Index: doc/theses/thierry_delisle_PhD/thesis/.gitignore
===================================================================
--- doc/theses/thierry_delisle_PhD/thesis/.gitignore	(revision d95969a75f9a2102e5866017daba99c54b1bb621)
+++ doc/theses/thierry_delisle_PhD/thesis/.gitignore	(revision d95969a75f9a2102e5866017daba99c54b1bb621)
@@ -0,0 +1,1 @@
+back_text/
Index: doc/theses/thierry_delisle_PhD/thesis/Makefile
===================================================================
--- doc/theses/thierry_delisle_PhD/thesis/Makefile	(revision 71582027d4aee596817893608c7bef096d15cb5b)
+++ doc/theses/thierry_delisle_PhD/thesis/Makefile	(revision d95969a75f9a2102e5866017daba99c54b1bb621)
@@ -43,5 +43,5 @@
 ## Define the documents that need to be made.
 all: thesis.pdf
-thesis.pdf: ${TEXTS} ${FIGURES} ${PICTURES} glossary.tex local.bib
+thesis.pdf: ${TEXTS} ${FIGURES} ${PICTURES} thesis.tex glossary.tex local.bib
 
 DOCUMENT = thesis.pdf
Index: doc/theses/thierry_delisle_PhD/thesis/text/core.tex
===================================================================
--- doc/theses/thierry_delisle_PhD/thesis/text/core.tex	(revision 71582027d4aee596817893608c7bef096d15cb5b)
+++ doc/theses/thierry_delisle_PhD/thesis/text/core.tex	(revision d95969a75f9a2102e5866017daba99c54b1bb621)
@@ -49,8 +49,8 @@
 
 \section{Design}
-In general, a na\"{i}ve \glsxtrshort{fifo} ready-queue does not scale with increased parallelism from \glspl{hthrd}, resulting in decreased performance. The problem is adding/removing \glspl{thrd} is a single point of contention. As shown in the evaluation sections, most production schedulers do scale when adding \glspl{hthrd}. The common solution to the single point of contention is to shard the ready-queue so each \gls{hthrd} can access the ready-queue without contention, increasing performance though lack of contention.
+In general, a na\"{i}ve \glsxtrshort{fifo} ready-queue does not scale with increased parallelism from \glspl{hthrd}, resulting in decreased performance. The problem is adding/removing \glspl{thrd} is a single point of contention. As shown in the evaluation sections, most production schedulers do scale when adding \glspl{hthrd}. The common solution to the single point of contention is to shard the ready-queue so each \gls{hthrd} can access the ready-queue without contention, increasing performance.
 
 \subsection{Sharding} \label{sec:sharding}
-An interesting approach to sharding a queue is presented in \cit{Trevors paper}. This algorithm presents a queue with a relaxed \glsxtrshort{fifo} guarantee using an array of strictly \glsxtrshort{fifo} sublists as shown in Figure~\ref{fig:base}. Each \emph{cell} of the array has a timestamp for the last operation and a pointer to a linked-list with a lock and each node in the list is marked with a timestamp indicating when it is added to the list. A push operation is done by picking a random cell, acquiring the list lock, and pushing to the list. If the cell is locked, the operation is simply retried on another random cell until a lock is acquired. A pop operation is done in a similar fashion except two random cells are picked. If both cells are unlocked with non-empty lists, the operation pops the node with the oldest cell timestamp. If one of the cells is unlocked and non-empty, the operation pops from that cell. If both cells are either locked or empty, the operation picks two new random cells and tries again.
+An interesting approach to sharding a queue is presented in \cit{Trevors paper}. This algorithm presents a queue with a relaxed \glsxtrshort{fifo} guarantee using an array of strictly \glsxtrshort{fifo} sublists as shown in Figure~\ref{fig:base}. Each \emph{cell} of the array has a timestamp for the last operation and a pointer to a linked-list with a lock. Each node in the list is marked with a timestamp indicating when it is added to the list. A push operation is done by picking a random cell, acquiring the list lock, and pushing to the list. If the cell is locked, the operation is simply retried on another random cell until a lock is acquired. A pop operation is done in a similar fashion except two random cells are picked. If both cells are unlocked with non-empty lists, the operation pops the node with the oldest timestamp. If one of the cells is unlocked and non-empty, the operation pops from that cell. If both cells are either locked or empty, the operation picks two new random cells and tries again.
 
 \begin{figure}
@@ -100,10 +100,10 @@
 \paragraph{Local Information} Figure~\ref{fig:emptytls} shows an approach using dense information, similar to the bitmap, but each \gls{hthrd} keeps its own independent copy. While this approach can offer good scalability \emph{and} low latency, the liveliness and discovery of the information can become a problem. This case is made worst in systems with few processors where even blind random picks can find \glspl{thrd} in a few tries.
 
-I built a prototype of these approaches and none of these techniques offer satisfying performance when few threads are present. All of these approach hit the same 2 problems. First, randomly picking sub-queues is very fast but means any improvement to the hit rate can easily be countered by a slow-down in look-up speed when there are empty lists. Second, the array is already as sharded to avoid contention bottlenecks, so any denser data structure tends to become a bottleneck. In all cases, these factors meant the best cases scenario, \ie many threads, would get worst throughput, and the worst-case scenario, few threads, would get a better hit rate, but an equivalent poor throughput. As a result I tried an entirely different approach.
+I built a prototype of these approaches and none of these techniques offer satisfying performance when few threads are present. All of these approach hit the same 2 problems. First, randomly picking sub-queues is very fast. That speed means any improvement to the hit rate can easily be countered by a slow-down in look-up speed, whether or not there are empty lists. Second, the array is already sharded to avoid contention bottlenecks, so any denser data structure tends to become a bottleneck. In all cases, these factors meant the best cases scenario, \ie many threads, would get worst throughput, and the worst-case scenario, few threads, would get a better hit rate, but an equivalent poor throughput. As a result I tried an entirely different approach.
 
 \subsection{Dynamic Entropy}\cit{https://xkcd.com/2318/}
-In the worst-case scenario there are only few \glspl{thrd} ready to run, or more precisely given $P$ \glspl{proc}\footnote{For simplicity, this assumes there is a one-to-one match between \glspl{proc} and \glspl{hthrd}.}, $T$ \glspl{thrd} and $\epsilon$ a very small number, than the worst case scenario can be represented by $\epsilon \ll P$, than $T = P + \epsilon$. It is important to note in this case that fairness is effectively irrelevant. Indeed, this case is close to \emph{actually matching} the model of the ``Ideal multi-tasking CPU'' on page \pageref{q:LinuxCFS}. In this context, it is possible to use a purely internal-locality based approach and still meet the fairness requirements. This approach simply has each \gls{proc} running a single \gls{thrd} repeatedly. Or from the shared ready-queue viewpoint, each \gls{proc} pushes to a given sub-queue and then popes from the \emph{same} subqueue. In cases where $T \gg P$, the scheduler should also achieves similar performance without affecting the fairness guarantees.
+In the worst-case scenario there are only few \glspl{thrd} ready to run, or more precisely given $P$ \glspl{proc}\footnote{For simplicity, this assumes there is a one-to-one match between \glspl{proc} and \glspl{hthrd}.}, $T$ \glspl{thrd} and $\epsilon$ a very small number, than the worst case scenario can be represented by $T = P + \epsilon$, with $\epsilon \ll P$. It is important to note in this case that fairness is effectively irrelevant. Indeed, this case is close to \emph{actually matching} the model of the ``Ideal multi-tasking CPU'' on page \pageref{q:LinuxCFS}. In this context, it is possible to use a purely internal-locality based approach and still meet the fairness requirements. This approach simply has each \gls{proc} running a single \gls{thrd} repeatedly. Or from the shared ready-queue viewpoint, each \gls{proc} pushes to a given sub-queue and then pops from the \emph{same} subqueue. The challenge is for the the scheduler to achieve good performance in both the $T = P + \epsilon$ case and the $T \gg P$ case, without affecting the fairness guarantees in the later.
 
-To handle this case, I use a pseudo random-number generator, \glsxtrshort{prng} in a novel way. When the scheduler uses a \glsxtrshort{prng} instance per \gls{proc} exclusively, the random-number seed effectively starts an encoding that produces a list of all accessed subqueues, from latest to oldest. The novel approach is to be able to ``replay'' the \glsxtrshort{prng} backwards and there exist \glsxtrshort{prng}s that are fast, compact \emph{and} can be run forward and backwards. Linear congruential generators~\cite{wiki:lcg} are an example of \glsxtrshort{prng}s that match these requirements.
+To handle this case, I use a \glsxtrshort{prng}\todo{Fix missing long form} in a novel way. There exist \glsxtrshort{prng}s that are fast, compact and can be run forward \emph{and} backwards.  Linear congruential generators~\cite{wiki:lcg} are an example of \glsxtrshort{prng}s of such \glsxtrshort{prng}s. The novel approach is to use the ability to run backwards to ``replay'' the \glsxtrshort{prng}. The scheduler uses an exclusive \glsxtrshort{prng} instance per \gls{proc}, the random-number seed effectively starts an encoding that produces a list of all accessed subqueues, from latest to oldest. Replaying the \glsxtrshort{prng} to identify cells accessed recently and which probably have data still cached.
 
 The algorithm works as follows:
Index: doc/theses/thierry_delisle_PhD/thesis/text/runtime.tex
===================================================================
--- doc/theses/thierry_delisle_PhD/thesis/text/runtime.tex	(revision 71582027d4aee596817893608c7bef096d15cb5b)
+++ doc/theses/thierry_delisle_PhD/thesis/text/runtime.tex	(revision d95969a75f9a2102e5866017daba99c54b1bb621)
@@ -11,5 +11,5 @@
 
 \section{Clusters}
-\CFA allows the option to group user-level threading, in the form of clusters. Both \glspl{thrd} and \glspl{proc} belong to a specific cluster. \Glspl{thrd} are only be scheduled onto \glspl{proc} in the same cluster and scheduling is done independently of other clusters. Figure~\ref{fig:system} shows an overview of the \CFA runtime, which allows programmers to tightly control parallelism. It also opens the door to handling effects like NUMA, by pining clusters to a specific NUMA node\footnote{This is not currently implemented in \CFA, but the only hurdle left is creating a generic interface for cpu masks.}.
+\CFA allows the option to group user-level threading, in the form of clusters. Both \glspl{thrd} and \glspl{proc} belong to a specific cluster. \Glspl{thrd} are only scheduled onto \glspl{proc} in the same cluster and scheduling is done independently of other clusters. Figure~\ref{fig:system} shows an overview of the \CFA runtime, which allows programmers to tightly control parallelism. It also opens the door to handling effects like NUMA, by pining clusters to a specific NUMA node\footnote{This is not currently implemented in \CFA, but the only hurdle left is creating a generic interface for cpu masks.}.
 
 \begin{figure}
@@ -25,12 +25,13 @@
 
 \section{\glsxtrshort{io}}\label{prev:io}
-Prior to this work, the \CFA runtime did not add any particular support for \glsxtrshort{io} operations. %\CFA being built on C, this means that,
-While all I/O operations available in C are available in \CFA, \glsxtrshort{io} operations are designed for the POSIX threading model~\cite{pthreads}. Using these 1:1 threading operations in an M:N threading model means I/O operations block \glspl{proc} instead of \glspl{thrd}. While this can work in certain cases, it limits the number of concurrent operations to the number of \glspl{proc} rather than \glspl{thrd}. It also means deadlock can occur because all \glspl{proc} are blocked even if at least one \gls{thrd} is ready to run. A simple example of this type of deadlock would be as follows:
+Prior to this work, the \CFA runtime did not add any particular support for \glsxtrshort{io} operations. While all \glsxtrshort{io} operations available in C are available in \CFA, \glsxtrshort{io} operations are designed for the POSIX threading model~\cite{pthreads}. Using these 1:1 threading operations in an M:N threading model means \glsxtrshort{io} operations block \glspl{proc} instead of \glspl{thrd}. While this can work in certain cases, it limits the number of concurrent operations to the number of \glspl{proc} rather than \glspl{thrd}. It also means deadlock can occur because all \glspl{proc} are blocked even if at least one \gls{thrd} is ready to run. A simple example of this type of deadlock would be as follows:
+
 \begin{quote}
 Given a simple network program with 2 \glspl{thrd} and a single \gls{proc}, one \gls{thrd} sends network requests to a server and the other \gls{thrd} waits for a response from the server. If the second \gls{thrd} races ahead, it may wait for responses to requests that have not been sent yet. In theory, this should not be a problem, even if the second \gls{thrd} waits, because the first \gls{thrd} is still ready to run and should be able to get CPU time to send the request. With M:N threading, while the first \gls{thrd} is ready, the lone \gls{proc} \emph{cannot} run the first \gls{thrd} if it is blocked in the \glsxtrshort{io} operation of the second \gls{thrd}. If this happen, the system is in a synchronization deadlock\footnote{In this example, the deadlocked could be resolved if the server sends unprompted messages to the client. However, this solution is not general and may not be appropriate even in this simple case.}.
 \end{quote}
-Therefore, one of the objective of this work is to introduce \emph{User-Level \glsxtrshort{io}}, like \glslink{uthrding}{User-Level \emph{Threading}} blocks \glspl{thrd} rather than \glspl{proc} when doing \glsxtrshort{io} operations, which entails multiplexing the \glsxtrshort{io} operations of many \glspl{thrd} onto fewer \glspl{proc}. This multiplexing requires that a single \gls{proc} be able to execute multiple I/O operations in parallel. This requirement cannot be done with operations that block \glspl{proc}, \ie \glspl{kthrd}, since the first operation would prevent starting new operations for its blocking duration. Executing I/O operations in parallel requires \emph{asynchronous} \glsxtrshort{io}, sometimes referred to as \emph{non-blocking}, since the \gls{kthrd} does not block.
 
-\section{Interoperating with C}
+Therefore, one of the objective of this work is to introduce \emph{User-Level \glsxtrshort{io}}, like \glslink{uthrding}{User-Level \emph{Threading}} blocks \glspl{thrd} rather than \glspl{proc} when doing \glsxtrshort{io} operations, which entails multiplexing the \glsxtrshort{io} operations of many \glspl{thrd} onto fewer \glspl{proc}. This multiplexing requires that a single \gls{proc} be able to execute multiple \glsxtrshort{io} operations in parallel. This requirement cannot be done with operations that block \glspl{proc}, \ie \glspl{kthrd}, since the first operation would prevent starting new operations for its blocking duration. Executing \glsxtrshort{io} operations in parallel requires \emph{asynchronous} \glsxtrshort{io}, sometimes referred to as \emph{non-blocking}, since the \gls{kthrd} does not block.
+
+\section{Interoperating with \texttt{C}}
 While \glsxtrshort{io} operations are the classical example of operations that block \glspl{kthrd}, the non-blocking challenge extends to all blocking system-calls. The POSIX standard states~\cite[\S~2.9.1]{POSIX17}:
 \begin{quote}
@@ -44,5 +45,5 @@
 \begin{enumerate}
 	\item Precisely identifying blocking C calls is difficult.
-	\item Introducing new code can have a significant impact on general performance.
+	\item Introducing control points code can have a significant impact on general performance.
 \end{enumerate}
-Because of these consequences, this work does not attempt to ``sandbox'' calls to C. Therefore, it is possible for an unidentified library calls to block a \gls{kthrd} leading to deadlocks in \CFA's M:N threading model, which would not occur in a traditional 1:1 threading model. Currently, all M:N thread systems interacting with UNIX without sandboxing suffer from this problem but manage to work very well in the majority of applications. Therefore, a complete solution to this problem is outside the scope of this thesis.
+Because of these consequences, this work does not attempt to ``sandbox'' calls to C. Therefore, it is possible calls from an unidentified library will block a \gls{kthrd} leading to deadlocks in \CFA's M:N threading model, which would not occur in a traditional 1:1 threading model. Currently, all M:N thread systems interacting with UNIX without sandboxing suffer from this problem but manage to work very well in the majority of applications. Therefore, a complete solution to this problem is outside the scope of this thesis.
Index: doc/theses/thierry_delisle_PhD/thesis/thesis.tex
===================================================================
--- doc/theses/thierry_delisle_PhD/thesis/thesis.tex	(revision 71582027d4aee596817893608c7bef096d15cb5b)
+++ doc/theses/thierry_delisle_PhD/thesis/thesis.tex	(revision d95969a75f9a2102e5866017daba99c54b1bb621)
@@ -81,4 +81,5 @@
 %\usepackage{nomencl} % For a nomenclature (optional; available from ctan.org)
 \usepackage{amsmath,amssymb,amstext} % Lots of math symbols and environments
+\usepackage{xcolor}
 \usepackage{graphicx} % For including graphics
 
@@ -120,5 +121,14 @@
 % although it's supposed to be in both the TeX Live and MikTeX distributions. There are also documentation and
 % installation instructions there.
-\renewcommand*{\glstextformat}[1]{\textsf{#1}}
+\makeatletter
+\newcommand*{\glsplainhyperlink}[2]{%
+  \colorlet{currenttext}{.}% store current text color
+  \colorlet{currentlink}{\@linkcolor}% store current link color
+  \hypersetup{linkcolor=currenttext}% set link color
+  \hyperlink{#1}{#2}%
+  \hypersetup{linkcolor=currentlink}% reset to default
+}
+\let\@glslink\glsplainhyperlink
+\makeatother
 
 \usepackage{csquotes}