I am controlling a simple set up, 9 leds, 3.3v and 20mA each, each connected to a 100ohm resistor and plugged into pins 3-13 (skipping a couple) and they are turning on but they are very dim. Is it because they are not receiving enough voltage?
By default all the pins are set as inputs. If you do a digitalWrite(pin, HIGH) to an input pin it will turn on the internal pull-up resistor (just like pinMode(pin,INPUT_PULLUP)). This will turn an LED on dimly. Make sure you set each output pin to OUTPUT mode:
for (int pin=3; pin <= 13; pin++)
pinMode(pin, OUTPUT);
What John said. if you do not Write to the pin a high voltage then the resistor is in place and severely limiting your power.
They are set to output so I'm not sure what's going on.
Is there another way to set the pin to high voltage?
Perhaps this detailed LED tutorial will help you figure out what is going wrong:
http://www.ladyada.net/learn/arduino/LEDs.html