mem: Move ruby protocols into a directory called ruby_protocol.

Now that the gem5 protocols are split out, it would be nice to put them
in their own protocol directory. It's also confusing to have files
called *_protocol which are not in the protocol directory.

Change-Id: I7475ee111630050a2421816dfd290921baab9f71
Reviewed-on: https://gem5-review.googlesource.com/c/public/gem5/+/20230
Reviewed-by: Gabe Black <gabeblack@google.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Gabe Black <gabeblack@google.com>
Tested-by: kokoro <noreply+kokoro@google.com>

mem-ruby: Enable set size increase

Add NUMBER_BITS_PER_SET environment variable to control
the size of the bitmask in Set.hh (default=64).
Necessary for configs which require >64 instances of a given
machine type. This can be set in the build_opts file, e.g.
by adding the following line:
NUMBER_BITS_PER_SET = <number>

Change-Id: I314a3cadca8ce975fcf4a60d9022494751688e88
Reviewed-on: https://gem5-review.googlesource.com/c/public/gem5/+/18968
Reviewed-by: Tiago Mück <tiago.muck@arm.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Nikos Nikoleris <nikos.nikoleris@arm.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Tested-by: kokoro <noreply+kokoro@google.com>

style: fix amd license and style issues

Change-Id: I26136fb49f743c4a597f8021cfd27f78897267b5
Reviewed-on: https://gem5-review.googlesource.com/10463
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Anthony Gutierrez <anthony.gutierrez@amd.com>

mem: Standardize mem folder header guards

Standardize all header guards in the mem directory according to the most
frequent patterns. In general they have the form:
mem: __FOLDER_TREE_FILE_NAME_HH__
ruby: __FOLDER_TREE_FILENAME_HH__

Change-Id: I983853e292deb302becf151bf0e970057dc24774
Reviewed-on: https://gem5-review.googlesource.com/7881
Reviewed-by: Nikos Nikoleris <nikos.nikoleris@arm.com>
Maintainer: Nikos Nikoleris <nikos.nikoleris@arm.com>

misc: Rename misc.(hh|cc) to logging.(hh|cc)

These files aren't a collection of miscellaneous stuff, they're the
definition of the Logger interface, and a few utility macros for
calling into that interface (panic, warn, etc.).

Change-Id: I84267ac3f45896a83c0ef027f8f19c5e9a5667d1
Reviewed-on: https://gem5-review.googlesource.com/6226
Reviewed-by: Brandon Potter <Brandon.Potter@amd.com>
Maintainer: Gabe Black <gabeblack@google.com>

ruby: Refactor some Event subclasses to lambdas

Change-Id: I9f47a20a869553515a759d9a29c05f6ce4b42d64
Signed-off-by: Sean Wilson <spwilson2@wisc.edu>
Reviewed-on: https://gem5-review.googlesource.com/3930
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>

style: [patch 1/22] use /r/3648/ to reorganize includes

ruby: add default ctor for MachineID type

not all uses of MachineID initialize its fields, so here we add a default
ctor.

style: eliminate explicit boolean comparisons

Result of running 'hg m5style --skip-all --fix-control -a' to get
rid of '== true' comparisons, plus trivial manual edits to get
rid of '== false'/'== False' comparisons.

Left a couple of explicit comparisons in where they didn't seem
unreasonable:
invalid boolean comparison in src/arch/mips/interrupts.cc:155
>> DPRINTF(Interrupt, "Interrupts OnCpuTimerINterrupt(tc) == true\n");<<
invalid boolean comparison in src/unittest/unittest.hh:110
>> "EXPECT_FALSE(" #expr ")", (expr) == false)<<

mem: write combining for ruby protocols

This patch adds support for write-combining in ruby.

mem: misc flags for AMD gpu model

This patch add support to mark memory requests/packets with attributes defined
in HSA, such as memory order and scope.

ruby: added stl vector of ints to be used by SLICC

ruby: add BoolVec

The BoolVec typedef and insertion operator overload function simplify usage of
vectors of type bool

misc: Remove redundant compiler-specific defines

This patch moves away from using M5_ATTR_OVERRIDE and the m5::hashmap
(and similar) abstractions, as these are no longer needed with gcc 4.7
and clang 3.1 as minimum compiler versions.

ruby: print addresses in hex
Changeset 4872dbdea907 replaced Address by Addr, but did not make changes to
print statements. So the addresses which were being printed in hex earlier
along with their line address, were now being printed in decimals. This patch
adds a function printAddress(Addr) that can be used to print the address in hex
along with the lines address. This function has been put to use in some of the
places. At other places, change has been made to print just the address in
hex.

ruby: rename System.{hh,cc} to RubySystem.{hh,cc}

The eventual aim of this change is to pass RubySystem pointers through to
objects generated from the SLICC protocol code.

Because some of these objects need to dereference their RubySystem pointers,
they need access to the System.hh header file.

In src/mem/ruby/SConscript, the MakeInclude function creates single-line header
files in the build directory that do nothing except include the corresponding
header file from the source tree.

However, SLICC also generates a list of header files from its symbol table, and
writes it to mem/protocol/Types.hh in the build directory. This code assumes
that the header file name is the same as the class name.

The end result of this is the many of the generated slicc files try to include
RubySystem.hh, when the file they really need is System.hh. The path of least
resistence is just to rename System.hh to RubySystem.hh.

ruby: set: reimplement using std::bitset
The current Set data structure is slow and therefore is being reimplemented
using std::bitset. A maximum limit of 64 is being set on the number of
controllers of each type. This means that for simulating a system with more
controllers of a given type, one would need to change the value of the variable
NUMBER_BITS_PER_SET

ruby: eliminate type uint64 and int64
These types are being replaced with uint64_t and int64_t.

ruby: reverts to changeset: bf82f1f7b040

ruby: DataBlock: adds a comment

ruby: SubBlock: refactor code

ruby: eliminate type uint64 and int64

These types are being replaced with uint64_t and int64_t.

ruby: replace Address by Addr
This patch eliminates the type Address defined by the ruby memory system.
This memory system would now use the type Addr that is in use by the
rest of the system.

ruby: replace global g_abs_controls with per-RubySystem var

This is another step in the process of removing global variables
from Ruby to enable multiple RubySystem instances in a single simulation.

The list of abstract controllers is per-RubySystem and should be
represented that way, rather than as a global.

Since this is the last remaining Ruby global variable, the
src/mem/ruby/Common/Global.* files are also removed.

ruby: replace global g_system_ptr with per-object pointers

This is another step in the process of removing global variables
from Ruby to enable multiple RubySystem instances in a single simulation.

With possibly multiple RubySystem objects, we can no longer use a global
variable to find "the" RubySystem object. Instead, each Ruby component
has to carry a pointer to the RubySystem object to which it belongs.

ruby: replace g_ruby_start with per-RubySystem m_start_cycle

This patch begins the process of removing global variables from the Ruby
source with the goal of eventually allowing users to create multiple Ruby
instances in a single simulation. Currently, users cannot do so because
several global variables and static members are referenced by the RubySystem
object in a way that assumes that there will only ever be a single RubySystem.
These need to be replaced with per-RubySystem equivalents.

This specific patch replaces the global var g_ruby_start, which is used
to calculate throughput statistics for Throttles in simple networks and
links in Garnet networks, with a RubySystem instance var m_start_cycle.

ruby: drop NetworkMessage class

This patch drops the NetworkMessage class. The relevant data members and functions
have been moved to the Message class, which was the parent of NetworkMessage.

ruby: set: replace long by unsigned long
UBSan complains about negative value being shifted

mem: Add const getters for write packet data

This patch takes a first step in tightening up how we use the data
pointer in write packets. A const getter is added for the pointer
itself (getConstPtr), and a number of member functions are also made
const accordingly. In a range of places throughout the memory system
the new member is used.

The patch also removes the unused isReadWrite function.

mem: Dynamically determine page bytes in memory components

This patch takes a step towards an ISA-agnostic memory
system by enabling the components to establish the page size after
instantiation. The swap operation in the memory is now also allowing
any granularity to avoid depending on the IntReg of the ISA.

base: Use the global Mersenne twister throughout

This patch tidies up random number generation to ensure that it is
done consistently throughout the code base. In essence this involves a
clean-up of Ruby, and some code simplifications in the traffic
generator.

As part of this patch a bunch of skewed distributions (off-by-one etc)
have been fixed.

Note that a single global random number generator is used, and that
the object instantiation order will impact the behaviour (the sequence
of numbers will be unaffected, but if module A calles random before
module B then they would obviously see a different outcome). The
dependency on the instantiation order is true in any case due to the
execution-model of gem5, so we leave it as is. Also note that the
global ranom generator is not thread safe at this point.

Regressions using the memtest, TrafficGen or any Ruby tester are
affected and will be updated accordingly.

arch: Cleanup unused ISA traits constants

This patch prunes unused values, and also unifies how the values are
defined (not using an enum for ALPHA), aligning the use of int vs Addr
etc.

The patch also removes the duplication of PageBytes/PageShift and
VMPageSize/LogVMPageSize. For all ISAs the two pairs had identical
values and the latter has been removed.

ruby: remove typedef of Index as int64
The Index type defined as typedef int64 does not really provide any help
since in most places we use primitive types instead of Index. Also, the name
Index is very generic that it does not merit being used as a typename.

ruby: eliminate type Time
There is another type Time in src/base class which results in a conflict.

ruby: move files from ruby/system to ruby/structures

The directory ruby/system is crowded and unorganized. Hence, the files the
hold actual physical structures, are being moved to the directory
ruby/structures. This includes Cache Memory, Directory Memory,
Memory Controller, Wire Buffer, TBE Table, Perfect Cache Memory, Timer Table,
Bank Array.

The directory ruby/systems has the glue code that holds these structures
together.

ruby: consumer: avoid accessing wakeup times when waking up
Each consumer object maintains a set of tick values when the object is supposed
to wakeup and do some processing. As of now, the object accesses this set both
when scheduling a wakeup event and when the object actually wakes up. The set
is accessed during wakeup to remove the current tick value from the set. This
functionality is now being moved to the scheduling function where ticks are
removed at a later time.

ruby: remove some of the unnecessary code

ruby: remove few not required #includes

ruby: add support for clusters

A cluster over here means a set of controllers that can be accessed only by a
certain set of cores. For example, consider a two level hierarchy. Assume
there are 4 L1 controllers (private) and 2 L2 controllers. We can have two
different hierarchies here:

a. the address space is partitioned between the two L2 controllers. Each L1
controller accesses both the L2 controllers. In this case, each L1 controller
is a cluster initself.

b. both the L2 controllers can cache any address. An L1 controller has access
to only one of the L2 controllers. In this case, each L2 controller
along with the L1 controllers that access it, form a cluster.

This patch allows for each controller to have a cluster ID, which is 0 by
default. By setting the cluster ID properly, one can instantiate hierarchies
with clusters. Note that the coherence protocol might have to be changed as
well.

ruby: some small changes

ruby: declare variables to be unsigned in Address.hh

ruby: profiler: lots of inter-related changes
The patch started of with removing the global variables from the profiler for
profiling the miss latency of requests made to the cache. The corrresponding
histograms have been moved to the Sequencer. These are combined together when
the histograms are printed. Separate histograms are now maintained for
tracking latency of all requests together, of hits only and of misses only.

A particular set of histograms used to use the type GenericMachineType defined
in one of the protocol files. This patch removes this type. Now, everything
that relied on this type would use MachineType instead. To do this, SLICC has
been changed so that multiple machine types can be declared by a controller
in its preamble.

ruby: remove undefined functions in Address class

ruby: patch checkpoint restore with garnet
Due to recent changes to clocking system in Ruby and the way Ruby restores
state from a checkpoint, garnet was failing to run from a checkpointed state.
The problem is that Ruby resets the time to zero while warming up the caches.
If any component records a local copy of the time (read calls curCycle())
before the simulation has started, then that component will not operate until
that time is reached. In the context of this particular patch, the Garnet
Network class calls curCycle() at multiple places. Any non-operational
component can block in requests in the memory system, which the system
interprets as a deadlock. This patch makes changes so that Garnet can
successfully run from checkpointed state.

It adds a globally visible time at which the actual execution started. This
time is initialized in RubySystem::startup() function. This variable is only
meant for components with in Ruby. This replaces the private variable that
was maintained within Garnet since it is not possible to figure out the
correct time when the value of this variable can be set.

The patch also does away with all cases where curCycle() is called with in
some Ruby component before the system has actually started executing. This
is required due to the quirky manner in which ruby restores from a checkpoint.

ruby: consumer: avoid using receiver side clock
A set of patches was recently committed to allow multiple clock domains
in ruby. In those patches, I had inadvertently made an incorrect use of
the clocks. Suppose object A needs to schedule an event on object B. It
was possible that A accesses B's clock to schedule the event. This is not
possible in actual system. Hence, changes are being to the Consumer class
so as to avoid such happenings. Note that in a multi eventq simulation,
this can possibly lead to an incorrect simulation.

There are two functions in the Consumer class that are used for scheduling
events. The first function takes in the relative delay over the current time
as the argument and adds the current time to it for scheduling the event.
The second function takes in the absolute time (in ticks) for scheduling the
event. The first function is now being moved to protected section of the
class so that only objects of the derived classes can use it. All other
objects will have to specify absolute time while scheduling an event
for some consumer.

ruby: set: corrects csprintf() call introduced by 7d95b650c9b6

scons: Fix warnings issued by clang 3.2svn (XCode 4.6)

This patch fixes the warnings that clang3.2svn emit due to the "-Wall"
flag. There is one case of an uninitialised value in the ARM neon ISA
description, and then a whole range of unused private fields that are
pruned.

ruby: replace Time with Cycles (final patch in the series)
This patch is as of now the final patch in the series of patches that replace
Time with Cycles.This patch further replaces Time with Cycles in Sequencer,
Profiler, different protocols and related entities.

Though Time has not been completely removed, the places where it is in use
seem benign as of now.

ruby: replaces Time with Cycles in many places
The patch started of with replacing Time with Cycles in the Consumer class.
But to get ruby to compile, the rest of the changes had to be carried out.
Subsequent patches will further this process, till we completely replace
Time with Cycles.

ruby: modifies histogram add() function
This patch modifies the Histogram class' add() function so that it can add
linear histograms as well. The function assumes that the left end point of
the ranges of the two histograms are the same. It also assumes that when
the ranges of the two histogram are changed to accomodate an element not in
the range, the factor used in changing the range is same for both the
histograms.

This function is then used in removing one of the calls to the global
profiler*. The histograms for recording the delays incurred in processing
different requests are now maintained by the controllers. The profiler
adds these histograms when it needs to print the stats.

ruby: record fully busy cycle with in the controller
This patch does several things. First, the counter for fully busy cycles for a
controller is now kept with in the controller, instead of being part of the profiler.
Second, the topology class no longer keeps an array of controllers which was only
used for printing stats. Instead, ruby system will now ask each controller to print
the stats. Thirdly, the statistical variable for recording how many different types
were created is being moved in to the controller from the profiler. Note that for
printing, the profiler will collate results from different controllers.

Ruby: remove reference to g_system_ptr from class Message
This patch was initiated so as to remove reference to g_system_ptr,
the pointer to Ruby System that is used for getting the current time.
That simple change actual requires changing a lot many things in slicc and
garnet. All these changes are related to how time is handled.

In most of the places, g_system_ptr has been replaced by another clock
object. The changes have been done under the assumption that all the
components in the memory system are on the same clock frequency, but the
actual clocks might be distributed.

Ruby: use ClockedObject in Consumer class
Many Ruby structures inherit from the Consumer, which is used for scheduling
events. The Consumer used to relay on an Event Manager for scheduling events
and on g_system_ptr for time. With this patch, the Consumer will now use a
ClockedObject to schedule events and to query for current time. This resulted
in several structures being converted from SimObjects to ClockedObjects. Also,
the MessageBuffer class now requires a pointer to a ClockedObject so as to
query for time.

ruby: add functions for computing next stride/page address

ruby: eliminate typedef integer_t

ruby: avoid using g_system_ptr for event scheduling
This patch removes the use of g_system_ptr for event scheduling. Each consumer
object now needs to specify upfront an EventManager object it would use for
scheduling events. This makes the ruby memory system more amenable for a
multi-threaded simulation.

Ruby: Use uint32_t instead of uint32 everywhere

Ruby: Use uint8_t instead of uint8 everywhere

Ruby System: Convert to Clocked Object
This patch moves Ruby System from being a SimObject to recently introduced
ClockedObject.

Ruby: Correct DataBlock =operator
The =operator for the DataBlock class was incorrectly interpreting the class
member m_alloc. This variable stands for whether the assigned memory for the
data block needs to be freed or not by the class itself. It seems that the
=operator interpreted the variable as whether the memory is assigned to the
data block. This wrong interpretation was causing values not to propagate
to RubySystem::m_mem_vec_ptr. This caused major issues with restoring from
checkpoints when using a protocol which verified that the cache data was
consistent with the backing store (i.e. MOESI-hammer).

Ruby: Remove RubyEventQueue
This patch removes RubyEventQueue. Consumer objects now rely on RubySystem
or themselves for scheduling events.

Ruby NetDest: add assert for bad element in netdest

Ruby: Remove the unused src/mem/ruby/common/Driver.* files.

clang/gcc: Fix compilation issues with clang 3.0 and gcc 4.6

This patch addresses a number of minor issues that cause problems when
compiling with clang >= 3.0 and gcc >= 4.6. Most importantly, it
avoids using the deprecated ext/hash_map and instead uses
unordered_map (and similarly so for the hash_set). To make use of the
new STL containers, g++ and clang has to be invoked with "-std=c++0x",
and this is now added for all gcc versions >= 4.6, and for clang >=
3.0. For gcc >= 4.3 and <= 4.5 and clang <= 3.0 we use the tr1
unordered_map to avoid the deprecation warning.

The addition of c++0x in turn causes a few problems, as the
compiler is more stringent and adds a number of new warnings. Below,
the most important issues are enumerated:

1) the use of namespaces is more strict, e.g. for isnan, and all
headers opening the entire namespace std are now fixed.

2) another other issue caused by the more stringent compiler is the
narrowing of the embedded python, which used to be a char array,
and is now unsigned char since there were values larger than 128.

3) a particularly odd issue that arose with the new c++0x behaviour is
found in range.hh, where the operator< causes gcc to complain about
the template type parsing (the "<" is interpreted as the beginning
of a template argument), and the problem seems to be related to the
begin/end members introduced for the range-type iteration, which is
a new feature in c++11.

As a minor update, this patch also fixes the build flags for the clang
debug target that used to be shared with gcc and incorrectly use
"-ggdb".

Ruby: Fix Set::print for 32-bit hosts

This patch fixes a compilation error caused by a length mismatch on
32-bit hosts. The ifdef and sprintf is replaced by a csprintf.

Scons: Remove Werror=False in SConscript files

This patch removes the overriding of "-Werror" in a handful of
cases. The code compiles with gcc 4.6.3 and clang 3.0 without any
warnings, and thus without any errors. There are no functional changes
introduced by this patch. In the future, rather than ypassing
"-Werror", address the warnings.

Ruby Set: Move NUMBER_WORDS_PER_SET to Set.hh
This constant is currently in System.hh, but is only used in Set.hh. It
is being moved to Set.hh to remove this artificial dependence of Set.hh
on System.hh.

Ruby: Remove some unused typedefs
This patch removes some of the unused typedefs. It also moves
some of the typedefs from Global.hh to TypeDefines.hh. The patch
also eliminates the file NodeID.hh.

Ruby: Remove some unused code

Ruby: Eliminate modulo op for computing set size.

BuildEnv: Eliminate RUBY as build environment variable
This patch replaces RUBY with PROTOCOL in all the SConscript files as
the environment variable that decides whether or not certain components
of the simulator are compiled.

Ruby: Remove files and includes not in use

Ruby: Correct set LONG_BITS and INDEX_SHIFT in class Set.
The code for Set class was written under the assumption that
std::numeric_limits<long>::digits returns the number of bits used for
data type long, which was presumed to be either 32 or 64. But return value
is actually one less, that is, it is either 31 or 63. The value is now
being incremented by 1 so as to correctly set it.

trace: reimplement the DTRACE function so it doesn't use a vector
At the same time, rename the trace flags to debug flags since they
have broader usage than simply tracing. This means that
--trace-flags is now --debug-flags and --trace-help is now --debug-help

includes: sort all includes

Ruby: Make Address.hh independent of RubySystem
This patch changes Address.hh so that it is not dependent on RubySystem.
This dependence seems unecessary. All those functions that depend on
RubySystem have been moved to Address.cc file.

Ruby: Make DataBlock.hh independent of RubySystem
This patch changes DataBlock.hh so that it is not dependent on RubySystem.
This dependence seems unecessary. All those functions that depende on
RubySystem have been moved to DataBlock.cc file.

ruby: cleaning up RubyQueue and RubyNetwork dprintfs
Overall, continue to progress Ruby debug messages to more of the normal M5
debug message style
- add a name() to the Ruby Throttle & PerfectSwitch objects so that the debug output
isn't littered w/"global:" everywhere.
- clean up messages that print over multiple lines when possible
- clean up duplicate prints in the message buffer

Ruby: Improve Change PerfectSwitch's wakeup function
Currently the wakeup function for the PerfectSwitch contains three loops -

loop on number of virtual networks
loop on number of incoming links
loop till all messages for this (link, network) have been routed

With an 8 processor mesh network and Hammer protocol, about 11-12% of the
was observed to have been spent in this function, which is the highest
amongst all the functions. It was found that the innermost loop is executed
about 45 times per invocation of the wakeup function, when each invocation
of the wakeup function processes just about one message.

The patch tries to do away with the redundant executions of the innermost
loop. Counters have been added for each virtual network that record the
number of messages that need to be routed for that virtual network. The
inner loops are only executed when the number of messages for that particular
virtual network > 0. This does away with almost 80% of the executions of the
innermost loop. The function now consumes about 5-6% of the total execution
time.

ruby: get rid of ruby's Debug.hh

Get rid of the Debug class
Get rid of ASSERT and use assert
Use DPRINTFR for ProtocolTrace

Make commenting on close namespace brackets consistent.

Ran all the source files through 'perl -pi' with this script:

s|\s*(};?\s*)?/\*\s*(end\s*)?namespace\s*(\S+)\s*\*/(\s*})?|} // namespace $3|;
s|\s*};?\s*//\s*(end\s*)?namespace\s*(\S+)\s*|} // namespace $2\n|;
s|\s*};?\s*//\s*(\S+)\s*namespace\s*|} // namespace $1\n|;

Also did a little manual editing on some of the arch/*/isa_traits.hh files
and src/SConscript.

This patch removes the WARN_* and ERROR_* from src/mem/ruby/common/Debug.hh file. These statements have been replaced with warn(), panic() and fatal() defined in src/base/misc.hh

ruby: remove Ruby asserts for m5.fast

This diff is for changing the way ASSERT is handled in Ruby. m5.fast
compiles out the assert statements by using the macro NDEBUG. Ruby uses the
macro RUBY_NO_ASSERT to do so. This macro has been removed and NDEBUG has
been put in its place.

ruby: Converted old ruby debug calls to M5 debug calls

This patch developed by Nilay Vaish converts all the old GEMS-style ruby
debug calls to the appropriate M5 debug calls.

ruby: fixed DirectoryMemory's numa_high_bit configuration

This fix includes the off-by-one bit selection bug for numa mapping.

ruby: get rid of Vector and use STL
add a couple of helper functions to base for deleteing all pointers in
a container and outputting containers to a stream

ruby: get rid of RefCnt and Allocator stuff use base/refcnt.hh

This was somewhat tricky because the RefCnt API was somewhat odd. The
biggest confusion was that the the RefCnt object's constructor that
took a TYPE& cloned the object. I created an explicit virtual clone()
function for things that took advantage of this version of the
constructor. I was conservative and used clone() when I was in doubt
of whether or not it was necessary. I still think that there are
probably too many instances of clone(), but hopefully not too many.

I converted several instances of const MsgPtr & to a simple MsgPtr.
If the function wants to avoid the overhead of creating another
reference, then it should just use a regular pointer instead of a ref
counting ptr.

There were a couple of instances where refcounted objects were created
on the stack. This seems pretty dangerous since if you ever
accidentally make a reference to that object with a ref counting
pointer, bad things are bound to happen.

style: clean up ruby's Set class

Further cleanup should probably be done to make this class be non-Ruby
specific and put it in src/base.

There are probably several cases where this class is used, std::bitset
could be used instead.