%I had used the following tex code to compile my MS thesis. If you face any problem with typesetting, let me know. I may not be available immediately; but definitely, Google is there! :-p..
% MOSLEM UDDIN, E-mail: moslem.cu47@gmail.com
%Alumni, Dept. of Mathematics(47th batch) University of Chittagong, Chittagong-4331, Bangladesh
\documentclass[a4paper,12pt]{report}
\usepackage[left=1.5in,top=1in,right=1in]{geometry}
\usepackage[utf8]{inputenc}
\usepackage{calligra}
%\usepackage{commath}
\usepackage{anyfontsize}
\usepackage{nomencl}
\makenomenclature
%{if u have problem with nomenclature,Copy the given code and paste into Texmaker/Texstudio setting : Path- Option - Configure -Texmaker/Texstudio -Commands- Makeindex
%Code: makeindex %.nlo -s nomencl.ist -o %.nls -t %.nlg}
\usepackage{imakeidx}
\makeindex[columns=2, title= Index, intoc]
\usepackage{amsmath}
\usepackage{mathrsfs}
\usepackage[usenames, dvipsnames]{color}
\usepackage[bottom]{footmisc}
\usepackage{verbatim}
\usepackage{subcaption}
\usepackage{latexsym}
\usepackage[backend=biber,style=ieee,sorting=nyt]{biblatex}
\addbibresource{bibliography.bib}
%\include{bibliograph.bib.tex}
\usepackage[acronym,automake]{glossaries}
\makeglossaries
\newacronym{fm}{FM}{Fluid Mechanics}
\newacronym{pde}{PDE}{Partial Differential Equation}
\usepackage{textcomp}
\usepackage{frcursive}
\usepackage{graphicx}
\graphicspath{ {Pictures/} }
\usepackage{wrapfig}
\usepackage[Lenny]{fncychap}
\usepackage{minitoc}
\usepackage{fancyhdr}
\usepackage{lastpage}
\pagestyle{fancy}
\fancyhead{}
\fancyhead[R]{\fontsize{5}{5} \selectfont\leftmark}
\fancyhead[L]{\fontsize{5}{5} \selectfont\rightmark}
\fancyfoot{}
\fancyfoot[C]{\thepage}
\renewcommand{\headrulewidth}{0.4pt}
\renewcommand{\footrulewidth}{0.4pt}
\renewcommand{\listfigurename}{List of Plots}
\renewcommand{\listtablename}{List of Tables}
\renewcommand{\nomname}{List of Symbols}
\numberwithin{equation}{section}
\linespread{1.5}
\pagenumbering{gobble}
\title{
{thesis title \\thesis title}
\vspace{.5 in}
\begin{figure}[h]
\centering
\includegraphics[width=0.26\linewidth]{"Pictures/CUlogo"}
\end{figure}
}
\author{\Large Submitted By\\\ \LARGE \textbf{Moslem Uddin}\\ \Large Examination Roll No. : \\\Large Registration No. : \\\Large Session : \vspace{.5cm}\\A Thesis Submitted to the \textbf{University of Chittagong} \\in Partial Fulfillment of the Requirements for the \\Degree of Master of Science in Mathematics(Applied).\vspace{.7cm}\\\LARGE \textbf{Department of Mathematics}\\\LARGE University of Chittagong\\\Large Chittagong -4331, Bangladesh}
\date{\today}
%\thispagestyle{plain}
\thispagestyle{plain}
\begin{document}
\dominitoc
\maketitle
\pagenumbering{roman}
\pagestyle{plain}
\chapter*{Dedication}
\addcontentsline{toc}{chapter}{Dedication}\mtcaddchapter
\chapter*{Declaration}
\addcontentsline{toc}{chapter}{Declaration}\mtcaddchapter
\chapter*{Certification}
\addcontentsline{toc}{chapter}{Certification}\mtcaddchapter
\chapter*{Acknowledgments}
\addcontentsline{toc}{chapter}{Acknowledgments}\mtcaddchapter
\chapter*{Abstract}
\addcontentsline{toc}{chapter}{Abstract}\mtcaddchapter
\cleardoublepage
\addcontentsline{toc}{chapter}{List of Plots}\mtcaddchapter
\listoffigures
\cleardoublepage
\addcontentsline{toc}{chapter}{List of Symbols}\mtcaddchapter
\printnomenclature
\cleardoublepage
\addcontentsline{toc}{chapter}{List of Acronyms}\mtcaddchapter
\printglossary[type=\acronymtype,title=List of Acronyms]
\cleardoublepage
\tableofcontents
\clearpage
\pagenumbering{arabic}\cfoot{Page \thepage \hspace{1pt} of \pageref{Lastpage}}
\pagestyle{fancy}
\chapter{Introduction}
\minitoc
\acrfull{fm} is the branch of physics concerned with the mechanics of fluids (liquids, gases, and plasmas) and the forces on them. It has applications in a wide range of disciplines, including mechanical, civil, chemical and biomedical engineering, geophysics, astrophysics, and biology.
\section{1}
Latex \index{latex} is widely used in academia for the communication and publication of scientific documents in many fields, including mathematics, statistics, computer science, engineering, chemistry\cite{stok}, physics, economics, linguistics, quantitative psychology, philosophy, and political science\cite{li,cur}.\\
Distance $x$ \nomenclature{$x$}{distance}
\subsubsection{1a}
\section{2}
\chapter{Literature Review}
\minitoc
\section{1}
\subsubsection{1}
\section{2}
\chapter{Main body}
\minitoc
\section{1}
\subsubsection{1}
\section{2}
\chapter{Conclusion}\label{c6}
\minitoc
\label{Lastpage}
\clearpage
\pagenumbering{Alph}\cfoot{Page \thepage \hspace{1pt} of \pageref{Lastpage1}}
\appendix
\chapter{Appendix}\label{A1}
\clearpage
\addcontentsline{toc}{chapter}{Bibliography }
%\bibliographystyle{acm}
%\bibliography{bibliography/bibliograph}
\printbibliography
\printindex
\label{Lastpage1}
\end{document}
