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Getting Started with Perlmutter

2FA and Log-In

You can set up the two-factor authentication (2FA) and log into Perlmutter following the intructions here. You can access Perlmutter server by following the instruction here. Be sure to set up the sshproxy following the directions on that page to avoid typing your 2FA every time you log in.

Command Line

Once logged into Perlmutter, you are be presented with a bash shell.

Some important commands are:

ls                          # list files in currect directory
ls *.txt                    # list files in currect directory that end in .txt
cd [DIRNAME]                # change current directory
cd ~                        # change to your home directory
cd ..                       # go up one directory
cat [FILENAME]              # print file content
cat [FILENAME] | less       # print file content, scroll with arrows, quit with q
grep "needle" [FILENAME]    # searches for "needle" in file
man [COMMAND]               # display the manual for COMMAND, use q to quit
exit                        # close shell

You can go back to the last used command by using ↑ key. Press Enter if you want to use the command, use Backspace to edit the command before using it. Use Ctrl+R to search through your command history. Use cat ~/.bash_history | less to view your complete command history.

Editor

One of the easiest ways to implement your homework is to directly change the code on the server. For this you need to use a command line editor like nano or vim.

For beginners we recommend taking your first steps with nano. You can use it on Perlmutter like this:

[demmel@login10 cs267_hw1_2019]$ module load nano
[demmel@login10 cs267_hw1_2019]$ nano dgemm-blocked.c

Use Ctrl+X to exit.

For a more complete code editor try vim which is loaded by default:

[demmel@login10 cs267_hw1_2019]$ vim dgemm-blocked.c

Use Esc and :q to exit. (:q! if you want to discard changes). Try out the interactive vim tutorial to learn more.

Compiler

Compilers on Perlmutter are selected using a "programming environment" module. No matter which compiler you use, you always compile on Perlmutter using the CC (for C++) or cc commands, which use special wrappers that invoke the compilers for you with some specially tuned flags enabled (such as -march=native).

Unlike Cori using Intel compilers by default, Perlmutter uses GNU by default. You don't have to switch to using the GNU compiler as previous years. To check the loaded modules, you can use command module list. Now, when you invoke CC or cc, you will be using the GNU compilers.

Additionally, most homeworks require cmake version > 3.14, which can be loaded using the command module load cmake. You can confirm your module configuration is correct by running module list. For more details on modules, see the documentation on modules here.

Compiler Explorer

You can examine the assembly produced for your code by using the -S flag in your compiler.

[demmel@blasboss ~] cc -S hello.c -o hello.s
[demmel@blasboss ~]$ head hello.s
        .file   "hello.c"
        .text
        .section        .rodata
.LC0:
        .string "Hi, fam!"

While this can be useful, it's often cumbersome to constantly edit a sourcefile and then have to recompile to view the assembly. There's a nice tool called the GodBolt Compiler Explorer that let's you interactively edit code and view the assembly interactively as you optimize. It also has a couple of nice features that you won't find just using your local C/C++ compiler: it will color code lines of code to visually match them up with the corresponding lines of assembly, and it will use some advanced symbol lookup techniques to place more human-readable names for your functions and variables in the assembly output.

Acknowledgements

Thanks to Kevin Laeufer to create this tutorial.