Toggling a GPIO pin by ARM software is very limited.

There're 19 pins at the board for hardware PWM output, 13 of them can work 
simultanously:

| Pin   | Subsystem       | Frequency Range        | Notice            |
| ----- | :-------------: | :--------------------- | :---------------- |
| P8_07 | TIMER-4         | 0.000010914 to 6e6 Hz  | free              |
| P8_09 | TIMER-5         | 0.000010914 to 6e6 Hz  | free              |
| P8_10 | TIMER-6         | 0.000010914 to 6e6 Hz  | free              |
| P8_08 | TIMER-7         | 0.000010914 to 6e6 Hz  | free              |
| P8_13 | PWMSS-2, PWM B  | 0.42 to 50e6 Hz        | free              |
| P8_19 | PWMSS-2, PWM A  | 0.42 to 50e6 Hz        | free              |
| P9_14 | PWMSS-1, PWM A  | 0.42 to 50e6 Hz        | free              |
| P9_16 | PWMSS-1, PWM B  | 0.42 to 50e6 Hz        | free              |
| P9_21 | PWMSS-0, PWM B  | 0.42 to 50e6 Hz        | free              |
| P9_22 | PWMSS-0, PWM A  | 0.42 to 50e6 Hz        | free              |
| P8_34 | PWMSS-1, PWM B  | 0.42 to 50e6 Hz        | HDMI              |
| P8_36 | PWMSS-1, PWM A  | 0.42 to 50e6 Hz        | HDMI              |
| P8_45 | PWMSS-2, PWM B  | 0.42 to 50e6 Hz        | HDMI              |
| P8_46 | PWMSS-2, PWM A  | 0.42 to 50e6 Hz        | HDMI              |
| P9_29 | PWMSS-0, PWM B  | 0.42 to 50e6 Hz        | MCASP0            |
| P9_31 | PWMSS-0, PWM A  | 0.42 to 50e6 Hz        | MCASP0            |
| P9_28 | PWMSS-2, CAP    | 0.0233 to 50e6 Hz      | MCASP0            |
| P9_42 | PWMSS-0, CAP    | 0.0233 to 50e6 Hz      | free (double pin) |
| JT_05 | PWMSS-1, PRUCAP | 0.0233 to 50e6 Hz      | JTag (UART0_TXD)  |

If those are not enough, you can use direct PRU pins to generate PWM. When 
both PRUSS are used, up to 24 PWM outputs are possible (ie. 
https://github.com/omcaree/bbb-prupwm).

BR

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