Use Ghost Script from commandline
gs -sDEVICE=pdfwrite -dNOPAUSE -dQUIET -dBATCH -dPDFSETTINGS=/screen -dCompatibilityLevel=1.6 -sOutputFile=pdfoutsmallfile.pdf pdfinputlargefile.pdf
-dNOPAUSE – disable the interactive prompting
pdfwrite – create pdf files
-dCompatibilityLevel=1.6 – compatibility with each versions of adobe. Use 1.3,1.4,1.6,1.7
-sOutputFile – name of the output file.