The Profile GPU Rendering checkbox in the Developer Options controls value of the debug.hwui.profile system property:

/**
  * System property used to enable or disable hardware rendering profiling.
  * The default value of this property is assumed to be false.
  *
  * When profiling is enabled, the adb shell dumpsys gfxinfo command will
  * output extra information about the time taken to execute by the last
  * frames.
  *
  * Possible values:
  * "true", to enable profiling
  * "visual_bars", to enable profiling and visualize the results on screen
  * "false", to disable profiling
  *
  * @see #PROFILE_PROPERTY_VISUALIZE_BARS
  *
  * @hide
  */
public static final String PROFILE_PROPERTY = "debug.hwui.profile";

So you can use setprop debug.hwui.profile visual_bars command to enable profiling and setprop debug.hwui.profile false to disable it.

I have noticed that Instant Run causes this kind of issues. Try turning off instant run:

Mac - Android Studio > Preferences > Build, execution, deploy > Instant Run.

Windows - File > Setting

In regards to the GPU issue, the documentation states the following:

To enable GPU monitoring, make sure you turn on monitoring for your Android hardware device or emulator under Setting → Developer Options → Profile GPU rendering → In adb shell dumpsys gfxinfo

One you enabled GPU rendering in adb shell dumpsys gfxinfo, you have to untoggle the pause icon in Android Studio (on the left of the graph) for the GPU profiling to start for the selected app.

Hope this helps.

To edit the run configuration choose "Run/Run..." in AndroidStudio and then select "Edit Configurations". Choose tab "profiling" and there select "Capture GPU Commands".

Rooting the device should not be necessary as far as I know.