If env_conf.xml or env_mach_pes.xml variables need to be changed after configure has been called, the case scripts will need to be reconfigured. To do this, run
> cd $CASEROOT > configure -cleanall > configure -case
This will update the buildnml and buildexe files in the Buildconf directory and the case build and run scripts in the CASEROOT directory. If only variables in env_conf.xml have change, clean and reconfigure just the files in Buildconf by doing
> cd $CASEROOT > configure -cleannamelist > configure -case
If only variables in env_mach_pes.xml have changed, clean and reconfigure the build and run scripts by doing
> cd $CASEROOT > configure -cleanmach > configure -case
Note that the -cleanall option does a combination of the -cleannamelist and -cleanmach options. Reconfiguring with -cleanall results in the loss of all local modifications to the component buildnml or buildexe files in Buildconf as well as the loss of all local modifications to the local build and run scripts.