just for completeness, i am giving the whole list of commands( shown within modelsim) when i start simulation from within quartusII (via EDA Simulation Tool --> Run Gate level Simulation ):
Reading C:/altera/71sp1/modelsim_ae/tcl/vsim/pref.tcl
# do loopaccelerator_run_msim_gate_verilog.do
# if {[file exists gate_work]} {
# vdel -lib gate_work -all
# }
# vlib gate_work
# vmap work gate_work
# Copying
C:\altera\71sp1\modelsim_ae\win32aloem/../modelsim.ini to modelsim.ini
# Modifying modelsim.ini
# ** Warning: Copied
C:\altera\71sp1\modelsim_ae\win32aloem/../modelsim.ini to modelsim.ini.
# Updated modelsim.ini.
#
# vlog -vlog01compat -work work +incdir+. {loopaccelerator.vo}
# Model Technology ModelSim ALTERA vlog 6.1g Compiler 2006.08 Aug 12 2006
# -- Compiling module LoopAccelerator
#
# Top level modules:
# LoopAccelerator
#
# vlog -vlog01compat -work work +incdir+D:/AnuChaudhary/Study/Project/Quartus/24Septonwards/loopacc/synth_result {D:/AnuChaudhary/Study/Project/Quartus/24Septonwards/loopacc/synth_result/testbench_mod.v}
# Model Technology ModelSim ALTERA vlog 6.1g Compiler 2006.08 Aug 12 2006
# -- Compiling module testbench_MOD
#
# Top level modules:
# testbench_MOD
#
# vsim -t 1ps -L cycloneii_ver -L gate_work -L work testbench_MOD
# vsim -L cycloneii_ver -L gate_work -L work -t 1ps testbench_MOD
# // ModelSim ALTERA 6.1g Aug 12 2006
# //
# // Copyright 2006 Mentor Graphics Corporation
# // All Rights Reserved.
# //
# // THIS WORK CONTAINS TRADE SECRET AND
# // PROPRIETARY INFORMATION WHICH IS THE PROPERTY
# // OF MENTOR GRAPHICS CORPORATION OR ITS LICENSORS
# // AND IS SUBJECT TO LICENSE TERMS.
# //
# Loading gate_work.testbench_MOD
# Loading gate_work.LoopAccelerator
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_lcell_ff
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_lcell_comb
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_io
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_mux21
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_dffe
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_asynch_io
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_clkctrl
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_mux41
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.cycloneii_ena_reg
# ** Error: (vsim-3043) D:/AnuChaudhary/Study/Project/Quartus/24Septonwards/loopacc/synth_result/testbench_mod.v(56): Unresolved reference to '_processor_0_done' in loop_accelerator._processor_0_done.
# Region: /testbench_MOD
# Loading
C:\altera\71sp1\modelsim_ae\win32aloem/../altera/verilog/cycloneii.CYCLONEII_PRIM_DFFE
# ** Warning: (vsim-3620) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(104): Specify path destination port 'Q' has no drivers on it.
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/input_reg
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (1st connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (2nd connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (3rd connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (4th connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (5th connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (6th connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Error: (vsim-3389) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Port '(null)' not found in the connected module (7th connection).
# Region: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux
# ** Fatal: (vsim-3365) C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v(5764): Too many port connections. Expected 4, found 11.
# Time: 0 ps Iteration: 0 Instance: /testbench_MOD/loop_accelerator/\CLK~I\/outreg_D_mux File: C:/altera/71sp1/modelsim_ae/win32aloem/../altera/verilog/src/cycloneii_atoms.v
# FATAL ERROR while loading design
# Error loading design
# Error: Error loading design
# Pausing macro execution
# MACRO ./loopaccelerator_run_msim_gate_verilog.do PAUSED at line 12