There is a fairly deep issue when comparing GDX files if one of the GDX files has the following properties:
     - It is produced by GDXDUMP 
     - It contains Equation records 
  
  The following illustrates the problem: 
              |           C:\projects\tmp>gamslib indus89                   Copy ASCII: indus89.gms           C:\projects\tmp>gams indus89 lo=0 gdx=1           C:\projects\tmp>gdxdump 1.gdx output=2.gms                *  GDX dump of 1.gdx                *  Library in use : C:\PROGRA~1\GAMS23.7                *  Library version: GDX Library      BETA  8Jun11 23.7.0 WEX 25828.25830 WEI x86_64/MS Windows                *  File version   : GDX Library      BETA  8Jun11 23.7.0 WEX 25828.25830 WEI x86_64/MS Windows                *  Producer       : GAMS Base Module BETA  8Jun11 23.7.0 WEX 25828.25830 WEI x86_64/MS Windows                *  File format    :    7                *  Compression    :    0                *  Symbols        :  281                *  Unique Elements:  245           C:\projects\tmp>gams 2.gms lo=0 gdx=2           C:\projects\tmp>gdxdiff 1.gdx 2.gdx eps=1.0e-6                   GDXDIFF          BETA  8Jun11 23.7.0 WEX 25828.25830 WEI x86_64/MS Windows                File1 : 1.gdx                File2 : 2.gdx                Summary of differences:                   bdraft   Data are different                   brepco   Data are different                  ccombal   Data are different                  consbal   Data are different                     cost   Data are different                   demnat   Data are different                divcnlsea   Data are different                   divsea   Data are different                   fodder   Data are different                   grnfdr   Data are different                   laborc   Data are different                     nbal   Data are different                  nwfpalc   Data are different                     objn   Data are different                    objnn   Data are different                     objz   Data are different                    objzn   Data are different                  protein   Data are different                   prseaw   Data are different                  qcombal   Data are different                  subirrc   Data are different                   tdraft   Data are different                watalcpro   Data are different                watalcsea   Data are different                  watalcz   Data are different                waterbaln   Data are different                Output: diffile.gdx                GDXDiff finished           C:\projects\tmp>gdxdump diffile.gdx Symbols                *  GDX dump of diffile.gdx                *  Library in use : C:\PROGRA~1\GAMS23.7                *  Library version: GDX Library      BETA  8Jun11 23.7.0 WEX 25828.25830 WEI x86_64/MS Windows                *  File version   : GDX Library      BETA  8Jun11 23.7.0 WEX 25828.25830 WEI x86_64/MS Windows                *  Producer       : GDXDIFF                *  File format    :    7                *  Compression    :    0                *  Symbols        :   26                *  Unique Elements:  249                   Symbol    Dim Type  Explanatory text                1 bdraft      4  Equ  Differences                2 brepco      3  Equ  Differences                3 ccombal     4  Equ  Differences                4 consbal     4  Equ  Differences                5 cost        3  Equ  Differences                6 demnat      3  Equ  Differences                7 divcnlsea   3  Equ  Differences                8 divsea      2  Equ  Differences                9 fodder      4  Equ  Differences                10 grnfdr      4  Equ  Differences                11 laborc      4  Equ  Differences                12 nbal        3  Equ  Differences                13 nwfpalc     2  Equ  Differences                14 objn        1  Equ  Differences                15 objnn       1  Equ  Differences                16 objz        1  Equ  Differences                17 objzn       1  Equ  Differences                18 protein     4  Equ  Differences                19 prseaw      3  Equ  Differences                20 qcombal     4  Equ  Differences                21 subirrc     4  Equ  Differences                22 tdraft      4  Equ  Differences                23 watalcpro   3  Equ  Differences                24 watalcsea   3  Equ  Differences                25 watalcz     4  Equ  Differences                26 waterbaln   4  Equ  Differences           C:\projects\tmp>         |      
   
  Apart from a small bug related to $ONEMPTY, it turns out that the way GDXDUMP exports equations records, it looses information about the equation type. This leads to the above results. Luckily in practice this will not be an issue, as equations are not often part of such an exercise.
  Background.
  During a course I taught about GAMS I was asked if it is possible to edit GDX files. The answer is: GDXDUMP will give you a GAMS representation of a GDX file which you can edit. Using the call:
     GAMS gmsfile gdx=newgdxfile
 
  you can make a new GDX file with the changes incorporated. The tool GDXDIFF will allow you to monitor the changes. 
  Although this is correct, I chose the INDUS89 example as illustration. That was unfortunate, as that failed because of the exotic Equation problem.