Hopefully this will help.
The file transfer protocol depends what you have configured on the PBS Servers /etc/pbs.conf for STAGEIN (server to compute nodes) and PBS MOMs $PBS_HOME/mom_priv/config for STAGEOUT (if $usecp does not exists in mom_priv/config then it follows what is configured in /etc/pbs.conf on the MOM)
Key words to search in the PBS Pro admin guide : $usecp
Default copy mechanism is : RCP , otherwise SCP and CP if they are configured in pbs.conf / mom_priv/config
#PBS -W stagein = <execution_path>@:<storage_path>
#PBS -W stageout = <execution_path>@:<storage_path>
stagein: location of input files ( copy input files to the execution directory or job directory)
stageout: location of output files (copy results from job directory or execution directory back to you intended location )
execution_path: execution directory on the compute node
storage_path: filename on host hostname
The ‘@’ character separates execution path specification from storage path specification
@ character is just a separator, it does not represent username@hostname kind of specification
Sample:
#!/bin/bash
#PBS -N pbsproapplicaton
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -W sandbox=PRIVATE
#copy the box.fem file from the current location to headnode:/home/pbsdata/optistruct with the same file name box.fem
#PBS -W stagein=box.fem@headnode:/home/pbsdata/optistruct/box.fem
#copy all the results from the sandbox or jobdir to headnode:/home/pbsdata/output
#PBS -W stageout=*@headnode:/home/pbsdata/output
#!/bin/bash
#PBS -N pbsproapplication
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -W sandbox=PRIVATE
#copy the box.fem and box.inc files from the current location to headnode:/home/pbsdata/optistruct with the same file name box.fem
#PBS -W stagein=box.fem@headnode:/home/pbsdata/optistruct/box.fem,box.inc@@headnode:/home/pbsdata/optistruct/box.fem
#copy *.out and *.log result files from the sandbox or jobdir to headnode:/home/pbsdata/output
#PBS -W stageout=*.out@headnode:/home/pbsdata/output,*.log@headnode:/home/pbsdata/output