In case of the logn-time calculations, it is useful to run a mathematica program on some remote Linux server.
My way of doing it is the following:
1) it is convenient to edit the program code in the notebook form.
2) then rewrite the code into InputForm, it can be done by converting all cells into InputForm, crt-a, main menu -> cell -> convert to InputForm
3) Save as .txt file
4) put the .txt file on the remote Linux machine
5) run mathematica kernel: math < file.txt > output.txt
6) In the output.txt the output is recorded.
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