The board is Arduino Due (Programming port). It works fine with the program bossac.exe, which one Arduino system uses to program the Due version. Visual Micro system uses avrdude.exe. The output is listed here:
n/arm-none-eabi-g++" -Os -Wl,--gc-sections -mcpu=cortex-m3 uino_due_x/linker_scripts/gcc/flash.ld" _due_x_dbg/HelloWorld.map" -o g/HelloWorld.elf" dbg" -lm -lgcc -mthumb -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -Wl,--start-group g/syscalls_sam3.c.o" g\HelloWorld.cpp.o" g\LiquidCrystal\LiquidCrystal.cpp.o" no_due_x/libsam_sam3x8e_gcc_rel.a" g/core.a" -Wl,--end-group
n/arm-none-eabi-objcopy" -O binary g/HelloWorld.elf" g/HelloWorld.bin"
Binary sketch size: 11048 bytes (2% of a 524288 byte maximum) (0.32 secs)
Uploading to I/O board using 'arduinoisp'
"C:\temp\arduino-1.5.2-windows\arduino-1.5.2\hardware\tools\avr\bin/avrdude" nf" -v -v -v -v -pcortex-m3 -cstk500v1 -P\\.\COM17 -b9600 o_due_x_dbg\HelloWorld.hex":i
avrdude: Version 5.11, compiled on Sep 2 2011 at 19:38:36
Copyright (c) 2000-2005 Brian Dean,
http://www.bdmicro.com/ Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "
avrdude: AVR Part "cortex-m3" not found.
Valid parts are:
t10 = ATtiny10 [C:\temp\arduino-1.5.2-windows\arduino-1.5.2\hardware/tools/avr/etc/avrdude.conf:16880]
t9 = ATtiny9 [C:\temp\arduino-1.5.2-windows\arduino-1.5.2\hardware/tools/avr/etc/avrdude.conf:16836]
t5 = ATtiny5 [C:\temp\arduino-1.5.2-windows\arduino-1.5.2\hardware/tools/avr/etc/avrdude.conf:16792]