Batch-computing

= Introduction to Using Earlham's Linux Cluster Computer =

This exercise will help you learn to use Al-Salam, the Linux cluster computer administered by the Earlham College Cluster Computing Group (CCG), a speciality group of the Computer Science department.

Actions and commands that you should perform or enter are in the '''computer boldface '''font.

After each Unix command you type at the Unix prompt (explained below), press the <tt>Enter</tt> key.

An account has been set up for you. Your user name is denoted here as yourusername, but may actually be of the form ncsi####, where ### is a specific user ID number. Or, if you’re a permanent CCG user, your user name may be tied to your name; for example, fitz (Andrew Fitz Gibbon).

If you have any difficulty with the steps outlined here, then please send e-mail to [mailto:ccg@cs.earlham.edu ccg@cs.earlham.edu]

This intro is adapted from Henry Neeman's ''Intro to Batch Computing'' at OSCER. Check out his page [http://www.oscer.ou.edu/education.php here] for more info.

== Log In ==
<ol>
<li>From the PC of your choice (Windows, MacOS, Linux or whatever), bring up your web browser (Internet Explorer, Firefox, Opera, Safari, Chrome or whatever) and go to:</li>

[http://www.oscer.ou.edu/ssh_install.php http://www.oscer.ou.edu/ssh_install.php]

'''NOTICE''' the underscore in the URL, between ssh and install.

Following the instructions on that page, log in to:

'''cluster.earlham.edu'''

<li>Once you log in, you’ll get some text, and then a ''Unix prompt'' – but probably not necessarily a percent sign – with the cursor after it, like so:</li>

<pre>
%
</pre>

There may be some information before the prompt character, such as the name of the computer that you’ve logged in to (which may be different from cluster.earlham.edu), your user name, and so on. For purposes of these materials, we’ll generally use the percent sign % to indicate the Unix prompt.

<li><tt>cluster.earlham.edu</tt>, also called <tt>hopper </tt>is what's called a ''login node.'' It is not a cluster and you should not run things there! Instead, you should actually be on Al-Salam. You can do this by simply entering:</li>

 % <b>ssh al-salam</b>

<li>Check the lines of text immediately above the Unix prompt.</li>

'''If''' there are lines of text that read something like:

<pre>
No directory /cluster/home/yourusername! Logging in with home = "/".
</pre>

then you should log out immediately by entering

 % <b>exit</b>

and then log back in. If you repeatedly have this problem, then please send e-mail to:

[mailto:ccg@cs.earlham.edu ccg@cs.earlham.edu]

<li>Check to be sure that you’re in your ''home directory'' (a ''directory'' in Unix is like a folder in Windows, and your ''home directory'' in Unix is like your desktop in Windows):</li>

 % <b>pwd</b>
 /cluster/home/yourusername

This command is short for “Print working directory;” that is, “print the full name of the directory that I’m currently in.” The output is the name of the directory that you’re currently in.

If your current working directory is just a slash (which means the ''root directory'', which is like C:\ in Windows), rather than something like /cluster/home/yourusername, then you should log out immediately (as above), then log back in.

If you repeatedly have this problem, then please send e-mail to:

[mailto:ccg@cs.earlham.edu ccg@cs.earlham.edu]
</ol>

== Set Up (First Time Logging In ONLY) ==

<ol>
<li>You should ''immediately'' do the following to change your password away from the default:</li>

<pre>
% ldpasswd
</pre>

It will ask you for your old password (this is the one you used to log in with the first time) and then your new password ''twice ''(to make sure you didn't mistype it the first time).

You '''ONLY''' have to do this for the first time logging in.

<li>Please '''IMMEDIATELY''' enter the following:</li>

<pre>
% echo youremailaddress@yourinstitution.edu > ~/.forward
</pre>

You '''WON’T''' have to do this for future logins.

'''NOTES'''

* You should replace '''youremailaddress@yourinstitution.edu '''with your e-mail address.
* After your e-mail address comes a blank space, then a greater-than symbol, then another blank space, then tilde slash period <tt>'''forwad'''</tt>, with no spaces between them.
* The Unix copy command is cp.
* The first filename after cp is the ''source'' (the thing that you’re making a copy of); the second is the ''destination'' (the name and/or location of the copy).
* The filename .forward begins with a period (very important). The filename is pronounced “dot forward.”
* In Unix, filename s are ''case sensitive'', meaning that it matters whether you use ''upper case'' (capital) or ''lower case'' (small) for each letter in a filename.
* In Unix, pieces of a filename (or actually of the directory that it’s in) are separated by slashes, '''NOT''' by backslashes as in Windows.
* The symbol <tt>˜</tt> (known as a ''tilde'', pronounced “TILL-duh”) denotes your home directory (another way to denote your home directory is ˜yourusername).
* The substring <tt>˜fitz</tt> means “the home directory of the user named fitz.”

<li>Create a ''subdirectory'' of your home directory named MPI_exercises, like so:</li>

<pre>
% mkdir ~/MPI_exercises
</pre>

'''NOTICE''': In the subdirectory name MPI_exercises, the MPI '''MUST BE CAPITALIZED'''; that is, the directory name is “capital-M capital-P capital-I underscore exercises” with no spaces or other characters in between.

This command means: “Create a directory named MPI_exercises as a subdirectory inside my home directory” (it’s like creating a new folder named MPI_exercises on your desktop in Windows).

You '''WON’T''' have to do this for future logins.

<li>Confirm that you have successfully created your MPI_exercises directory by listing the contents of the current working directory:</li>

<pre>
% ls
MPI_exercises
</pre>

This command means: “List the names of the files and subdirectories in my current working directory.”

'''NOTICE''' that the command is “ell ess” — that is, small-L small-S — rather than “one ess” and that ls is short for “list.”

<li>Set the ''permissions'' on your MPI_exercises directory so that only you can access it:</li>

<pre>
% chmod u=rwx,go= MPI_exercises
</pre>

This command means: “Change the ''mode'' (list of permissions) on my subdirectory named MPI_exercises so that I (the user) can read files in it, write files in it, and go into (execute) it, but nobody else can.”

Your MPI_exercises directory is now accessible only to you. The only other people who can access it are the ''system administrator's'' (''sysadmins'' for short) of this Linux cluster computer; that is, the Earlham CCG cluster maintainers.

You '''WON’T''' have to do this for future logins.

<li>Log out of the Linux cluster computer by entering the following command:</li>

<pre>
% exit
</pre>

Once you have completed the setup steps in this section, you '''WON’T''' have to do them again when you log in later.

</ol>

== Copy Fitz's Intro Directory Into Your MPI_exercises Directory ==

<ol>
<li>Log in again, and make sure you're on Al-Salam, not the login server:</li>

 %''' hostname'''

The result of this command should be <tt>as0.cluster.earlham.edu</tt>. ''as'' in this case is short for ''Al-Salam'' and the ''0 ''(that's a zero) means it's what we call the ''head node. ''You'll learn more about what that means later.

<li>Confirm that you’re in your home directory:</li>

 % '''pwd'''

/cluster/home/yourusername

<li>Check that you still have a MPI_exercises subdirectory inside your home directory:</li>

 % '''ls'''
 MPI_exercises

<li>Go into your MPI_exercises subdirectory:</li>

 % '''cd MPI_exercises'''

This command means: “Change the working directory to MPI_exercises, which is a subdirectory of my current working directory.” (This is like double-clicking a folder in Windows.)

<li>Confirm that you’re in your MPI_exercises subdirectory:</li>

 % '''pwd'''
 /cluster/home/yourusername/MPI_exercises

<li>See what files or subdirectories (if any) are in the current working directory:</li>

 % '''ls'''

You may get no output, just the Unix prompt; if so, that indicates that your current working directory has no files or subdirectories in it.

<li>'''SIDEBAR''': To learn more about a particular Unix command, enter:</li>

 % '''man ''commandname'''''

for some command. For example, try

 % '''man chmod'''

which will give you the online ''manual page'' for the chmod command.

The output of man goes through another command, more, which shows one screenful at a time. To get the next screenful, press the spacebar; to get the next line, press the '''Enter '''key. To quit the more command, press the '''Q '''key.

<li>Copy the subdirectory named Intro from Fitz’s MPI_exercises directory into your MPI_exercises directory:</li>

 % '''cp -r ~fitz/MPI_exercises/Intro ~/MPI_exercises/'''

This command means: “Copy the subdirectory named Intro inside the directory named MPI_exercises under the home directory of user fitz into my directory MPI_exercises under my home directory.”

<li>Confirm that the Intro subdirectory was copied into your MPI_exercises directory:</li>

 % '''ls'''
 Intro

<li>Go into your Intro subdirectory:</li>

 % '''cd Intro'''

<li>Confirm that you’re in your Intro subdirectory:</li>

 % '''pwd'''
 /cluster/home/yourusername/MPI_exercises/Intro

<li>See what files or subdirectories (if any) are in the current working directory (Intro):</li>

 % '''ls'''

C Fortran90

<li>Go into either your C subdirectory or your Fortran90 subdirectory ('''BUT NOT BOTH'''):</li>

 % '''cd C'''

OR

 % '''cd Fortran90'''

<li>Confirm that you’re in your C or Fortran90 subdirectory:</li>

 % '''pwd'''
 /cluster/home/yourusername/MPI_exercises/Intro/C

OR the output of the pwd command might be:

 % '''pwd'''
 /cluster/home/yourusername/MPI_exercises/Intro/Fortran90

<li>See what files or subdirectories (if any) are in the current working directory:</li>

 % '''ls'''
 makefile my_number.bsub my_number.c my_number_input.txt

OR the source file might be named my_number.f90 instead of my_number.c.
</ol>

== Edit the Batch Script File To Create Your Own Unique Version ==

<ol>
<li>Before you can run the original version of the program, you need to modify your copy of the batch script file my_number.qsub to create a version that’s uniquely yours.</li>

Using your preferred Unix text editor (whether nano, pico, vim, vi, emacs or whatever), edit your copy of my_number.qsub.

For example, if you’re using nano, then the edit command would be:

 % '''nano my_number.qsub'''

This command means: “Edit the text in the file named my_number.qsub that’s in my current working directory, using the text editor program named nano.”

<li>In nano, notice the little help messages at the bottom of the screen:</li>

 ^G Get Help ^O WriteOut ^R Read File ^Y Prev Pg ^K Cut Text ^C Cur Pos
 ^X Exit ^J Justify ^W Where is ^V Next Pg ^U UnCut Text ^T To Spell

For example, consider

ˆW Where is

This means that you should press '''Ctrl-W''' (the caret ^ indicates the Ctrl key) to search for a particular string of characters.

Another example:

ˆC Cur Pos

This is short for “Cursor Position” and causes nano to tell you what line number the cursor is located at.

Another example:

ˆK Cut Text

This means “delete the line that the cursor is currently on.”

<li>Using the text editor, make the following changes to my_number.qsub:</li>

<li>Everywhere throughout the file, change yourusername to your user name (which might be of the form ncsi####, or perhaps is based on your name). '''THIS IS EXTREMELY IMPORTANT!'''</li>
<li>Everywhere throughout the file, change</li>

youremailaddress@yourinstitution.edu

to your full e-mail address. '''THIS IS EXTREMELY IMPORTANT!'''

<li>'''IMPORTANT!''' Every few minutes while you’re editing, you should save the work that you’ve done so far, in case your work is interrupted by a computer crashing. In nano, enter''' Ctrl-O '''(the letter oh), at which point nano will ask you, near the bottom of the screen:</li>

 File Name to write : my_number.qsub

That is, nano wants to know what filename to save the edited text into, with a default filename of my_number.qsub). Press '''Enter''' to save to the default filename my_number.qsub.

<li>The lines of text in the batch script file my_number.qsub should be less than 80 characters long, and ideally at most 72 characters long. (Your PuTTY window should be 80 characters wide.)</li>
<li>Some text editors, including nano, try to help keep text lines short, by breaking a long line into multiple short lines. For example, nano might break a line like the following into two separate lines:</li>

 #PBS –o
 /cluster/home/yourusername/MPI_exercises/Intro/C/my_number_%J_stdout.txt

That is, nano automatically puts a carriage return when the line starts getting too long for its taste.

Unfortunately, the batch scheduler (PBS, for Portable Batch System) will consider this to be an error. Why? Because the batch scheduler cannot allow an individual batch directive – that is, a line starting with #PBS – to use more than one line.

For example, the batch script directive above should be on a single line:

 #BSUB –o /cluster/home/yourusername/MPI_exercises/Intro/C/my_number_%J_stdout.txt

So, you’ll need to correct any such occurrences.

<li>After you’ve finished editing, go back up to the top of the batch script file, and '''CAREFULLY READ THE ENTIRE BATCH SCRIPT FILE FROM START TO FINISH.''' This will give you a much clearer understanding of what batch computing is and how it works.</li>
=== Understanding batch computing ===

As an analogy, imagine that you’re at a football game and you want a drink. You get up and walk to the concession stand. If there are a lot of people at the concession stand, then you’re going to have to wait a while before a server serves you, but if you’re the only person in line, or more generally if there are at least as many servers behind the counter as customers lined up to buy, then you’ll be served quickly.

Batch computing is analogous, except that instead of food and drink, you and the other users want your jobs to be run, and instead of food servers, the servers are computers that can run jobs. Typically, for a production cluster supercomputer, the number of resources requested by the users – that is, total servers requested – is much larger than the number of available resources (servers).

The only way to make this work is for a program known as a ''scheduler'' – in this case, LSF (Load Share Facility) – to decide whose jobs run on which servers, and when.

Compare getting food at a football game to getting food at home, where you just walk up to your fridge or cupboard or whatever, and take out what you want. But if you’ve got hundreds of people getting food, that method won’t work: it doesn’t ''scale'' to hundreds of people sharing one source of food, because you can’t fit all of them in front of the one fridge; instead, everyone has to wait their turn at the counter, and work with a server to get served.

Likewise with computing: your normal way of interacting with your laptop won’t work when hundreds of people are sharing one source of computing.

<li>After you’ve finished editing and reading the batch script file, exit the text editor.</li>

For example, in nano, enter''' Ctrl-X'''. If you have made any changes since the last time you entered Ctrl-O, then nano will ask you, near the bottom of the screen,

Save modified buffer (ANSWERING "No" WILL DESTROY CHANGES)? 

To save your most recent changes to the file (which is probably what you want to do), press the '''Y '''key; to avoid saving your most recent changes, press the '''N '''key.

After that, nano will behave the same as if you had entered '''Ctrl-O'''.
</ol>

== Look At, Make (Compile), and Run the Original Version ==

<ol>
<li>For your own understanding, look at the contents of the source file:</li>

 % '''cat my_number.c'''

OR:

 % '''cat my_number.f90 '''

This command means: “Output the contents of the text file named my_number.c (or my_number.f90) to the terminal screen.”

'''NOTICE''' that the command to output the contents of a text file to the terminal screen without using the more command is cat, which is short for “concatenate,” a word that means “output one text file after another in sequence.”

The output of the cat command goes to the terminal screen (known as “standard output,” or “standard out” for short, abbreviated stdout), and in this case, we are only concatenating a single text file, so we’re simply outputting the text file’s contents to the terminal screen.

If you’re using PuTTY as your SSH client, and the contents of the file exceeds the height of the PuTTY window, then you can scroll up or down using the scrollbar on the right side of the window; most other SSH clients have similar capability. 

<li>For your own understanding, look at the contents of the input file:</li>

 % '''cat my_number_input.txt'''

<li>For your own understanding, look at the contents of the makefile:</li>

 % '''cat makefile'''

<li>''Make'' (compile) the ''executable'' program for the original version of my_number.c (or my_number.f90):</li>

 % '''make my_number'''
 gcc -O -c my_number.c
 gcc -O -o my_number my_number.o

(It could be the case that the compiler is gfortran and the source file is my_number.f90.)

'''NOTICE''':

* In the make command, the ''command line argument'' my_number is the name of the ''executable'' (the file that can actually be run) that you are making.
* The make command runs the C compiler gcc (OR the Fortran90 compiler gfortran) to compile the source file named my_number.c (OR my_number.f90).
* In the compile command, the ''command line option''

-o my_number

indicates that my_number is to be the name of the executable.

If that option had been left out, then by default the name of the executable would be a.out (“the output of the assembler”), '''WHICH WOULD BE BAD''', because then the executable’s filename wouldn’t explain the executable’s purpose.

<li>Submit the batch script file my_number.bsub to the batch scheduler:</li>

 % '''qsub my_number.qsub'''

You should get back output something like this:

 ######.as0.al-salam.loc

where ###### is replaced by the batch job ID for the batch job that you’ve just submitted.

<li>Check the status of your batch job:</li>

 % '''qstat'''

You’ll get one of the following outputs, either nothing at all—that is, the Unix prompt immediately returns (if you get this right after the qstat command, try it several more times, because sometimes there’s a pause just before the batch job starts showing up, as below)—OR:

<pre>
Job id                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
######.as0                my_number        yourusername           0 Q ec
</pre>

where ###### is replaced by a batch job ID number, and yourusername is replaced by your user name, and where Q is short for “queued,” meaning that your job is waiting to start,

OR:

<pre>
Job id                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
######.as0                my_number        yourusername    00:00:05 R ec
</pre>

<li>You may need to check the status of your batch job repeatedly, using the qstat command, until it runs to completion. '''This may take several minutes (occasionally much longer).'''</li>

You’ll know that the batch job has finished running when it no longer appears in the list of your batch jobs, or it simply returns nothing.

<li>Once your job has finished running, and the ''standard output'' and ''standard error'' files from your job:</li>

 % '''ls -ltr '''

'''NOTICE''' that the command is “ell ess space hyphen ell tee are” – that is, small-L small-S blank hyphen small-L small-T small-R – rather than “one ess” or “one tee are” and that ls is short for “list” and -ltr is short for “long detailed listing, sorted by time of most recent modification, in reverse order so that the most recently modified file is at the bottom.”

Using this command, you should see files named 

 my_number_######_stdout.txt 

and

 my_number_######_stderr.txt

(where ###### is replaced by the batch job ID).

These files should contain the output of my_number. Ideally, the file length of my_number_######_stderr.txt should be zero. 

Look at the contents of the standard output file:

 % '''cat my_number_######_stdout.txt'''

(where ###### is replaced by the batch job ID).

You may want to look at the stderr file as well:

 % '''cat my_number_######_stdout.txt'''

<li>Congratulations! You’ve just run your first batch job. Now continue on.</li>
</ol>

== Edit the C Source File To Create Your Own Unique Version ==

<ol>
<li>Now that you’ve run the original version of the program, it’s time to modify your copy of the source file my_number.c (or my_number.f90) to create a version that’s uniquely yours.</li>

Using your preferred Unix text editor (whether nano, pico, vim, vi, emacs or whatever), edit your copy of my_number.c (or my_number.f90).

For example, if you’re using nano, then the edit command would be:

 % '''nano my_number.c''' 

OR

 % '''nano my_number.f90'''

<li>Using the text editor, make the following changes to my_number.c (or my_number.f90):</li>
<ol>
<li>In the ''declaration section'', change the constant values assigned to minimum_number, maximum_number, close_distance and computers_number.</li>

You may select any integer values you want, which must be different from 1, 5, 10 and 1 respectively, and minimum_number &lt; computers_number &lt; maximum_number, and they are sufficiently spread out that you can actually do the runs properly.

'''DON’T CHANGE THE VALUE OF maximum_guesses!!!'''

<li>In the ''execution ''sectio''n'' (also known as the ''body'' of the program), change the following sequences of character text to your own words:</li>
<pre>
Hey!
That’s amazing!
Close, but no cigar.
Bzzzt! Not even close.
</pre>

<li>Every few minutes while you’re editing, you should save the work that you’ve done so far, in case your work is interrupted by a computer crashing.</li>

In nano, enter '''Ctrl-O '''(the letter oh), at which point nano will ask you, near the bottom of the screen:

<pre>File Name to Write [Backup]: my_number.c</pre>

That is, nano wants to know what filename to save the edited text into, with a default filename of my_number.c (or my_number.f90). Press '''Enter '''to save to the default filename my_number.c (or my_number.f90).

<li>A ''character string literal constant'', also known as a ''character string literal'' or a ''string literal'' for short, is a sequence of characters between a pair of double quotes.</li>

For example, in the C printf statement

 printf("This is a printf statement.\n");

the following is a string literal:

 "This is a printf statement.\n"

Likewise, in the Fortran90 PRINT statement

 PRINT *, "This is a PRINT statement."

the following is a string literal:

 "This is a PRINT statement." 

We say that the pair of double quotes ''delimits'' the sequence of characters in the string literal. Note that, in C, the \n at the end of the string literal tells the program to output a carriage return (also known as a ''newline'') at the end of the line of output text. (In Fortran90, the carriage return is implied by the end of the PRINT statement.) 

<li>The lines of text in the source file my_number.c (or my_number.f90) should be less than 80 characters long, and ideally no more than 72 characters long. (Your PuTTY window should be 80 characters wide.)</li>
<li>Some text editors, including nano, try to help keep text lines short, by breaking a long line into multiple short lines. For example, nano might break a line like:</li>

 printf("This is a long line and nano will probably break part of it off.\n");

into two separate lines:

<pre>
printf("This is a long line and nano will probably break part
of it off.\n");
</pre>

That is, nano automatically puts a carriage return when the line starts getting too long for nano’s taste.

Unfortunately, the C compiler (or the Fortran90 compiler) will consider this to be an error. Why? Because C (or Fortran90) cannot allow an individual string literal to use more than one line (in Fortran90, there’s a goofy way to do it, but it’s bad practice). So, the correct way to write the above example is:

<pre>
printf("This is a long line and nano will probably");
printf(" break part of it off.\n"); 
</pre>

OR:

<pre>
PRINT *, "This is a long line and nano will probably"
PRINT *, " break part of it off."
</pre>

<li>Like the lines of source text, the lines of output text should be less than 80 characters long, and ideally no more than 72 characters long. You can break a long line of output text into shorter pieces by making it into two printf (or PRINT) statements.</li>

For example:

<pre>
printf("Why you big old stinker! That’s not between %d and %d!\n",
minimum_number, maximum_number);
</pre>

This single printf statement can be converted into two printf statements, like so: 

<pre>
printf("Why you big old stinker! That’s not between\n");
printf(" %d and %d!\n", minimum_number, maximum_number);
</pre>

OR:

<pre>
PRINT *, "Why you big old stinker! That’s not between"
PRINT *, minimum_number, " and ", maximum_number, "!"
</pre>
</ol>

<li>After you’ve finished editing, exit the text editor. For example, in nano, enter '''Ctrl-X'''.</li>

If you have made any changes since the last time you entered '''Ctrl-O''', then nano will ask you, near the bottom of the screen:

Save modified buffer (ANSWERING "No" WILL DESTROY CHANGES)?

To save your most recent changes to the file (which is probably what you want to do), press the '''Y '''key; to avoid saving your most recent changes, press the '''N '''key. After that, nano will behave the same as if you had entered '''Ctrl-O'''.

<li>Edit the input file my_number_input.txt to replace the original input values with input values relevant to your new unique version of the program, specifically:</li>
# an integer value less than your value for minimum_number<nowiki>;</nowiki>
# an integer value greater than your value for maximum_number<nowiki>;</nowiki>
# an integer value between your value for minimum_number and your value for maximum_number (inclusive), but far from your value for computers_number<nowiki>;</nowiki>
# an integer value close to your value for computers_number (that is, within your value for close_distance of your value for computers_number);
# your value for computers_number.
</ol>

== Make (Compile), Run and Debug Your Own Unique Version ==

<ol>
<li>Make (compile) your own unique version of the executable program:</li>

 % '''make my_number'''
 gcc -O -c my_number.c
 gcc -O -o my_number my_number.o

(It could be the case that the compiler is gfortran and the source file is my_number.f90.)

<li>If the program doesn’t compile, then you’ll need to edit it and figure out where things went wrong. In the worst case, if you’re totally stumped, then copy the original from Henry’s directory again, and start editing from the beginning.</li>
<li>Repeat the instructions in section V, items 5-9, above.</li>
<li>Congratulations! You’ve just completed this exercise.</li>
</ol>