The logs are inline with your comment...
So if that many columns and rows are removable, may be I can also simplify my model at the very first step. I remember there was a presentation about the methods used in Presolve
*************** BIP***********************
Gurobi 7.0.2 (win64, .NET) logging started 06/19/17 00:39:29
Optimize a model with 1213501 rows, 1225635 columns and 6542569 nonzeros
Variable types: 1213500 continuous, 12135 integer (12135 binary)
Coefficient statistics:
Matrix range [1e+00, 1e+00]
Objective range [1e+00, 1e+00]
Bounds range [1e+00, 1e+00]
RHS range [7e+00, 7e+00]
Found heuristic solution: objective 1100
Presolve removed 1019994 rows and 1020000 columns (presolve time = 5s) ...
Presolve removed 1025546 rows and 1025552 columns (presolve time = 10s) ...
Presolve removed 1025546 rows and 1025602 columns (presolve time = 15s) ...
Presolve removed 1025546 rows and 1025602 columns
Presolve time: 18.48s
Presolved: 187955 rows, 200033 columns, 3207676 nonzeros
Variable types: 187954 continuous, 12079 integer (12076 binary)
Root simplex log...
Iteration Objective Primal Inf. Dual Inf. Time
0 4.9951600e+05 1.879540e+05 0.000000e+00 20s
15472 4.3223000e+05 1.704480e+05 0.000000e+00 20s
75326 1.8983700e+05 1.009900e+05 0.000000e+00 25s
120245 1.0360900e+05 6.528500e+04 0.000000e+00 30s
141729 7.6626000e+04 3.908100e+04 0.000000e+00 35s
151969 6.7543000e+04 4.134200e+04 0.000000e+00 40s
161212 6.1271000e+04 1.971000e+04 0.000000e+00 45s
169981 5.5776000e+04 1.505200e+04 0.000000e+00 50s
178276 5.1429000e+04 8.285000e+03 0.000000e+00 55s
185623 4.8716000e+04 8.786000e+03 0.000000e+00 60s
191289 4.7583000e+04 0.000000e+00 0.000000e+00 63s
Root relaxation: objective 4.758300e+04, 191289 iterations, 44.15 seconds
Nodes | Current Node | Objective Bounds | Work
Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time
* 0 0 0 47583.000000 47583.0000 0.00% - 64s
Explored 0 nodes (191289 simplex iterations) in 64.33 seconds
Thread count was 8 (of 8 available processors)
Solution count 2: 47583 1100
Pool objective bound 47583
Optimal solution found (tolerance 1.00e-04)
Best objective 4.758300000000e+04, best bound 4.758300000000e+04, gap 0.0000%
*************** LP RELAX ***********************
Gurobi 7.0.2 (win64, .NET) logging started 06/19/17 00:40:54
Optimize a model with 1213501 rows, 1225635 columns and 6542569 nonzeros
Coefficient statistics:
Matrix range [1e+00, 1e+00]
Objective range [1e+00, 1e+00]
Bounds range [1e+00, 1e+00]
RHS range [7e+00, 7e+00]
Concurrent LP optimizer: dual simplex and barrier
Showing barrier log only...
Presolve removed 714684 rows and 714740 columns (presolve time = 5s) ...
Presolve removed 714684 rows and 714740 columns
Presolve time: 5.56s
Presolved: 498817 rows, 510895 columns, 5079739 nonzeros
Elapsed ordering time = 5s
Elapsed ordering time = 10s
Ordering time: 12.50s
Barrier statistics:
Dense cols : 2198
AA' NZ : 4.287e+07
Factor NZ : 5.315e+07 (roughly 800 MBytes of memory)
Factor Ops : 1.395e+10 (less than 1 second per iteration)
Threads : 3
Objective Residual
Iter Primal Dual Primal Dual Compl Time
0 2.38037001e+07 1.78083157e+07 2.36e+05 1.39e+01 6.83e+02 31s
1 2.05161397e+07 1.71703066e+07 2.04e+05 1.59e+01 5.47e+02 32s
2 1.30386780e+07 1.66086918e+07 1.27e+05 7.24e+00 3.33e+02 34s
3 9.46917567e+06 1.60777995e+07 9.13e+04 3.35e+00 2.31e+02 36s
4 6.77534460e+06 1.55917224e+07 6.46e+04 1.72e+00 1.62e+02 37s
5 4.88234016e+06 1.49358868e+07 4.60e+04 9.63e-01 1.15e+02 39s
6 3.70631731e+06 1.39278922e+07 3.45e+04 5.05e-01 8.48e+01 41s
7 2.75959535e+06 1.28050389e+07 2.52e+04 3.07e-01 6.13e+01 42s
8 1.98296837e+06 1.17244607e+07 1.76e+04 1.91e-01 4.29e+01 44s
9 1.41130038e+06 9.59020200e+06 1.20e+04 8.38e-02 2.85e+01 45s
10 8.66126422e+05 7.48497802e+06 6.73e+03 3.44e-02 1.63e+01 47s
11 6.71848429e+05 5.57378293e+06 4.92e+03 1.04e-02 1.13e+01 48s
12 4.81670425e+05 3.98026568e+06 3.18e+03 6.10e-10 7.26e+00 50s
13 4.18932530e+05 3.18738001e+06 2.64e+03 4.31e-10 5.82e+00 52s
14 3.28580992e+05 2.42403564e+06 1.89e+03 2.96e-10 4.20e+00 53s
15 2.88334550e+05 1.73505633e+06 1.57e+03 1.70e-10 3.25e+00 55s
16 1.91621249e+05 1.25674542e+06 8.23e+02 1.13e-10 1.91e+00 57s
17 1.38201463e+05 8.09598559e+05 4.58e+02 1.06e-10 1.13e+00 58s
18 1.14381357e+05 5.21289172e+05 3.23e+02 1.73e-10 7.78e-01 59s
19 8.18166938e+04 1.75247237e+05 1.52e+02 1.57e-10 3.18e-01 61s
20 6.75652499e+04 7.52496864e+04 7.63e+01 1.34e-10 1.37e-01 63s
21 6.32457283e+04 6.66318554e+04 5.55e+01 1.08e-10 9.94e-02 64s
22 6.05776967e+04 6.32836905e+04 4.40e+01 8.50e-11 7.94e-02 66s
23 5.88236081e+04 5.86739538e+04 3.67e+01 1.20e-10 6.54e-02 67s
24 5.68447245e+04 5.36391426e+04 2.63e+01 6.58e-11 4.59e-02 69s
25 5.58484444e+04 5.28222644e+04 2.26e+01 1.06e-10 3.94e-02 71s
26 5.43662066e+04 5.22893273e+04 1.78e+01 6.25e-11 3.14e-02 72s
27 5.30684727e+04 5.15476564e+04 1.32e+01 1.80e-10 2.35e-02 73s
28 5.14794342e+04 4.81960980e+04 5.65e+00 9.14e-11 9.05e-03 75s
29 4.82498010e+04 4.76944799e+04 1.81e+00 1.76e-10 3.38e-03 77s
30 4.76078702e+04 4.75999954e+04 1.14e-01 1.79e-10 2.32e-04 79s
31 4.75830013e+04 4.75830170e+04 6.72e-06 1.97e-10 2.43e-08 80s
32 4.75830000e+04 4.75830000e+04 1.54e-11 1.82e-10 5.69e-14 82s
Barrier solved model in 32 iterations and 81.84 seconds
Optimal objective 4.75830000e+04
Crossover log...
45246 DPushes remaining with DInf 0.0000000e+00 85s
34807 DPushes remaining with DInf 0.0000000e+00 90s
23709 DPushes remaining with DInf 0.0000000e+00 95s
12648 DPushes remaining with DInf 0.0000000e+00 100s
894 DPushes remaining with DInf 0.0000000e+00 105s
0 DPushes remaining with DInf 0.0000000e+00 106s
0 PPushes remaining with PInf 0.0000000e+00 106s
Push phase complete: Pinf 0.0000000e+00, Dinf 0.0000000e+00 106s
Iteration Objective Primal Inf. Dual Inf. Time
494331 4.7583000e+04 0.000000e+00 0.000000e+00 106s
494331 4.7583000e+04 0.000000e+00 0.000000e+00 108s
Solved with barrier
Solved in 494331 iterations and 107.77 seconds
Optimal objective 4.758300000e+04