Yes, the fitter defaults in Quartus® II software version 12.1 have changed when PLL/CDR Reconfiguration is enabled on Stratix® V GX devices. Quartus II will try to implement a separate CMU/ATX PLL per channel within the given instance. You must explicitly identify which TX PLLs can be merged using either QSF assignments or the Assignment Editor.
Assignment Editor
Apply the assignment name “XCVR TX PLL Reconfiguration Group Setting” and set the group number the same for all of the TX PLLs you wish to merge.
Manual QSF assignments
Use the ‘XCVR_TX_PLL_RECONFIG_GROUP” assignment and set the group number the same for all of the TX PLLs you wish to merge. For example, to merge the ATX PLLs for a two channel instance, you would set the group number to 1 for both PLLs.
set_instance_assignment -name XCVR_TX_PLL_RECONFIG_GROUP 1 -to “ native_phy:txrx10g_40b_4ch_qsfp|altera_xcvr_native_sv:native_phy_inst|sv_xcvr_plls:gen_native_inst.
xcvr_native_insts[0].gen_bonded_group_plls.gen_tx_plls.tx_plls|pll[0].pll.atx_pll.tx_pll“
set_instance_assignment -name XCVR_TX_PLL_RECONFIG_GROUP 1 -to "native_phy:txrx10g_40b_4ch_qsfp|altera_xcvr_native_sv:native_phy_inst|sv_xcvr_plls:gen_native_inst.
xcvr_native_insts[1].gen_bonded_group_plls.gen_tx_plls.tx_plls|pll[0].pll.atx_pll.tx_pll“