Normal alignment time and solution for reducing time to run on laptop

I am new user of mothur. I appreciate because of your nice workflow. I have a questions regarding the alignment of high number of unique sequence (around 2 million) using the align.seq().
As, I have 32 paired-end reads/ samples so it seems for me that it take too much time for the alignment because I run it and then stop it, I am not sure that if is good idea to run it on my laptop? maybe it take 12 hours based on my estimation.
Could anyone guide me that what should I do?
Could I align my samples in different sets like (6 samples) and then merge them?!
or you may have better solution.

Many thanks

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