Critical change about using $PFSDIR directory at OSC

Category: 
Batch
Resolution: 
Resolved

Starting from Thursday, Feb 2nd, the $PFSDIR directory on scratch (/fs/scratch) won’t be created by job prologue. For example, if you simply use the command cd $PFSDIR, you will get an error indicating that this directory does not exist. The reason we are making this change is to address recent problems with the batch environments on OSC’s clusters. You will have to create the $PFSDIR directory by yourself if you use this directory. Please include the following additional lines in the job script.

If you use bash:

1. Right after PBS directives, create the $PFSDIR directory with the following commands:

if [ -n "$PFSDIR" -a ! -d $PFSDIR ]; then
 export PFSDIR=/fs/scratch/`whoami`/$PBS_JOBID
 if [ ! -d $PFSDIR ]; then
  mkdir -p $PFSDIR
 fi
fi

2. At the end, remove this directory with the following commands:

if [ -n "$PFSDIR" -a -d $PFSDIR ]; then
 rm -rf $PFSDIR
fi

If you use csh/tcsh:

1. Right after PBS directives, create the $PFSDIR directory with the following commands:

if ( $?PFSDIR && ! -d $PFSDIR ) then
 setenv PFSDIR /fs/scratch/`whoami`/$PBS_JOBID
 if ( ! -d $PFSDIR ) then
  mkdir -p $PFSDIR
 endif
endif

2. At the end, remove this directory with the following commands:

if ( $?PFSDIR && -d $PFSDIR ) then
 rm -rf $PFSDIR
endif