> How should I calculate [the following] for my sparse matrix?
> Bigarr =: a1 =/ a2.

Well, I would've advised you to first make  a1  and  a2  sparse themselves, 
i.e.:

           a1 =/&:$. a2.

But, when I tried some experiments:

           a1 =. i. 4000
           a2 =. 60e3 $ 78

           $ a1 =/ a2
        4000 60000
           sa1 =. $. a1
           sa2 =. $. a2
      
           $ sa1 =/ sa2
        |non-unique sparse elements: scriptd
        |   $sa1    =/sa2
        |[-7] c:\app\dev\lang\j\601c\temp\13.ijs
   
Which looks like a bug (to me), and is reducible to :
           
           =/~ $. , 1
        |non-unique sparse elements
        |       =/~$.,1
-Dan

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