These didn't help.
But I am puzzled as to why none of the clocking and calibration features such as PLLs, DLLs, calibration blocks, etc. are not included in the design partition statistics.
Altera support asked me to add this to quartus.ini - fsac_clock_manager_merge_all_hssi_tx_pcs_in_same_quad=off
Not sure what it does but I have since then started getting internal error when I recompile with an existing database.
----------error msg begin ----------
Internal Error: Sub-system: CDB_ATOM, File: /quartus/db/cdb_atom/cdb_atom_tgx_lcell.cpp, Line: 854
Atom# 406195 - get_lutmask() called for non-consistent arithmetic lcell comb
Stack Trace:
0x13d66d: CDB_ATOM_TGX_LCELL_COMB::get_transformed_lutmask + 0x57d (db_cdb_atom)
0x13dd60: CDB_ATOM_TGX_LCELL_COMB::get_lutmask + 0x160 (db_cdb_atom)
0x18744e: CDB_ATOM_LUTMASK_CACHE::visit_atom_tgx_lcell_comb + 0xae (db_cdb_atom)
0x186aff: CDB_ATOM_LUTMASK_CACHE::init_data + 0x7f (db_cdb_atom)
0x186dd2: CDB_ATOM_LUTMASK_CACHE::CDB_ATOM_LUTMASK_CACHE + 0x92 (db_cdb_atom)
0x188967: CDB_ATOM_LUTMASK_CACHE::init_lutmask_cache + 0xe7 (db_cdb_atom)
0xb62a: a2t_call_update_tdb_netlist_for_atoms + 0x9f7a (tsm_a2t)
0xbf74: a2t_call_update_tdb_netlist_for_atoms + 0xa8c4 (tsm_a2t)
0xd54a: a2t_call_recursive_visitor + 0xa (tsm_a2t)
0x3fa7: sta_update_tdb_netlist_for_atoms + 0xe67 (TSM_STA)
0xb98b: sta_build_and_preprocess_tdb + 0x15b (TSM_STA)
0x164a4: tdc_get_accessories + 0x53c4 (TSM_TDC)
0xef93a: FITCC_TDC_UTILITY::setup_tdc_utility + 0x4ba (FITTER_FITCC)
0xf1fa9: FITCC_TDC_UTILITY::FITCC_TDC_UTILITY + 0x1e9 (FITTER_FITCC)
0x3a42b: FITCC_ENV::get_tdc_utility_or_create_if_necessary + 0x35b (FITTER_FITCC)
0x217e3e: FSAC_AUTO_DELAY_CHAIN_OP::work_new + 0x1be (FITTER_FSAC)
0x1fda49: FSAC_DELAY_CHAIN_OP::work + 0x1d9 (FITTER_FSAC)
0x84ce: FTITAN_LUT_RAM_CONVERSION_UTIL::lutram_iterm_port_is_internal_registered + 0x4c1e (fitter_ftitan)
0x462f7: FITCC_EXPERT::fitter_post_operations + 0x1a7 (FITTER_FITCC)
0x475c5: FITCC_EXPERT::invoke_fitter + 0xa55 (FITTER_FITCC)
0x29c5: ftitan_execute + 0x265 (fitter_ftitan)
0xb55d: fmain_start + 0x7cd (FITTER_FMAIN)
0x1264b: qexe_get_command_line + 0x1c5b (comp_qexe)
0x1588d: qexe_process_cmdline_arguments + 0x5ad (comp_qexe)
0x159a1: qexe_standard_main + 0xa1 (comp_qexe)
0x1a48: MSG_INITIALIZER::~MSG_INITIALIZER + 0x118 (CCL_MSG)
0x19ec: MSG_INITIALIZER::~MSG_INITIALIZER + 0xbc (CCL_MSG)
0x53d4: MEM_INITIALIZER::~MEM_INITIALIZER + 0x244 (ccl_mem)
0x3379f: msg_exe_main + 0x8f (CCL_MSG)
0x1652c: BaseThreadInitThunk + 0xc (kernel32)
0x2c520: RtlUserThreadStart + 0x20 (ntdll)
End-trace
Quartus II 64-Bit Version 11.1 Build 259 01/25/2012 SJ Full Version
Service Pack Installed: 2
----------- error msg end -------------