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  1. 28 Dec, 2015 1 commit
  3. 14 Dec, 2015 1 commit
  5. 10 Dec, 2015 2 commits
  7. 09 Dec, 2015 3 commits
  9. 20 Nov, 2015 12 commits
  11. 15 Nov, 2015 1 commit
    • Andrew Jeffery's avatar
      strgrp: Cache cosine popcounts to reduce computation · 4a439212
      Andrew Jeffery authored 
      Neatly, this reduces some of the OpenMP-related noise in the
implementation by removing the need for the include. The loop body of
grp_for() is also clearer as a result of the change; the changes to the
function interfaces motivated a re-think of the complexity here.
      4a439212
  13. 13 Nov, 2015 1 commit
  15. 12 Nov, 2015 1 commit
  17. 08 Nov, 2015 1 commit
    • Andrew Jeffery's avatar
      strgrp: Add cosine similarity filter · e95575c4
      Andrew Jeffery authored 
      The cosine similarity measure[1] (O(m + n)) contributes a decent runtime
reduction when used as a filter prior to execution of more expensive
algorithms such as LCS[2] (O(m * n)).

A private test set of 3500 strings was used to quantify the improvement.
The shape of the test set is described by Python's Pandas module as:

    >>> frames.apply(len).describe()
    count    3500.000000
    mean       47.454286
    std        14.980197
    min        10.000000
    25%        37.000000
    50%        45.000000
    75%        61.000000
    max       109.000000
    dtype: float64
    >>>

The tests were performed on a lightly loaded Lenovo X201s stocked with a
Intel Core i7 L 640 @ 2.13GHz CPU with 3.7 GiB of memory. The test was
compiled with GCC 4.9.3:

    $ gcc --version
    gcc (Gentoo 4.9.3 p1.0, pie-0.6.2) 4.9.3
    Copyright (C) 2015 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions.  There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Using the test program outlined below, ten runs for input set sizes
incrementing in batches of 500 were taken prior to filtering with cosine
similarity:

    500:  0.61, 0.25, 0.08, 0.07, 0.07, 0.07, 0.09, 0.07, 0.07, 0.07
    1000: 0.33, 0.32, 0.34, 0.32, 0.32, 0.33, 0.32, 0.32, 0.34, 0.32
    1500: 0.72, 1.53, 0.72, 0.70, 0.72, 0.70, 0.72, 0.71, 1.46, 0.71
    2000: 1.22, 1.20, 1.22, 1.98, 1.20, 1.20, 1.22, 1.94, 1.20, 1.20
    2500: 1.97, 2.72, 1.94, 2.33, 2.44, 1.94, 2.82, 1.93, 1.94, 2.69
    3000: 2.69, 3.41, 2.66, 3.38, 2.67, 3.42, 2.63, 3.44, 2.65, 3.39
    3500: 4.18, 3.65, 4.21, 4.21, 3.56, 4.21, 4.16, 3.63, 4.20, 4.13

After adding the cosine similarity filter the runtimes became:

    500:  0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02
    1000: 0.08, 0.07, 0.07, 0.07, 0.08, 0.07, 0.07, 0.08, 0.07, 0.07
    1500: 0.16, 0.16, 0.15, 0.16, 0.16, 0.15, 0.15, 0.15, 0.16, 0.16
    2000: 0.26, 0.26, 0.25, 0.26, 0.26, 0.26, 0.25, 0.26, 0.26, 0.26
    2500: 0.41, 0.41, 0.41, 0.40, 0.42, 0.42, 0.42, 0.41, 0.41, 0.41
    3000: 0.58, 0.56, 0.57, 0.56, 0.58, 0.57, 0.56, 0.56, 0.57, 0.55
    3500: 0.75, 0.74, 0.73, 0.74, 0.74, 0.73, 0.72, 0.75, 0.75, 0.75

As such, on average the runtime improvements are:

    N       Avg Pre         Avg Post        Improvement (Pre / Post)
    500     0.145           0.02            7.25
    1000    0.326           0.073           4.47
    1500    0.869           0.156           5.57
    2000    1.358           0.258           5.26
    2500    2.272           0.412           5.51
    3000    3.034           0.566           5.36
    3500    4.014           0.74            5.42

The test driver is as below, where both it and its dependencies were
compiled with 'CFLAGS=-O2 -fopenmp' and linked with 'LDFLAGS=-fopenmp',
'LDLIBS=-lm':

    $ cat test.c
    #include "config.h"
    #include <stdio.h>
    #include <stdlib.h>
    #include <string.h>
    #include "ccan/strgrp/strgrp.h"

    int main(void) {
        FILE *f;
        char *buf;
        struct strgrp *ctx;
        f = fdopen(0, "r");
    #define BUF_SIZE 512
        buf = malloc(BUF_SIZE);
        ctx = strgrp_new(0.85);
        while(fgets(buf, BUF_SIZE, f)) {
            buf[strcspn(buf, "\r\n")] = '\0';
            if (!strgrp_add(ctx, buf, NULL)) {
                printf("Failed to classify %s\n", buf);
            }
        }
        strgrp_free(ctx);
        free(buf);
        fclose(f);
        return 0;
    }

[1] https://en.wikipedia.org/wiki/Cosine_similarity
[2] https://en.wikipedia.org/wiki/Longest_common_subsequence_problem
      e95575c4
  19. 03 Nov, 2015 2 commits
    • David Gibson's avatar
      aga: Error codes · afae9c82
      David Gibson authored 
      Add an enum to record error codes for aga routines.  The current
algorithms, dfs and bfs don't have any error conditions except those
reported by callbacks.  So, for now, the only code is "no error", but this
will be expanded in future.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      afae9c82
    • David Gibson's avatar
      aga: Fix initialization bug in aga_for_each_edge_info · 2ab26c62
      David Gibson authored 
      The aga_for_each_edge_info macro is constructed so that if the edge_info
callback returns an error, the for loop terminates early and leaves the
_err parameter set to the error.  On successful completion of the loop,
_err should be zero.

However, on a node with no edges, _err will not be initialized, meaning
that it could be non-zero even on successful (trivial) completion of the
loop.  This fixes the bug.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      2ab26c62
  21. 02 Nov, 2015 1 commit
  23. 27 Oct, 2015 1 commit
  25. 25 Oct, 2015 8 commits
    • David Gibson's avatar
      lqueue: Streamline interface with TCON_CONTAINER · 42b7ab48
      David Gibson authored 
      The interfaces the lqueue module currently has implement (partial) type
safety in a somewhat clunky way - types and member names need to be passed
to a number of entry points.

This patch uses the new TCON_CONTAINER magic to stash the typing
information into the declaration of the queue object, so it no longer needs
to be explicitly passed to later calls.

This does alter the lqueue interface incompatibly.  I think the module
is young enough that we can reasonably do that.  One other module,
'aga', was using lqueue, and this also includes fixes so that it still
works.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      42b7ab48
    • David Gibson's avatar
      lstack: Streamline interface with TCON_CONTAINER · e47d78e9
      David Gibson authored 
      The interfaces the lstack module currently has implement (partial) type
safety in a somewhat clunk way - types and member names need to be passed
to a number of entry points.

This patch uses the new TCON_CONTAINER magic to stash the typing
information into the declaration of the stack object, so it no longer needs
to be explicitly passed to later calls.

This does alter the lstack interface incompatibly.  I think the module
is young enough that we can reasonably do that.  One other module,
'aga', was using lstack, and this also includes fixes so that it still
works.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      e47d78e9
    • David Gibson's avatar
      tcon: Encode information on container members in "type" canaries · 0ddea413
      David Gibson authored 
      Add "container canaries" to tcon.  This allows information about a specific
member of a container structure to be encoded with TCON or TCON_WRAP.  Once
that's done, tcon_container_of() and tcon_member_of() can be used to
translate between member and container pointers based on the canary
information, without having to repeat the type and member details.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      0ddea413
    • David Gibson's avatar
      tcon: Encode integer values into "type" canaries · fd48aee6
      David Gibson authored 
      Add the ability to encode, as well as types, integer values (must be
positive, compile time constant and in the range of size_t) into TCON
constructed "type" canaries.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      fd48aee6
    • David Gibson's avatar
      tcon: Add tcon_sizeof() helper · cc3db07e
      David Gibson authored 
      Add a new tcon_sizeof() helper macro which returns the size of a type for
which a canary has been constructed with TCON or TCON_WRAP.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      cc3db07e
    • David Gibson's avatar
      tcon: Add an alternate way of building type canaries · 43992de4
      David Gibson authored 
      The tcon module allows you to add "type canaries" to a structures, which
can be used for later typechecks.  The canaries are implemented using
a flexible array member, to avoid them taking any actual space at runtime.
That means the canaries must go at the end of your structure.

That doesn't seem like a big limitation, except that it also means the
structure containing the canaries must be at the end of any structure it
is embedded in in turn, which is a rather more serious limitation.

This patch adds a TCON_WRAP() macro which wraps a given type in a new type
which also contains type canaries, and doesn't suffer the last member
limitation.  The drawback is that if the wrapped type has smaller size than
a pointer, the type canaries will pad the wrapped type out to the size of a
pointer.

By constructing the wrappers carefully, the existing tcon macros will work
on both wrapper types constructed with TCON_WRAP and on structures
explicitly including TCON type canaries.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      43992de4
    • David Gibson's avatar
      lstack, lqueue: Move from MODS_WITH_SRC to MODS_NO_SRC · fced03d3
      David Gibson authored 
      The lstack and lqueue modules are entirely implemented in a single header.
However, in Makefile-ccan they're listed in MODS_WITH_SRC, instead of
MODS_NO_SRC.  This appears to be harmless, but this patch moves them to
the correct category anyway.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      fced03d3
    • David Gibson's avatar
      ptrint: ptr2int and int2ptr are constant functions · 14addbab
      David Gibson authored 
      By construction these functions depend only on their arguments, so declare
them as CONST_FUNCTION using the helper from ccan/compiler.
Signed-off-by: default avatarDavid Gibson <david@gibson.dropbear.id.au>
      14addbab
  27. 21 Oct, 2015 2 commits
  29. 20 Oct, 2015 1 commit
  31. 18 Oct, 2015 2 commits
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