With the exception of the -j option, specifying -R on the command line as well as in the MPRUN_FLAGS environment variable combines the two sets of values--that is, the command line does not override the environment variable settings. For example, if you have
% setenv MPRUN_FLAGS '-R "load1 < 1"'
and issue the command
% mprun -R "load5 < 1" -R "load15 < 1" a.out
this would be the same as issuing the command
% mprun -R "(load1<1) & (load5<1) & (load15<1)" a.out
This combining behavior does not happen with the -j option. When -j is specified by MPRUN_FLAGS as well as on the mprun command line, the command line use overrides the environment variable setting.