Application Note 532 showcases an example where PCIe interfaces with the DMA using the Avalon-MM interface. The design example given operates correctly in Quartus II 8.0, but due to changes made in the SOPC Builder, the design does not simulate or compile correctly when you are doing the DMA test if you create the design in Quartus II 9.1 or later. This is because of the PCIe interrupt is not being connected correctly by SOPC Builder.
As a workaround, open the <sopc variation>.v file and find the following lines:
// pcie_compiler_0_Rx_Interface_irq of type irq does not connect to anything so wire it to default (0)
assign pcie_compiler_0_Rx_Interface_irq = 0;
Change that connection to the following:
assign pcie_compiler_0_Rx_Interface_irq = dma_0_control_port_slave_irq;