working with too many files

I have a lot of files in a UNIX subdirectory and I need to perform some calculations on the data for each pair of files . I need to know an efficient way of do that taking on account the characteristics of the network file system (nfs).
Thank you!

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_______________________________________________________________
  Osvaldo Olmea, PhD                             | Phone: (212) 241 8191
  Department of Physiology & Biophysics |  Fax: (212) 860 3369
  Mount Sinai School of Medicine            | email:
Osvaldo.Olmea_at_inka.mssm.edu
  One Gustave Levy Pl., Box 1218
  New York, NY 10029