CIS(theta)Computing Independent Study2009-2011

Saturday, November 19, 2011

Quarter II, Week 2: ScreenCasts, SmartNotes and Code, oh my!

This was a long week making up for last week with Veteran's day on Friday and my being sick on Thursday....

AP Calculus BC finished CH5 on Anti Derivatives and will have a test next week. We covered Riemann Sums, definite vs. indefinite integrals, Fundamental Theorem of Calculus Parts I & II as well as U-Substitution!
BC 506 LRTE.p89

Calculus 506 LRTE Program

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BC 507 MTSE.p89

Calculus 507 MTSE Program

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BC 508 Fundamental Theorems

Calculus 508 Fundamental Theorem of Calculus Parts I and II

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BC 509 Indefinite Integrals

Calculus 509 Definite Integral

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BC 510 U-Substitution

Calculus 510 U-Substitution

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PreCalculus for Seniors finished CH5 on using Inverse Functions to solve equations analytically and graphically. We focused mostly on exponential and logarithmic functions. We had a test yesterday, but it didn't seem to go over well! Maybe we'll review some more on Monday and reTest on Tuesday before GameDay on Wednesday (Thursday is TurkeyDay).

PRE 506 Compound Interest

preCalculus 506 Compounded Interest

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PRE 507 Exponential Growth and Decay Word Problems

preCalculus 507 Exponential Growth and Decay

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AP Computer Science started CH5 about conditional statements and predicate methods! We started with C4X6, renaming it C5X0, which we said needed if statements, but really didn't! C5X1 was a rewrite of C4X13 using a predicate method to guard against square rooting the discriminant of the quadratic formula when its negative! C5X2 was about using if statements to parse String input. C5X3 used if statements to sort 3 doubles. What about Math.min(Math.min(num1,num2),num3)???

C5X0+C5X1 DataSet.java and QuadraticEquation.java

C5X2 Card.java

C5X3 Sorter.java

Computer Math is finishing Chapter 4 on Sequences and Series. I'm looking ahead toward a final project this year involving python's turtle graphics module or VPython 3D modeling or TI83/89 BASIC programming.
Note:
python 2.6 is already installed by default in Ubuntu
turtle.py is already installed by default in Ubuntu.
run apt-get install idle to use python
get vpython from the Ubuntu Software Center
vpython needs apt-get install libgtkglextmm-x11-1.2-dev

CM 404 Infinite Series
https://clemix.clemson.edu:34567/home/pub/251

CM 405 Iteration and While loops in Python 2.6

https://clemix.clemson.edu:34567/home/pub/252

Calculus Research Lab continued Lab 4.10 (even exercises) so we have nothing new to post. Recall, I only post new material. I do not post review sheets, labs, quizzes, tests or solutions as these are graded materials.

XTRA CREDIT:
Can you figure out what the frak the following file is for???

HTH and I hope you enjoyed this week's notes!

Learning with Technology,

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Monday, November 14, 2011

The Paperless Office: How's your 21st Century Classroom's workflow?

OK, I've got this down to a science! This year, I'm ScreenCasting from a Linux desktop with a real SmartBoard as needed and focusing on AP Computer Science with java. I hope you have been enjoying all the new recordings! However, I'm also using recordings from prior years for preCalculus and AP Calculus. Next year I hope to record Computer Math and Calculus Research Lab.

Typically, I start a Math unit on http://www.edmodo.com with an assignment sheet listing daily topics, homeworks, quizzes and tests for a whole chapter of the textbook. These assignment sheets usually span 2-4 school weeks. I link to the appropriate MP4 file from http://www.youtube.com/calcpage2009 to Edmodo daily and Blogspot weekly. I also link the current PDF from http://www.slideshare.net/calcpage2011 to Blogspot weekly. Note: I don't record, upload or link anything to do with review material, quizzes, tests or solutions. For example, today I linked to pre506.mp4 on Compounded Bank Interest from Youtube to Edmodo as shown above. I also uploaded pre506.pdf to Slideshare for future reference!

A Computer unit on Edmodo usually starts with uploading the current chapter as a PDF of our etext. Then I upload the exercises for that chapter. Finally, I give out hardcopies only of the curent lab assignment or test. Again, I link MP4s from http://www.youtube.com/calcpage2009 to Edmodo daily and to Blogspot weekly. I also link from http://pastebin.com/u/calcpage or SAGE to Blogspot weekly. For example, I recorded C5X0X1.mp4 today and uploaded it to Youtube and linked it to Edmodo as shown above. Further, I uploaded C5X0_DataSet.java and C5X1_QuadraticEquation.java to Pastebin for the weeekly blog.

preCalculus 506 Compounded Interest

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In my Math classes, everything I do at the SmartBoard, including what I say, is recorded in real time! I attach a wireless lapel mic to my SmartBoard PC and run http://screencast-o-matic.com in the background. Screencast-o-matic renders the recording as an MP4 file that I upload to YouTube. SmartNotebook files can be exported to PDF and I upload these files to Slideshare as shown above. Actually, I'm using Xournal on 64bit Ubuntu this year instead of SmartNotebook as there's only a 32bit version for Linux, but the result is the same (I only use SmartNotebook as a pen app anyway).

My Computing classes are a little more keyboard intensive. I still use the lapel mic to record what I say as I type. However, for these classes I'm stuck at my desktop in the back of the room. I use a Bluetooth Wacom Gaphire 6x8 tablet to write on the SmartBoard remotely if need be. TXT files I type for these classes get uploaded to Pastebin as shown above. I also upload new MP4s from Screencast-o-matic for these classes to YouTube.

https://clemix.clemson.edu:34567/home/pub/251

I link all these files to my blog weekly and to Edmodo daily for students that are absent or want to review old topics. However, I do not link files from pastebin or slideshare to Edmodo anymore. I find that doing so just clutters up the Edmodo page for each class (Edmodo looks and feels a lot like Facebook). The result is a huge number of links from the beginning of a unit to the end making it hard to find the first postings when needed. The files on pastebin and slideshare do get linked to my blog on a weekly basis so students have access to written class notes whether it be SmartNotes as PDFs or code as TXTs. BTW, code for Computer Math and Calculus Research Lab is linked from my account on a SAGE server as shown above (CM 4.4 Infinite Series).

Well, that's all folks!

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Friday, November 11, 2011

Quarter II, Week 1: ScreenCasts, SmartNotes and Code, oh my!

AP Calculus BC continued CH5 on Anti Derivatives.
BC 505 Left, Right and Trap Riemann Sums!

Calculus 505 Left, Right, Trap Riemann Sums!

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PreCalculus for Seniors continued CH5 on using Inverse Functions to solve equations analytically and graphically.
PRE 504 Log Rules

preCalculus 504 Log Rules

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PRE 505 Solving Equations using Logs!

preCalculus 505 Solving Log Equations

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AP Computer Science finished Lab 4 so I have nothing new to post. Sorry, I don't post anything to do with Labs, Quizzes or Tests. I only record new material, so I don't post anything to do with Homework Assignments or Review Sheets either!

Computer Math continued Chapter 4 on Sequences and Series.
CM 403 Series
https://clemix.clemson.edu:34567/home/pub/246

Calculus Research Lab continued the odd exercises in 4.10 and started Lab 4.10 (even exercises)!
CRL 410 Differentiation Rules
https://clemix.clemson.edu:34567/home/pub/234

This was a very short week as we had Veteran's Day on Friday and I got sick on Thursday....

HTH and I hope you enjoyed this week's notes!

Learning with Technology,

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Wednesday, November 9, 2011

CIS(theta) 2011-2012 - Install openMPI and Stress the Cluster! - Meeting V

The following is a summary of what we've accomplished so far with the 2011-2012 CIS(theta) team. Our new Shadowfax Cluster is coming along quite well. We have a nice base OS in the 64bit Ubuntu 11.04 Natty Narwhal Desktop on top of our AMD dualcore Athlons and gigE LAN. The Unity Desktop isn't that different from the Gnome Desktop we've been using these past few years on Fedora and Ubuntu. Natty is proving very user friendly and easy to maintain! This week we installed openMPI and we used flops.f to stress our mini 8-core cluster! We needed public keys so openMPI can scatter/gather cluster jobs without the overhead of logging into each node as needed. We created a new user common to all cluster nodes called "jobs" in memory of Steve Jobs. Now, the cluster user can simply log into one node and be logged into all nodes at once (you can actually shh into each node as "jobs" without specifying a userid or passwd)!

InstantCluster Step 1: Infrastructure

Make sure your cores have enough ventilation. The room has to have powerful air conditioning too. These two factors may seem trivial but will become crucial when running the entire cluster for extended periods of time! Also, you need to have enough electrical power, preferably with the cabling out of the way, to run all cores simultaneously. Don't forget to do the same with all your Ethernet cabling. We have CAT6E cables to support our gigE Ethernet cards and switches. We are lucky that this step was taken care of for us already!

InstantCluster Step 2: Hardware

You need up to date Ethernet switches plus Ethernet cards and cores as well as plenty of RAM in each Linux box. As stated above, our gigE LAN and switches were already setup for us. Also, we have 64bit dual-core AMD Athlons and our HP boxes have 2GB of RAM. We are still waiting for our quad-core AMD Phenom upgrade!

InstantCluster Step 3: Firmware

We wasted way too much time two years ago (2009-2010 CIS(theta)) trying out all kinds of Linux distros looking for a good 64bit base for our cluster. Last year (2010-2011 CIS(theta)) we spent way too much time testing out different liveCD distros. Last year, we also downgraded from 64bit Ubuntu 10.04 Desktop edition to the 32bit version on our Linux partitions. 64bit gives us access to more RAM and a larger maxint, but was proving to be a pain to maintain. Just to name one problem, jre and flash were hard to install and update on FireFox. Two years ago, we tried Fedora, Rocks, Oscar, CentOS, Scientific Linux and, finally, Ubuntu. We've done this several times over the years using everything from Slakware and KNOPPIX to Fedora and Ubuntu! This year, 64bit Ubuntu has proven very easy to use and maintain, so I think we'll stick with it for the cluster!

InstantCluster Step 4: Software Stack I

On top of Ubuntu we need to add openSSH, public-key authentication (step 4) and openMPI (step 5). Then we have to scale the cluster (step 6). In steps 7-10, we can discuss several applications to scatter/gather over the cluster whether it be graphical (fractals, povray, blender, openGL, animations) or number crunching (C++ or python app for Mersenne Primes or Beal's Conjecture). So, what follows is a summary of what we did to get up to plublic-key authentication. This summary is based on the http://cs.calvin.edu/curriculum/cs/374/MPI/ link listed below. First, we installed openSSH-server from http://packages.ubuntu.com, then:

If you have no .ssh directory in your home directory, ssh to some other machine in the lab; then Ctrl-d to close the connection, creating .ssh and some related files.
From your home directory, make .ssh secure by entering:
```
chmod 700 .ssh
```
Next, make .ssh your working directory by entering:
```
cd .ssh
```
To list/view the contents of the directory, enter:
```
ls -a [we used ls -l]
```
To generate your public and private keys, enter:
```
ssh-keygen -t rsa
```
The first prompt is for the name of the file in which your private key will be stored; press Enter to accept the default name (id_rsa).The next two prompts are for the password you want, and since we are trying to avoid entering passwords, just press Enter at both prompts, returning you to the system prompt.
To compare the previous output of ls and see what new files have been created, enter:
```
ls -a [we used ls -l]
```
You should see id_rsa containing your private key, and id_rsa.pub containing your public key.

To make your public key the only thing needed for you to ssh to a different machine, enter:

cat id_rsa.pub >> authorized_keys

[The Linux boxes on our LAN, soon to be cluster, have IPs ranging from 10.5.129.1 to

10.5.129.24 So, we copied each id_rsa.pub file to temp01-temp24 and uploaded these

files via ssh to the teacher station. Then we just ran cat tempnn >> authorized_keys

for each temp file to generate one master authorized_keys file for all nodes that we could

just download to each node's .ssh dir.]

[optional] To make it so that only you can read or write the file containing your private key, enter:

chmod 600 id_rsa [optional] To make it so that only you can read or write the file containing your authorized keys, enter: chmod 600 authorized_keys

InstantCluster Step 5: Software Stack II

We then installed openMPI (we had a lot less dependencies this year with Natty 11.04 64bit) and tested multi-core with flops. Testing the cluster as a whole will have to wait until the next meeting when we scale the cluster! We followed openMPI install instructions for Ubuntu from http://www.cs.ucsb.edu/~hnielsen/cs140/openmpi-install.html

These instructions say to use sudo and run run apt-get install openmpi-bin openmpi-doc libopenmpi-dev However, the way our firewall is setup at school, I can never update my apt-get sources files properly. So, I used http://packages.ubunutu.com and installed openmpi-bin, gfortran and libopenmpi-dev. That's it!



Then we used the following FORTRAN code to test multi-core. FORTRAN, really? I haven't used FORTRAN77 since 1979! ...believe it or don't!

We compiled flops.f on the Master Node (any node can be a master):
mpif77 -o flops flops.f


and tested openmpi and got just under 800 MFLOPS using 2 cores (one PC):
mpirun -np 2 flops


Next, we generated a "machines" file to tell mpirun where all the nodes (Master and Workers) are (2 PCs or nodes with 2 cores each for example):
mpirun -np 4 --hostfile machines flops



Every node has the same "machines" text file in /home/jobslisting all the IPs, one per line. Every node has the same "flops" executable file (or whatever your executable will be) in /home/jobs. Every node has the same "authorized_keys" text file with all 25 keys in /home/jobs/.ssh

Note: last year we got about 900 MFLOPS per node. This year we still have 64bit AMD athlon dualcore processors. However, these are new PCs, so these athlons have slightly different specs. Also, last year we were running Maverick 10.04 32bit ... and ... these new PCs were supposed to be quadcores! We are still awaiting shipment.

===================================================

What we are researching III 
(look at some clustering environments we've used in the past):
We used PVM PVMPOV in the 1990s.
http://www.csm.ornl.gov/pvm
http://pvmpov.sourceforge.net
openMOSIX and kandel were fun in the 2000s.




http://openmosix.sourceforge.net/instant_openmosix_clusters.html
https://zworykin.elec.uow.edu.au/~daniel/Projects/Software/kandel
Let's try out openMPI and Blender now!




http://www.open-mpi.org
http://www.blender.org



===================================================
What we are researching II 
(look what other people are doing with MPI):
MPI intro, nice!
http://www.ualberta.ca/CNS/RESEARCH/Courses/2001/PPandV/Intro_to_MPI.pdf
MPI on Ubuntu
   http://ubuntuforums.org/showthread.php?t=1327253
Sample MPI code
   http://www.cc.gatech.edu/projects/ihpcl/mpi.html   ===================================================
What we are researching I 
(look what this school did in the 80s and 90s): 
Thomas Jefferson High courses
http://academics.tjhsst.edu/compsci/parallel/
Thomas Jefferson High paper
http://www.tjhsst.edu/~rlatimer/techlab07/BWardPaperQ3-07.pdf
Thomas Jefferson High ftp
http://www.tjhsst.edu/~rlatimer/techlab07/
Thomas Jefferson High teacher
http://www.tjhsst.edu/~rlatimer/   ===================================================
Today's Topic:
CIS(theta) 2011-2012 - Install openMPI and Stress the Cluster! - Meeting V
Today's Attendance:
CIS(theta) 2011-2012: GeorgeA, GrahamS, KennyK, LucasE
Today's Reading:
Chapter 3 Building Parallel Programs (BPP) using clusters and parallelJava   ===================================================
Well, that's all folks, enjoy!
Happy Clustering,
calcpage@aol.com
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Saturday, November 5, 2011

School Week 9: ScreenCasts, SmartNotes and Code, oh my!

AP Computer Science finished CH4 this past week and we started Lab 4. We are going at a really good pace. I think we should have plenty of time for review before the AP Exam! We are going to do CH5 Conditional Expressions and Predicates as well as CH6 Loops before we start the GridWorld CaseStudy. BTW, we are working through the text faster than last year as I'm not giving written unit tests... yet.
APCS Chapter 4 Exercise 4 Pair.java

APCS Chapter 4 Exercise 5 DataSet.java

Computer Math started Chapter 4 on Sequences and Series. We also had contract day yesterday where we decided who is taking this class for Honors credit and who is taking this class for Regents credit. Remember, Honors students complete all Lab Exercises. Regents students need only complete half those problems in the same time frame.
CM 402 Sequences
https://clemix.clemson.edu:34567/home/pub/232

Calculus Research Lab started Chapter 4 about General Differentiation Rules! We focused on the Product, Quotient, Power and Chain Rules. We just started the odd exercises in 4.10 and will start Lab 4.10 (even exercises) soon!
CRL 401 General Rules
https://clemix.clemson.edu:34567/home/pub/233
CRL 410 Odd Exercises
https://clemix.clemson.edu:34567/home/pub/234

AP Calculus BC had a MCQ Monday last week. We tried 2003 AB Part IB which is Graphing Calculator active. Then we started CH5 on Anti Derivatives. BTW, we just got a new eText for Calculus! We've been using DWFT since the 1st edition in 1995. Now we have the 6th edition on http://csps.coursesmart.com Only preCalc has a traditional text. We have to work on that.
BC 501 Anti Derivatives

Calculus 501 Anti Differentiation

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BC 502 Differential Equations

Calculus 502 Differential Equations

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BC 503 Riemann Sums I

Calculus 503 Riemann Sums!

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BC 504 Riemann Sums II

Calculus 504 more Riemann Sums?

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PreCalculus for Seniors started CH5 on using Inverse Functions to solve equations analytically and graphically. We focused on exponential vs. logarithmic functions.
PRE 501 Inverse Functions

preCalculus 501 Inverse Functions

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PRE 502 Exponential Functions

PreCalculus 502 Exponential Functions

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PRE 503 Logarithmic Functions

PreCalculus 503 Logarithms

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No, say it ain't so! Quarter I just ended yesterday? OMG, I can't believe we're starting Quarter II this coming Monday! Wow, here's to a great start to the year.

HTH, I hope you enjoyed this week's notes!

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Friday, November 4, 2011

Math YouTube Wednesdays are back!

I tried TED.com Tuesdays for a while, but I really missed my good old YouTube Wednesdays! So, just for fun, I thought I'd share some of my most recent YouTubes. On these Wednesdays, I try to show different YouTubes in Math class as opposed to Computing classes. I have 2 sections of preCalculus for Seniors and 1 section of AP Calculus BC. What follows are YouTubes I've been sharing with those classes. In fact, we managed a theme of "Tom Lehrer" related videos though out the entire 1st Quarter of this school year! We started with "Mathematicious," but then we went right into Lehrer filks such as: "The New Math," "Lobachevsky," "Santa Monica" (since it was Roshashana), and "The Elements!"