This document will be updated throughout the course.
Here are links to scans of the writeups of two exemplary projects from 2012.
This should provide you with some idea of what a good project might look
like.
Feel free to try to raise the bar, and perhaps yours will be gracing these web pages in 2016!
As those of you who were in the lab this afternoon know, the machine that
acts as the "server" for the
course--laplace.phas.ubc.ca--(hosts the web site and the file system
/phys210) was down for an extended period.
I was doing some reconfiguration of equipment in my office that necessitated a restart of the machine, and due to a technical issue that I won't bore you with, the machine was rendered unbootable. After 90 mins or so of flailing around trying various futile fixes, I finally downloaded a DVD of the most recent version of Mageia, which includes a "rescue" facility that allowed me to remedy the problem.
You shouldn't have lost any data due to this snafu, but if you think you did, let me know and I will check the backups for you.
I apologize for the inconvenience this caused, as well as the fact that I was unavailable for most of the afternoon.
Note, however, that I will be in the lab tomorrow (I'll try to post the hours so somewhat beforehand) as well as for a few hours both Saturday and Sunday.
Lots of gravitational physics in this movie [TRAILER]
Kip Thorne, an executive producer and chief scientific consultant for the film has a very readable book on the science that underpins the movie: The Science of Interstellar
The full Homework 3 handout is now available HERE as well as from the course home page and the homework page. I'm sure that you'll find a bug or two or three, but it's definitely in good enough shape to allow you to get working on Problem 4.
Since Problem 4 of the current homework---which I consider to the most important homework question in the entire course by a substantial margin---has developed in length beyond by initial expectations, Problem 3 is now OPTIONAL, and for bonus credit.
From my snooping, it appears that only on the order of five of you have started and/or completed it, and if you are among those, you will all receive bonus marks for what you have done, with a level of bonus commensurate with how well you have completed it.
HOWEVER, NOTE THE FOLLOWING
I still urge all of you to attempt to complete it. Newton's method plays an extremely important role in many areas of computational science, and is an absolute must for the toolbox of anyone who wants to consider themselves even moderately educated in scientific computing. For example, the last part of the question has you solve a nonlinear equation that arises directly from the material on quantum mechanics most of you are currently studying in Physics 200.
If you think you can solve it quickly, then I would go ahead and do so before you start with Problem 4; otherwise I recommend that you focus your attention on finishing Problems 1 and 2 soon, and then move on to Problem 4
Most importantly: since I have already mentioned in class that I expect that Problem 4 will be quite challenging for many of you, and that you shouldn't be too concerned about how well you solve it will impact your final grade, I am concerned that some of you might be inclined not to put enough effort into it.
Now that Problem 3 is optional I expect that most, if not all of you, should be able to do a good job with Problem 4, particularly if you get assistance from your instructors and classmates as needed. The TAs and I will be able to tell from your code the amount of effort that you have expended, and if the effort is low you can expect your performance to have a substantial negative impact on your final grade.
To summarize, the effort you have invested in working on Problem 4 definitely matters, and the amount of effort you have invested in Problem 3 also matters in that regard; i.e. we will be considering the sum total of what you have done when we decide what grade you should receive.
My expectation is that most of you will need to spend more time on this problem set than the others; that should be your expectation as well.
However, I firmly believe that as you work on your term projects you will find the return on your investment to be substantial.
As always, the online version of the homework is up to date. Be sure to clear your browser cache as necessary so that you get the most recent version.
Download it from HERE (or from the course home page or course homework page.)
Mona reported a problem with the grading of her Quiz 2 which, due
to the fact that I used a script, was probably not isolated
to her work alone. I have thus re-run the script, and hope that the
updated /phys210/$LOGNAME/matlab/README_q2_$LOGNAME files are now
correct. Let me know if there are appear to be further problems.
I think I have everyone's lab section sorted out, so the presentation schedule for next week is available HERE.
I will greatly appreciate if everyone can have a quick look at the page to ensure that you are scheduled to speak in the section in which you are enrolled.
Once again, please refer to the instructions in the
for full details concerning how your presentations should be prepared and e-mailed to Arman.
Presentations must be e-mailed to Arman in PDF form by
Noon, Monday October 20
and this is a firm deadline.
The MATLAB issue on hyper has been fixed. Let me know if you encounter any problems running it there.
I've run your MATLAB Quiz 1 scripts (q1.m) through a grading
script. Results are in
/phys210/$LOGNAME/matlab/README_q1_$LOGNAME
Class averages (won't add to 12 due to some missing scripts)
Well done!
All those Hello World!'s:
Variant Frequency count.
'Hello WOrld' 1
'Hello World!!!!' 1
'Hello World!' 5
'Hello World' 3
'Hello word' 1
'Hello world !' 1
'Hello world!!!!!!!!!!!!!!!!!!!!!!!!!!! LOLZ' 1
'Hello world!' 16
'Hello world' 27
'hello world!' 1
'hello world' 3
Anarchists indeed ...
A couple of you have noticed that executing matlab on hyper doesn'
t work. There's a small system issue that needs to be addressed and
I hope that it will be fixed soon. For the time being there are at
least two work-arounds:
Use the full pathname to start the application
hyper% /opt/matlab/R2013a/phas/bin/matlab -nosplash -nodesktop
Secure-shell to tau.phas.ubc.ca and start matlab there (recall that tau
is the server I mentioned a while ago that will eventually replace
hyper).
I need to emphasize that all projects must be implemented in MATLAB unless you have my explicit approval to use a different language. So if you do want to use some other language, you will need to speak with me soon about the matter.
As I was discussing with a few of you in the lab yesterday, the ray tracing optics project is reasonably challenging and, I think, fun to do. You can see an example of the results from a nice implementation of it last year by Alex Fang here: MPEG and MPEG.
Note that this is not a pre-approved topic: I ask you to speak with me (i.e. in person if at all possible) should you wish to try it since students have tended to struggle with it in the past for a variety of reasons.
Since there has been some confusion about this, note that for Problem 2, the only subproblem that involves a plot is 2.5. For the others, your expression should evaluate to either
So, in summary, generate one plot for Problem 2.
See THIS PAGE for detailed information concerning the selection of your term project topics, how your choice of topic is to be e-mailed to me, and how you should prepare for your presentation to your peers and myself on Oct 21 and 23.
Amanda and Arman have finished grading your first homeworks and comments along with your marks are available in a README file (what else?) in your hw1 directory, i.e. in
/phys210/$LOGNAME/hw1/README
Note that the grading was split in the following way:
Amanda marked: 1, 2 and 5.
Arman marked: 3 and 4.
Should you have questions or concerns about the grading of one or more problems, please direct your questions in the first instance to the TA (or TAs) who graded the question(s). Should the issue(s) not be resolved to your satisfaction you are then absolutely free to consult me about the matter.
"Except" for the homework, we're done with Maple and will move on to new topics this coming week:
The complete handout for Homework 2 is now available HERE. There will likely be some bug fixes, but I hope not too many.
20 pages of handout, but, in principle, less than 100 lines of procedure code to write, so don't panic, but please em do read the handout. It's to be viewed as part of the course notes as well as an assignment.
Deadlines
Now that part of Homework 2 is out, the bug reports are coming in! To minimize confusion and the number of detailed Connect messages that I will need to send, I have started a SPECIAL PAGE that will enumerate the bugs, along with a summary of what action you will need to take, relative to the original handout, to deal with the defects.
So far, all the bugs are harmless; i.e. require no action on your part.
Nonetheless, I surely appreciate the reports, no matter how trivial the issue might seem to be, so keep at it!
The bug page is also available from the course home page, under the homework link.
Finally, I will keep the online handout and any other related online material (such as my version of the worksheet for Problem 1) updated approrpriately. Just remember to clear your cache as necessary (again, Safari users are likely to have to do this), to ensure that you get the latest version of any document.
In what I consider to be a bit of a cosmic coincidence, given that the
first homework had a significant bash component, the server outage
was due to the recently discovered
"Shellshock" vulnerabilities
in the bash.
I predict that there will be quite a few more problems unearthed with this particular piece of software before all the dust settles.
The course web server http://laplace.phas.ubc.ca is back up. The course
home page and links within, including your own course pages, should now
be visible from any browser per usual.
Those parts of homework 1 for which the deadline was extended are now due tonight at 11:59 PM.
For your amusement, here's a pipeline which tells me how many students were still working on the homework today:
% ls -lR /phys210/*/hw1 | grep 'Sep 25' | awk '{print $3}' | sort | uniq | wc -l
(note that you can't execute this since you don't have access to anyone's hw1 directories but your own).
The first student who e-mails me the integer that this command produced at 9:46 PM on Sept. 25 can collect $10.00 from me.
One entry per student only --- no generation of 65 messages covering all the bases
If you play the game, make sure that I can identify your name from the message.
P.S. Sorry Arman & Amanda, only undergraduate students can play!
The PHAS system administrators are in the process of replacing the aging hyper.phas.ubc.ca, with a new server
tau.phas.ubc.ca
and although the configuration is not quite complete (as we
shall see in today's lab),
you should now be able to ssh to that machine, both from the
lab machines, and on your own systems. Additionally, provided that
you have the appopriate software installed, X-based applications
(kate, gedit, gnuplot, maple, etc) running on tau should also work
for you, modulo the fact that some packages including gnuplot and
kate have not yet been installed.
Once we (the sys admins and I) feel that tau is properly set up,
I will recommend that
you start using it rather than hyper, not
least so that we can get any remaining bugs worked out quickly.
Please note the following:
For HW 1, Problem 2, be sure to check that all of the intended contents of your page---most notably the images---appear when the page is accessed outside the lab, e.g. using a browser on your laptop or home machine. To facilitate this, make sure that the image files are located in
/phys210/$LOGNAME/public_html
not somewhere within your home directory /home2/$LOGNAME.
I've made a small amendment to the Homework 1 handout. In Problem 4, I have modified all three instances of the text
Using a single pipeline of commands ...
to
Using a single command or pipeline of commands ...
I.e. if you can solve any/all of the problems with a single command, that is fine.
The online version of the handout has been updated to reflect the change, and thanks go to Mona for bringing to my attention the need for the clarification.
The online version of the handout has been updated to reflect the change.
If you are having difficulties transferring files from personal machines to the lab machines, see HERE for a workaround. Please e-mail me immediately if you encounter problems with the workaround.
Sample solution of gnuplot exercise.
As emphasized in the lab notes, I would like you to get in the habit of scripting commands that you would normally type at the command-line (when using any command-line driven software), and then using the software's facility to redirect input to execute the commands in the file.
## Display the contents of the script file, created using my text editor
% cat gnuplot-input
# Enable dashed lines ...
set terminal wxt dashed
# Plot the title ...
# - tc rgb "blue" -> title color is blue
set title "My plot of cos(x**2)" tc rgb "blue"
# Make the plot ...
# - lt 2 -> line type is 2, i.e. dashed (use test command to see this)
# - lc rgb "green" -> line color is green
plot cos(x)**2 lt 2 lc rgb "green"
## Start gnuplot and load the script file to generate the plot
% gnuplot
gnuplot> load "gnuplot-input"
Sample solution of sed exercise. We can't use redirection directly to change myfireice so introduce a temporary file.
% cd ~/redirect
% cp fireice myfireice
% sed 's/say/state/g' < myfireice > foo
% MV foo myfireice
_Or ..._
% my foo fireice
_... and answer 'y' to the overwrite prompt._
Sample solution of optional pipeline exercise
% sed 's/ .*$//g' < poems | grep -v '^[ ]*$' | sort | uniq | wc -l
Sample solution of backquotes exercise.
Part a)
% mylist=`ls`
% cd ~phys210t
% mylist=`ls`
% echo $mylist
cmd dir1/ dir2/
Part b)
First, determine the full pathname to the "real" ls using the
which command, then use that pathname within the backquotes:
% which ls
/usr/bin/ls
% mylist=`/usr/bin/ls`
% cd ~phys210t
% mylist=`/usr/bin/ls`
% echo $mylist
cmd dir1 dir2
Sample solution of Pattern matching exercise 2
% mkdir -p /tmp/$LOGNAME/mywords
% cd ~phys210/words
% cp [aeiouAEIUO]*ing /tmp/$LOGNAME/mywords
For Safari users:
lease see HERE for instructions to clear Safari's cache. Knowing how to do this is important to ensure, for example, that when you click on a homework handout link you will retrieve the most recent version.
See the course Software page for information about FileZilla, an application you may want to install on your personal machines to allow you to easily transfer files to and from hyper.
If you are working remotely using PuTTY/Xming (Windows) or with a Mac, I suggest that you use the text editor gedit rather than kate. gedit appears to have much better performance than kate when used remotely and is just as good a text editor for the purposes of this course.
Sample solution to Lab 2 aliases exercise
Some RESULTS from Lab Exercise 1.2
