## Friday, February 17, 2012

### Quarter III, Week 3: ScreenCasts, SmartNotes and Code, oh my!

This was the last week before February Break! AP Calculus BC enjoyed their first BC MCQ Monday exam (2003 BC IA). There was no TED Tuesday this week. I'm such a slave driver! We had our last Grace Hopper related YouTube Wednesday. We had an informal Think-a-lot Thursday reviewing Completing the Square and graphing Conic Sections from Standard Form Equations for my preCalculus for Seniors Quiz on FRQ Friday! Note: Not every Monday is an MCQ Monday, not every Tuesday is a TED Tuesday, not every Wednesday is a YouTube Wednesday, not every Thursday is a Think-a-lot Thursday and not every Friday is a FRQ Friday. Gotta switch it up sometimes!

AP Calculus BC continued Chapter 8 on integration techniques. We also had our first BC MCQ (2003 BC IA).

BC Calc 0809 Partial Fractions!

BC Calc 0811 Solving DiffEqus Graphically and Numerically: Slope Fields!

preCalculus for Seniors started Chapter 10 on Conic Section.

preCalc 10-02 Parabolas

preCalc 10-03 + 10-04 Ellipses and Hyperbolas

AP Computer Science continued CH8/EX7 on arrays and ArrayLists! We wrote the DataSet class using static arrays. What follows is the final product. Please view C7X8 and C7X8a on my YouTube Channel, Calcpage2009, as well!
C7X8 - C7X8b AltSum.java Calculus Research Lab continued our new anti-derivatives eText!

CRL 1.1 Reimann Sums Intro
https://sage.math.clemson.edu:34567/home/pub/285

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

Learning with Technology,

## Friday, February 10, 2012

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

OOPs, almost forgot to post last week's materials, sorry! Let's see, AP Calculus BC had a post MCQ Monday. I had a TED Tuesday about 3D Printers of all things! Since it was my BDay, I also had to have a YouTube Wednesday with Grace Hopper on David Letterman. We had a CML Thursday in AP Calculus BC. Last, but not least, we had a FRQ Friday in preCalculus for Seniors!

AP Calculus BC started off the week going over the last MCQ Monday (1997 AB IB). We continued with some advanced integration techniques (Integration By Parts and Trig Sub). We also had the second Meet for the Continental Mathematics League Calculus Division on Thursday.

BC Calc 805 Integration By Parts I

BC Calc 806 Integration By Parts II

BC Calc 807 Integrating powers of sin(x) and cos(x)

BC Calc 808 Trig Sub

preCalculus for Seniors finished Chapter 8 with harmonic Motion, Trig Regression and a test.

preCalc 805 Harmonic Motion

AP Computer Science continued CH8/EX7 on arrays and ArrayLists! We wrote the Purse class using ArrayList. Below, you will find the finished product. Please see C7X2, C7X2a, C7X2b, C7X2c and C7X2d for all 6 screencasts!
C7X2 - C7X2e Purse.java
Calculus Research Lab continued our new anti-derivatives eText!

CRL 1.1 Reimann Sums Intro
https://sage.math.clemson.edu:34567/home/pub/285

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

Learning with Technology,

## Thursday, February 9, 2012

### CIS(theta) 2011-2012 - Scaling the Cluster! - Meeting IX

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! We installed openMPI and we used flops.f to scale our cluster up to 50 cores! Remember, we needed openSSH public keys so openMPI can scatter/gather cluster jobs without the overhead of logging into each node as needed. We created a user common to all cluster nodes called "jobs" in memory of Steve Jobs so the cluster user can simply log into one node and be logged into all nodes at once (you can actually ssh 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 (Meeting III)
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 (Meeting IV)
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:
1. 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.
2. From your home directory, make .ssh secure by entering:
`chmod 700 .ssh`
3. Next, make .ssh your working directory by entering:
`cd .ssh`
4. To list/view the contents of the directory, enter:
`ls -a [we used ls -l]`
5. 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.
6. 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.
7. 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.]`
8. [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 (Meeting V)`
`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.htmlThese 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.fand tested openmpi and got just under 800 MFLOPS using 2 cores (one PC):mpirun -np 2 flopsNext, 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 flopsEvery node has the same "machines" text file in /home/jobs listing 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.`
`InstantCluster Step 6: Scaling the cluster`
`UPDATE: 2011.1126 (Meeting VI)`
`Including myself, we only had 3 members attending this week. So, we added 3 new nodes. We had nodes 21-24 working well last time. Now we have nodes 19-25 for a total of 7 nodes, 14 cores and over 5 GFLOPS! This is how we streamlined the process: `
`(1) adduser jobs and login as jobs `
`(2) goto http://packages.ubuntu.com and install openssh-server from the natty repository `
`(3) create /home/jobs/.ssh dir and cd there `
`(4) run ssh-keygen -t rsa `
`(5) add new public keys to /home/jobs/.ssh/authenticated_keys to all nodes `
`(6) add new IPs to /home/jobs/machines to all nodes`
`(7) goto http://packages.ubuntu.com and install openmpi-bin, gfortran and libopenmpi-devfrom the natty repository`
`(8) download flops.f to /home/jobs from our ftpsite compile and run: `
`mpif77 -o flops flops.f and `
`mpirun -np 2 flops or `
`mpirun -np 4 --hostfile machines flops `
`NB: since we are using the same hardware, firmware and compiler everywhere, we don't need to recompile flops.f on every box, just copy flops from another node!`
`(9) The secret is setting up each node identically:`
`/home/jobs/flops`
`/home/jobs/machines`
`/home/jobs/.ssh/authenticated_keys`
```
```
```
```
`UPDATE: 2011.1214 (Meeting VII)`
`We had 5 members slaving away today. Nodes 19-25 were running at about 5 GFLOPS last meeting. Today we added nodes 10, 11, 12, 17 and 18. However, we ran into some errors when testing more than the 14 cores we had last time. We should now have 24 cores and nearly 10 GFLOPS but that will have to wait until next time when we debug everything again....`
`UPDATE: 2012.0111 (Meeting VIII)`
`We found that some nodes did not have gfortran installed and many of the authorized_keys files were in consistent. So, we made sure every node had a user called jobs. Then we made sure we installed openssh-server, openmpi-bin, openmpi-doc (optional), libopenmpi-dev and gfortran installed. We generated all the public ssh keys and copied then over to one master authorized_keys file on shadowfax using ssh. Then we copied the master file back to each node over ssh to /home/jobs/.ssh and we tested everything with flops, and then I wrote this on FB:`
###### Eureka, success! By Jove I think we've done it! I give you joy, gentlemen! After you guys left, I was still trying to find the bottleneck in the cluster network. So, I just ran "mpirun -np 2 flops" on each box without the ---hostfile machines. Guess, what I found: all the cores ran at about 388 MFLOPS except the 2 cores in PC12. These cores were only running half that speed, about 194 MFLOPS each. So, all I had to do was delete the PC12 line from the machines file on the Master Node and run "mpirun -np 48 --hostfile machines flops" and every core ran over 300 MFLOPS! What's weird is is that when I ran "mpirun -np 2 flops" on any PC other that PC12, the cores would always yield over 380 MFLOPS no matter how many times I tried it. However, when running "mpirun -np 48 --hostfile machines flops" the yield varied greatly. Each core ran somewhere between 310 and 410 MFLOPS. I ran this several times as well. I'd say I got a mean of about 15.5 GFLOPS with a standard deviation of 2.25 GFLOPS. In other words, a typical run would fall in the range of 13.25 to 17.75 GFLOPS. What's even weirder is that the pelicanHPC liveCD ran all 50 cores last week at nearly 20 GFLOPS with each core running more than 350 MFLOPS. What's up with that? So, we are back on track. We got the cluster fully operational before midterms! Our next meeting (2/8/12) will be about what applications we can run over openMPI. You each should google for beginners' projects using mpicc, mpiCC, mpif77 or mpif90 and maybe even mpi4py. Simple number crunching or graphics would do! Maybe I'll also show you how pelicanHPC liveCD can PXE boot the whole room into an openMPI cluster in 5-10 minutes!
`UPDATE: 2012.0209 (Meeting IX)`
`(1) While testing the cluster, we got up to 32 cores and 12 GFLOPS. Anything more than 16 nodes had very power efficiency (the more cores we added, the less GFLOPS we got)! We will need to isolate the bottle necks. We isolated node #12, but there must be more. Is it the Ethernet cards or cables? Do we have defective cores? Did we install some nodes inconsistently?`
`(2) There are recruiting screencasts for CSH, CSAP and CRL, but none for CIS? So, we made one:`
`http://shadowfaxrant.blogspot.com/2012/01/cis-computing-independent-study.html`
`(3) Then we booted the whole room in about 5 minutes using the pelicanHPC liveCD. We got up to 48 cores and 18 GFLOPS. This tells us that probably not the cores or the Ethernet causing problems. We may have to reinstall a couple of nodes.`
` `
`===================================================`
What we are researching VI (Feb)
(let's learn from other's MPI code!):
pelicanHPC liveCD
BCCD liveCD
NVidia's CUDA and GPUs?
`===================================================`
```What we are researching V (Jan)(we used to use the BCCD liveCD, look at their openMPI code):HelloWorldhttp://bccd.net/wiki/index.php/Hello_World_for_MPI
Conway's 2D Game of Lifehttp://bccd.net/wiki/index.php/Game_of_Life
N-Body Orbitshttp://bccd.net/wiki/index.php/GalaxSee
Code

http://bccd-ng.cluster.earlham.edu/svn/bccd-ng/tags/bccd-3.1/trees/home/bccd/```
`===================================================`
```What we are researching IV (Dec)(maybe we can use Python on our MPI cluster?):MPI4pyhttp://blog.mikael.johanssons.org/archive/2008/05/parallell-and-cluster-mpi4py/Parallel Pythonhttp://www.parallelpython.com/IPythonhttp://ipython.scipy.org/moin/

===================================================```
```What we are researching III (Nov)(look at some clustering environments we've used in the past):We used PVM PVMPOV in the 1990s.http://www.csm.ornl.gov/pvmhttp://pvmpov.sourceforge.netopenMOSIX and kandel were fun in the 2000s.http://openmosix.sourceforge.net/instant_openmosix_clusters.htmlhttps://zworykin.elec.uow.edu.au/~daniel/Projects/Software/kandelLet's try out openMPI and Blender now!http://www.open-mpi.orghttp://www.blender.org

===================================================What we are researching II (Oct)(look what other people are doing with MPI):MPI intro, nice!http://www.ualberta.ca/CNS/RESEARCH/Courses/2001/PPandV/Intro_to_MPI.pdfMPI on Ubuntuhttp://ubuntuforums.org/showthread.php?t=1327253Sample MPI codehttp://www.cc.gatech.edu/projects/ihpcl/mpi.html

===================================================What we are researching I (Sept)(look what this school did in the 80s and 90s): Thomas Jefferson High courseshttp://academics.tjhsst.edu/compsci/parallel/Thomas Jefferson High paperhttp://www.tjhsst.edu/~rlatimer/techlab07/BWardPaperQ3-07.pdfThomas Jefferson High ftphttp://www.tjhsst.edu/~rlatimer/techlab07/Thomas Jefferson High teacherhttp://www.tjhsst.edu/~rlatimer/

===================================================Today's Topic:CIS(theta) 2011-2012 - Scaling the Cluster! - MeetingIXToday's Attendance:CIS(theta) 2011-2012: GeorgeA, GrahamS, KennyK, LucasE; CIS(theta) Today's Reading:Chapter 6: Building Parallel Programs (BPP) using clusters and parallelJava

===================================================Well, that's all folks, enjoy!Happy Clustering,calcpage@aol.comhttp://shop.ebay.com/items/_ti_calculator_activehttp://mathforum.org/kb/profile.jspa?userID=32552```

## Saturday, February 4, 2012

### CSH: Computer Science Honors Recruiting Office!

Welcome to Computing at Baldwin Senior High School! My name is Mr. Garcia. I teach in the Math Department at good old BSHS. I'm here today to encourage you to take Computer Science Honors aka CSH.

CSH is a new course I've been teaching since 1975 replacing Computer Math and Advanced Computer Math. How is that possible, you ask? Well, CSH is an introduction to programming and I've been teaching people how to program ever since I learned how. What's new about this course is that we just started using Python as our programming language of choice. We also just started using a new textbook about Discerete Mathematics using Python, http://www.skylit.com/mathandpython.html, pictured above. BTW, all your work is stored online and we use an eText, so you don't even have to bring anything to class!

Also, the first thing you'll notice is that I don't do Windows, and neither does my maid! We are currently using the 64bit Ubuntu 11.04 Linux Desktop which is a rock solid, programmer friendly system designed with network security, multitasking, multiprocessing and multiuser support built-in from the ground up. Please see the video above and sign-up sheet below:

## Friday, February 3, 2012

### APCS: AP Computer Science Recruiting Office!

Welcome to Computing at Baldwin Senior High School! My name is Mr. Garcia. I teach in the Math Department at good old BSHS. I'm here today to encourage you to take AP Computer Science aka APCS.

APCS is a fun course I've been teaching since the CollegeBoard introduced it in 1984. APCS is an extension of CSH where we use the Java programming language as a vehicle to learn about Object Oriented Programming which is all the rage these days! Programming with Objects makes it very easy to do lots of Number Crunching and Graphics! We use a great textbook by Cay Horstmann, a world reknown expert in Java, http://horstmann.com/bigjava.html, pictured above. BTW, all your work is stored online and we use an eText, so you don't even have to bring anything to class!

Also, the first thing you'll notice is that I don't do Windows, and neither does my maid! We are currently using the 64bit Ubuntu 11.04 Linux Desktop which is a rock solid, programmer friendly system designed with network security, multitasking, multiprocessing and multiuser support built-in from the ground up. Please see the video above and sign-up sheet below:

Generally Speaking,

## Thursday, February 2, 2012

### CRL: Calculus Research Lab Recruiting Office!

Welcome to Computing at Baldwin Senior High School! My name is Mr. Garcia. I teach in the Math Department at good old BSHS. I'm here today to encourage you to take Calculus Research Lab aka CRL.

CRL is meant to enhance your experience in AP Calculus. We meet every other day like a Science Lab. We use a Python based Computer Algebra System called SAGE, http://sagemath.org, to investigate problems symbolically.  We use a Super Computer, http://www.sagenb.org, at the University of Washington setup for our use. BTW, all your work is stored online and we use an eText, so you don't even have to bring anything to class!

Also, the first thing you'll notice is that I don't do Windows, and neither does my maid! We are currently using the 64bit Ubuntu 11.04 Linux Desktop which is a rock solid, programmer friendly system designed with network security, multitasking, multiprocessing and multiuser support built-in from the ground up. Please see the video above and sign-up sheet below:

Generally Speaking,

## Wednesday, February 1, 2012

### CIS: Computing Independent Study Recruiting Office!

Welcome to Computing at Baldwin Senior High School! My name is Mr. Garcia. I teach in the Math Department at good old BSHS. I'm here today to encourage you to take Computing Independent Study aka CIS.

CIS is an independent study class that meets every other Wednesday after school like a club. We build, test, maintain and program a Super Computer of our own design. Some have described this course as: "the care and feeding of a linux cluster!" We use openMPI, http://www.open-mpi.org, to link all the 50 cores in Room 429 as one massive computer or Linux Cluster. Several programming languages and environments are useful here: Fortran, C, C++, Java, Python, POV-Ray, Blender. What we do is a lot like PelicanHPC, http://www.pelicanhpc.org, and Bootable Cluster CD, http://www.bccd.net. BTW, all your work is stored online and we use an eText, so you don't even have to bring anything to class!

Also, the first thing you'll notice is that I don't do Windows, and neither does my maid! We are currently using the 64bit Ubuntu 11.04 Linux Desktop which is a rock solid, programmer friendly system designed with network security, multitasking, multiprocessing and multiuser support built-in from the ground up. Please see the video above and sign-up sheet below:

Generally Speaking,