Getting Started

EECS E6870: Speech Recognition

January 20, 2016

Table of Contents

1. Getting set up for remote login

Introduction We will be using Linux workstations in one of the labs in the EE department (1214/1218 Mudd). The room has badge access and we don't have permission to enter the lab, so you will need to log in remotely. To do this, use the program ssh. For basic information, see EE Computing Lab Remote Access. If you want to do graphical stuff like Matlab plots, you will also need to install X Windows. However, the labs don't require any graphics, so installing X Windows is entirely optional.

Getting ssh and X on Windows The EE department recommends using MobaXTerm. To install, click on the preceding link, select Installer edition, and run the installer. After running, click on Start local terminal to start a shell and then you can follow the directions in Section 2. You can also click on the + to open a new tab/shell.

If you want to have access to the full suite of Linux commands on your local computer, another way to go is to install Cygwin, which provides a Linux-like environment on top of Windows. See Cygwin/X User's Guide for information on how to install X Windows on Cygwin. Installing Cygwin is complex, so we don't recommend this.

Getting ssh and X on OS X The program ssh should be preinstalled. If you want X Windows, you can get this at XQuartz.

Getting ssh and X on Linux This stuff should be preinstalled.

2. Getting an EE account and logging on

Getting an account After the first class, we will submit a request to create accounts for all students who are currently registered for the class according to Courseworks. If you are not registered but are planning to register, E-mail Stan to get the process started (include your UNI and E-mail address). When an account has been created, a username and password will be E-mailed to you.

Lab Policy Note that you will be expected to follow EE Computer Lab Policy. Since we do not have physical access to the lab, many of the rules do not apply. Still, there will be students sitting in front of the machines that we will be logging into, so please be considerate. If you do not follow lab policy, your account may be revoked.

Logging in Once you have a username and password, you can try logging onto a machine in the cluster. The machines are named cadpc01.ee.columbia.edu through cadpc42.ee.columbia.edu. To be able to use graphical programs like Matlab when using X Windows, you need to use the -X flag with ssh, e.g., 

ssh -X <username>@cadpc08.ee.columbia.edu
Do not be alarmed if you see the following error message: 
Warning: untrusted X11 forwarding setup failed: xauth key data not generated
Warning: No xauth data; using fake authentication data for X11 forwarding.
Not all of the machines may be up at a given time, so if you are having trouble with one machine, try another. To log out, type 
exit

To change your password On any machine, type the command 

kpasswd
and follow the directions.

If your machine seems slow If many people are using the same machine, the machine may get slow and you may want to consider switching to a different machine. To see how busy a machine is, you can use the command w. This will list all the users on the machine, and the numbers after load average are the average number of programs currently running (averaged over the past 1, 5, and 15 minutes).

3. Learning basic UNIX commands and text editing

For those of you who are not familiar with Linux or other variants of UNIX, you need to learn how to use UNIX for basic tasks such as making directories, moving/copying files, redirection, etc., and for editing text files. You're basically on your own for this, but we did some quick Google searches and here are some pointers.

Linux/Unix Here is one Unix tutorial and here is another Unix tutorial. Type UNIX tutorial or some other relevant string into Google for pointers to more material.

Text editing To edit text files, if you do not already know a UNIX text editor, one option is to use X Windows as described in Section 1 and run emacs. In this scenario, emacs acts pretty much like a generic text editor.

Otherwise, the two most popular editing tools for UNIX are emacs and vi. The editor vi has weird key mappings, but is simple and compact. The editor emacs is extremely powerful and also has some weird key mappings. Here is an emacs tutorial and here is a vi tutorial.

If you are not running X Windows; don't already know emacs or vi; and are too lazy to read a real tutorial, here is a 1-minute tutorial for emacs. To edit the file foo, type 

emacs foo
You can edit in an intuitive fashion; the arrow keys and page up/down keys work as expected. To do stuff like save, exit, etc., you can use the menu bar at the top. Press the F10 key to get to the menu bar. When you do this, a window opens at the bottom of the screen with a list of options. Press the letter corresponding to the option you want. Menus can be deep, so you may need to do this several times. (Press Esc three times to abort.) For example, saving is F10 f s and exiting is F10 f e. When editing files that end in a C or C++ extension (e.g., .cc), emacs will enter a special mode that does automatic indenting and highlighting.

4. Setting up your EE account

In this section, we discuss the things you need to do to set up your account for this course. By default, you will be assigned the shell bash. If you don't know what I'm talking about, you are probably using bash. If you are using a different shell, then you will have to adjust the commands in this section appropriately, but if you are using a different shell, you should know how.

If your account was newly created, first backup the default .bash_profile and .bashrc files in your home directory: 

cp ~/.bash_profile ~/.bash_profile.bak
cp ~/.bashrc ~/.bashrc.bak
(The ~ character is an abbreviation for your home directory.) Then, copy in versions of these files from /user1/faculty/stanchen/e6870/, i.e.: 
cp /user1/faculty/stanchen/e6870/.bash_profile ~
cp /user1/faculty/stanchen/e6870/.bashrc ~
These files set environment variables as needed for the labs. If your account was not newly created and you have modified these files, then manually merge the contents of the version we supply with your existing version.

You can type . ~/.bashrc (or logout and login again) to have these changes take effect.

Problems with the backspace key If when you press the backspace key you see a ^? printed instead (e.g., in vi on a Mac), then try adding the following line at the end of your .bashrc file (and logout and login again): 

stty erase '^?'

5. Language-specific setup

We will be supporting only C++ for the labs. This is the language the majority of speech recognition software is written in. We'll also mention a little about Matlab and Python, in case you want to play around in these languages by yourself.

We will be providing a small C++ library supplying basic input/output routines and some key data structures. To provide access to this library in Python, we are using SWIG to generate the wrapping code necessary for making this happen. (The library isn't accessible from Matlab.) Documentation for this library will be given in the labs.

5.1. C++

We'll be using the GNU C++ compiler, g++. To compile a program, one can use an incantation like 

g++ -g -Wall <source-files> -o <output-file> -lm
The flag -g signals that debugging information should be included in the executable (see Section 6); the flag -Wall signals to print lots of warnings about questionable programming constructs; and the flag -lm signals that the math library should be linked in, which you'll probably need for all of the labs. We'll be using version 4.9.3 of g++, a recent version that includes support for many modern features of C++. To turn on support for C++14, use the flag -std=c++14.

To automate the compilation process, one can use make; here's a make tutorial. Here's a sample Makefile: 

CXX = g++
CXXFLAGS = -g -Wall
LDLIBS = -lm

hello : hello.C
        $(CXX) $(CXXFLAGS) hello.C -o hello $(LDLIBS)
Note that the indentation in the last line must be the tab character, not spaces. If placed in the current directory in the file Makefile, one can recompile by typing the command make hello.

5.2. Matlab

Typing matlab should start up Matlab. If you are running X Windows (and used the -X flag with ssh), you should see the graphical interface; otherwise, the command-line interface will start up (see Section 1). If you can't find Matlab, the full path is 

/usr/local/bin/matlab
If for some reason you are having trouble with the Matlab license server, another option is to use octave, which is open-source software mimicking Matlab. This uses the same syntax for most things, though its function library is not as extensive.

5.3. Python

If you completed Section 4 correctly, your PATH and PYTHONPATH environment variables should be set up correctly to use the desired version of Python and the course Python libraries. (Don't forget to logout and login again after updating your .bashrc file.) In particular, you should be using the Python from 

/user1/faculty/stanchen/pub/exec/
(type type python to check) and PYTHONPATH should include the directory 
/user1/faculty/stanchen/e6870/lib/
To print the value of PYTHONPATH, type 
echo $PYTHONPATH

The course Python module is named asr_lib. To test things are working, you can try: 

python
from asr_lib import *
print g_zeroLogProb

6. Learning how to debug programs

For those of you who are not robots or cyborgs, you will undoubtedly introduce bugs into your source code at some time or another. One simple way to debug stuff is to place print statements everywhere. However, it will make your life much easier in the long run if you learn how to use a debugger. A debugger lets you stop the execution of your program at any point and examine any values you wish, which makes this much more general and powerful than the print statement technique.

For C++, the GNU gdb debugger is available. Here is one gdb tutorial and here is another gdb tutorial; you can also get some documentation within gdb by typing help. To start gdb, type gdb <program>. Within gdb, type run <arguments> to start the program. Commands that you should know about include breakpoint, print, cont, step, next, where, up, down, and finish. Don't forget to compile your program with the -g flag (see Section 5.1).

Tip: in the provided C++ library, errors are reported either as assert() failures or as exceptions. It's useful to be able to set breakpoints on these events when debugging. To set a breakpoint on an assert() failure, you can do 

b __assert_fail
If you're asked Make breakpoint pending ... library load?, say yes. To set a breakpoint on the throwing of any exception, you can do 
b __cxa_throw

For future reference, in the interest of preempting debugging questions, here are three procedures you should perform before asking for help in finding a bug: