Fall 2020 – HONR268N

Entry #1 | 09/10/2020 – 09/14/2020

TL;DR

• 1. Your shell determines the format of your command inputs; read up on it online to find out more.

  2. The terminal help function is very thorough, but I found that a google search with a dumbed-down explanation serves as a better primer for commands.

  3. If you run a command and it seems to be unresponsive or you want to stop it for whatever reason, try ‘control + c’.

  4. Don’t use ‘sudo’ on the cluster! You will get reported (oops).

What is my shell?

That depends. A shell essentially provides you with a means to communicate with your computer—tell it what to do. There are different shell types that give you different features which may sway your preference of choosing one over another. I have no clue what those are, but that’s ok for now.

Entering “echo $0” into my laptop’s terminal window returned “-bash”. This tells me that -bash is the current shell I’m working in. A useful command if I’m switching between shells and forgot which one I’m using.

Entering “echo $SHELL” tells me what my default shell is; “bin/bash”. This command tells me that if I open a new terminal window, the shell will default to -bash.

That changed when I logged into the cluster though. There, the shell defaults to -tcsh and it behaves differently from -bash.

Typing in “help” on the -bash shell my laptop defaults to actually wasn’t very helpful. If I want information on what certain commands do in that environment, then I need to type “info” followed by a space and then the command. That takes me to a separate screen which gives in-depth information on the command. It took me a bit to figure out how to exit that screen, but it’s done by hitting “q” on my computer.

On the other hand, typing a command followed by “--help” on the -tcsh shell while on the cluster does yield helpful information.

What does the ‘touch’ command do?

After my first try with the command, it seems to create a file within a directory (defaults to working dir.) without any extension with the name I specified, and the help function confirmed that. It creates an empty file if it doesn’t exist already. But it also updates the latest access and modification times to the current time if the file does exist. There are a bunch of arguments you can use (I think of them as modifiers) to do different things. Just to test one out I changed the date my file was last accessed and modified to the day the world was supposed to end.

It worked. But, it still shows the time the last change was made. Oh well.

Why do we include ‘.’ after the ‘find’ command?

From my first use, I think that the search only happens within the working directory. Otherwise it searches for the keyword everywhere within the home directory.

It worked fine.

I was going to demonstrate how it didn’t work with the GUI, but now that I was going to log the error of course it’s working.

When it wasn’t working, my issue was that the GUI was unresponsive to any inputs—text or clicks. In fact, the file would open empty despite the fact there was already text in it. I saw that some of the icons I had hovered over would randomly appear to respond. No matter how long I waited though, there would be no sign of inputs working. My suspicion is that during class I was using a lot of bandwidth with Zoom since I saw my video lagging. Now that I’m not on Zoom it’s working just fine. Both times, I accessed the GUI through Terminal and had XQuartz running.

Which leads me to the next point. XQuartz is necessary, but only for the remote GUI access.

Here’s what I saw when it was working.

All the buttons were working, I could edit the file, no issues.

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Entry #3 | 9/20/2020

Shell Scripts

Write first shell script

I created my first shell script using the emac command and made edit in the terminal.

Of course, it’s important to not confuse apostrophes ‘ with backticks `. Now that those errors have been fixed The script runs as intended.

Write a script that searches and logs rogs results for a given input

I modified the first script after this. Deleted all the echos and and added in the line which prompts a search via find. Attempting to run the script without the tcsh command resulted in a “permission denied” response from the system. Using chmod to give me permissions with the -x modifier changed that.

The -x is for execute and it gave not only me, but all users access to execute my file.

I wrote the homesearch.tcsh script and realized that using the * didn’t work quite how I thought it would when I put it in the argument. To make it behave more predictably, I put it into the find command.

What is piping? 

Piping takes the output of one command and “pipes” it through another command. In other words, it takes the output of the first command as the input for the second.

Here’s an example which uses ‘ls’ to list the contents of a directory and ‘wc -l’ to count the lines output by ‘ls’. In essence, this pipe results in outputting the amount of files in the directory to the console.

How to change strings in a .txt file 

‘sed’ is a powerful command. It can substitute strings of characters in a variety of ways defined by the user. In the following example, the command substitutes the string “was” for “is” everywhere in the ‘hw3.txt.’ file

It worked

Using -n returned the line on which the hit was on.

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Entry #4 | 10/1/2020

Muons and C++

Why do muons travel farthest in particle detectors?

I started my search in our class text. I found that muons are relatively heavy compared to other particles being physically detected post-collision in accelerator experiments.

The muon is two orders of magnitude more massive than the components of a proton, and by extension, much more massive than even protons and neutrons. A quick google search shows that a proton is made up of two up quarks and one down quark. It makes sense since that adds up to a +1 charge. We know from discussion in class, that the top quark is extremely unstable. So, I would assume that the lighter particles are more stable than the heavier ones.

The muon must sit in a nice sweet spot, be special in some way, or both since it doesn’t decay before going so far out. It has a charge so it will interact with magnetic fields. If it is heavier than other charged particles being detected, for a given velocity or energy, it should have a larger arc radius as it travels through its curved path within the CMS.

The lhc-closer.es website kind of confirms that since it explains that the more energy a particle has, the shallower the curve of its arc through the detectors is. Muons are in fact special in some way because they can travel meters through iron without interacting, according to CERN’s CMS site.

Running first C++ script

First, I created the script, main.cpp, in emacs. Then, I ran it with g++ and had the contents of the script read with ./a.out.

What’s going on under the hood?

Using g++ -dumpspecs showed me that I was using v4.4.7

...

I used cat on a couple of math files in the bits folder

It looks like the trig functions above are composites of other functions.

More C++ scripts—simple calculators, T/F, and loops

The first run of my second C++ script resulted in some error. I debugged it by using cat and comparing the first script, which I knew was error free, with the one that was having issues. The error description gave me a clue that I had mistyped something. Sure enough I had omitted an ‘l’ (lowercase “L”) after ‘end’ on the first line after main().

Example three had an error in it to begin with, it was missing a set of quotation marks.

But before running, I fixed that and it went without any hiccups.

The ++ and -- operators add 1 and subtract 1, respectively. It makes no difference if they are before or after the variable. I guess it’s called C++ because adding 1 and subtracting 1 in this simple manner must be frequently used. Just a guess though.

Example 4 went well, too.

For the for loop exercise, I wrote it without testing what was on the hw page first. I got the same numbers but in very different formats. At first, I thought is was because I had ‘endl’ in a spot and that removing it would solve the discrepancy, but it’s definitely a bit more than that.

After removing the ‘<<endl’ after ‘m’, this is what I got:

Success! After playing around with it a few times it worked. This is the condensed “for” version of the hw’s “while” loop.

After moving ‘return 0’ down a line:

Just for fun, I tried making ‘p’ a double pointer to see what would happen. The compiler told me that it couldn’t be done.

Ok this is beautiful! Of course program 2 shows how to do it. By pointing to the variable i’s address, we can always get the most current value instead of having to reset j everytime like in the previous example. Mind blown.

My pi pointer took a bit to get right, but I figured it out. The main issue I had was that I was trying to put the value of p1 into the pointer p2 without using ‘new’ and got an error saying that double can’t be converted to double*.

Computing 

• 1. Write a small C++ code that shows examples of if and while logic statements.

For my loop example I created an outline of what could be a “Voyage into Space” simulator. I found the altitudes of our atmosphere’s layers and made the program print out statements according to the height. After a bit of fine tuning, it worked!

The biggest issue I had was that I didn’t use the logic statement correctly. Instead of ‘==’ I was using ‘=’ which made my program get stuck in my first ‘if’ loop. At first, I thought it was stuck because ‘x’ wouldn’t increment in that loop so I added ‘x++;’ at the end of each if and else if loop. Turned out that wasn’t necessary since if the ‘if’ statement were true, then that block should finish and then the program should move on. I forgot a bracket but the compiler easily pointed that out.

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Speed of light, Phase and Group Velocity, and Speeds Higher than c

The speed of light in a vacuum is the constant c. This is the speed we refer to when referencing "the speed of light" in equations, concepts and discussion regarding reference frames in special relativity and the like—299,792,458 m/s.

When two waves interfere, they can produce a wide variety of "new" waves. Two waves of the same frequency, amplitude and on phase with each other will create an identical wave with double the amplitude but the same as their original components otherwise. If they were 180º off phase with each other, then they would cancel out. If they are traveling in opposite directions, they could create standing waves which would stand still over time. But a special case is where two waves are traveling in opposite directions at ever so slightly different frequencies. The resulting interference would create apparent pulses traveling much faster than either of the component waves. This screenshot taken from Michael Richmond's page on phase and group velocities demonstrates the effect.

If the waves are light waves, the resulting phase velocity—movement of the green dot over time—can actually be faster than light. The group velocity—movement of the magenta dot over time—will not however. There are special conditions for this phenomena that I'm not 100% sure of. From what I gathered, this can happen in a 'waveguide'. So maybe that means a wire, fiber optic cable, some other thing? I'm not sure. But I also found that this phenomena doesn't really mean much physically since the wave's energy is not traveling faster than c. It's just a mathematical representation of interference

 Raymond Rumpf and Gifuni Angelo provide answers in regarding a question on the topic posted on ResearchGate.

How are elements distributed in columns and rows? 

Essentially, what is happening is that a matrix is being created. In the first loop, ‘ii’ is a matrix of 3 rows by 1 column, with its elements being 1, 2, and 3 in that order. ‘j’ is the variable which specifies the element to be returned with each iteration of the loop. Here is a visualization of the ‘ii’ matrix:

The second loop has ‘LL’, a 2 by 3 matrix, being cycled through with both ‘j’ and ‘k’:

Now change N to 10.  What do you find? 

Now, I would say it’s between 40 and 130 GeV with the center being around 80 GeV, but there is a much larger room for error.

Change N to 1000.  What do you find? 

The data is centered around 95 GeV with a range from about 22 GeV to 155 GeV. Again, the margin of error looks even smaller since the peak keeps getting closer to a certain energy.

Now open secretparameters.txt and change the first number in it to 1.  Repeat with N=1,10,100,1000.  What have you learned? 

Issues with MadGraph 

• 1. One issue with MadGraph was that the version available from the download site is too updated to work with the default python on the cluster. For compatibility’s sake, copying the MG5_aMC_v2.2.3.tar.gz file from /home/HONR268N/SIMULATION into the MC… folder was the way to go.

  2. Another problem I ran into was forgetting to use “cmsenv” before running the subsequent steps to generate the pp → ttbar processes. Everytime we use MadGraph or ROOT we have to use “cmsenv” prior, otherwise some issues will arise. In this case, I had an error when trying to generate the MG5 run that said Fortran compiler could not be found.

  3. The third problem now is that I cannot successfully open the “converted” root file ‘MY_FIRST_MG5_RUN.root’. However, I don’t think it even converted correctly because when running ‘unweighted_events.lhe’ through the lhe2root.py script, all I see returned to the console is “Problem with line:... Skipping… “.

     1. Turns out this is not a problem, it’s how the program works. The real issue I had was that I was not following up with the root command: ‘TBrowser’ followed by a space and some variable, call it “T”. That opened up the root browser so that I could see the data.

Which color tracks are electrons? 

Electrons are represented with green tracks.

Which color tracks are muon? 

Muons are represented with red tracks.

Which color track missing energy is represented with? 

Purple/Pink

How are jets depicted in this visualization? 

Orange cones

Can you figure out if a track has clockwise curvature, it is  +vely charged or negatively charged? (when looking at the x-y view, with x along the horizontal axis) 

If a particle tracks with a clockwise curvature, it is positively charged.

Study at least 2 events from each category in the files available with the display and specify how many objects of each kind are seen in every event? 

Event 1: DoubleElectron_Run2012C_0.ig:Events/Run_202016/Event_616969809 

Open the output file and paste the Z_ee and H_zz histograms in your HW file

Exercise: Using the pre-declared variables, calculate the area of a circle, and assign it to a new variable named 'area'. Print 'area' to the console.

Try to figure out why one works and the other doesn't.

Method 1 doesn't work because once 'a' is set to 'b' and the program prints 'b', it will print 'a's new value, which is still 'b'.

Method 2 works because 'temp' holds 'a's original value, so when the program prints 'b' it will return 'temp' which is 'a's original value.

Exercise: Using temporary variables, switch the following data so that it makes sense. Print the new variables to the console.

Exercise: Write a function that will round a number to 'n' digits. Test your function using a print statement. Make sure the print statement is outside of your function.

What do you see when you execute this code?

Exercise: Write a function that takes in two lists as arguments. Your function must first find the max of both lists. It must return the product ('*') of the maxes. Test your function by printing to the console.

What is the output of the above code?

Exercise:  Using print statements, and built-in functions min(), max(), sum(), write some code that either evaluates to True or False.

For the assigned values of variables a and b, what is the output?

Exercise: Change values of a and b such that the other two conditions are met.

What is the output of the above code?

Exercise: Write a function to determine if the absolute value of the minimum in a list is odd. If it is odd, print 'odd' to the console. Else, print 'even' to the console

Add the following lines one by one to the above code and add comments to explain what they mean.

Exercise: Final is between the two teams. Complete the function below to select the captain of the losing team and print to console.

Complete the function below to implement the Purple Shell's effect. Pass the list 'standings' into your function and print the updated standings to the console.

Exercise: Your lucky number is 7. You really like 7. You even like numbers divisible by 7 (do I smell a modulus operator?). Write a function that counts the frequency of numbers divisible by 7 in a list, and print that frequency to the console.

It's important to understand the instructions before coding so that the right program is written. Otherwise, you spend time writing something that wasn't asked for:

The correct program is as follows:

Exercise:

MatPlotLib and Numpy

WOW! This is awesome. This is a very simple, but very powerful tool I'm sure will come in handy.

Exercise. Google the functions used by the matplotlib and numpy libraries to get an understanding of the flow of the code. In the blank code space below, import the matplotlib and numpy libraries and make any plot of your own. Use the above examples and the documentation pages to help you.

Paste the output of the above code to your HW.

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