Presentation
Project Final Catastasis (Group 5)
Lisa Gentry Molly Meyer Anthony Morton Daniel O'Neil
26 APR 05
catastasis
(n.)
1. The intensified part of the action directly preceding the catastrophe in classical tragedy. 2. The climax of a drama. - Dictionary.com
(So in retrospect, this was a bad, prophetic thing to name our group... oops.)
Design Use Case and Goals
Handheld device intended to be carried by emergency responders This means:
Small database (2 MB) Ability to communicate results Minimal hardware additions Wireless transmission of results back to emergency response dispatch center
Intended addition to project
Final System Architecture
Audio
A/D
receive_am_fdm
3
Hardware Handshake
neighbor_words b62_score Hardware Handshake 5
nuc2aa
FPGA
DSP
AVR
Terminal Driver Serialization for TNC
7
extend_hit find_hsps find_seeds 8 Memory Controller
ARM
TNC
FSK
8 21 Audio Bank0
(4 Mbit)
NIOS Proc.
Bank1
(4 Mbit)
Bank2
(4 Mbit)
Bank3
(4 Mbit)
Flash
DSP Voodoo
Filtering is easy as a concept, but... Finding threshold values is Hell
(But yes, this code works consistently...)
BLOSUM62 Architecture
AA Shift Register
1024:1 Lookup Table
1024:1 Lookup Table
1024:1 Lookup Table
Amino Acid from DSP
...
...
...
+
AA Iterator
b62 Score to Comparator
Neighbor Words ARM
Potential for timing nightmare here is huge
If ARM doesn't read fast enough, have to interlock (or mask through buffers) the entire hardware behind the ARM handshake Two handshakes, queue loading, amino acid iteration, seed collection
Custom hardware has 5 FSMs!
Dozens and dozens of control lines and flags
BLOSUM62 FPGA usage
lookup_table (one B62 table)
0/8,320 logic elements (0% ) 4,096/106,496 memory bits (3.8%)
top_blosum
309/8,320 logic elements (3%) 13,248/106,496 memory bits (12%)
BLOSUM62 Runtime
Timing requirements
Longest delay 21.874 ns Max clock frequency 45.72 MHz
Estimated runtime of example
Analysis of 3 character Amino Acid sequence
3
* 21^3 + 4 = # of clock cycles [3 * 21^3 + 4] * 21.874 ns = 0.6078 ms per seed Independent of number of neighbor words for seed because they're sent while 21^3 iterations are running
Memory
Many groups opted to use Compact Flash storage to put entire database on "chip"
Required knowledge of FAT Required more complicated hardware Constructed a 2MB array of Atmel Flash chips Able to order chips from DigiKey quickly
But, we wanted a simpler option...
What Analog Realities?
Everyone expressed concerns that our rat's nest of wires and flash chips might not work
Who could blame them? Turns out limitations of flash chips were hit long before limitations of our wiring
Packet Radio TNC
Takes input from terminal ATmega8 TNC ATmega8 programmed to handle packet assembly and transmission
Encode data with audio frequency shift keying Send data packets using AX.25 protocol to handheld transceiver
System Performance
So, how long does all of this take?
We don't know yet...
Review of our design metric from DR#1:
I: Virus correctly identified II: Identification transmitted wirelessly to receiving computer, results printed
(Vote) Yes on I, No on II
The Soda Can Conspiracy...
On the day of the second demo, very, very early in the morning Team Catastasis sat at the bench and stared bleakly at their growing collection of soda cans. As the group consumed approximately 1 soda per person every three hours the set of ten to fifteen soda cans currently sitting on the bench was very sad indeed Additionally, at the current rate of growth the collection seemed to be on track to take over the entire lab bench in a few hours What to do? What to do?
Soda Can Conspiracy, cont.
Then suddenly a flash of insight (aided by the amount of caffeine consumed by the group) gave them a solution to their problem A Monumental Work of Art would be constructed from all of the soda cans:
A great pyramid, where Lisa and Molly's Diet Pepsi cans would constitute the bulk of the pyramid with an inlaid design consisting of Daniel's Mountain Dew cans
Armed with this new insight the group quickly got back to work and continued to build up their supply of cans
Soda Can Conspiracy...Revealed!
The next day, having gotten a little sleep, the group came back into the lab expecting to construct their structure However, only the Mountain Dew cans remained! Where were the Diet Pepsi cans?! What nefarious had plot removed them (and only them), and thus prevented the creation of the Monumental Work of Art? The group may never know...
Lisa's Lessons Learned
All things are better when powered Just because Quartus says it works doesn't mean it works Compared to the DSP documentation, Quartus's documentation is very user friendly Many things can be powered by a single serial port
A Late-Night Mystery
It was the middle of the night. Molly was battling the DSP and had been all day. Filtering worked for DaqGen signals. She added a bunch of code for marker wave delimiting to her working code, but it was all commented out. For sanity's sake, she tried to re-run the code to make sure it hadn't changed When she typed the load command, DSK3DW closed abruptly. Power-cycling the board didn't fix it But what was going on? How could comments destroy the loadability of a program??
A Late-Night Mystery, cont.
Molly tried commenting out everything but basic echo functionality. The program still would not load Then she tried deleting all the comments. This time, the program loaded and ran perfectly She added the comments back in and tried every method of commenting allowed in C. Nothing would make the file load in DSK3DW And then, she figured it out...
The Answer!
The DSK3DW has a columns limit! If any line in the .c file exceeds a certain number of characters, the .out file will bring DSK3DW to its knees No idea why this would be, but there you have it!
The Moral is...
When working with hardware you don't know very well and for which you don't have much documentation...
ASSUME NOTHING!!!
Solder-ific
Started working on the DSP, but switched to the TNC and wireless transmission Got to have the fun soldering part of the project
Anthony's Lessons Learned
Nothing is as easy as it seems Being the only person at CMU without Internet access at home really sucks The ATmega8 can operate at up to -30 degrees Celsius on balloon flights!
Pin Compatible, Right?
Not having to deal with Compact Flash seemed like the right call
After all, the 4Mbit chips seemed like they should be pretty much the same as the 2Mbit ones we'd been issued Knowing what to connect where was pretty important, though
What's this? The datasheet only has pin-outs for surface mount parts??
Atmel.com, c. 2000 A.D.
After an hour or so of fruitless poking on atmel.com, it became clear to me that this part I wanted to order had been thoroughly disavowed
But how could I find an old version of the data sheet? archive.org, of course!
Morals of the story:
Nobody uses discreet flash or DIPs anymore Always make sure you have documentation before ...