Commit 2951b12d authored by aiss's avatar aiss
Browse files

push v0.6.18 version

parent e8309f27
/*!
* Bootstrap Responsive v2.1.0
*
* Copyright 2012 Twitter, Inc
* Licensed under the Apache License v2.0
* http://www.apache.org/licenses/LICENSE-2.0
*
* Designed and built with all the love in the world @twitter by @mdo and @fat.
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/*!
* Bootstrap v2.1.0
*
* Copyright 2012 Twitter, Inc
* Licensed under the Apache License v2.0
* http://www.apache.org/licenses/LICENSE-2.0
*
* Designed and built with all the love in the world @twitter by @mdo and @fat.
* Augmented by Eric Kryski @ekryski
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.bar-warning{background-color:#faa732;background-image:-moz-linear-gradient(top,#fbb450,#f89406);background-image:-webkit-gradient(linear,0 0,0 100%,from(#fbb450),to(#f89406));background-image:-webkit-linear-gradient(top,#fbb450,#f89406);background-image:-o-linear-gradient(top,#fbb450,#f89406);background-image:linear-gradient(to bottom,#fbb450,#f89406);background-repeat:repeat-x;filter:progid:dximagetransform.microsoft.gradient(startColorstr='#fffbb450',endColorstr='#fff89406',GradientType=0)}.progress-warning.progress-striped .bar,.progress-striped .bar-warning{background-color:#fbb450;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.accordion{margin-bottom:20px}.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px}.accordion-heading{border-bottom:0}.accordion-heading .accordion-toggle{display:block;padding:8px 15px}.accordion-toggle{cursor:pointer}.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5}.carousel{position:relative;margin-bottom:20px;line-height:1}.carousel-inner{position:relative;width:100%;overflow:hidden}.carousel .item{position:relative;display:none;-webkit-transition:.6s ease-in-out left;-moz-transition:.6s ease-in-out left;-o-transition:.6s ease-in-out left;transition:.6s ease-in-out left}.carousel .item>img{display:block;line-height:1}.carousel .active,.carousel .next,.carousel .prev{display:block}.carousel .active{left:0}.carousel .next,.carousel .prev{position:absolute;top:0;width:100%}.carousel .next{left:100%}.carousel .prev{left:-100%}.carousel .next.left,.carousel .prev.right{left:0}.carousel .active.left{left:-100%}.carousel .active.right{left:100%}.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#fff;text-align:center;background:#222;border:3px solid #fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:15px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{line-height:20px;color:#fff}.carousel-caption h4{margin:0 0 5px}.carousel-caption p{margin-bottom:0}.hero-unit{padding:60px;margin-bottom:30px;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit p{font-size:18px;font-weight:200;line-height:30px;color:inherit}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden}.affix{position:fixed}
\ No newline at end of file
/***
colors.css v2.0.0
http://clrs.cc
@mrmrs
MIT License
***/
/*
SKINS
- Backgrounds
- Colors
- Border colors
- SVG fills
- SVG Strokes
*/
/* Backgrounds */
.bg-navy {
background-color: #001F3F; }
.bg-blue {
background-color: #0074D9; }
.bg-aqua {
background-color: #7FDBFF; }
.bg-teal {
background-color: #39CCCC; }
.bg-olive {
background-color: #3D9970; }
.bg-green {
background-color: #2ECC40; }
.bg-lime {
background-color: #01FF70; }
.bg-yellow {
background-color: #FFDC00; }
.bg-orange {
background-color: #FF851B; }
.bg-red {
background-color: #FF4136; }
.bg-fuchsia {
background-color: #F012BE; }
.bg-purple {
background-color: #B10DC9; }
.bg-maroon {
background-color: #85144B; }
.bg-white {
background-color: #fff; }
.bg-gray {
background-color: #aaa; }
.bg-silver {
background-color: #ddd; }
.bg-black {
background-color: #111; }
/* Colors */
.navy {
color: #001F3F; }
.blue {
color: #0074D9; }
.aqua {
color: #7FDBFF; }
.teal {
color: #39CCCC; }
.olive {
color: #3D9970; }
.green {
color: #2ECC40; }
.lime {
color: #01FF70; }
.yellow {
color: #FFDC00; }
.orange {
color: #FF851B; }
.red {
color: #FF4136; }
.fuchsia {
color: #F012BE; }
.purple {
color: #B10DC9; }
.maroon {
color: #85144B; }
.white {
color: #fff; }
.silver {
color: #ddd; }
.gray {
color: #aaa; }
.black {
color: #111; }
/* Border colors
Use with another border utility that sets border-width and style
i.e .border { border-width: 1px; border-style: solid; }
*/
.border--navy {
border-color: #001F3F; }
.border--blue {
border-color: #0074D9; }
.border--aqua {
border-color: #7FDBFF; }
.border--teal {
border-color: #39CCCC; }
.border--olive {
border-color: #3D9970; }
.border--green {
border-color: #2ECC40; }
.border--lime {
border-color: #01FF70; }
.border--yellow {
border-color: #FFDC00; }
.border--orange {
border-color: #FF851B; }
.border--red {
border-color: #FF4136; }
.border--fuchsia {
border-color: #F012BE; }
.border--purple {
border-color: #B10DC9; }
.border--maroon {
border-color: #85144B; }
.border--white {
border-color: #fff; }
.border--gray {
border-color: #aaa; }
.border--silver {
border-color: #ddd; }
.border--black {
border-color: #111; }
/* Fills for SVG */
.fill-navy {
fill: #001F3F; }
.fill-blue {
fill: #0074D9; }
.fill-aqua {
fill: #7FDBFF; }
.fill-teal {
fill: #39CCCC; }
.fill-olive {
fill: #3D9970; }
.fill-green {
fill: #2ECC40; }
.fill-lime {
fill: #01FF70; }
.fill-yellow {
fill: #FFDC00; }
.fill-orange {
fill: #FF851B; }
.fill-red {
fill: #FF4136; }
.fill-fuchsia {
fill: #F012BE; }
.fill-purple {
fill: #B10DC9; }
.fill-maroon {
fill: #85144B; }
.fill-white {
fill: #fff; }
.fill-gray {
fill: #aaa; }
.fill-silver {
fill: #ddd; }
.fill-black {
fill: #111; }
/* Strokes for SVG */
.stroke-navy {
stroke: #001F3F; }
.stroke-blue {
stroke: #0074D9; }
.stroke-aqua {
stroke: #7FDBFF; }
.stroke-teal {
stroke: #39CCCC; }
.stroke-olive {
stroke: #3D9970; }
.stroke-green {
stroke: #2ECC40; }
.stroke-lime {
stroke: #01FF70; }
.stroke-yellow {
stroke: #FFDC00; }
.stroke-orange {
stroke: #FF851B; }
.stroke-red {
stroke: #FF4136; }
.stroke-fuchsia {
stroke: #F012BE; }
.stroke-purple {
stroke: #B10DC9; }
.stroke-maroon {
stroke: #85144B; }
.stroke-white {
stroke: #fff; }
.stroke-gray {
stroke: #aaa; }
.stroke-silver {
stroke: #ddd; }
.stroke-black {
stroke: #111; }
/* PRETTIER LINKS */
a {
text-decoration: none;
-webkit-transition: color .3s ease-in-out;
transition: color .3s ease-in-out; }
a:link {
-webkit-transition: color .3s ease-in-out;
transition: color .3s ease-in-out; }
a:visited { }
a:hover {
color: #001F3F;
-webkit-transition: color .3s ease-in-out;
transition: color .3s ease-in-out; }
a:active {
-webkit-transition: color .3s ease-in-out;
transition: color .3s ease-in-out; }
/* main stylesheet */
@import url(http://fonts.googleapis.com/css?family=Signika);
html {
overflow-y: scroll;
}
body {
font-size: 15px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, sans-serif;
color: #332;
}
h1, h2, h3, h4, h5 {
color: #332;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, sans-serif;
font-weight: 400;
font-size: 1.4em;
line-height: 1.1;
margin-top: 30px;
}
pre code {
font: 14px/19px Inconsolata, Monaco,"Lucida Console",Terminal,"Courier New",Courier;
}
.figure {
text-align: center;
}
.small .figure img {
height: 200px;
}
.pagetitle .figure {
text-align: left !important;
}
.pagetitle .figure img {
height: 36px;
}
table{
background:#fff;
border:1px solid #ccc;
border-width:2px;
border-collapse:collapse;
margin:5px 0 10px;
margin-top: 20px;
margin-bottom: 20px;
}
th, td{
border:1px solid #ccc;
padding:3px 10px;
text-align:left;
vertical-align:top;
}
tr.even td{
background:#f7f7f7;
}
th{
background:#edeff0;
}
td code {
border: 0px;
}
img {
max-width: 100%;
height: auto;
}
hr {
border: 0px;
height: 0;
border-bottom: 1px solid #ccc;
margin-bottom: 100px;
}
/* Logo */
.logo {
text-align: center;
}
.tagline {
font-family: Georgia;
font-size: 18px;
font-style: italic;
line-height: 1.45;
color: #383838;
}
.author {
}
.halfbreak {
padding-bottom: 100px;
}
.break {
padding-bottom: 200px;
}
/* TOC Links */
a {
color: #111111;
text-decoration: none;
}
.body li a {
text-decoration: underline;
}
/* Math */
.MathJax_Display {
padding-top: 20px;
padding-bottom: 20px;
}
/* Body Links */
p a {
text-decoration: underline;
}
li code, p code {
font-size: 12px;
border: 1px solid #ccc;
margin-left: 3px;
margin-right: 3px;
padding-left: 2px;
padding-right: 2px;
}
/* */
.center {
text-align: center;
}
.bigger img {
width: 120%;
height: 120%;
}
pre {
font-size: 0.9em;
margin-bottom: 18px;
margin-top: 18px;
border-left: 1px solid #ccc;
}
h1 {
margin-top: 0px;
}
.annotation {
font-size: 10pt;
}
.annotation pre {
display: block;
margin: 0;
padding: 7px 10px;
overflow-x: auto;
}
.annotation.span2 {
/* Override bootstrap */
margin-left: 0px !important;
margin-top: 18px !important;
}
.annotation pre code {
border: 0;
padding: 0;
background: transparent;
}
blockquote {
border-left: 1px solid #ccc;
font-family: Georgia, serif;
font-size: 14px;
font-style: italic;
margin: 0.25em 0;
padding-left: 10px;
line-height: 1.45;
color: #383838;
left: 20px;
}
blockquote cite {
color: #999999;
font-size: 14px;
display: block;
margin-top: 5px;
}
ul.sections {
list-style: none;
padding:0 0 5px 0;
margin:0;
}
code.sourceCode {
padding: 0;
background: inherit;
}
pre.sourceCode {
padding: 10px;
}
ul.sections > li > div {
-moz-box-sizing: border-box; /* firefox */
-ms-box-sizing: border-box; /* ie */
-webkit-box-sizing: border-box; /* webkit */
-khtml-box-sizing: border-box; /* konqueror */
box-sizing: border-box; /* css3 */
}
/* Make the naviation centered and larger on small screens */
/*---------------------- (> 481px) ---------------------*/
@media only screen and (max-width: 481px) {
}
@media only screen and (min-width: 1025px) {
body {
padding: 10px;
}
.side {
position: fixed;
width: 120px !important;
margin-left: 0px;
z-index: 1000;
}
.side ul ul {
display: none;
}
.side ul ul.active {
display: block;
}
.side .active {
font-weight: bold;
}
.body {
margin-left: 120px !important;
}
}
// Silly program just to test the natvis file for Visual Studio
// ------------------------------------------------------------
#include <string>
#include "parallel_hashmap/phmap.h"
template<class Set, class F>
void test_set(const F &f)
{
Set s;
typename Set::iterator it;
for (int i=0; i<100; ++i)
s.insert(f(i));
it = s.begin();
++it;
it = s.end();
it = s.begin();
while(it != s.end())
++it;
it = s.begin();
}
int main(int, char **)
{
using namespace std;
auto make_int = [](int i) { return i; };
auto make_string = [](int i) { return std::to_string(i); };
auto make_2int = [](int i) { return std::make_pair(i, i); };
auto make_2string = [](int i) { return std::make_pair(std::to_string(i), std::to_string(i)); };
test_set<phmap::flat_hash_set<int>>(make_int);
test_set<phmap::flat_hash_set<string>>(make_string);
test_set<phmap::node_hash_set<int>>(make_int);
test_set<phmap::node_hash_set<string>>(make_string);
test_set<phmap::flat_hash_map<int, int>>(make_2int);
test_set<phmap::flat_hash_map<string, string>>(make_2string);
test_set<phmap::node_hash_map<int, int>>(make_2int);
test_set<phmap::node_hash_map<string, string>>(make_2string);
test_set<phmap::parallel_flat_hash_set<int>>(make_int);
test_set<phmap::parallel_flat_hash_set<string>>(make_string);
test_set<phmap::parallel_node_hash_set<int>>(make_int);
test_set<phmap::parallel_node_hash_set<string>>(make_string);
test_set<phmap::parallel_flat_hash_map<int, int>>(make_2int);
test_set<phmap::parallel_flat_hash_map<string, string>>(make_2string);
test_set<phmap::parallel_node_hash_map<int, int>>(make_2int);
test_set<phmap::parallel_node_hash_map<string, string>>(make_2string);
// example of using default parameters in order to specify the mutex type.
//
// Please be aware that the iterators returned (by find for example) cannot
// be safely read in a multithreaded environment. Instead use if_contains(),
// which passes a reference value to the callback while holding the submap lock.
// Similarly, write access can be done safely using modify_if, try_emplace_l
// or lazy_emplace_l.
// ----------------------------------------------------------------------------
using Map = phmap::parallel_flat_hash_map<std::size_t, std::size_t,
std::hash<size_t>,
std::equal_to<size_t>,
std::allocator<std::pair<const size_t, size_t>>,
4,
std::mutex>;
auto make_2size_t = [](size_t i) { return std::make_pair(i, i); };
test_set<Map>(make_2size_t);
}
#include <iostream>
#include <string>
#include <parallel_hashmap/phmap.h>
using phmap::flat_hash_map;
int main()
{
// Create an unordered_map of three strings (that map to strings)
flat_hash_map<std::string, std::string> email =
{
{ "tom", "tom@gmail.com"},
{ "jeff", "jk@gmail.com"},
{ "jim", "jimg@microsoft.com"}
};
// Iterate and print keys and values
for (const auto& n : email)
std::cout << n.first << "'s email is: " << n.second << "\n";
// Add a new entry
email["bill"] = "bg@whatever.com";
// and print it
std::cout << "bill's email is: " << email["bill"] << "\n";
return 0;
}
#include <inttypes.h>
#ifdef STL_UNORDERED
#include <unordered_map>
#define MAPNAME std::unordered_map
#define EXTRAARGS
#elif defined(PHMAP_FLAT)
#include "parallel_hashmap/phmap.h"
#define MAPNAME phmap::flat_hash_map
#define NMSP phmap
#define EXTRAARGS
#else
#include "parallel_hashmap/phmap.h"
#if 1
#include <mutex>
#define MTX std::mutex
#elif 0
// Abseil's mutexes are very efficient (at least on windows)
#include "absl/synchronization/mutex.h"
#define MTX phmap::AbslMutex
#elif 1
#include <boost/thread/locks.hpp>
#if 1
#include <boost/thread/mutex.hpp>
#define MTX boost::mutex // faster if all we do is exclusive locks like this bench
#else
#include <boost/thread/shared_mutex.hpp>
#define MTX boost::upgrade_mutex
#endif
#elif 1
#include <windows.h>
class srwlock {
SRWLOCK _lock;
public:
srwlock() { InitializeSRWLock(&_lock); }
void lock() { AcquireSRWLockExclusive(&_lock); }
void unlock() { ReleaseSRWLockExclusive(&_lock); }
};
#define MTX srwlock
#else
// spinlocks - slow!
#include <atomic>
class spinlock {
std::atomic_flag flag = ATOMIC_FLAG_INIT;
public:
void lock() { while(flag.test_and_set(std::memory_order_acquire)); }
void unlock() { flag.clear(std::memory_order_release); }
};
#define MTX spinlock
#endif
#define MAPNAME phmap::parallel_flat_hash_map
#define NMSP phmap
#define MT_SUPPORT 1
#if MT_SUPPORT == 1
// create the parallel_flat_hash_map without internal mutexes, for when
// we programatically ensure that each thread uses different internal submaps
// --------------------------------------------------------------------------
#define EXTRAARGS , NMSP::priv::hash_default_hash<K>, \
NMSP::priv::hash_default_eq<K>, \
std::allocator<std::pair<const K, V>>, 4, NMSP::NullMutex
#elif MT_SUPPORT == 2
// create the parallel_flat_hash_map with internal mutexes, for when
// we read/write the same parallel_flat_hash_map from multiple threads,
// without any special precautions.
// --------------------------------------------------------------------------
#define EXTRAARGS , NMSP::priv::hash_default_hash<K>, \
NMSP::priv::hash_default_eq<K>, \
std::allocator<std::pair<const K, V>>, 4, MTX
#else
#define EXTRAARGS
#endif
#endif
#define phmap_xstr(s) phmap_str(s)
#define phmap_str(s) #s
template <class K, class V>
using HashT = MAPNAME<K, V EXTRAARGS>;
using hash_t = HashT<int64_t, int64_t>;
using str_hash_t = HashT<const char *, int64_t>;
const char *program_slug = phmap_xstr(MAPNAME); // "_4";
#include <cassert>
#include <ctime>
#include <cstring>
#include <cstdlib>
#include <cstdio>
#include <cmath>
#include <thread>
#include <chrono>
#include <ostream>
#include "parallel_hashmap/meminfo.h"
#include <vector>
using std::vector;
int64_t _abs(int64_t x) { return (x < 0) ? -x : x; }
#ifdef _MSC_VER
#pragma warning(disable : 4996)
#endif // _MSC_VER
// --------------------------------------------------------------------------
class Timer
{
typedef std::chrono::high_resolution_clock high_resolution_clock;
typedef std::chrono::milliseconds milliseconds;
public:
explicit Timer(bool run = false) { if (run) reset(); }
void reset() { _start = high_resolution_clock::now(); }
milliseconds elapsed() const
{
return std::chrono::duration_cast<milliseconds>(high_resolution_clock::now() - _start);
}
private:
high_resolution_clock::time_point _start;
};
// --------------------------------------------------------------------------
// from: https://github.com/preshing/RandomSequence
// --------------------------------------------------------------------------
class RSU
{
private:
unsigned int m_index;
unsigned int m_intermediateOffset;
static unsigned int permuteQPR(unsigned int x)
{
static const unsigned int prime = 4294967291u;
if (x >= prime)
return x; // The 5 integers out of range are mapped to themselves.
unsigned int residue = ((unsigned long long) x * x) % prime;
return (x <= prime / 2) ? residue : prime - residue;
}
public:
RSU(unsigned int seedBase, unsigned int seedOffset)
{
m_index = permuteQPR(permuteQPR(seedBase) + 0x682f0161);
m_intermediateOffset = permuteQPR(permuteQPR(seedOffset) + 0x46790905);
}
unsigned int next()
{
return permuteQPR((permuteQPR(m_index++) + m_intermediateOffset) ^ 0x5bf03635);
}
};
// --------------------------------------------------------------------------
char * new_string_from_integer(uint64_t num)
{
int ndigits = num == 0 ? 1 : (int)log10(num) + 1;
char * str = (char *)malloc(ndigits + 1);
sprintf(str, "%u", (unsigned int)num);
return str;
}
// --------------------------------------------------------------------------
template <class T>
void _fill(vector<T> &v)
{
srand(1); // for a fair/deterministic comparison
for (size_t i = 0, sz = v.size(); i < sz; ++i)
v[i] = (T)(i * 10 + rand() % 10);
}
// --------------------------------------------------------------------------
template <class T>
void _shuffle(vector<T> &v)
{
for (size_t n = v.size(); n >= 2; --n)
std::swap(v[n - 1], v[static_cast<unsigned>(rand()) % n]);
}
// --------------------------------------------------------------------------
template <class T, class HT>
Timer _fill_random(vector<T> &v, HT &hash)
{
_fill<T>(v);
_shuffle<T>(v);
Timer timer(true);
for (size_t i = 0, sz = v.size(); i < sz; ++i)
hash.insert(typename HT::value_type(v[i], 0));
return timer;
}
// --------------------------------------------------------------------------
void out(const char* test, int64_t cnt, const Timer &t, bool = false)
{
printf("%s,time,%u,%s,%f\n", test, (unsigned int)cnt, program_slug,
(float)((double)t.elapsed().count() / 1000));
}
// --------------------------------------------------------------------------
void outmem(const char*, int64_t cnt, uint64_t mem, bool final = false)
{
static uint64_t max_mem = 0;
static uint64_t max_keys = 0;
if (final)
printf("peak memory usage for %u values: %.2f GB\n", (unsigned int)max_keys,
max_mem / ((double)1000 * 1000 * 1000));
else {
if (mem > max_mem)
max_mem = mem;
if ((uint64_t)cnt > max_keys)
max_keys = cnt;
}
}
static bool all_done = false;
static int64_t s_num_keys[16] = { 0 };
static int64_t loop_idx = 0;
static int64_t inner_cnt = 0;
static const char *test = "random";
// --------------------------------------------------------------------------
template <class HT>
void _fill_random_inner(int64_t cnt, HT &hash, RSU &rsu)
{
for (int64_t i=0; i<cnt; ++i)
{
hash.insert(typename HT::value_type(rsu.next(), 0));
++s_num_keys[0];
}
}
// --------------------------------------------------------------------------
template <class HT>
void _fill_random_inner_mt(int64_t cnt, HT &hash, RSU &rsu)
{
constexpr int64_t num_threads = 8; // has to be a power of two
std::unique_ptr<std::thread> threads[num_threads];
auto thread_fn = [&hash, cnt, num_threads](size_t thread_idx, RSU rsu_) {
#if MT_SUPPORT
size_t modulo = hash.subcnt() / num_threads; // subcnt() returns the number of submaps
for (int64_t i=0; i<cnt; ++i) // iterate over all values
{
unsigned int key = rsu_.next(); // get next key to insert
#if MT_SUPPORT == 1
size_t hashval = hash.hash(key); // compute its hash
size_t idx = hash.subidx(hashval); // compute the submap index for this hash
if (idx / modulo == thread_idx) // if the submap is suitable for this thread
#elif MT_SUPPORT == 2
if (i % num_threads == thread_idx)
#endif
{
hash.insert(typename HT::value_type(key, 0)); // insert the value
++(s_num_keys[thread_idx]); // increment count of inserted values
}
}
#endif
};
// create and start 8 threads - each will insert in their own submaps
// thread 0 will insert the keys whose hash direct them to submap0 or submap1
// thread 1 will insert the keys whose hash direct them to submap2 or submap3
// --------------------------------------------------------------------------
for (size_t i=0; i<num_threads; ++i)
threads[i].reset(new std::thread(thread_fn, i, rsu));
// rsu passed by value to threads... we need to increment the reference object
for (int64_t i=0; i<cnt; ++i)
rsu.next();
// wait for the threads to finish their work and exit
for (size_t i=0; i<num_threads; ++i)
threads[i]->join();
}
// --------------------------------------------------------------------------
size_t total_num_keys()
{
size_t n = 0;
for (int i=0; i<16; ++i)
n += s_num_keys[i];
return n;
}
// --------------------------------------------------------------------------
template <class HT>
Timer _fill_random2(int64_t cnt, HT &hash)
{
test = "random";
unsigned int seed = 76687;
RSU rsu(seed, seed + 1);
Timer timer(true);
const int64_t num_loops = 10;
inner_cnt = cnt / num_loops;
for (int i=0; i<16; ++i)
s_num_keys[i] = 0;
for (loop_idx=0; loop_idx<num_loops; ++loop_idx)
{
#if 1 && MT_SUPPORT
// multithreaded insert
_fill_random_inner_mt(inner_cnt, hash, rsu);
#else
_fill_random_inner(inner_cnt, hash, rsu);
#endif
out(test, total_num_keys(), timer);
}
fprintf(stderr, "inserted %.2lfM\n", (double)hash.size() / 1000000);
outmem(test, total_num_keys(), spp::GetProcessMemoryUsed());
return timer;
}
// --------------------------------------------------------------------------
template <class T, class HT>
Timer _lookup(vector<T> &v, HT &hash, size_t &num_present)
{
_fill_random(v, hash);
num_present = 0;
size_t max_val = v.size() * 10;
Timer timer(true);
for (size_t i = 0, sz = v.size(); i < sz; ++i)
{
num_present += (size_t)(hash.find(v[i]) != hash.end());
num_present += (size_t)(hash.find((T)(rand() % max_val)) != hash.end());
}
return timer;
}
// --------------------------------------------------------------------------
template <class T, class HT>
Timer _delete(vector<T> &v, HT &hash)
{
_fill_random(v, hash);
_shuffle(v); // don't delete in insertion order
Timer timer(true);
for(size_t i = 0, sz = v.size(); i < sz; ++i)
hash.erase(v[i]);
return timer;
}
// --------------------------------------------------------------------------
void memlog()
{
std::this_thread::sleep_for(std::chrono::milliseconds(10));
uint64_t nbytes_old_out = spp::GetProcessMemoryUsed();
uint64_t nbytes_old = spp::GetProcessMemoryUsed(); // last non outputted mem measurement
outmem(test, 0, nbytes_old);
int64_t last_loop = 0;
while (!all_done)
{
uint64_t nbytes = spp::GetProcessMemoryUsed();
if ((double)_abs(nbytes - nbytes_old_out) / nbytes_old_out > 0.03 ||
(double)_abs(nbytes - nbytes_old) / nbytes_old > 0.01)
{
if ((double)(nbytes - nbytes_old) / nbytes_old > 0.03)
outmem(test, total_num_keys() - 1, nbytes_old);
outmem(test, total_num_keys(), nbytes);
nbytes_old_out = nbytes;
last_loop = loop_idx;
}
else if (loop_idx > last_loop)
{
outmem(test, total_num_keys(), nbytes);
nbytes_old_out = nbytes;
last_loop = loop_idx;
}
nbytes_old = nbytes;
std::this_thread::sleep_for(std::chrono::milliseconds(1));
}
}
// --------------------------------------------------------------------------
int main(int argc, char ** argv)
{
int64_t num_keys = 100000000;
const char *bench_name = "random";
int64_t i, value = 0;
if(argc > 2)
{
num_keys = atoi(argv[1]);
bench_name = argv[2];
}
hash_t hash;
str_hash_t str_hash;
srand(1); // for a fair/deterministic comparison
Timer timer(true);
#if MT_SUPPORT
if (!strcmp(program_slug,"absl::parallel_flat_hash_map") ||
!strcmp(program_slug,"phmap::parallel_flat_hash_map"))
program_slug = phmap_xstr(MAPNAME) "_mt";
#endif
std::thread t1(memlog);
try
{
if(!strcmp(bench_name, "sequential"))
{
for(i = 0; i < num_keys; i++)
hash.insert(hash_t::value_type(i, value));
}
#if 0
else if(!strcmp(bench_name, "random"))
{
vector<int64_t> v(num_keys);
timer = _fill_random(v, hash);
out("random", num_keys, timer);
}
#endif
else if(!strcmp(bench_name, "random"))
{
fprintf(stderr, "size = %zu\n", sizeof(hash));
timer = _fill_random2(num_keys, hash);
}
else if(!strcmp(bench_name, "lookup"))
{
vector<int64_t> v(num_keys);
size_t num_present;
timer = _lookup(v, hash, num_present);
//fprintf(stderr, "found %zu\n", num_present);
}
else if(!strcmp(bench_name, "delete"))
{
vector<int64_t> v(num_keys);
timer = _delete(v, hash);
}
else if(!strcmp(bench_name, "sequentialstring"))
{
for(i = 0; i < num_keys; i++)
str_hash.insert(str_hash_t::value_type(new_string_from_integer(i), value));
}
else if(!strcmp(bench_name, "randomstring"))
{
for(i = 0; i < num_keys; i++)
str_hash.insert(str_hash_t::value_type(new_string_from_integer((int)rand()), value));
}
else if(!strcmp(bench_name, "deletestring"))
{
for(i = 0; i < num_keys; i++)
str_hash.insert(str_hash_t::value_type(new_string_from_integer(i), value));
timer.reset();
for(i = 0; i < num_keys; i++)
str_hash.erase(new_string_from_integer(i));
}
//printf("%f\n", (float)((double)timer.elapsed().count() / 1000));
fflush(stdout);
//std::this_thread::sleep_for(std::chrono::seconds(1000));
}
catch (...)
{
}
all_done = true;
outmem(test, 0, 0, true);
t1.join();
return 0;
}
#include <iostream>
#include "btree_fwd.h"
#include <parallel_hashmap/btree.h>
int main()
{
// initialise map with some values using an initializer_list
phmap::btree_map<std::string, int> map =
{ { "John", 35 },
{ "Jane", 32 },
{ "Joe", 30 },
};
// add a couple more values using operator[]()
map["lucy"] = 18;
map["Andre"] = 20;
auto it = map.find("Joe");
map.erase(it);
map.insert(std::make_pair("Alex", 16));
map.emplace("Emily", 18); // emplace uses pair template constructor
for (auto& p: map)
std::cout << p.first << ", " << p.second << '\n';
IntString map2; // IntString is declared in btree_fwd.h
map2.emplace(std::piecewise_construct, std::forward_as_tuple(0), std::forward_as_tuple(10, 'c'));
map2.try_emplace(1, 10, 'a'); // phmap::btree_map supports c++17 API
for (auto& p: map2)
std::cout << p.first << ", " << p.second << '\n';
// create a btree_set of tuples
using X = std::tuple<float, std::string>;
phmap::btree_set<X> set;
for (int i=0; i<10; ++i)
set.insert(X((float)i, std::to_string(i)));
set.emplace(15.0f, "15");
set.erase(X(1.0f, "1"));
for (auto& e: set)
std::cout << std::get<0>(e) << ", \"" << std::get<1>(e) << "\" \n";
return 0;
}
#include <string>
#include <parallel_hashmap/phmap_fwd_decl.h>
using IntString = phmap::btree_map<int, std::string>;
#include <iostream>
#include <parallel_hashmap/phmap_dump.h>
void dump_load_uint64_uint32() {
phmap::flat_hash_map<uint64_t, uint32_t> mp1 = { {100, 99}, {300, 299} };
for (const auto& n : mp1)
std::cout << n.first << "'s value is: " << n.second << "\n";
{
phmap::BinaryOutputArchive ar_out("./dump.data");
mp1.phmap_dump(ar_out);
}
phmap::flat_hash_map<uint64_t, uint32_t> mp2;
{
phmap::BinaryInputArchive ar_in("./dump.data");
mp2.phmap_load(ar_in);
}
for (const auto& n : mp2)
std::cout << n.first << "'s value is: " << n.second << "\n";
}
void dump_load_parallel_flat_hash_map() {
phmap::parallel_flat_hash_map<uint64_t, uint32_t> mp1 = {
{100, 99}, {300, 299}, {101, 992} };
for (const auto& n : mp1)
std::cout << "key: " << n.first << ", value: " << n.second << "\n";
{
phmap::BinaryOutputArchive ar_out("./dump.data");
mp1.phmap_dump(ar_out);
}
phmap::parallel_flat_hash_map<uint64_t, uint32_t> mp2;
{
phmap::BinaryInputArchive ar_in("./dump.data");
mp2.phmap_load(ar_in);
}
for (const auto& n : mp2)
std::cout << "key: " << n.first << ", value: " << n.second << "\n";
}
int main()
{
dump_load_uint64_uint32();
dump_load_parallel_flat_hash_map();
return 0;
}
/*
*
* Example of dumping a map, containing values which are phmap maps or sets
* building this requires c++17 support
*
*/
#include <iostream>
#include <parallel_hashmap/phmap_dump.h>
template <class K, class V>
class MyMap : public phmap::flat_hash_map<K, phmap::flat_hash_set<V>>
{
public:
using Set = phmap::flat_hash_set<V>;
void dump(const std::string &filename)
{
phmap::BinaryOutputArchive ar_out (filename.c_str());
ar_out.dump(this->size());
for (auto& [k, v] : *this)
{
ar_out.dump(k);
v.dump(ar_out);
}
}
void load(const std::string & filename)
{
phmap::BinaryInputArchive ar_in(filename.c_str());
size_t size;
ar_in.load(&size);
this->reserve(size);
while (size--)
{
K k;
Set v;
ar_in.load(&k);
v.load(ar_in);
this->insert_or_assign(std::move(k), std::move(v));
}
}
void insert(K k, V v)
{
Set &set = (*this)[k];
set.insert(v);
}
friend std::ostream& operator<<(std::ostream& os, const MyMap& map)
{
for (const auto& [k, m] : map)
{
os << k << ": [";
for (const auto& x : m)
os << x << ", ";
os << "]\n";
}
return os;
}
};
int main()
{
MyMap<size_t, size_t> m;
m.insert(1, 5);
m.insert(1, 8);
m.insert(2, 3);
m.insert(1, 15);
m.insert(1, 27);
m.insert(2, 10);
m.insert(2, 13);
std::cout << m << "\n";
m.dump("test_archive");
m.clear();
m.load("test_archive");
std::cout << m << "\n";
return 0;
}
#include <map>
#include <unordered_map>
#include <string>
#include <iostream>
#include <chrono>
#include <vector>
#include <parallel_hashmap/phmap.h>
#include <sstream>
template <typename T>
using milliseconds = std::chrono::duration<T, std::milli>;
// type containing std::string. Seems to take a long time to construct (and maybe move)
// ------------------------------------------------------------------------------------
class custom_type
{
std::string one = "one";
std::string two = "two";
std::uint32_t three = 3;
std::uint64_t four = 4;
std::uint64_t five = 5;
public:
custom_type() = default;
// Make object movable and non-copyable
custom_type(custom_type &&) = default;
custom_type& operator=(custom_type &&) = default;
// should be automatically deleted per http://www.slideshare.net/ripplelabs/howard-hinnant-accu2014
//custom_type(custom_type const&) = delete;
//custom_type& operator=(custom_type const&) = delete;
};
// type containing only integrals. should be faster to create.
// -----------------------------------------------------------
class custom_type_2
{
std::uint32_t three = 3;
std::uint64_t four = 4;
std::uint64_t five = 5;
std::uint64_t six = 6;
public:
custom_type_2() = default;
// Make object movable and non-copyable
custom_type_2(custom_type_2 &&) = default;
custom_type_2& operator=(custom_type_2 &&) = default;
// should be automatically deleted per http://www.slideshare.net/ripplelabs/howard-hinnant-accu2014
//custom_type_2(custom_type_2 const&) = delete;
//custom_type_2& operator=(custom_type_2 const&) = delete;
};
// convert std::size_t to appropriate key
// --------------------------------------
template <class K>
struct GenKey
{
K operator()(std::size_t j);
};
template <>
struct GenKey<std::string>
{
std::string operator()(std::size_t j) {
std::ostringstream stm;
stm << j;
return stm.str();
}
};
template <>
struct GenKey<int>
{
int operator()(std::size_t j) {
return (int)j;
}
};
// emplace key + large struct
// --------------------------
template <class Map, class K, class V, class T> struct _emplace
{
void operator()(Map &m, std::size_t j);
};
// "void" template parameter -> use emplace
template <class Map, class K, class V> struct _emplace<Map, K, V, void>
{
void operator()(Map &m, std::size_t j)
{
m.emplace(GenKey<K>()(j), V());
}
};
// "int" template parameter -> use emplace_back for std::vector
template <class Map, class K, class V> struct _emplace<Map, K, V, int>
{
void operator()(Map &m, std::size_t j)
{
m.emplace_back(GenKey<K>()(j), V());
}
};
// The test itself
// ---------------
template <class Map, class K, class V, class T, template <class, class, class, class> class INSERT>
void _test(std::size_t iterations, std::size_t container_size, const char *map_name)
{
std::size_t count = 0;
auto t1 = std::chrono::high_resolution_clock::now();
INSERT<Map, K, V, T> insert;
for (std::size_t i=0; i<iterations; ++i)
{
Map m;
for (std::size_t j=0; j<container_size; ++j)
insert(m, j);
count += m.size();
}
auto t2 = std::chrono::high_resolution_clock::now();
auto elapsed = milliseconds<double>(t2 - t1).count();
if (count != iterations*container_size)
std::clog << " invalid count: " << count << "\n";
std::clog << map_name << std::fixed << int(elapsed) << " ms\n";
}
template <class K, class V, template <class, class, class, class> class INSERT>
void test(std::size_t iterations, std::size_t container_size)
{
std::clog << "bench: iterations: " << iterations << " / container_size: " << container_size << "\n";
_test<std::map<K, V>, K, V, void, INSERT>(iterations, container_size, " std::map: ");
_test<std::unordered_map<K, V>, K, V, void, INSERT>(iterations, container_size, " std::unordered_map: ");
_test<phmap::flat_hash_map<K, V>, K, V, void, INSERT>(iterations, container_size, " phmap::flat_hash_map: ");
_test<std::vector<std::pair<K, V>>, K, V, int, INSERT> (iterations, container_size, " std::vector<std::pair>: ");
std::clog << "\n";
}
int main()
{
std::size_t iterations = 100000;
// test with custom_type_2 (int key + 32 byte value). This is representative
// of the hash table insertion speed.
// -------------------------------------------------------------------------
std::clog << "\n\n" << "testing with <int, custom_type_2>" "\n";
std::clog << "---------------------------------" "\n";
test<int, custom_type_2, _emplace>(iterations,10);
test<int, custom_type_2, _emplace>(iterations,100);
test<int, custom_type_2, _emplace>(iterations,500);
// test with custom_type, which contains two std::string values, and use
// a generated string key. This is not very indicative of the speed of the
// hash itself, as a good chunk of the time is spent creating the keys and
// values (as shown by the long times even for std::vector).
// -----------------------------------------------------------------------
std::clog << "\n" << "testing with <string, custom_type>" "\n";
std::clog << "---------------------------------" "\n";
test<std::string, custom_type, _emplace>(iterations,1);
test<std::string, custom_type, _emplace>(iterations,10);
test<std::string, custom_type, _emplace>(iterations,50);
}
/*
* Make sure that the phmap.h header builds fine when included in two separate
* source files
*/
#include <string>
#include <parallel_hashmap/phmap.h>
using phmap::flat_hash_map;
int main()
{
// Create an unordered_map of three strings (that map to strings)
using Map = flat_hash_map<std::string, std::string>;
Map email =
{
{ "tom", "tom@gmail.com"},
{ "jeff", "jk@gmail.com"},
{ "jim", "jimg@microsoft.com"}
};
extern void f2(Map&);
f2(email);
return 0;
}
/*
* Make sure that the phmap.h header builds fine when included in two separate
* source files
*/
#include <iostream>
#include <string>
#include <parallel_hashmap/phmap.h>
using phmap::flat_hash_map;
using Map = flat_hash_map<std::string, std::string>;
void f2(Map& email)
{
// Iterate and print keys and values
for (const auto& n : email)
std::cout << n.first << "'s email is: " << n.second << "\n";
// Add a new entry
email["bill"] = "bg@whatever.com";
// and print it
std::cout << "bill's email is: " << email["bill"] << "\n";
}
#include "hash_std.h" // defines Person with std::hash specialization
#include <iostream>
#include <parallel_hashmap/phmap.h>
int main()
{
// As we have defined a specialization of std::hash() for Person,
// we can now create sparse_hash_set or sparse_hash_map of Persons
// ----------------------------------------------------------------
phmap::flat_hash_set<Person> persons =
{ { "John", "Mitchell", 35 },
{ "Jane", "Smith", 32 },
{ "Jane", "Smith", 30 },
};
for (auto& p: persons)
std::cout << p._first << ' ' << p._last << " (" << p._age << ")" << '\n';
}
#ifndef phmap_example_hash_std_
#define phmap_example_hash_std_
#include <parallel_hashmap/phmap_utils.h> // minimal header providing phmap::HashState()
#include <string>
using std::string;
struct Person
{
bool operator==(const Person &o) const
{
return _first == o._first && _last == o._last && _age == o._age;
}
string _first;
string _last;
int _age;
};
namespace std
{
// inject specialization of std::hash for Person into namespace std
// An alternative is to provide a hash_value() friend function (see hash_value.h)
// ------------------------------------------------------------------------------
template<> struct hash<Person>
{
std::size_t operator()(Person const &p) const
{
return phmap::HashState().combine(0, p._first, p._last, p._age);
}
};
}
#endif // phmap_example_hash_std_
#include "hash_value.h" // defines Person with std::hash specialization
#include <iostream>
#include <parallel_hashmap/phmap.h>
int main()
{
// As we have defined a specialization of std::hash() for Person,
// we can now create sparse_hash_set or sparse_hash_map of Persons
// ----------------------------------------------------------------
phmap::flat_hash_set<Person> persons =
{ { "John", "Mitchell", 35 },
{ "Jane", "Smith", 32 },
{ "Jane", "Smith", 30 },
};
for (auto& p: persons)
std::cout << p._first << ' ' << p._last << " (" << p._age << ")" << '\n';
}
#ifndef phmap_example_hash_value_
#define phmap_example_hash_value_
#include <parallel_hashmap/phmap_utils.h> // minimal header providing phmap::HashState()
#include <string>
using std::string;
struct Person
{
bool operator==(const Person &o) const
{
return _first == o._first && _last == o._last && _age == o._age;
}
// Demonstrates how to provide the hash function as a friend member function of the class
// This can be used as an alternative to providing a std::hash<Person> specialization
// --------------------------------------------------------------------------------------
friend size_t hash_value(const Person &p)
{
return phmap::HashState().combine(0, p._first, p._last, p._age);
}
string _first;
string _last;
int _age;
};
#endif // phmap_example_hash_value_
#include <string>
#include <array>
#include <cstdint>
#include <limits>
#include <random>
#include <utility>
#define PHMAP_ALLOCATOR_NOTHROW 1
#include <parallel_hashmap/phmap.h>
// this is probably the fastest high quality 64bit random number generator that exists.
// Implements Small Fast Counting v4 RNG from PractRand.
class sfc64 {
public:
using result_type = uint64_t;
// no copy ctors so we don't accidentally get the same random again
sfc64(sfc64 const&) = delete;
sfc64& operator=(sfc64 const&) = delete;
sfc64(sfc64&&) = default;
sfc64& operator=(sfc64&&) = default;
sfc64(std::array<uint64_t, 4> const& _state)
: m_a(_state[0])
, m_b(_state[1])
, m_c(_state[2])
, m_counter(_state[3]) {}
static constexpr uint64_t(min)() {
return (std::numeric_limits<uint64_t>::min)();
}
static constexpr uint64_t(max)() {
return (std::numeric_limits<uint64_t>::max)();
}
sfc64()
: sfc64(UINT64_C(0x853c49e6748fea9b)) {}
sfc64(uint64_t _seed)
: m_a(_seed)
, m_b(_seed)
, m_c(_seed)
, m_counter(1) {
for (int i = 0; i < 12; ++i) {
operator()();
}
}
void seed() {
*this = sfc64{std::random_device{}()};
}
uint64_t operator()() noexcept {
auto const tmp = m_a + m_b + m_counter++;
m_a = m_b ^ (m_b >> right_shift);
m_b = m_c + (m_c << left_shift);
m_c = rotl(m_c, rotation) + tmp;
return tmp;
}
// this is a bit biased, but for our use case that's not important.
uint64_t operator()(uint64_t boundExcluded) noexcept {
#ifdef PHMAP_HAS_UMUL128
uint64_t h;
(void)umul128(operator()(), boundExcluded, &h);
return h;
#else
return 0;
#endif
}
std::array<uint64_t, 4> state() const {
return {{m_a, m_b, m_c, m_counter}};
}
void state(std::array<uint64_t, 4> const& s) {
m_a = s[0];
m_b = s[1];
m_c = s[2];
m_counter = s[3];
}
private:
template <typename T>
T rotl(T const x, int k) {
return (x << k) | (x >> (8 * sizeof(T) - k));
}
static constexpr int rotation = 24;
static constexpr int right_shift = 11;
static constexpr int left_shift = 3;
uint64_t m_a;
uint64_t m_b;
uint64_t m_c;
uint64_t m_counter;
};
int main()
{
// Create an unordered_map of three strings (that map to strings)
using Map = phmap::parallel_node_hash_map<int, int>;
static size_t const n = 50000000;
sfc64 rng(123);
size_t checksum = 0;
if (0)
{
size_t const max_rng = n / 20;
Map map;
for (size_t i = 0; i < n; ++i) {
checksum += ++map[static_cast<int>(rng(max_rng))];
}
}
if (0)
{
size_t const max_rng = n / 4;
Map map;
for (size_t i = 0; i < n; ++i) {
checksum += ++map[static_cast<int>(rng(max_rng))];
}
}
if (1)
{
size_t const max_rng = n / 2;
Map map;
for (size_t i = 0; i < n; ++i) {
checksum += ++map[static_cast<int>(rng(max_rng))];
}
}
if (0)
{
Map map;
for (size_t i = 0; i < n; ++i) {
checksum += ++map[static_cast<int>(rng())];
}
}
printf("%zu\n", checksum);
}
>ONE Homo sapiens alu
GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA
TCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACT
AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG
GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG
CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGT
GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA
GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA
TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAG
AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA
GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGT
AATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACC
AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTG
GTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC
CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAG
AGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTT
TGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA
TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT
GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGG
TTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT
CTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG
CGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCG
TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTA
CTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG
AGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCG
GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACC
TGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAA
TACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA
GGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT
GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTC
ACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGT
TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC
CGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG
CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG
GGCGACAGAGCGAGACTCCG
>TWO IUB ambiguity codes
cttBtatcatatgctaKggNcataaaSatgtaaaDcDRtBggDtctttataattcBgtcg
tactDtDagcctatttSVHtHttKtgtHMaSattgWaHKHttttagacatWatgtRgaaa
NtactMcSMtYtcMgRtacttctWBacgaaatatagScDtttgaagacacatagtVgYgt
cattHWtMMWcStgttaggKtSgaYaaccWStcgBttgcgaMttBYatcWtgacaYcaga
gtaBDtRacttttcWatMttDBcatWtatcttactaBgaYtcttgttttttttYaaScYa
HgtgttNtSatcMtcVaaaStccRcctDaataataStcYtRDSaMtDttgttSagtRRca
tttHatSttMtWgtcgtatSSagactYaaattcaMtWatttaSgYttaRgKaRtccactt
tattRggaMcDaWaWagttttgacatgttctacaaaRaatataataaMttcgDacgaSSt
acaStYRctVaNMtMgtaggcKatcttttattaaaaagVWaHKYagtttttatttaacct
tacgtVtcVaattVMBcttaMtttaStgacttagattWWacVtgWYagWVRctDattBYt
gtttaagaagattattgacVatMaacattVctgtBSgaVtgWWggaKHaatKWcBScSWa
accRVacacaaactaccScattRatatKVtactatatttHttaagtttSKtRtacaaagt
RDttcaaaaWgcacatWaDgtDKacgaacaattacaRNWaatHtttStgttattaaMtgt
tgDcgtMgcatBtgcttcgcgaDWgagctgcgaggggVtaaScNatttacttaatgacag
cccccacatYScaMgtaggtYaNgttctgaMaacNaMRaacaaacaKctacatagYWctg
ttWaaataaaataRattagHacacaagcgKatacBttRttaagtatttccgatctHSaat
actcNttMaagtattMtgRtgaMgcataatHcMtaBSaRattagttgatHtMttaaKagg
YtaaBataSaVatactWtataVWgKgttaaaacagtgcgRatatacatVtHRtVYataSa
KtWaStVcNKHKttactatccctcatgWHatWaRcttactaggatctataDtDHBttata
aaaHgtacVtagaYttYaKcctattcttcttaataNDaaggaaaDYgcggctaaWSctBa
aNtgctggMBaKctaMVKagBaactaWaDaMaccYVtNtaHtVWtKgRtcaaNtYaNacg
gtttNattgVtttctgtBaWgtaattcaagtcaVWtactNggattctttaYtaaagccgc
tcttagHVggaYtgtNcDaVagctctctKgacgtatagYcctRYHDtgBattDaaDgccK
tcHaaStttMcctagtattgcRgWBaVatHaaaataYtgtttagMDMRtaataaggatMt
ttctWgtNtgtgaaaaMaatatRtttMtDgHHtgtcattttcWattRSHcVagaagtacg
ggtaKVattKYagactNaatgtttgKMMgYNtcccgSKttctaStatatNVataYHgtNa
BKRgNacaactgatttcctttaNcgatttctctataScaHtataRagtcRVttacDSDtt
aRtSatacHgtSKacYagttMHtWataggatgactNtatSaNctataVtttRNKtgRacc
tttYtatgttactttttcctttaaacatacaHactMacacggtWataMtBVacRaSaatc
cgtaBVttccagccBcttaRKtgtgcctttttRtgtcagcRttKtaaacKtaaatctcac
aattgcaNtSBaaccgggttattaaBcKatDagttactcttcattVtttHaaggctKKga
tacatcBggScagtVcacattttgaHaDSgHatRMaHWggtatatRgccDttcgtatcga
aacaHtaagttaRatgaVacttagattVKtaaYttaaatcaNatccRttRRaMScNaaaD
gttVHWgtcHaaHgacVaWtgttScactaagSgttatcttagggDtaccagWattWtRtg
ttHWHacgattBtgVcaYatcggttgagKcWtKKcaVtgaYgWctgYggVctgtHgaNcV
taBtWaaYatcDRaaRtSctgaHaYRttagatMatgcatttNattaDttaattgttctaa
ccctcccctagaWBtttHtBccttagaVaatMcBHagaVcWcagBVttcBtaYMccagat
gaaaaHctctaacgttagNWRtcggattNatcRaNHttcagtKttttgWatWttcSaNgg
gaWtactKKMaacatKatacNattgctWtatctaVgagctatgtRaHtYcWcttagccaa
tYttWttaWSSttaHcaaaaagVacVgtaVaRMgattaVcDactttcHHggHRtgNcctt
tYatcatKgctcctctatVcaaaaKaaaagtatatctgMtWtaaaacaStttMtcgactt
taSatcgDataaactaaacaagtaaVctaggaSccaatMVtaaSKNVattttgHccatca
cBVctgcaVatVttRtactgtVcaattHgtaaattaaattttYtatattaaRSgYtgBag
aHSBDgtagcacRHtYcBgtcacttacactaYcgctWtattgSHtSatcataaatataHt
cgtYaaMNgBaatttaRgaMaatatttBtttaaaHHKaatctgatWatYaacttMctctt
ttVctagctDaaagtaVaKaKRtaacBgtatccaaccactHHaagaagaaggaNaaatBW
attccgStaMSaMatBttgcatgRSacgttVVtaaDMtcSgVatWcaSatcttttVatag
ttactttacgatcaccNtaDVgSRcgVcgtgaacgaNtaNatatagtHtMgtHcMtagaa
attBgtataRaaaacaYKgtRccYtatgaagtaataKgtaaMttgaaRVatgcagaKStc
tHNaaatctBBtcttaYaBWHgtVtgacagcaRcataWctcaBcYacYgatDgtDHccta
>THREE Homo sapiens frequency
aacacttcaccaggtatcgtgaaggctcaagattacccagagaacctttgcaatataaga
atatgtatgcagcattaccctaagtaattatattctttttctgactcaaagtgacaagcc
ctagtgtatattaaatcggtatatttgggaaattcctcaaactatcctaatcaggtagcc
atgaaagtgatcaaaaaagttcgtacttataccatacatgaattctggccaagtaaaaaa
tagattgcgcaaaattcgtaccttaagtctctcgccaagatattaggatcctattactca
tatcgtgtttttctttattgccgccatccccggagtatctcacccatccttctcttaaag
gcctaatattacctatgcaaataaacatatattgttgaaaattgagaacctgatcgtgat
tcttatgtgtaccatatgtatagtaatcacgcgactatatagtgctttagtatcgcccgt
gggtgagtgaatattctgggctagcgtgagatagtttcttgtcctaatatttttcagatc
gaatagcttctatttttgtgtttattgacatatgtcgaaactccttactcagtgaaagtc
atgaccagatccacgaacaatcttcggaatcagtctcgttttacggcggaatcttgagtc
taacttatatcccgtcgcttactttctaacaccccttatgtatttttaaaattacgttta
ttcgaacgtacttggcggaagcgttattttttgaagtaagttacattgggcagactcttg
acattttcgatacgactttctttcatccatcacaggactcgttcgtattgatatcagaag
ctcgtgatgattagttgtcttctttaccaatactttgaggcctattctgcgaaatttttg
ttgccctgcgaacttcacataccaaggaacacctcgcaacatgccttcatatccatcgtt
cattgtaattcttacacaatgaatcctaagtaattacatccctgcgtaaaagatggtagg
ggcactgaggatatattaccaagcatttagttatgagtaatcagcaatgtttcttgtatt
aagttctctaaaatagttacatcgtaatgttatctcgggttccgcgaataaacgagatag
attcattatatatggccctaagcaaaaacctcctcgtattctgttggtaattagaatcac
acaatacgggttgagatattaattatttgtagtacgaagagatataaaaagatgaacaat
tactcaagtcaagatgtatacgggatttataataaaaatcgggtagagatctgctttgca
attcagacgtgccactaaatcgtaatatgtcgcgttacatcagaaagggtaactattatt
aattaataaagggcttaatcactacatattagatcttatccgatagtcttatctattcgt
tgtatttttaagcggttctaattcagtcattatatcagtgctccgagttctttattattg
ttttaaggatgacaaaatgcctcttgttataacgctgggagaagcagactaagagtcgga
gcagttggtagaatgaggctgcaaaagacggtctcgacgaatggacagactttactaaac
caatgaaagacagaagtagagcaaagtctgaagtggtatcagcttaattatgacaaccct
taatacttccctttcgccgaatactggcgtggaaaggttttaaaagtcgaagtagttaga
ggcatctctcgctcataaataggtagactactcgcaatccaatgtgactatgtaatactg
ggaacatcagtccgcgatgcagcgtgtttatcaaccgtccccactcgcctggggagacat
gagaccacccccgtggggattattagtccgcagtaatcgactcttgacaatccttttcga
ttatgtcatagcaatttacgacagttcagcgaagtgactactcggcgaaatggtattact
aaagcattcgaacccacatgaatgtgattcttggcaatttctaatccactaaagcttttc
cgttgaatctggttgtagatatttatataagttcactaattaagatcacggtagtatatt
gatagtgatgtctttgcaagaggttggccgaggaatttacggattctctattgatacaat
ttgtctggcttataactcttaaggctgaaccaggcgtttttagacgacttgatcagctgt
tagaatggtttggactccctctttcatgtcagtaacatttcagccgttattgttacgata
tgcttgaacaatattgatctaccacacacccatagtatattttataggtcatgctgttac
ctacgagcatggtattccacttcccattcaatgagtattcaacatcactagcctcagaga
tgatgacccacctctaataacgtcacgttgcggccatgtgaaacctgaacttgagtagac
gatatcaagcgctttaaattgcatataacatttgagggtaaagctaagcggatgctttat
ataatcaatactcaataataagatttgattgcattttagagttatgacacgacatagttc
actaacgagttactattcccagatctagactgaagtactgatcgagacgatccttacgtc
gatgatcgttagttatcgacttaggtcgggtctctagcggtattggtacttaaccggaca
ctatactaataacccatgatcaaagcataacagaatacagacgataatttcgccaacata
tatgtacagaccccaagcatgagaagctcattgaaagctatcattgaagtcccgctcaca
atgtgtcttttccagacggtttaactggttcccgggagtcctggagtttcgacttacata
aatggaaacaatgtattttgctaatttatctatagcgtcatttggaccaatacagaatat
tatgttgcctagtaatccactataacccgcaagtgctgatagaaaatttttagacgattt
ataaatgccccaagtatccctcccgtgaatcctccgttatactaattagtattcgttcat
acgtataccgcgcatatatgaacatttggcgataaggcgcgtgaattgttacgtgacaga
gatagcagtttcttgtgatatggttaacagacgtacatgaagggaaactttatatctata
gtgatgcttccgtagaaataccgccactggtctgccaatgatgaagtatgtagctttagg
tttgtactatgaggctttcgtttgtttgcagagtataacagttgcgagtgaaaaaccgac
gaatttatactaatacgctttcactattggctacaaaatagggaagagtttcaatcatga
gagggagtatatggatgctttgtagctaaaggtagaacgtatgtatatgctgccgttcat
tcttgaaagatacataagcgataagttacgacaattataagcaacatccctaccttcgta
acgatttcactgttactgcgcttgaaatacactatggggctattggcggagagaagcaga
tcgcgccgagcatatacgagacctataatgttgatgatagagaaggcgtctgaattgata
catcgaagtacactttctttcgtagtatctctcgtcctctttctatctccggacacaaga
attaagttatatatatagagtcttaccaatcatgttgaatcctgattctcagagttcttt
ggcgggccttgtgatgactgagaaacaatgcaatattgctccaaatttcctaagcaaatt
ctcggttatgttatgttatcagcaaagcgttacgttatgttatttaaatctggaatgacg
gagcgaagttcttatgtcggtgtgggaataattcttttgaagacagcactccttaaataa
tatcgctccgtgtttgtatttatcgaatgggtctgtaaccttgcacaagcaaatcggtgg
tgtatatatcggataacaattaatacgatgttcatagtgacagtatactgatcgagtcct
ctaaagtcaattacctcacttaacaatctcattgatgttgtgtcattcccggtatcgccc
gtagtatgtgctctgattgaccgagtgtgaaccaaggaacatctactaatgcctttgtta
ggtaagatctctctgaattccttcgtgccaacttaaaacattatcaaaatttcttctact
tggattaactacttttacgagcatggcaaattcccctgtggaagacggttcattattatc
ggaaaccttatagaaattgcgtgttgactgaaattagatttttattgtaagagttgcatc
tttgcgattcctctggtctagcttccaatgaacagtcctcccttctattcgacatcgggt
ccttcgtacatgtctttgcgatgtaataattaggttcggagtgtggccttaatgggtgca
actaggaatacaacgcaaatttgctgacatgatagcaaatcggtatgccggcaccaaaac
gtgctccttgcttagcttgtgaatgagactcagtagttaaataaatccatatctgcaatc
gattccacaggtattgtccactatctttgaactactctaagagatacaagcttagctgag
accgaggtgtatatgactacgctgatatctgtaaggtaccaatgcaggcaaagtatgcga
gaagctaataccggctgtttccagctttataagattaaaatttggctgtcctggcggcct
cagaattgttctatcgtaatcagttggttcattaattagctaagtacgaggtacaactta
tctgtcccagaacagctccacaagtttttttacagccgaaacccctgtgtgaatcttaat
atccaagcgcgttatctgattagagtttacaactcagtattttatcagtacgttttgttt
ccaacattacccggtatgacaaaatgacgccacgtgtcgaataatggtctgaccaatgta
ggaagtgaaaagataaatat
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