Overview:

This portion of the class is devoted to making sure we are all starting from the same starting point on stampede. This tutorial was developed as a combined version of multiple other tutorials which were previously given credit here. Anyone wishing to use this tutorial is welcome.

This is probably the longest tutorial in the entire class. It is designed to take between 1/2 and 3/4 of the first class. Do not stress if you feel people are moving through it faster than you are, or if you do not get it done before the next presentation. There will be links back to this tutorial from other tutorials as needed, and by the 2nd half of Wednesday's class when we start with the specialized tutorials, you can circle back to this tutorial as well. 

Class Structure

As mentioned in the email that went out last week, the course is being offered in a hybrid format with some participants being in person and some attending only on zoom. Everyone is welcome to attend in either format on any day. If you have any questions please dont hesitate to reach out. Each day during class, I'll walk around the room while you work on the tutorials and look at various screens to see if I notice any issues individuals are running into, but please just get my attention if you know you are running into a problem. For those on zoom I'll have an ear bud in my ear so the easiest way to get my attention will be to just unmute and say something, but i will also circle by my computer and check if anyone has sent a chat message about an issue.

Objectives:

1. Familiarize yourself with the way course material will be presented.
2. Log into stampede2.
3. Change your stampede2 profile to the course specific format.
4. Refresh understanding of basic linux commands with some course organization.
5. Review use of the nano text editor program, and become familiar with several other text editor programs.

Example things you will encounter in the course:

As this is the first real tutorial you are encountering in this course, some housekeeping matters to familiarize you with how information will be presented.

• Code blocks

There will be 4 types of code blocks used throughout this class. Text inside of code blocks represent at least 1 possible correct answer, and should either be typed EXACTLY into the terminal window as they are, or copy pasted. There is a notable exception that text between <> symbols represent something that you need to replace before sending it to the terminal. Yes, the <> marks themselves also need to be replaced. We try to put informative text within the brackets so you know what to replace it with. If you are ever unsure of what to replace the <> text with, just ask.

1. Visible
   1. These are code blocks that you would likely have no idea what to type without help. This is common when a new command is being introduced, or when things you might be able to guess at are wrong in some way.
   2. These will typically be associated with longer/more detailed text above the text box explaining things.

   3. An example code block showing you the command you need to type into the prompt to list what directory you are currently in:

      pwd

2. Hinted
   
   1. These are code blocks that you can probably figure out what to type with a hint that goes beyond what the tutorial is requesting. Access the hint by clicking the triangle or hint hyperlink text.
   2. These exist to force you to think about what command you need, and hopefully make some connections to help you remember what you will need to type in the future.
   3. These should all come with additional explanation as to what is going on.
   4. Rather than just expanding these by reflex, I strongly suggest seeing if you can figure out what the command will be, and checking your work

   5. Example:

       what command would you use to Print your current Working Directory

      In this example the letters P W and D are all capitalized to try to help you focus on the command itself

      pwd 

3. Hidden:
   1. These code blocks represent things that you should have seen or used several times already, or things that can be succinctly explained.

   2. Example:

      use the pwd command to print your current working directory Expand source

      pwd

4. Speed bump:

   1. This combines the previous 2 types to deliberately slow you down and be cumbersome. 
   2. If you find yourself consistently wrong about what eventually shows up in the text box, slow down, step back, think about whats going on, and consider asking a question.
   3. These should only come after you have seen the same (or very similar) commands in the other formats previously

   4. Example:

       print your current working directory

      Remember, the command you need is "pwd".

      This command needs no options Expand source

      pwd

• Warnings

• Info boxes

• Tip boxes

Tutorial:

• Logging into stampede2

I think everyone was able to log into stampede2 last week as part of the pre-class assignment. If not make sure the instructor is aware as there are additional elements that still need to be addressed (potentially adding you to the project allocation and definitely being added to the reservation that we will use starting tomorrow). 

ssh <username>@stampede2.tacc.utexas.edu

When prompted enter your password, and digital security code from the app, and answer "yes" to the security question if you see one. If you previously have logged in you will not see such a question prompt.

As a reminder, the ssh command, and launching programs to give you the prompt to type them was provided as part of the pre-class assignment. Convenient links incase you need them or want to refresh your memory:

• Windows users

• Mac users

• Setting up your stampede2 profile

There are many flavors of Linux/Unix shells. The default for TACC's Linux (and most other Linuxes) is bash (bourne again shell), which we will use throughout. I am not aware of any others being used by biologists, so this is likely just something you will always default to.

Whenever you login via an interactive shell as you did above, a well-known script is executed by the shell to establish your favorite environment settings. I've set up a common profile for you to start with that will help you know where you are in the file system and make it easier to access some of our shared resources. If you already have a profile set up on stampede2 that you like, we want to make sure that we don't destroy it but it is critical to make sure that we change it temporarily so everyone is working from the same place through the class. Use the ls command to check if you have a profile already set up in your home directory.

cdh
ls .profile
ls .bashrc

If you already have a .profile or .bashrc file, use the mv command to change the name to something descriptive (for example ".profile_pre_GVA_backup"). Otherwise continue to creating a new files.

mv .profile profile_pre_GVA_backup
mv .bashrc bashrc_pre_GVA_backup

Now that we have backed up your profiles so you won't lose any previous settings, you can copy our predefined GVA.bashrc file from the /corral-repl/utexas/BioITeam/gva_course/ folder to your $HOME folder as .bashrc and the predefined GVA.profile as .profile from the same location before using the chmod command to change the permissions to read and write for the user only.

cp /corral-repl/utexas/BioITeam/gva_course/GVA.bashrc .bashrc
cp /corral-repl/utexas/BioITeam/gva_course/GVA.profile .profile
chmod 700 .bashrc
chmod 700 .profile

The chmod 700 <FILE> command marks the file as readable/writable/executable only by you. The .bashrc script file will not be executed unless it has these permissions settings. 

ls              #ignore everything that comes after the # mark. There is a problem on this wiki page but things after a # wont effect commands  

ls -a

ls -a -1

ls -a -l

ls -a -1

ls -al

Getting back to your profile... Since .bashrc is executed when you login, to ensure it is set up properly you should first logout:

logout
# or
exit

then log back in:

ssh <username>@stampede2.tacc.utexas.edu

If everything is working correctly you should now see this as your prompt:  

tacc:~$

It is also likely or expected that upon logging in you see the following:

The following have been reloaded with a version change:
  1) impi/18.0.2 => impi/17.0.3     2) intel/18.0.2 => intel/17.0.4     3) python2/2.7.15 => python2/2.7.14

These messages have to do with some of the core compilers and associated tools on TACC. You could use the module spider commands detailed below to find out more information of any of these modules and track down why such changes might be being made, but they are not concerning.

• Setting up other shortcuts:

In order to make navigating to the different file systems on stampede2 a little easier ($SCRATCH and $WORK), you can set up some shortcuts with these commands that create folders that "link" to those locations. Run these commands when logged into stampede2 with a terminal, from your home directory.

cdh
ln -s $SCRATCH scratch
ln -s $WORK work
ln -s $BI BioITeam

In previous years, several people have report seeing an error message stating "ln: failed to create symbolic link 'BioITeam/BioITeam': Permission denied." This seems to be related to different project allocations. I do not think it will be an issue for anyone this year.

• Understanding what your .bashrc file actually does.

cat .bashrc

• Editing files

There are a number of options for editing files at TACC. These fall into three categories:

• Linux text editors installed at TACC (nano, vi, emacs). These run in your terminal window. vi and emacs are extremely powerful but also quite complex, so nano is the best choice as a first local text editor. It is also powerful enough that you can still accomplish whatever you are working on, it just might be more difficult if you try to do more complex edits. If you are already familiar with one of the other programs you are welcome to continue using it. If this is something you plan to use long term, it is worth spending the time to learn to rely on something other than nano after this class.
• A former lab member suggested that vs code may be the best current platform to combine much of this, and while I trust his experience and suggestion I don't have personal familiarity with it https://code.visualstudio.com/docs/remote/ssh .
• Text editors or IDEs that run on your local computer but have an SFTP (secure FTP) interface that lets you connect to a remote computer (Notepad++ or Komodo Edit). Once you connect to the remote host, you can navigate its directory structure and edit files. When you open a file, its contents are brought over the network into the text editor's edit window, then saved back when you save the file.
• Software that will allow you to mount your home directory on TACC as if it were a normal disk e.g. MacFuse/MacFusion for Mac, or ExpanDrive for Windows or Mac ($$, but free trial). Then, you can use any text editor to open files and copy them to your computer with the usual drag-drop.

We'll go over nano together in class, but you may find these other options more useful for your day-to-day work so feel free to go over these sections in your free time to familiarize yourself with their workings to see if one is better for you.

As we will be using nano throughout the class, it is a good idea to review some of the basics. nano is a very simple editor available on most Linux systems. If you are able to use ssh, you can use nano. To invoke it, just type:

nano

You'll see a short menu of operations at the bottom of the terminal window. The most important are:

• ctl-o - write out the file
• ctl-x - exit nano
  You can just type in text, and navigate around using arrow keys. A couple of other navigation shortcuts:
• ctl-a - go to start of line
• ctl-e - go to end of line

• How should we name files and folders?

In general you will want to adopt a consistent pattern of naming, and it should be your own and something that makes sense to you. After that there are some tips:

1. The most important thing to get used to is the convention of using . _  or capitalizing the first letter in each word in names rather than spaces in names, and limiting your use of any other punctuation. Spaces are great for mac and windows folder names when you are using visual interfaces, but on the command line, a space is a signal to start doing something different. Imagine instead of a BioITeam folder you wanted to make it a little easier to read and wanted to call it "Bio Informatics Team" certainly everyone would agree its easier to read that way, but because of the spaces, bash will think you want to create 3 folders, 1 named Bio another named Informatics and a third named Team. Now this is certainly behavior you can use when appropriate to your advantage, but generally speaking spaces will not be your friend. Early on in my computational learning I was told "A computer will always do exactly what you told it to do. The trick is correctly telling it to do what you want it to do". 
2. Name things something that makes it obvious to you what the contents are not just today but next week, next month, and next year even if you don't touch the it for weeks-months-years.
3. Prefixing file/folder names with international date format (YYYY-MM-DD) will ensure that listing the contents will print in an order in which they were created. This can be useful when doing the same or similar analysis on new samples as new data is generated.

cd this\ is\ really\ annoying\ to\ use\ but\ I\ don\'t\ know\ it\ yet

• Understanding TACC

Now that we've been using stampede2 for a little bit, and have it behaving in a way that is a little more useful to us, let's get more of a functional understanding of what exactly it is and how it works.

Diagram of Stampede2 directories: What connects to what, how fast, and for how long.

Stampede2 is a computer cluster connected to three file servers (each with unique characteristics), and other computer infrastructure. For the purpose of this class, and your own work, you only need to understand the basics of the 3 file servers to know how to use them effectively. The 3 servers are named, "HOME", "WORK", and "SCRATCH", and we will work with them all over the next 5 days

Executables that aren't available on TACC through the "module" command should be stored in $HOME.

If you plan to be using a set of files frequently or would like to save the results of a job, they should be stored in $WORK. While 1TB may seem like a lot of space you can easily fill it up with just a few sequencing projects, particularly if you store files in a non-compressed manner, or wish to store analyzed intermediates. Best practice would be to store the most important files (raw > scripts > final > analysis files) on a system such as corral or backed up to something else such as UTbox. 

If you're going to run a job, it's a good idea to keep your input files in a directory in $WORK and copy them to a directory in $SCRATCH where you plan to run your job.

 cp $WORK/my_fastq_data/*fastq $SCRATCH/my_project/

Understanding "jobs" and compute nodes.

When you log into stampede2 using ssh you are connected to what is known as the login node or "the head node". There are several different head nodes, but they are shared by everyone that is logged into stampede2 (not just in this class, or from campus, or even from Texas, but everywhere in the world). Anything you type onto the command line has to be executed by the head node. The longer something takes to complete, or the more commands you send at once the slower the head node will work for you and everybody else. Get enough people running large jobs on the head node all at once (say a class of summer school students) and stampede2 can actually crash leaving nobody able to execute commands or even log in for minutes -> hours -> perhaps even days if something goes really wrong. To try to avoid crashes, TACC tries to monitor things and proactively stop things before they get too out of hand. If you guess wrong on if something is safe to run on the head node, you may eventually see a message like the one pasted below. If you do, it's not the end of the world, but repeated messages will lead to revoked TACC access and emails where you have to explain what you are doing to TACC and your PI and how you are going to fix it and avoid it in the future.  

Message from root@login1.ls4.tacc.utexas.edu on pts/127 at 09:16 ...
Please do not run scripts or programs that require more than a few minutes of
CPU time on the login nodes.  Your current running process below has been
killed and must be submitted to the queues, for usage policy see
http://www.tacc.utexas.edu/user-services/usage-policies/
If you have any questions regarding this, please submit a consulting ticket.

So you may be asking yourself what the point of using stampede2 is at all if it is wrought with so many issues. The answer comes in the form of compute nodes. There are nearly 6,000 compute nodes with different configurations that can only be accessed by a single person for a specified amount of time. For the duration of the class, each student will interact with a single compute node using an interactive DEVelopment (iDEV) session so that you get immediate feedback of seeing commands being run and know when to use the next command. This is not the typical way you will analyze your own data. Friday's tutorial will deal with the queue system.

While stampede2 is tremendously powerful and will greatly speed up your analysis, it doesn't have much in the way of a GUI (graphical user interface). The lack of a GUI means it can't visualize graphs or other meaningful representations of our data that we are used to seeing. In order to do these types of things, we have to get our data off of stampede2 and onto our own computers. This course uses the scp ("secure copy command") exclusively to move files back to your local computer, as mentioned there are other programs that can be configured to more easily transfer files back and forth as you progress in your analysis.

Transferring files to and from stampede2 with scp

When this class was taught in person, it was helpful to have a small set of steps on transferring files between stampede2 and your local computer which tended to give people problems. The idea being that some problems on the first day would eventually work themselves out through the week as the SCP command was repeatedly used. Given how zoom makes it more difficult for problems to be identified, this tutorial has been moved to its own tutorial page so that it can be more referenced more easily when files are to be transferred in future tutorials. for now, focus on transferring the