Overhauled the docs. Removed all the HTML files, put in XML files as

converted by Donna.  Hooked it into the build system so they are only
built when specifically asked for, and when doing "make dist".

They're not perfect;  in particular, there are the following problems:
- The plain-text FAQ should be built from FAQ.xml, but this is not
  currently done.  (The text FAQ has been left in for now.)

- The PS/PDF building doesn't work -- it fails with an incomprehensible
  error message which I haven't yet deciphered.

Nonetheless, I'm putting it in so others can see it.



git-svn-id: svn://svn.valgrind.org/valgrind/trunk@3153 a5019735-40e9-0310-863c-91ae7b9d1cf9

1 files changed, 1012 insertions, 0 deletions

diff --git a/cachegrind/docs/cg-manual.xml b/cachegrind/docs/cg-manual.xml
new file mode 100644
index 000000000..58df4988e
--- /dev/null
+++ b/cachegrind/docs/cg-manual.xml
@@ -0,0 +1,1012 @@
+<?xml version="1.0"?> <!-- -*- sgml -*- -->
+<!DOCTYPE chapter PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
+  "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd">
+
+<chapter id="cg-manual" xreflabel="Cachegrind: a cache-miss profiler">
+<title>Cachegrind: a cache profiler</title>
+
+<para>Detailed technical documentation on how Cachegrind works is
+available in <xref linkend="cg-tech-docs"/>.  If you only want to know
+how to <command>use</command> it, this is the page you need to
+read.</para>
+
+
+<sect1 id="cg-manual.cache" xreflabel="Cache profiling">
+<title>Cache profiling</title>
+
+<para>To use this tool, you must specify
+<computeroutput>--tool=cachegrind</computeroutput> on the
+Valgrind command line.</para>
+
+<para>Cachegrind is a tool for doing cache simulations and
+annotating your source line-by-line with the number of cache
+misses.  In particular, it records:</para>
+<itemizedlist>
+  <listitem>
+    <para>L1 instruction cache reads and misses;</para>
+  </listitem>
+  <listitem>
+    <para>L1 data cache reads and read misses, writes and write
+    misses;</para>
+  </listitem>
+  <listitem>
+    <para>L2 unified cache reads and read misses, writes and
+    writes misses.</para>
+  </listitem>
+</itemizedlist>
+
+<para>On a modern x86 machine, an L1 miss will typically cost
+around 10 cycles, and an L2 miss can cost as much as 200
+cycles. Detailed cache profiling can be very useful for improving
+the performance of your program.</para>
+
+<para>Also, since one instruction cache read is performed per
+instruction executed, you can find out how many instructions are
+executed per line, which can be useful for traditional profiling
+and test coverage.</para>
+
+<para>Any feedback, bug-fixes, suggestions, etc, welcome.</para>
+
+
+
+<sect2 id="cg-manual.overview" xreflabel="Overview">
+<title>Overview</title>
+
+<para>First off, as for normal Valgrind use, you probably want to
+compile with debugging info (the
+<computeroutput>-g</computeroutput> flag).  But by contrast with
+normal Valgrind use, you probably <command>do</command> want to turn
+optimisation on, since you should profile your program as it will
+be normally run.</para>
+
+<para>The two steps are:</para>
+<orderedlist>
+  <listitem>
+    <para>Run your program with <computeroutput>valgrind
+    --tool=cachegrind</computeroutput> in front of the normal
+    command line invocation.  When the program finishes,
+    Cachegrind will print summary cache statistics. It also
+    collects line-by-line information in a file
+    <computeroutput>cachegrind.out.pid</computeroutput>, where
+    <computeroutput>pid</computeroutput> is the program's process
+    id.</para>
+
+    <para>This step should be done every time you want to collect
+    information about a new program, a changed program, or about
+    the same program with different input.</para>
+  </listitem>
+
+  <listitem>
+    <para>Generate a function-by-function summary, and possibly
+    annotate source files, using the supplied
+    <computeroutput>cg_annotate</computeroutput> program. Source
+    files to annotate can be specified manually, or manually on
+    the command line, or "interesting" source files can be
+    annotated automatically with the
+    <computeroutput>--auto=yes</computeroutput> option.  You can
+    annotate C/C++ files or assembly language files equally
+    easily.</para>
+
+    <para>This step can be performed as many times as you like
+    for each Step 2.  You may want to do multiple annotations
+    showing different information each time.</para>
+  </listitem>
+
+</orderedlist>
+
+<para>The steps are described in detail in the following
+sections.</para>
+
+</sect2>
+
+
+<sect2>
+<title>Cache simulation specifics</title>
+
+<para>Cachegrind uses a simulation for a machine with a split L1
+cache and a unified L2 cache.  This configuration is used for all
+(modern) x86-based machines we are aware of.  Old Cyrix CPUs had
+a unified I and D L1 cache, but they are ancient history
+now.</para>
+
+<para>The more specific characteristics of the simulation are as
+follows.</para>
+
+<itemizedlist>
+
+  <listitem>
+    <para>Write-allocate: when a write miss occurs, the block
+    written to is brought into the D1 cache.  Most modern caches
+    have this property.</para>
+  </listitem>
+
+  <listitem>
+    <para>Bit-selection hash function: the line(s) in the cache
+    to which a memory block maps is chosen by the middle bits
+    M--(M+N-1) of the byte address, where:</para>
+    <itemizedlist>
+      <listitem>
+        <para>line size = 2^M bytes</para>
+      </listitem>
+      <listitem>
+        <para>(cache size / line size) = 2^N bytes</para>
+      </listitem>
+    </itemizedlist> 
+  </listitem>
+
+  <listitem>
+    <para>Inclusive L2 cache: the L2 cache replicates all the
+    entries of the L1 cache.  This is standard on Pentium chips,
+    but AMD Athlons use an exclusive L2 cache that only holds
+    blocks evicted from L1.  Ditto AMD Durons and most modern
+    VIAs.</para>
+  </listitem>
+
+</itemizedlist>
+
+<para>The cache configuration simulated (cache size,
+associativity and line size) is determined automagically using
+the CPUID instruction.  If you have an old machine that (a)
+doesn't support the CPUID instruction, or (b) supports it in an
+early incarnation that doesn't give any cache information, then
+Cachegrind will fall back to using a default configuration (that
+of a model 3/4 Athlon).  Cachegrind will tell you if this
+happens.  You can manually specify one, two or all three levels
+(I1/D1/L2) of the cache from the command line using the
+<computeroutput>--I1</computeroutput>,
+<computeroutput>--D1</computeroutput> and
+<computeroutput>--L2</computeroutput> options.</para>
+
+
+<para>Other noteworthy behaviour:</para>
+
+<itemizedlist>
+  <listitem>
+    <para>References that straddle two cache lines are treated as
+    follows:</para>
+    <itemizedlist>
+      <listitem>
+        <para>If both blocks hit --&gt; counted as one hit</para>
+      </listitem>
+      <listitem>
+        <para>If one block hits, the other misses --&gt; counted
+        as one miss.</para>
+      </listitem>
+      <listitem>
+        <para>If both blocks miss --&gt; counted as one miss (not
+        two)</para>
+      </listitem>
+    </itemizedlist>
+  </listitem>
+
+  <listitem>
+    <para>Instructions that modify a memory location
+    (eg. <computeroutput>inc</computeroutput> and
+    <computeroutput>dec</computeroutput>) are counted as doing
+    just a read, ie. a single data reference.  This may seem
+    strange, but since the write can never cause a miss (the read
+    guarantees the block is in the cache) it's not very
+    interesting.</para>
+
+    <para>Thus it measures not the number of times the data cache
+    is accessed, but the number of times a data cache miss could
+    occur.</para>
+  </listitem>
+
+</itemizedlist>
+
+<para>If you are interested in simulating a cache with different
+properties, it is not particularly hard to write your own cache
+simulator, or to modify the existing ones in
+<computeroutput>vg_cachesim_I1.c</computeroutput>,
+<computeroutput>vg_cachesim_D1.c</computeroutput>,
+<computeroutput>vg_cachesim_L2.c</computeroutput> and
+<computeroutput>vg_cachesim_gen.c</computeroutput>.  We'd be
+interested to hear from anyone who does.</para>
+
+</sect2>
+
+</sect1>
+
+
+
+<sect1 id="cg-manual.profile" xreflabel="Profiling programs">
+<title>Profiling programs</title>
+
+<para>To gather cache profiling information about the program
+<computeroutput>ls -l</computeroutput>, invoke Cachegrind like
+this:</para>
+
+<programlisting><![CDATA[
+valgrind --tool=cachegrind ls -l]]></programlisting>
+
+<para>The program will execute (slowly).  Upon completion,
+summary statistics that look like this will be printed:</para>
+
+<programlisting><![CDATA[
+==31751== I   refs:      27,742,716
+==31751== I1  misses:           276
+==31751== L2  misses:           275
+==31751== I1  miss rate:        0.0%
+==31751== L2i miss rate:        0.0%
+==31751== 
+==31751== D   refs:      15,430,290  (10,955,517 rd + 4,474,773 wr)
+==31751== D1  misses:        41,185  (    21,905 rd +    19,280 wr)
+==31751== L2  misses:        23,085  (     3,987 rd +    19,098 wr)
+==31751== D1  miss rate:        0.2% (       0.1%   +       0.4%)
+==31751== L2d miss rate:        0.1% (       0.0%   +       0.4%)
+==31751== 
+==31751== L2 misses:         23,360  (     4,262 rd +    19,098 wr)
+==31751== L2 miss rate:         0.0% (       0.0%   +       0.4%)]]></programlisting>
+
+<para>Cache accesses for instruction fetches are summarised
+first, giving the number of fetches made (this is the number of
+instructions executed, which can be useful to know in its own
+right), the number of I1 misses, and the number of L2 instruction
+(<computeroutput>L2i</computeroutput>) misses.</para>
+
+<para>Cache accesses for data follow. The information is similar
+to that of the instruction fetches, except that the values are
+also shown split between reads and writes (note each row's
+<computeroutput>rd</computeroutput> and
+<computeroutput>wr</computeroutput> values add up to the row's
+total).</para>
+
+<para>Combined instruction and data figures for the L2 cache
+follow that.</para>
+
+
+
+<sect2 id="cg-manual.outputfile" xreflabel="Output file">
+<title>Output file</title>
+
+<para>As well as printing summary information, Cachegrind also
+writes line-by-line cache profiling information to a file named
+<computeroutput>cachegrind.out.pid</computeroutput>.  This file
+is human-readable, but is best interpreted by the accompanying
+program <computeroutput>cg_annotate</computeroutput>, described
+in the next section.</para>
+
+<para>Things to note about the
+<computeroutput>cachegrind.out.pid</computeroutput>
+file:</para>
+
+<itemizedlist>
+  <listitem>
+    <para>It is written every time Cachegrind is run, and will
+    overwrite any existing
+    <computeroutput>cachegrind.out.pid</computeroutput>
+    in the current directory (but that won't happen very often
+    because it takes some time for process ids to be
+    recycled).</para>
+  </listitem>
+  <listitem>
+    <para>It can be huge: <computeroutput>ls -l</computeroutput>
+    generates a file of about 350KB.  Browsing a few files and
+    web pages with a Konqueror built with full debugging
+    information generates a file of around 15 MB.</para>
+  </listitem>
+</itemizedlist>
+
+<para>Note that older versions of Cachegrind used a log file
+named <computeroutput>cachegrind.out</computeroutput> (i.e. no
+<computeroutput>.pid</computeroutput> suffix).  The suffix serves
+two purposes.  Firstly, it means you don't have to rename old log
+files that you don't want to overwrite.  Secondly, and more
+importantly, it allows correct profiling with the
+<computeroutput>--trace-children=yes</computeroutput> option of
+programs that spawn child processes.</para>
+
+</sect2>
+
+
+
+<sect2 id="cg-manual.cgopts" xreflabel="Cachegrind options">
+<title>Cachegrind options</title>
+
+<para>Cache-simulation specific options are:</para>
+
+<screen><![CDATA[
+--I1=<size>,<associativity>,<line_size>
+--D1=<size>,<associativity>,<line_size>
+--L2=<size>,<associativity>,<line_size>
+
+[default: uses CPUID for automagic cache configuration]]]></screen>
+
+<para>Manually specifies the I1/D1/L2 cache configuration, where
+<computeroutput>size</computeroutput> and
+<computeroutput>line_size</computeroutput> are measured in bytes.
+The three items must be comma-separated, but with no spaces,
+eg:</para>
+
+<programlisting><![CDATA[
+valgrind --tool=cachegrind --I1=65535,2,64]]></programlisting>
+
+<para>You can specify one, two or three of the I1/D1/L2 caches.
+Any level not manually specified will be simulated using the
+configuration found in the normal way (via the CPUID instruction,
+or failing that, via defaults).</para>
+
+</sect2>
+
+
+  
+<sect2 id="cg-manual.annotate" xreflabel="Annotating C/C++ programs">
+<title>Annotating C/C++ programs</title>
+
+<para>Before using <computeroutput>cg_annotate</computeroutput>,
+it is worth widening your window to be at least 120-characters
+wide if possible, as the output lines can be quite long.</para>
+
+<para>To get a function-by-function summary, run
+<computeroutput>cg_annotate --pid</computeroutput> in a directory
+containing a <computeroutput>cachegrind.out.pid</computeroutput>
+file.  The <emphasis>--pid</emphasis> is required so that
+<computeroutput>cg_annotate</computeroutput> knows which log file
+to use when several are present.</para>
+
+<para>The output looks like this:</para>
+
+<programlisting><![CDATA[
+--------------------------------------------------------------------------------
+I1 cache:              65536 B, 64 B, 2-way associative
+D1 cache:              65536 B, 64 B, 2-way associative
+L2 cache:              262144 B, 64 B, 8-way associative
+Command:               concord vg_to_ucode.c
+Events recorded:       Ir I1mr I2mr Dr D1mr D2mr Dw D1mw D2mw
+Events shown:          Ir I1mr I2mr Dr D1mr D2mr Dw D1mw D2mw
+Event sort order:      Ir I1mr I2mr Dr D1mr D2mr Dw D1mw D2mw
+Threshold:             99%
+Chosen for annotation:
+Auto-annotation:       on
+
+--------------------------------------------------------------------------------
+Ir         I1mr I2mr Dr         D1mr   D2mr  Dw        D1mw   D2mw
+--------------------------------------------------------------------------------
+27,742,716  276  275 10,955,517 21,905 3,987 4,474,773 19,280 19,098  PROGRAM TOTALS
+
+--------------------------------------------------------------------------------
+Ir        I1mr I2mr Dr        D1mr  D2mr  Dw        D1mw   D2mw    file:function
+--------------------------------------------------------------------------------
+8,821,482    5    5 2,242,702 1,621    73 1,794,230      0      0  getc.c:_IO_getc
+5,222,023    4    4 2,276,334    16    12   875,959      1      1  concord.c:get_word
+2,649,248    2    2 1,344,810 7,326 1,385         .      .      .  vg_main.c:strcmp
+2,521,927    2    2   591,215     0     0   179,398      0      0  concord.c:hash
+2,242,740    2    2 1,046,612   568    22   448,548      0      0  ctype.c:tolower
+1,496,937    4    4   630,874 9,000 1,400   279,388      0      0  concord.c:insert
+  897,991   51   51   897,831    95    30        62      1      1  ???:???
+  598,068    1    1   299,034     0     0   149,517      0      0  ../sysdeps/generic/lockfile.c:__flockfile
+  598,068    0    0   299,034     0     0   149,517      0      0  ../sysdeps/generic/lockfile.c:__funlockfile
+  598,024    4    4   213,580    35    16   149,506      0      0  vg_clientmalloc.c:malloc
+  446,587    1    1   215,973 2,167   430   129,948 14,057 13,957  concord.c:add_existing
+  341,760    2    2   128,160     0     0   128,160      0      0  vg_clientmalloc.c:vg_trap_here_WRAPPER
+  320,782    4    4   150,711   276     0    56,027     53     53  concord.c:init_hash_table
+  298,998    1    1   106,785     0     0    64,071      1      1  concord.c:create
+  149,518    0    0   149,516     0     0         1      0      0  ???:tolower@@GLIBC_2.0
+  149,518    0    0   149,516     0     0         1      0      0  ???:fgetc@@GLIBC_2.0
+   95,983    4    4    38,031     0     0    34,409  3,152  3,150  concord.c:new_word_node
+   85,440    0    0    42,720     0     0    21,360      0      0  vg_clientmalloc.c:vg_bogus_epilogue]]></programlisting>
+
+
+<para>First up is a summary of the annotation options:</para>
+                    
+<itemizedlist>
+
+  <listitem>
+    <para>I1 cache, D1 cache, L2 cache: cache configuration.  So
+    you know the configuration with which these results were
+    obtained.</para>
+  </listitem>
+
+  <listitem>
+    <para>Command: the command line invocation of the program
+      under examination.</para>
+  </listitem>
+
+  <listitem>
+   <para>Events recorded: event abbreviations are:</para>
+   <itemizedlist>
+     <listitem>
+       <para><computeroutput>Ir </computeroutput>: I cache reads
+       (ie. instructions executed)</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>I1mr</computeroutput>: I1 cache read
+       misses</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>I2mr</computeroutput>: L2 cache
+       instruction read misses</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>Dr </computeroutput>: D cache reads
+       (ie. memory reads)</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>D1mr</computeroutput>: D1 cache read
+       misses</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>D2mr</computeroutput>: L2 cache data
+       read misses</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>Dw </computeroutput>: D cache writes
+       (ie. memory writes)</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>D1mw</computeroutput>: D1 cache write
+       misses</para>
+     </listitem>
+     <listitem>
+       <para><computeroutput>D2mw</computeroutput>: L2 cache data
+       write misses</para>
+     </listitem>
+   </itemizedlist>
+
+   <para>Note that D1 total accesses is given by
+   <computeroutput>D1mr</computeroutput> +
+   <computeroutput>D1mw</computeroutput>, and that L2 total
+   accesses is given by <computeroutput>I2mr</computeroutput> +
+   <computeroutput>D2mr</computeroutput> +
+   <computeroutput>D2mw</computeroutput>.</para>
+ </listitem>
+
+ <listitem>
+   <para>Events shown: the events shown (a subset of events
+   gathered).  This can be adjusted with the
+   <computeroutput>--show</computeroutput> option.</para>
+  </listitem>
+
+  <listitem>
+    <para>Event sort order: the sort order in which functions are
+    shown.  For example, in this case the functions are sorted
+    from highest <computeroutput>Ir</computeroutput> counts to
+    lowest.  If two functions have identical
+    <computeroutput>Ir</computeroutput> counts, they will then be
+    sorted by <computeroutput>I1mr</computeroutput> counts, and
+    so on.  This order can be adjusted with the
+    <computeroutput>--sort</computeroutput> option.</para>
+
+    <para>Note that this dictates the order the functions appear.
+    It is <command>not</command> the order in which the columns
+    appear; that is dictated by the "events shown" line (and can
+    be changed with the <computeroutput>--show</computeroutput>
+    option).</para>
+  </listitem>
+
+  <listitem>
+    <para>Threshold: <computeroutput>cg_annotate</computeroutput>
+    by default omits functions that cause very low numbers of
+    misses to avoid drowning you in information.  In this case,
+    cg_annotate shows summaries the functions that account for
+    99% of the <computeroutput>Ir</computeroutput> counts;
+    <computeroutput>Ir</computeroutput> is chosen as the
+    threshold event since it is the primary sort event.  The
+    threshold can be adjusted with the
+    <computeroutput>--threshold</computeroutput>
+    option.</para>
+  </listitem>
+
+  <listitem>
+    <para>Chosen for annotation: names of files specified
+    manually for annotation; in this case none.</para>
+  </listitem>
+
+  <listitem>
+    <para>Auto-annotation: whether auto-annotation was requested
+    via the <computeroutput>--auto=yes</computeroutput>
+    option. In this case no.</para>
+  </listitem>
+
+</itemizedlist>
+
+<para>Then follows summary statistics for the whole
+program. These are similar to the summary provided when running
+<computeroutput>valgrind
+--tool=cachegrind</computeroutput>.</para>
+  
+<para>Then follows function-by-function statistics. Each function
+is identified by a
+<computeroutput>file_name:function_name</computeroutput> pair. If
+a column contains only a dot it means the function never performs
+that event (eg. the third row shows that
+<computeroutput>strcmp()</computeroutput> contains no
+instructions that write to memory). The name
+<computeroutput>???</computeroutput> is used if the the file name
+and/or function name could not be determined from debugging
+information. If most of the entries have the form
+<computeroutput>???:???</computeroutput> the program probably
+wasn't compiled with <computeroutput>-g</computeroutput>.  If any
+code was invalidated (either due to self-modifying code or
+unloading of shared objects) its counts are aggregated into a
+single cost centre written as
+<computeroutput>(discarded):(discarded)</computeroutput>.</para>
+
+<para>It is worth noting that functions will come from three
+types of source files:</para>
+
+<orderedlist>
+  <listitem>
+    <para>From the profiled program
+    (<filename>concord.c</filename> in this example).</para>
+  </listitem>
+  <listitem>
+    <para>From libraries (eg. <filename>getc.c</filename>)</para>
+  </listitem>
+  <listitem>
+    <para>From Valgrind's implementation of some libc functions
+    (eg. <computeroutput>vg_clientmalloc.c:malloc</computeroutput>).
+    These are recognisable because the filename begins with
+    <computeroutput>vg_</computeroutput>, and is probably one of
+    <filename>vg_main.c</filename>,
+    <filename>vg_clientmalloc.c</filename> or
+    <filename>vg_mylibc.c</filename>.</para>
+  </listitem>
+
+</orderedlist>
+
+<para>There are two ways to annotate source files -- by choosing
+them manually, or with the
+<computeroutput>--auto=yes</computeroutput> option. To do it
+manually, just specify the filenames as arguments to
+<computeroutput>cg_annotate</computeroutput>. For example, the
+output from running <filename>cg_annotate concord.c</filename>
+for our example produces the same output as above followed by an
+annotated version of <filename>concord.c</filename>, a section of
+which looks like:</para>
+
+<programlisting><![CDATA[
+--------------------------------------------------------------------------------
+-- User-annotated source: concord.c
+--------------------------------------------------------------------------------
+Ir        I1mr I2mr Dr      D1mr  D2mr  Dw      D1mw   D2mw
+
+[snip]
+
+        .    .    .       .     .     .       .      .      .  void init_hash_table(char *file_name, Word_Node *table[])
+        3    1    1       .     .     .       1      0      0  {
+        .    .    .       .     .     .       .      .      .      FILE *file_ptr;
+        .    .    .       .     .     .       .      .      .      Word_Info *data;
+        1    0    0       .     .     .       1      1      1      int line = 1, i;
+        .    .    .       .     .     .       .      .      .
+        5    0    0       .     .     .       3      0      0      data = (Word_Info *) create(sizeof(Word_Info));
+        .    .    .       .     .     .       .      .      .
+    4,991    0    0   1,995     0     0     998      0      0      for (i = 0; i < TABLE_SIZE; i++)
+    3,988    1    1   1,994     0     0     997     53     52          table[i] = NULL;
+        .    .    .       .     .     .       .      .      .
+        .    .    .       .     .     .       .      .      .      /* Open file, check it. */
+        6    0    0       1     0     0       4      0      0      file_ptr = fopen(file_name, "r");
+        2    0    0       1     0     0       .      .      .      if (!(file_ptr)) {
+        .    .    .       .     .     .       .      .      .          fprintf(stderr, "Couldn't open '%s'.\n", file_name);
+        1    1    1       .     .     .       .      .      .          exit(EXIT_FAILURE);
+        .    .    .       .     .     .       .      .      .      }
+        .    .    .       .     .     .       .      .      .
+  165,062    1    1  73,360     0     0  91,700      0      0      while ((line = get_word(data, line, file_ptr)) != EOF)
+  146,712    0    0  73,356     0     0  73,356      0      0          insert(data->;word, data->line, table);
+        .    .    .       .     .     .       .      .      .
+        4    0    0       1     0     0       2      0      0      free(data);
+        4    0    0       1     0     0       2      0      0      fclose(file_ptr);
+        3    0    0       2     0     0       .      .      .  }]]></programlisting>
+
+<para>(Although column widths are automatically minimised, a wide
+terminal is clearly useful.)</para>
+  
+<para>Each source file is clearly marked
+(<computeroutput>User-annotated source</computeroutput>) as
+having been chosen manually for annotation.  If the file was
+found in one of the directories specified with the
+<computeroutput>-I / --include</computeroutput> option, the directory
+and file are both given.</para>
+
+<para>Each line is annotated with its event counts.  Events not
+applicable for a line are represented by a `.'; this is useful
+for distinguishing between an event which cannot happen, and one
+which can but did not.</para>
+
+<para>Sometimes only a small section of a source file is
+executed.  To minimise uninteresting output, Valgrind only shows
+annotated lines and lines within a small distance of annotated
+lines.  Gaps are marked with the line numbers so you know which
+part of a file the shown code comes from, eg:</para>
+
+<programlisting><![CDATA[
+(figures and code for line 704)
+-- line 704 ----------------------------------------
+-- line 878 ----------------------------------------
+(figures and code for line 878)]]></programlisting>
+
+<para>The amount of context to show around annotated lines is
+controlled by the <computeroutput>--context</computeroutput>
+option.</para>
+
+<para>To get automatic annotation, run
+<computeroutput>cg_annotate --auto=yes</computeroutput>.
+cg_annotate will automatically annotate every source file it can
+find that is mentioned in the function-by-function summary.
+Therefore, the files chosen for auto-annotation are affected by
+the <computeroutput>--sort</computeroutput> and
+<computeroutput>--threshold</computeroutput> options.  Each
+source file is clearly marked (<computeroutput>Auto-annotated
+source</computeroutput>) as being chosen automatically.  Any
+files that could not be found are mentioned at the end of the
+output, eg:</para>
+
+<programlisting><![CDATA[
+------------------------------------------------------------------
+The following files chosen for auto-annotation could not be found:
+------------------------------------------------------------------
+  getc.c
+  ctype.c
+  ../sysdeps/generic/lockfile.c]]></programlisting>
+
+<para>This is quite common for library files, since libraries are
+usually compiled with debugging information, but the source files
+are often not present on a system.  If a file is chosen for
+annotation <command>both</command> manually and automatically, it
+is marked as <computeroutput>User-annotated
+source</computeroutput>. Use the <computeroutput>-I /
+--include</computeroutput> option to tell Valgrind where to look
+for source files if the filenames found from the debugging
+information aren't specific enough.</para>
+
+<para>Beware that cg_annotate can take some time to digest large
+<computeroutput>cachegrind.out.pid</computeroutput> files,
+e.g. 30 seconds or more.  Also beware that auto-annotation can
+produce a lot of output if your program is large!</para>
+
+</sect2>
+
+
+<sect2 id="cg-manual.assembler" xreflabel="Annotating assembler programs">
+<title>Annotating assembler programs</title>
+
+<para>Valgrind can annotate assembler programs too, or annotate
+the assembler generated for your C program.  Sometimes this is
+useful for understanding what is really happening when an
+interesting line of C code is translated into multiple
+instructions.</para>
+
+<para>To do this, you just need to assemble your
+<computeroutput>.s</computeroutput> files with assembler-level
+debug information.  gcc doesn't do this, but you can use the GNU
+assembler with the <computeroutput>--gstabs</computeroutput>
+option to generate object files with this information, eg:</para>
+
+<programlisting><![CDATA[
+as --gstabs foo.s]]></programlisting>
+
+<para>You can then profile and annotate source files in the same
+way as for C/C++ programs.</para>
+
+</sect2>
+
+</sect1>
+
+
+<sect1 id="cg-manual.annopts" xreflabel="cg_annotate options">
+<title><computeroutput>cg_annotate</computeroutput> options</title>
+
+<itemizedlist>
+
+  <listitem>
+    <para><computeroutput>--pid</computeroutput></para>
+    <para>Indicates which
+    <computeroutput>cachegrind.out.pid</computeroutput> file to
+    read.  Not actually an option -- it is required.</para>
+  </listitem>
+    
+  <listitem>
+    <para><computeroutput>-h, --help</computeroutput></para>
+    <para><computeroutput>-v, --version</computeroutput></para>
+    <para>Help and version, as usual.</para>
+  </listitem>
+
+  <listitem>
+    <para><computeroutput>--sort=A,B,C</computeroutput> [default:
+    order in
+    <computeroutput>cachegrind.out.pid</computeroutput>]</para>
+    <para>Specifies the events upon which the sorting of the
+    function-by-function entries will be based.  Useful if you
+    want to concentrate on eg. I cache misses
+    (<computeroutput>--sort=I1mr,I2mr</computeroutput>), or D
+    cache misses
+    (<computeroutput>--sort=D1mr,D2mr</computeroutput>), or L2
+    misses
+    (<computeroutput>--sort=D2mr,I2mr</computeroutput>).</para>
+  </listitem>
+
+  <listitem>
+    <para><computeroutput>--show=A,B,C</computeroutput> [default:
+    all, using order in
+    <computeroutput>cachegrind.out.pid</computeroutput>]</para>
+    <para>Specifies which events to show (and the column
+    order). Default is to use all present in the
+    <computeroutput>cachegrind.out.pid</computeroutput> file (and
+    use the order in the file).</para>
+  </listitem>
+
+  <listitem>
+    <para><computeroutput>--threshold=X</computeroutput>
+    [default: 99%]</para>
+    <para>Sets the threshold for the function-by-function
+    summary.  Functions are shown that account for more than X%
+    of the primary sort event.  If auto-annotating, also affects
+    which files are annotated.</para>
+      
+    <para>Note: thresholds can be set for more than one of the
+    events by appending any events for the
+    <computeroutput>--sort</computeroutput> option with a colon
+    and a number (no spaces, though).  E.g. if you want to see
+    the functions that cover 99% of L2 read misses and 99% of L2
+    write misses, use this option:</para>
+    <para><computeroutput>--sort=D2mr:99,D2mw:99</computeroutput></para>
+  </listitem>
+
+  <listitem>
+    <para><computeroutput>--auto=no</computeroutput> [default]</para>
+    <para><computeroutput>--auto=yes</computeroutput></para>
+    <para>When enabled, automatically annotates every file that
+    is mentioned in the function-by-function summary that can be
+    found.  Also gives a list of those that couldn't be found.</para>
+  </listitem>
+
+  <listitem>
+    <para><computeroutput>--context=N</computeroutput> [default:
+    8]</para>
+    <para>Print N lines of context before and after each
+    annotated line.  Avoids printing large sections of source
+    files that were not executed.  Use a large number
+    (eg. 10,000) to show all source lines.</para>
+  </listitem>
+
+  <listitem>
+    <para><computeroutput>-I=&lt;dir&gt;,
+      --include=&lt;dir&gt;</computeroutput> [default: empty
+      string]</para>
+    <para>Adds a directory to the list in which to search for
+    files.  Multiple -I/--include options can be given to add
+    multiple directories.</para>
+  </listitem>
+
+</itemizedlist>
+  
+
+
+<sect2>
+<title>Warnings</title>
+
+<para>There are a couple of situations in which
+<computeroutput>cg_annotate</computeroutput> issues
+warnings.</para>
+
+<itemizedlist>
+  <listitem>
+    <para>If a source file is more recent than the
+    <computeroutput>cachegrind.out.pid</computeroutput> file.
+    This is because the information in
+    <computeroutput>cachegrind.out.pid</computeroutput> is only
+    recorded with line numbers, so if the line numbers change at
+    all in the source (eg.  lines added, deleted, swapped), any
+    annotations will be incorrect.</para>
+  </listitem>
+  <listitem>
+    <para>If information is recorded about line numbers past the
+    end of a file.  This can be caused by the above problem,
+    ie. shortening the source file while using an old
+    <computeroutput>cachegrind.out.pid</computeroutput> file.  If
+    this happens, the figures for the bogus lines are printed
+    anyway (clearly marked as bogus) in case they are
+    important.</para>
+  </listitem>
+</itemizedlist>
+
+</sect2>
+
+
+
+<sect2>
+<title>Things to watch out for</title>
+
+<para>Some odd things that can occur during annotation:</para>
+
+<itemizedlist>
+  <listitem>
+    <para>If annotating at the assembler level, you might see
+    something like this:</para>
+<programlisting><![CDATA[
+      1    0    0  .    .    .  .    .    .          leal -12(%ebp),%eax
+      1    0    0  .    .    .  1    0    0          movl %eax,84(%ebx)
+      2    0    0  0    0    0  1    0    0          movl $1,-20(%ebp)
+      .    .    .  .    .    .  .    .    .          .align 4,0x90
+      1    0    0  .    .    .  .    .    .          movl $.LnrB,%eax
+      1    0    0  .    .    .  1    0    0          movl %eax,-16(%ebp)]]></programlisting>
+
+    <para>How can the third instruction be executed twice when
+    the others are executed only once?  As it turns out, it
+    isn't.  Here's a dump of the executable, using
+    <computeroutput>objdump -d</computeroutput>:</para>
+<programlisting><![CDATA[
+      8048f25:       8d 45 f4                lea    0xfffffff4(%ebp),%eax
+      8048f28:       89 43 54                mov    %eax,0x54(%ebx)
+      8048f2b:       c7 45 ec 01 00 00 00    movl   $0x1,0xffffffec(%ebp)
+      8048f32:       89 f6                   mov    %esi,%esi
+      8048f34:       b8 08 8b 07 08          mov    $0x8078b08,%eax
+      8048f39:       89 45 f0                mov    %eax,0xfffffff0(%ebp)]]></programlisting>
+
+    <para>Notice the extra <computeroutput>mov
+    %esi,%esi</computeroutput> instruction.  Where did this come
+    from?  The GNU assembler inserted it to serve as the two
+    bytes of padding needed to align the <computeroutput>movl
+    $.LnrB,%eax</computeroutput> instruction on a four-byte
+    boundary, but pretended it didn't exist when adding debug
+    information.  Thus when Valgrind reads the debug info it
+    thinks that the <computeroutput>movl
+    $0x1,0xffffffec(%ebp)</computeroutput> instruction covers the
+    address range 0x8048f2b--0x804833 by itself, and attributes
+    the counts for the <computeroutput>mov
+    %esi,%esi</computeroutput> to it.</para>
+  </listitem>
+
+  <listitem>
+    <para>Inlined functions can cause strange results in the
+    function-by-function summary.  If a function
+    <computeroutput>inline_me()</computeroutput> is defined in
+    <filename>foo.h</filename> and inlined in the functions
+    <computeroutput>f1()</computeroutput>,
+    <computeroutput>f2()</computeroutput> and
+    <computeroutput>f3()</computeroutput> in
+    <filename>bar.c</filename>, there will not be a
+    <computeroutput>foo.h:inline_me()</computeroutput> function
+    entry.  Instead, there will be separate function entries for
+    each inlining site, ie.
+    <computeroutput>foo.h:f1()</computeroutput>,
+    <computeroutput>foo.h:f2()</computeroutput> and
+    <computeroutput>foo.h:f3()</computeroutput>.  To find the
+    total counts for
+    <computeroutput>foo.h:inline_me()</computeroutput>, add up
+    the counts from each entry.</para>
+
+    <para>The reason for this is that although the debug info
+    output by gcc indicates the switch from
+    <filename>bar.c</filename> to <filename>foo.h</filename>, it
+    doesn't indicate the name of the function in
+    <filename>foo.h</filename>, so Valgrind keeps using the old
+    one.</para>
+  </listitem>
+
+  <listitem>
+    <para>Sometimes, the same filename might be represented with
+    a relative name and with an absolute name in different parts
+    of the debug info, eg:
+    <filename>/home/user/proj/proj.h</filename> and
+    <filename>../proj.h</filename>.  In this case, if you use
+    auto-annotation, the file will be annotated twice with the
+    counts split between the two.</para>
+  </listitem>
+
+  <listitem>
+    <para>Files with more than 65,535 lines cause difficulties
+    for the stabs debug info reader.  This is because the line
+    number in the <computeroutput>struct nlist</computeroutput>
+    defined in <filename>a.out.h</filename> under Linux is only a
+    16-bit value.  Valgrind can handle some files with more than
+    65,535 lines correctly by making some guesses to identify
+    line number overflows.  But some cases are beyond it, in
+    which case you'll get a warning message explaining that
+    annotations for the file might be incorrect.</para>
+  </listitem>
+
+  <listitem>
+    <para>If you compile some files with
+    <computeroutput>-g</computeroutput> and some without, some
+    events that take place in a file without debug info could be
+    attributed to the last line of a file with debug info
+    (whichever one gets placed before the non-debug-info file in
+    the executable).</para>
+  </listitem>
+
+</itemizedlist>
+
+<para>This list looks long, but these cases should be fairly
+rare.</para>
+
+<formalpara>
+  <title>Note:</title>
+  <para><computeroutput>stabs</computeroutput> is not an easy
+  format to read.  If you come across bizarre annotations that
+  look like might be caused by a bug in the stabs reader, please
+  let us know.</para>
+</formalpara>
+
+</sect2>
+
+
+
+<sect2>
+<title>Accuracy</title>
+
+<para>Valgrind's cache profiling has a number of
+shortcomings:</para>
+
+<itemizedlist>
+  <listitem>
+    <para>It doesn't account for kernel activity -- the effect of
+    system calls on the cache contents is ignored.</para>
+  </listitem>
+
+  <listitem>
+    <para>It doesn't account for other process activity (although
+    this is probably desirable when considering a single
+    program).</para>
+  </listitem>
+
+  <listitem>
+    <para>It doesn't account for virtual-to-physical address
+    mappings; hence the entire simulation is not a true
+    representation of what's happening in the
+    cache.</para>
+  </listitem>
+
+  <listitem>
+    <para>It doesn't account for cache misses not visible at the
+    instruction level, eg. those arising from TLB misses, or
+    speculative execution.</para>
+  </listitem>
+
+  <listitem>
+    <para>Valgrind's custom threads implementation will schedule
+    threads differently to the standard one.  This could warp the
+    results for threaded programs.</para>
+  </listitem>
+
+  <listitem>
+    <para>The instructions <computeroutput>bts</computeroutput>,
+    <computeroutput>btr</computeroutput> and
+    <computeroutput>btc</computeroutput> will incorrectly be
+    counted as doing a data read if both the arguments are
+    registers, eg:</para>
+<programlisting><![CDATA[
+    btsl %eax, %edx]]></programlisting>
+
+    <para>This should only happen rarely.</para>
+  </listitem>
+
+  <listitem>
+    <para>FPU instructions with data sizes of 28 and 108 bytes
+    (e.g.  <computeroutput>fsave</computeroutput>) are treated as
+    though they only access 16 bytes.  These instructions seem to
+    be rare so hopefully this won't affect accuracy much.</para>
+  </listitem>
+
+</itemizedlist>
+
+<para>Another thing worth nothing is that results are very
+sensitive.  Changing the size of the
+<filename>valgrind.so</filename> file, the size of the program
+being profiled, or even the length of its name can perturb the
+results.  Variations will be small, but don't expect perfectly
+repeatable results if your program changes at all.</para>
+
+<para>While these factors mean you shouldn't trust the results to
+be super-accurate, hopefully they should be close enough to be
+useful.</para>
+
+</sect2>
+
+
+<sect2>
+<title>Todo</title>
+
+<itemizedlist>
+  <listitem>
+    <para>Program start-up/shut-down calls a lot of functions
+    that aren't interesting and just complicate the output.
+    Would be nice to exclude these somehow.</para>
+  </listitem>
+</itemizedlist> 
+
+</sect2>
+
+</sect1>
+</chapter>