From 8830fbbb2e0c8fc4ae6f5d9be9037d950f646b8b Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Thu, 15 Dec 2022 15:42:20 +0000
Subject: [PATCH] Simple pthread example

---
 c/examples/multichrom_wright_fisher.c | 73 ++++++++++++++++++++++-----
 c/meson.build                         |  4 +-
 2 files changed, 62 insertions(+), 15 deletions(-)

diff --git a/c/examples/multichrom_wright_fisher.c b/c/examples/multichrom_wright_fisher.c
index b64bad53e1..e4de79a1e8 100644
--- a/c/examples/multichrom_wright_fisher.c
+++ b/c/examples/multichrom_wright_fisher.c
@@ -4,6 +4,7 @@
 #include <err.h>
 #include <string.h>
 
+#include <pthread.h>
 #include <tskit/tables.h>
 
 #define check_tsk_error(val)                                                            \
@@ -51,6 +52,63 @@ dump_tables(tsk_table_collection_t *tcs, int num_chroms, const char *prefix)
     }
 }
 
+struct chrom_work {
+    int chrom;
+    tsk_table_collection_t *tc;
+    int *samples;
+    int N;
+};
+
+void *
+simplify_chrom(void *arg)
+{
+    int ret;
+    struct chrom_work *work = (struct chrom_work *) arg;
+    tsk_size_t edges_before = work->tc->edges.num_rows;
+
+    ret = tsk_table_collection_sort(work->tc, NULL, 0);
+    check_tsk_error(ret);
+    ret = tsk_table_collection_simplify(work->tc, work->samples, work->N,
+        TSK_SIMPLIFY_NO_FILTER_NODES | TSK_SIMPLIFY_NO_UPDATE_SAMPLE_FLAGS, NULL);
+    check_tsk_error(ret);
+    /* NOTE: this printf makes helgrind complain */
+    printf("\tchr %d: %lld -> %lld\n", work->chrom, (long long) edges_before,
+        (long long) work->tc->edges.num_rows);
+
+    return NULL;
+}
+
+void
+sort_and_simplify_all(tsk_table_collection_t *tcs, int num_chroms, int *samples, int N)
+{
+    int j, ret;
+    struct chrom_work work[num_chroms];
+    pthread_t threads[num_chroms];
+
+    for (j = 1; j < num_chroms; j++) {
+        tcs[j].nodes = tcs[0].nodes;
+    }
+
+    for (j = 0; j < num_chroms; j++) {
+        work[j].chrom = j;
+        work[j].tc = &tcs[j];
+        work[j].samples = samples;
+        work[j].N = N;
+
+        ret = pthread_create(&threads[j], NULL, simplify_chrom, (void *) &work[j]);
+        if (ret != 0) {
+            errx(EXIT_FAILURE, "Pthread create failed");
+        }
+        /* simplify_chrom((void *) &work[j]); */
+    }
+    for (j = 0; j < num_chroms; j++) {
+        ret = pthread_join(threads[j], NULL);
+        if (ret != 0) {
+            errx(EXIT_FAILURE, "Pthread join failed");
+        }
+    }
+}
+
 void
 simplify_tables(tsk_table_collection_t *tcs, int num_chroms, int *samples, int N)
 {
@@ -65,20 +123,7 @@ simplify_tables(tsk_table_collection_t *tcs, int num_chroms, int *samples, int N
     }
 
     printf("Simplify %lld nodes\n", (long long) tcs[0].nodes.num_rows);
-    for (j = 1; j < num_chroms; j++) {
-        tcs[j].nodes = tcs[0].nodes;
-    }
-
-    for (j = 0; j < num_chroms; j++) {
-        printf("\tchr %d: %lld", j, (long long) tcs[j].edges.num_rows);
-        ret = tsk_table_collection_sort(&tcs[j], NULL, 0);
-        /* tsk_table_collection_print_state(&tcs[j], stdout); */
-        check_tsk_error(ret);
-        ret = tsk_table_collection_simplify(&tcs[j], samples, N,
-            TSK_SIMPLIFY_NO_FILTER_NODES | TSK_SIMPLIFY_NO_UPDATE_SAMPLE_FLAGS, NULL);
-        check_tsk_error(ret);
-        printf(" -> %lld\n", (long long) tcs[j].edges.num_rows);
-    }
+    sort_and_simplify_all(tcs, num_chroms, samples, N);
 
     for (j = 0; j < num_nodes; j++) {
         delete_nodes[j] = true;
diff --git a/c/meson.build b/c/meson.build
index 77aea329a2..fba8e3caae 100644
--- a/c/meson.build
+++ b/c/meson.build
@@ -117,8 +117,10 @@ if not meson.is_subproject()
       executable('haploid_wright_fisher',
           sources: ['examples/haploid_wright_fisher.c'], 
           link_with: [tskit_lib], dependencies: lib_deps)
+
+      thread_dep = dependency('threads')
       executable('multichrom_wright_fisher',
           sources: ['examples/multichrom_wright_fisher.c'], 
-          link_with: [tskit_lib], dependencies: lib_deps)
+          link_with: [tskit_lib], dependencies: [m_dep, kastore_dep, thread_dep])
     endif
 endif