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I got a TQFP breakout board, soldered up a 2560 to it and all the headers.  I tried to setup basically a breadboard 2560.  Now the problem I am running into is the following whenever I try to do anything, what am I missing?  Thanks!

Code:
avrdude: Version 5.11, compiled on Sep  7 2011 at 19:34:16
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/usr/share/arduino/hardware/tools/avrdude.conf"
         User configuration file is "/home/matcat/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM0
         Using Programmer              : stk500v1
         Overriding Baud Rate          : 19200
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
         AVR Part                      : ATMEGA2560
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           flash         65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : STK500
         Description     : Atmel STK500 Version 1.x firmware
avrdude: Send: A [41] . [80]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [02]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [98]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
         Hardware Version: 2
         Firmware Version: 1.18
         Topcard         : Unknown
avrdude: Send: A [41] . [84]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [85]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [86]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [87]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [89]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
         Vtarget         : 0.0 V
         Varef           : 0.0 V
         Oscillator      : Off
         SCK period      : 0.1 us

avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: B [42] . [00] . [00] . [00] . [01] . [01] . [01] . [01] . [03] . [00] . [00] . [00] . [00] . [01] . [00] . [10] . [00] . [00] . [04] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: E [45] . [05] . [08] . [d7] . [a0] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: P [50]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: AVR device initialized and ready to accept instructions

Reading | avrdude: Send: V [56] 0 [30] . [00] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: V [56] 0 [30] . [00] . [01] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
################avrdude: Send: V [56] 0 [30] . [00] . [02] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
################################## | 100% 0.03s

avrdude: Device signature = 0x000000
avrdude: Yikes!  Invalid device signature.
         Double check connections and try again, or use -F to override
         this check.

avrdude: Send: Q [51]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]

avrdude done.  Thank you.
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A device signature of zero usually indicates a wiring problem, or that you have already programmed the fuses to use crystal oscillator but you have no crystal connected or the wrong capacitors connected.
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I see... assuming wiring is correct... Will having the crystal and caps on breadboard connected with jumpers be a problem with capacitance possibly?
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Ok I double checked my wiring and indeed I had the wiring wrong!  I wired it correctly and this time I get a proper device sig, and was able to set fuse bits for 16MHz crystal... however now when I try to upload a sketch:

Code:
avrdude: Version 5.11, compiled on Sep  7 2011 at 19:34:16
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/usr/share/arduino/hardware/tools/avrdude.conf"
         User configuration file is "/home/matcat/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM0
         Using Programmer              : stk500v1
         Overriding Baud Rate          : 19200
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
         AVR Part                      : ATMEGA2560
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           flash         65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : STK500
         Description     : Atmel STK500 Version 1.x firmware
avrdude: Send: A [41] . [80]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [02]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [98]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
         Hardware Version: 2
         Firmware Version: 1.18
         Topcard         : Unknown
avrdude: Send: A [41] . [84]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [85]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [86]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [87]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [89]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
         Vtarget         : 0.0 V
         Varef           : 0.0 V
         Oscillator      : Off
         SCK period      : 0.1 us

avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: B [42] . [00] . [00] . [00] . [01] . [01] . [01] . [01] . [03] . [00] . [00] . [00] . [00] . [01] . [00] . [10] . [00] . [00] . [04] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: E [45] . [05] . [08] . [d7] . [a0] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: P [50]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: AVR device initialized and ready to accept instructions

Reading | avrdude: Send: V [56] 0 [30] . [00] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [1e]
avrdude: Recv: . [10]
avrdude: Send: V [56] 0 [30] . [00] . [01] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [98]
avrdude: Recv: . [10]
################avrdude: Send: V [56] 0 [30] . [00] . [02] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
################################## | 100% 0.03s

avrdude: Device signature = 0x1e9801
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed
         To disable this feature, specify the -D option.
avrdude: Send: V [56] . [a0] . [0f] . [fc] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [ff]
avrdude: Recv: . [10]
avrdude: Send: V [56] . [a0] . [0f] . [fd] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [ff]
avrdude: Recv: . [10]
avrdude: Send: V [56] . [a0] . [0f] . [fe] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [ff]
avrdude: Recv: . [10]
avrdude: Send: V [56] . [a0] . [0f] . [ff] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [ff]
avrdude: Recv: . [10]
avrdude: erasing chip
avrdude: Send: V [56] . [ac] . [80] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: B [42] . [00] . [00] . [00] . [01] . [01] . [01] . [01] . [03] . [00] . [00] . [00] . [00] . [01] . [00] . [10] . [00] . [00] . [04] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: E [45] . [05] . [08] . [d7] . [a0] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: P [50]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: reading input file "/tmp/build3473976189903959033.tmp/Blink.cpp.hex"
avrdude: writing flash (1632 bytes):

Writing | avrdude: Send: U [55] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: d [64] . [01] . (Cut this line off so msg would fit)
avrdude: ser_recv(): programmer is not responding
avrdude: stk500_recv(): programmer is not responding
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How exactly are you trying to upload your sketch? Are you still using the Arduino as ISP and using the "Upload using programmer" menu option, or something different?
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Yes uploading using ISP.
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Does this version of AruinoISP make any difference...
http://arduino.cc/forum/index.php/topic,108797.msg824488.html#msg824488
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Does this version of AruinoISP make any difference...
http://arduino.cc/forum/index.php/topic,108797.msg824488.html#msg824488

I will try it when I get home!  At work now.
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Does this version of AruinoISP make any difference...
http://arduino.cc/forum/index.php/topic,108797.msg824488.html#msg824488

IT does seem to upload a sketch now but it seems the sketch isn't running... I tried blink sketch on a few different digital pins and nothing is happening... quite odd, picked up odd voltages too off the pins, from like .5v, or 1.25v, doesn't make any sense!  And I am tripple checking my connections...
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Add series resistors to everything (Vcc, MISO, MOSI, SCK).  220 ohms or higher (1K seems to be commonly used).  The resistors will protect both sides in case you make a wiring mistake.
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quite odd, picked up odd voltages too off the pins, from like .5v, or 1.25v
That sounds like you didn't set the pins as outputs, or you are looking at the wrong pins.

Post your sketch, and check this for analog/digitlal name to physical pin mapping
http://arduino.cc/en/Hacking/PinMapping2560
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Designing & building electrical circuits for over 25 years. Check out the ATMega1284P based Bobuino and other '328P & '1284P creations & offerings at  www.crossroadsfencing.com/BobuinoRev17.
Arduino for Teens available at Amazon.com.

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quite odd, picked up odd voltages too off the pins, from like .5v, or 1.25v
That sounds like you didn't set the pins as outputs, or you are looking at the wrong pins.

Post your sketch, and check this for analog/digitlal name to physical pin mapping
http://arduino.cc/en/Hacking/PinMapping2560
Yeah that is the pin mapping I am following...  I will check on it tonight, use my DSO Nano to figure out what's going on.

Could it simply be that the Arduino UNO as an ISP just isn't programming it properly?  I know I read something about 128k flash limit or something...
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Are you using NickGammon's programming sketch, or something else?
http://www.gammon.com.au/forum/?id=11635
http://www.gammon.com.au/forum/?id=11643

Your little LED blink sketis only 1 or 2K, yes?
I have a 21 page sketch when printed, its only 7K.
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Designing & building electrical circuits for over 25 years. Check out the ATMega1284P based Bobuino and other '328P & '1284P creations & offerings at  www.crossroadsfencing.com/BobuinoRev17.
Arduino for Teens available at Amazon.com.

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Yes only 1600 bytes, I am using the arduinoISP linked above...
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