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Subnets utilizing their own routing tables, are generally configured that way in order to separate environments. For example, separating staging and production environments.
That being said, the issue you have noted is quite common in this situation as by default, Amazon FSx uses your VPC's main route table[1].
A solution to this, would be to edit the route tables for the FSx. To do this, you can follow these steps:
- From your Fsx filesystem dashboard, select the filesystem you would like to update.
- Click 'Actions, Update file system, update route tables'.
- A new window will pop up, listing your route tables in the VPC.
- Select the route tables for your subnets and click 'Associate'.
- Once the association has been completed, click 'Close'
- Your route tables should now be correctly associated.
This then allows the FSx to utilize all of the route tables you have specified in that VPC
[1] https://docs.aws.amazon.com/fsx/latest/ONTAPGuide/unable-to-access.html#subnet-route-tables
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Thank you, this is it.