update submission examples

docs.it4i/general/capacity-computing.md

@@ -48,19 +48,21 @@ Then we create a jobscript:
 
 ```bash
 #!/bin/bash
-#PBS -A PROJECT_ID
+#PBS -A OPEN-00-00
 #PBS -q qprod
-#PBS -l select=1:ncpus=24,walltime=02:00:00
+#PBS -l select=1,walltime=02:00:00
 
 # change to scratch directory
-SCR=/scratch/work/user/$USER/$PBS_JOBID
-mkdir -p $SCR ; cd $SCR || exit
+SCRDIR=/scratch/project/${PBS_ACCOUNT,,}/${USER}/${PBS_JOBID}
+mkdir -p $SCRDIR
+cd $SCRDIR || exit
 
 # get individual tasks from tasklist with index from PBS JOB ARRAY
 TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist)
 
 # copy input file and executable to scratch
-cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
+cp $PBS_O_WORKDIR/$TASK input
+cp $PBS_O_WORKDIR/myprog.x .
 
 # execute the calculation
 ./myprog.x < input > output

docs.it4i/general/job-submission-and-execution.md

@@ -346,9 +346,12 @@ The recommended way to run production jobs is to change to the `/scratch` direct
 ```bash
 #!/bin/bash
 
-# change to scratch directory, exit on failure
-SCRDIR=/scratch/$USER/myjob
+cd $PBS_O_WORKDIR
+
+SCRDIR=/scratch/project/open-00-00/${USER}/myjob
 mkdir -p $SCRDIR
+
+# change to scratch directory, exit on failure
 cd $SCRDIR || exit
 
 # copy input file to scratch
@@ -389,10 +392,12 @@ Example jobscript for an MPI job with preloaded inputs and executables, options
 #PBS -q qprod
 #PBS -N MYJOB
 #PBS -l select=100:mpiprocs=1:ompthreads=16
-#PBS -A OPEN-0-0
+#PBS -A OPEN-00-00
+
+# job is run using project resources; here ${PBS_ACCOUNT,,} translates to "open-00-00"
+SCRDIR=/scratch/project/${PBS_ACCOUNT,,}/${USER}/myjob
 
 # change to scratch directory, exit on failure
-SCRDIR=/scratch/$USER/myjob
 cd $SCRDIR || exit
 
 # load the MPI module
@@ -407,7 +412,9 @@ mpirun ./mympiprog.x
 exit
 ```
 
-In this example, input and executable files are assumed to be preloaded manually in the `/scratch/$USER/myjob` directory. Note the `mpiprocs` and `ompthreads` qsub options controlling the behavior of the MPI execution. `mympiprog.x` is executed as one process per node, on all 100 allocated nodes. If `mympiprog.x` implements OpenMP threads, it will run 16 threads per node.
+In this example, input and executable files are assumed to be preloaded manually in the `/scratch/project/open-00-00/$USER/myjob` directory. Because we used the `qprod` queue, we had to specify which project's resources we want to use, and our `PBS_ACCOUNT` variable will be set accordingly (OPEN-00-00). `${PBS_ACCOUNT,,}` uses one of the bash's built-in functions to translate it into lower case.
+
+Note the `mpiprocs` and `ompthreads` qsub options controlling the behavior of the MPI execution. `mympiprog.x` is executed as one process per node, on all 100 allocated nodes. If `mympiprog.x` implements OpenMP threads, it will run 16 threads per node.
 
 ### Example Jobscript for Single Node Calculation