From 0d59870f3bcf0ddd862e38a82f0f81f38ab000d7 Mon Sep 17 00:00:00 2001
From: Danilo Horta <danilo.horta@pm.me>
Date: Mon, 12 Feb 2024 17:01:29 +0000
Subject: [PATCH] xsignal
---
c-core/CMakeLists.txt | 2 +-
c-core/scan.c | 26 +++++++++++++------------
c-core/thread.c | 30 ++++-------------------------
c-core/thread.h | 3 ++-
c-core/xsignal.c | 45 +++++++++++++++++++++++++++++++++++++++++++
c-core/xsignal.h | 12 ++++++++++++
6 files changed, 78 insertions(+), 40 deletions(-)
create mode 100644 c-core/xsignal.c
create mode 100644 c-core/xsignal.h
diff --git a/c-core/CMakeLists.txt b/c-core/CMakeLists.txt
index 1678b0c..ecdeedc 100644
--- a/c-core/CMakeLists.txt
+++ b/c-core/CMakeLists.txt
@@ -1,5 +1,5 @@
cmake_minimum_required(VERSION 3.20.2 FATAL_ERROR)
-project(deciphon VERSION 0.15.7 LANGUAGES C)
+project(deciphon VERSION 0.15.8 LANGUAGES C)
include(cmake/warnings.cmake)
include(cmake/sanitizers.cmake)
diff --git a/c-core/scan.c b/c-core/scan.c
index 2815b78..a93ca9c 100644
--- a/c-core/scan.c
+++ b/c-core/scan.c
@@ -1,9 +1,3 @@
-#if !defined(_POSIX_C_SOURCE) || _POSIX_C_SOURCE < 200809L
-#undef _POSIX_C_SOURCE
-#define _POSIX_C_SOURCE 200809L
-#endif
-#include <signal.h>
-
#include "scan.h"
#include "database_reader.h"
#include "debug.h"
@@ -15,6 +9,8 @@
#include "sequence_queue.h"
#include "thread.h"
#include "thread_params.h"
+#include "xsignal.h"
+#include <omp.h>
#include <stdlib.h>
struct scan
@@ -116,14 +112,13 @@ int scan_run(struct scan *x, char const *product_dir)
int rc = 0;
int num_threads = x->params.num_threads;
x->interrupted = false;
+ struct xsignal *xsignal = xsignal_new();
+
debug("%d thread(s)", num_threads);
if ((rc = product_open(&x->product, num_threads, product_dir)))
defer_return(rc);
- sigset_t signal_mask;
- sigprocmask(SIG_BLOCK, NULL, &signal_mask);
-
for (int i = 0; i < num_threads; ++i)
{
struct thread_params params = {&x->db.protein,
@@ -135,17 +130,24 @@ int scan_run(struct scan *x, char const *product_dir)
if ((rc = thread_setup(x->threads + i, params))) defer_return(rc);
}
-#pragma omp parallel for default(none) shared(x, num_threads, rc)
+#pragma omp parallel for default(none) shared(x, num_threads, rc, xsignal)
for (int i = 0; i < num_threads; ++i)
{
- int r = thread_run(x->threads + i, &x->sequences, &x->done_proteins);
+ struct xsignal *signal = omp_get_thread_num() == 0 ? xsignal : NULL;
+ int *proteins = &x->done_proteins;
+ int r = thread_run(x->threads + i, &x->sequences, proteins, signal);
+ if (!r)
+ {
+ for (int i = 0; i < num_threads; ++i)
+ x->threads[i].interrupted = true;
+ }
#pragma omp critical
if (r && !rc) rc = r;
}
defer:
- sigprocmask(SIG_SETMASK, &signal_mask, NULL);
+ xsignal_del(xsignal);
for (int i = 0; i < num_threads; ++i)
{
diff --git a/c-core/thread.c b/c-core/thread.c
index 9243d0e..778f5e8 100644
--- a/c-core/thread.c
+++ b/c-core/thread.c
@@ -1,9 +1,3 @@
-#if !defined(_POSIX_C_SOURCE) || _POSIX_C_SOURCE < 200809L
-#undef _POSIX_C_SOURCE
-#define _POSIX_C_SOURCE 200809L
-#endif
-#include <signal.h>
-
#include "thread.h"
#include "chararray.h"
#include "database_reader.h"
@@ -24,6 +18,7 @@
#include "trellis.h"
#include "viterbi.h"
#include "window.h"
+#include "xsignal.h"
void thread_init(struct thread *x)
{
@@ -85,20 +80,10 @@ static int process_window(struct thread *, int protein_idx,
struct window const *);
int thread_run(struct thread *x, struct sequence_queue const *sequences,
- int *done_proteins)
+ int *done_proteins, struct xsignal *xsignal)
{
int rc = 0;
- sigset_t sigmask;
- sigemptyset(&sigmask);
- sigaddset(&sigmask, SIGINT);
- sigaddset(&sigmask, SIGTERM);
- sigprocmask(SIG_BLOCK, &sigmask, NULL);
-
- sigset_t sigpend;
- sigemptyset(&sigpend);
- int signal = 0;
-
struct protein_iter *protein_iter = &x->iter;
if ((rc = protein_iter_rewind(protein_iter))) goto cleanup;
@@ -116,18 +101,11 @@ int thread_run(struct thread *x, struct sequence_queue const *sequences,
int last_hit_pos = -1;
while (window_next(&w, last_hit_pos))
{
+ if (x->interrupted) goto cleanup;
int protein_idx = protein_iter_idx(protein_iter);
if ((rc = process_window(x, protein_idx, &w))) break;
- sigpending(&sigpend);
- if (sigismember(&sigpend, SIGINT) || sigismember(&sigpend, SIGTERM))
- {
- if (sigwait(&sigmask, &signal) == 0)
- {
- x->interrupted = true;
- goto cleanup;
- }
- }
+ if (xsignal && xsignal_interrupted(xsignal)) x->interrupted = true;
}
}
diff --git a/c-core/thread.h b/c-core/thread.h
index a34c07d..f6ea352 100644
--- a/c-core/thread.h
+++ b/c-core/thread.h
@@ -13,6 +13,7 @@
struct product_thread;
struct sequence_queue;
struct viterbi;
+struct xsignal;
struct thread
{
@@ -34,7 +35,7 @@ struct thread
void thread_init(struct thread *);
int thread_setup(struct thread *, struct thread_params);
void thread_cleanup(struct thread *);
-int thread_run(struct thread *, struct sequence_queue const *, int *done_proteins);
+int thread_run(struct thread *, struct sequence_queue const *, int *done_proteins, struct xsignal *);
bool thread_interrupted(struct thread const *);
#endif
diff --git a/c-core/xsignal.c b/c-core/xsignal.c
new file mode 100644
index 0000000..8ac5e6b
--- /dev/null
+++ b/c-core/xsignal.c
@@ -0,0 +1,45 @@
+#if !defined(_POSIX_C_SOURCE) || _POSIX_C_SOURCE < 200809L
+#undef _POSIX_C_SOURCE
+#define _POSIX_C_SOURCE 200809L
+#endif
+#include <signal.h>
+
+#include "xsignal.h"
+#include <stdlib.h>
+
+struct xsignal
+{
+ sigset_t old_mask;
+ sigset_t new_sigmask;
+};
+
+
+struct xsignal *xsignal_new(void)
+{
+ struct xsignal *x = malloc(sizeof(*x));
+ sigemptyset(&x->new_sigmask);
+ sigaddset(&x->new_sigmask, SIGINT);
+ sigaddset(&x->new_sigmask, SIGTERM);
+ sigprocmask(SIG_BLOCK, &x->new_sigmask, &x->old_mask);
+ return x;
+}
+
+bool xsignal_interrupted(struct xsignal *x)
+{
+ sigset_t sigpend;
+ int signal = 0;
+
+ sigemptyset(&sigpend);
+ sigpending(&sigpend);
+
+ if (sigismember(&sigpend, SIGINT) || sigismember(&sigpend, SIGTERM))
+ {
+ if (sigwait(&x->new_sigmask, &signal) == 0) return true;
+ }
+ return false;
+}
+
+void xsignal_del(struct xsignal *x)
+{
+ sigprocmask(SIG_SETMASK, &x->old_mask, NULL);
+}
diff --git a/c-core/xsignal.h b/c-core/xsignal.h
new file mode 100644
index 0000000..19c1ba1
--- /dev/null
+++ b/c-core/xsignal.h
@@ -0,0 +1,12 @@
+#ifndef XSIGNAL_H
+#define XSIGNAL_H
+
+#include <stdbool.h>
+
+struct xsignal;
+
+struct xsignal *xsignal_new(void);
+bool xsignal_interrupted(struct xsignal *);
+void xsignal_del(struct xsignal *);
+
+#endif