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authorPádraig Brady <P@draigBrady.com>2011-05-13 18:41:42 +0100
committerPádraig Brady <P@draigBrady.com>2011-05-14 10:30:12 +0100
commit27873f1deb69745c79d403bbb8e1145bc18f55b8 (patch)
treed3b752eed0035e9ce767ea73c07f3b8577deaead
parent9d152a1ed72968ae3624a76e155fe16b240348dc (diff)
downloadcoreutils-27873f1deb69745c79d403bbb8e1145bc18f55b8.tar.xz
shuf: use memory more efficiently when returning a subset
* gl/lib/randperm.c (randperm_new): When the number of items to return H, is much smaller than the total number of items N, use a hash to represent the sparse permutations of the set N. This is currently enabled for N > 128K and N/H > 32. * tests/misc/shuf: Ensure shuf can quickly return 2 numbers from a large range. * gl/modules/randperm: Depend on hash. * NEWS: Mention the change.
-rw-r--r--NEWS5
-rw-r--r--gl/lib/randperm.c149
-rw-r--r--gl/modules/randperm1
-rwxr-xr-xtests/misc/shuf6
4 files changed, 154 insertions, 7 deletions
diff --git a/NEWS b/NEWS
index 82ce53c42..7a7f7612b 100644
--- a/NEWS
+++ b/NEWS
@@ -12,6 +12,11 @@ GNU coreutils NEWS -*- outline -*-
Note the use of single quotes, not double quotes.
That creates files named xaa.xz, xab.xz and xac.xz.
+** Improvements
+
+ shuf outputs small subsets of large permutations much more efficiently.
+ For example `shuf -i1-$((2**32-1)) -n2` no longer exhausts memory.
+
* Noteworthy changes in release 8.12 (2011-04-26) [stable]
diff --git a/gl/lib/randperm.c b/gl/lib/randperm.c
index 97c8d9a8b..26181b8a6 100644
--- a/gl/lib/randperm.c
+++ b/gl/lib/randperm.c
@@ -19,9 +19,11 @@
#include <config.h>
+#include "hash.h"
#include "randperm.h"
#include <limits.h>
+#include <stdlib.h>
#include "xalloc.h"
@@ -57,6 +59,94 @@ randperm_bound (size_t h, size_t n)
return bound;
}
+/* Swap elements I and J in array V. */
+
+static void
+swap (size_t *v, size_t i, size_t j)
+{
+ size_t t = v[i];
+ v[i] = v[j];
+ v[j] = t;
+}
+
+/* Structures and functions for a sparse_map abstract data type that's
+ used to effectively swap elements I and J in array V like swap(),
+ but in a more memory efficient manner (when the number of permutations
+ performed is significantly less than the size of the input). */
+
+struct sparse_ent_
+{
+ size_t index;
+ size_t val;
+};
+
+static size_t
+sparse_hash_ (void const *x, size_t table_size)
+{
+ struct sparse_ent_ const *ent = x;
+ return ent->index % table_size;
+}
+
+static bool
+sparse_cmp_ (void const *x, void const *y)
+{
+ struct sparse_ent_ const *ent1 = x;
+ struct sparse_ent_ const *ent2 = y;
+ return ent1->index == ent2->index;
+}
+
+typedef Hash_table sparse_map;
+
+/* Initialize the structure for the sparse map,
+ when a best guess as to the number of entries
+ specified with SIZE_HINT. */
+
+static sparse_map *
+sparse_new (size_t size_hint)
+{
+ return hash_initialize (size_hint, NULL, sparse_hash_, sparse_cmp_, free);
+}
+
+/* Swap the values for I and J. If a value is not already present
+ then assume it's equal to the index. Update the value for
+ index I in array V. */
+
+static void
+sparse_swap (sparse_map *sv, size_t* v, size_t i, size_t j)
+{
+ struct sparse_ent_ *v1 = hash_delete (sv, &(struct sparse_ent_) {i,0});
+ struct sparse_ent_ *v2 = hash_delete (sv, &(struct sparse_ent_) {j,0});
+
+ /* FIXME: reduce the frequency of these mallocs. */
+ if (!v1)
+ {
+ v1 = xmalloc (sizeof *v1);
+ v1->index = v1->val = i;
+ }
+ if (!v2)
+ {
+ v2 = xmalloc (sizeof *v2);
+ v2->index = v2->val = j;
+ }
+
+ size_t t = v1->val;
+ v1->val = v2->val;
+ v2->val = t;
+ if (!hash_insert (sv, v1))
+ xalloc_die ();
+ if (!hash_insert (sv, v2))
+ xalloc_die ();
+
+ v[i] = v1->val;
+}
+
+static void
+sparse_free (sparse_map *sv)
+{
+ hash_free (sv);
+}
+
+
/* From R, allocate and return a malloc'd array of the first H elements
of a random permutation of N elements. H must not exceed N.
Return NULL if H is zero. */
@@ -79,21 +169,66 @@ randperm_new (struct randint_source *r, size_t h, size_t n)
default:
{
+ /* The algorithm is essentially the same in both
+ the sparse and non sparse case. In the sparse case we use
+ a hash to implement sparse storage for the set of n numbers
+ we're shuffling. When to use the sparse method was
+ determined with the help of this script:
+
+ #!/bin/sh
+ for n in $(seq 2 32); do
+ for h in $(seq 2 32); do
+ test $h -gt $n && continue
+ for s in o n; do
+ test $s = o && shuf=shuf || shuf=./shuf
+ num=$(env time -f "$s:${h},${n} = %e,%M" \
+ $shuf -i0-$((2**$n-2)) -n$((2**$h-2)) | wc -l)
+ test $num = $((2**$h-2)) || echo "$s:${h},${n} = failed" >&2
+ done
+ done
+ done
+
+ This showed that if sparseness = n/h, then:
+
+ sparseness = 128 => .125 mem used, and about same speed
+ sparseness = 64 => .25 mem used, but 1.5 times slower
+ sparseness = 32 => .5 mem used, but 2 times slower
+
+ Also the memory usage was only significant when n > 128Ki
+ */
+ bool sparse = (n >= (128 * 1024)) && (n / h >= 32);
+
size_t i;
+ sparse_map *sv;
- v = xnmalloc (n, sizeof *v);
- for (i = 0; i < n; i++)
- v[i] = i;
+ if (sparse)
+ {
+ sv = sparse_new (h * 2);
+ if (sv == NULL)
+ xalloc_die ();
+ v = xnmalloc (h, sizeof *v);
+ }
+ else
+ {
+ sv = NULL; /* To placate GCC's -Wuninitialized. */
+ v = xnmalloc (n, sizeof *v);
+ for (i = 0; i < n; i++)
+ v[i] = i;
+ }
for (i = 0; i < h; i++)
{
size_t j = i + randint_choose (r, n - i);
- size_t t = v[i];
- v[i] = v[j];
- v[j] = t;
+ if (sparse)
+ sparse_swap (sv, v, i, j);
+ else
+ swap (v, i, j);
}
- v = xnrealloc (v, h, sizeof *v);
+ if (sparse)
+ sparse_free (sv);
+ else
+ v = xnrealloc (v, h, sizeof *v);
}
break;
}
diff --git a/gl/modules/randperm b/gl/modules/randperm
index 9cef78271..daf9e3215 100644
--- a/gl/modules/randperm
+++ b/gl/modules/randperm
@@ -8,6 +8,7 @@ lib/randperm.h
Depends-on:
randint
xalloc
+hash
configure.ac:
diff --git a/tests/misc/shuf b/tests/misc/shuf
index cdfe7052b..10d285846 100755
--- a/tests/misc/shuf
+++ b/tests/misc/shuf
@@ -18,6 +18,7 @@
. "${srcdir=.}/init.sh"; path_prepend_ ../src
print_ver_ shuf
+getlimits_
seq 100 > in || framework_failure
@@ -51,4 +52,9 @@ shuf --zero-terminated -i 1-1 > out || fail=1
printf '1\0' > exp || framework_failure
cmp out exp || { fail=1; echo "missing NUL terminator?" 1>&2; }
+# Ensure shuf -n operates efficiently for small n. Before coreutils-8.13
+# this would try to allocate $SIZE_MAX * sizeof(size_t)
+timeout 10 shuf -i1-$SIZE_MAX -n2 >/dev/null ||
+ { fail=1; echo "couldn't get a small subset" >&2; }
+
Exit $fail