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The same problem happened to me after upgrading from a 2.0.7 composer project to 2.1.0-rc3 while running the integration tests.
Turned out the DB dump in the sandbox directory was still from 2.0.7, and running the installation over the dump didn't add the column to the table sales_invoice_grid.
Once I removed the dump and the table, it got recreated with the base_grand_total column.
I didn't dig any deeper, but it seems that under some conditions during an upgrade over an existing table, the script \Magento\Sales\Setup\InstallSchema doesn't add the column.
Hi @quienti , @Vinai
thanks for reporting this issue. It is already being tracked by MAGETWO-54787 ticket and fix will be delivered soon.
This issue will be closed as duplicate of #4785.
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