From 58d9f76388303d4f90d98e1bcc90e3b6db1f2178 Mon Sep 17 00:00:00 2001
From: caubet_m <marc.caubet@psi.ch>
Date: Mon, 27 Apr 2020 16:58:43 +0200
Subject: [PATCH] Modified job submission examples

---
 .../03 Job Submission/slurm-examples.md       | 29 +++++++++----------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/pages/merlin6/03 Job Submission/slurm-examples.md b/pages/merlin6/03 Job Submission/slurm-examples.md
index 313f532..1c50114 100644
--- a/pages/merlin6/03 Job Submission/slurm-examples.md	
+++ b/pages/merlin6/03 Job Submission/slurm-examples.md	
@@ -27,8 +27,8 @@ single thread per core, doubling the memory is recommended (however, some applic
 #SBATCH --output=myscript.out   # Define your output file
 #SBATCH --error=myscript.err    # Define your error file
 
-module load $module       # ...
-My_Script || srun $task   # ...
+module load $MODULE_NAME # where $MODULE_NAME is a software in PModules
+srun $MYEXEC             # where $MYEXEC is a path to your binary file
 ```
 
 ### Example 2
@@ -49,7 +49,7 @@ more memory than the default (4000MB per thread) is very important to specify th
 #SBATCH --error=myscript.err    # Define your error file
 
 module load $module       # ...
-My_Script || srun $task   # ...
+srun $MYEXEC          # ...
 ```
 
 ## Multi core based job examples
@@ -73,8 +73,8 @@ thread is 4000MB; hence, in total this job can use up to 352000MB memory which i
 #SBATCH --output=myscript.out   # Define your output file
 #SBATCH --error=myscript.err    # Define your error file
 
-module load $module       # ...
-My_Script || srun $task  # ...
+module load $MODULE_NAME # where $MODULE_NAME is a software in PModules
+srun $MYEXEC             # where $MYEXEC is a path to your binary file
 ```
 
 ### Example 2: without Hyper-Threading
@@ -98,8 +98,8 @@ users need to increase it by either by setting ``--mem=352000`` or (exclusive) b
 #SBATCH --output=myscript.out   # Define your output file
 #SBATCH --error=myscript.err    # Define your output file
 
-module load $module       # ...
-My_Script || srun $task  # ...
+module load $MODULE_NAME # where $MODULE_NAME is a software in PModules
+srun $MYEXEC             # where $MYEXEC is a path to your binary file
 ```
 
 ## Advanced examples
@@ -118,8 +118,7 @@ e.g. for a parameter sweep, you can do this most easily in form of a **simple ar
 #SBATCH --array=1-8
 
 echo $(date) "I am job number ${SLURM_ARRAY_TASK_ID}"
-srun myprogram config-file-${SLURM_ARRAY_TASK_ID}.dat
-
+srun $MYEXEC config-file-${SLURM_ARRAY_TASK_ID}.dat
 ```
 
 This will run 8 independent jobs, where each job can use the counter
@@ -141,7 +140,7 @@ You also can use an array job approach to run over all files in a directory, sub
 
 ``` bash
 FILES=(/path/to/data/*)
-srun ./myprogram ${FILES[$SLURM_ARRAY_TASK_ID]}
+srun $MYEXEC ${FILES[$SLURM_ARRAY_TASK_ID]}
 ```
 
 Or for a trivial case you could supply the values for a parameter scan in form
@@ -149,7 +148,7 @@ of a argument list that gets fed to the program using the counter variable.
 
 ``` bash
 ARGS=(0.05 0.25 0.5 1 2 5 100)
-srun ./my_program.exe ${ARGS[$SLURM_ARRAY_TASK_ID]}
+srun $MYEXEC ${ARGS[$SLURM_ARRAY_TASK_ID]}
 ```
 
 ### Array jobs: running very long tasks with checkpoint files
@@ -168,10 +167,10 @@ strategy:
 #SBATCH --array=1-10%1   # Run a 10-job array, one job at a time.
 if test -e checkpointfile; then 
      # There is a checkpoint file;
-     myprogram --read-checkp checkpointfile
+     $MYEXEC --read-checkp checkpointfile
 else
      # There is no checkpoint file, start a new simulation.
-     myprogram
+     $MYEXEC
 fi
 ```
 
@@ -206,7 +205,7 @@ the corresponding parameters.
 #SBATCH --ntasks=44    # defines the number of parallel tasks
 for i in {1..1000}
 do
-   srun -N1 -n1 -c1 --exclusive ./myprog $i &
+   srun -N1 -n1 -c1 --exclusive $MYEXEC $i &
 done
 wait
 ```
@@ -231,7 +230,7 @@ module load gcc/9.2.0 openmpi/3.1.5-1_merlin6
 module list
 
 echo "Example no-MPI:" ; hostname        # will print one hostname per node
-echo "Example MPI:"    ; mpirun hostname # will print one hostname per ntask
+echo "Example MPI:"    ; srun hostname # will print one hostname per ntask
 ```
 
 In the above example are specified the options ``--nodes=2`` and ``--ntasks=44``. This means that up 2 nodes are requested,