How can I find points where I can measure all the frequencies that are generated on the board?

[MMust.5]

STM32F407
 

SYSCLK, HCLK, PCLK1, PCLK2, Ethernet PTP Clock, HCLK to AHB bus, To Cortex System Timer, FCLK Cortex Clock, APB1 peripheral clocks, APB1 timer clocks, APB2 peripheral clocks, APB2 timer clocks.

I only know where to measure HSE and HSI.

HSE frequency can be measured on quartz X2, PH1-OSC_OUT, pin PH1.

The HSI frequency can be measured on pin PA8 by enabling Master Clock Output 1 in the RCC Mode Configuration.

[waclawek.jan]

These clocks are not generated "on board" but inside the chip and cannot be measured directly. You know their frequency from the primary clock frequency and the clock chain setup - you can always verify that by reading out and checking the respective registers, mainly in RCC.

Primary clocks such as HSI or HSE can be measured by bringing them out to MCO or MCO2 pin. Some other clocks can be measured indirectly, e.g. you can measure APB clock frequency by setting up a timer on that APB bus to output PWM.

Never measure HSE directly on the crystal, it's an ultra-low-power circuit and the proble influences it significantly.

JW