);
}
if (match == NULL)
fail(ESRCH, file, line, "join_all lost");
// join the thread (will be almost immediate), remove from the threads
// list, update the reenter count, and free the thread
int ret = pthread_join(match->id, NULL);
if (ret)
fail(ret, file, line, "join");
threads_lock.value--;
*prior = match->next;
my_free(match);
count++;
}
// let go of the threads list and return the number of threads joined
release_(&(threads_lock), file, line);
return count;
}
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