ENH: Complete parameter sweep example 3; fixes #1

README.md

@@ -131,8 +131,9 @@ IDs.  The record ID is read by the program to find the corresponding
 input parameters, the program calculates the result from the
 parameters and saves the result in a directory.
 
-Once all records are completed, the results from the directory are
-aggregated into a single results file.
+Once all records are completed, the results from the directory can be
+aggregated by you into a single results file.  Aggregating files
+doesn't really require a SLURM job.
 
 GNU Parallel automatically feeds record IDs to task workers as the
 task workers complete records and become available.
@@ -142,16 +143,52 @@ task workers complete records and become available.
 module purge
 module load python/2.7.6-gcc-unicode
 cd ~/parallel-slurm/examples
-rm -rf joblog submit.out results/ results.csv
-for i in {1..5}; do sbatch 03-submit-param-sweep.slurm; done
+rm -rf joblog submit.out results/
+for i in {1..3}; do sbatch 03-submit-param-sweep.slurm; done
 touch submit.out && tail -f submit.out
 # Hit Ctrl+C to exit
 ```
 
 Output:
 
+```
+Started SLURM job 2346922
+Running 60 of total 60 simulations.
+1: Fitting model to parameters: x = 0.1, y = -0.1, z = control ...
+1: ... done!  Saved result  4.196 to results/01.dat
+2: Fitting model to parameters: x = 0.1, y = -0.1, z = positive ...
+2: ... done!  Saved result  1.574 to results/02.dat
+3: Fitting model to parameters: x = 0.1, y = -0.1, z = negative ...
+3: ... done!  Saved result 12.589 to results/03.dat
+...
+44: Fitting model to parameters: x = 0.8, y = -0.1, z = positive ...
+44: ... done!  Saved result  1.278 to results/44.dat
+slurmstepd: *** JOB 2346922 ON cn338 CANCELLED AT 2019-05-13T18:52:16 DUE TO TIME LIMIT ***
+Started SLURM job 2346923
+Running 15 of total 60 simulations.
+45: Fitting model to parameters: x = 0.8, y = -0.1, z = negative ...
+45: ... done!  Saved result 10.226 to results/45.dat
+...
+59: Fitting model to parameters: x = 1.0, y = 0.1, z = positive ...
+59: ... done!  Saved result  1.250 to results/59.dat
+60: Fitting model to parameters: x = 1.0, y = 0.1, z = negative ...
+60: ... done!  Saved result 10.000 to results/60.dat
+Completed SLURM job 2346923 in   00:00:32 
+Started SLURM job 2346924
+Nothing to run; all 60 simulations complete.
+Completed SLURM job 2346924 in   00:00:01 
 ```
 
+```console
+$ head -n 4 joblog; echo "..."; tail -n 3 joblog
+Seq     Host    Starttime       JobRuntime      Send    Receive Exitval Signal  Command
+1       cn236   1557787112.519       5.414      0       119     0       0       python model.py 1
+3       cn236   1557787112.750       5.250      0       120     0       0       python model.py 3
+2       cn236   1557787117.940       5.276      0       429     0       0       python model.py 2
+...
+58      cn338   1557787220.703       5.284      0       120     0       0       python model.py 58
+59      cn338   1557787220.815       5.267      0       121     0       0       python model.py 59
+60      cn338   1557787225.850       5.263      0       121     0       0       python model.py 60
 ```
 
 ## Next Steps

examples/03-submit-param-sweep.slurm

@@ -1,11 +1,10 @@
 #!/bin/bash
-#SBATCH --ntasks 5
+#SBATCH --ntasks 3
 #SBATCH --output submit.out
-
 #SBATCH --dependency singleton
 #SBATCH --job-name example-03-parameter-sweep
-# Kill job after 5 minutes seconds to show resuming feature.
-#SBATCH --time 5:00
+# Kill job after 1 minute to show resuming feature.
+#SBATCH --time 1:00
 
 parallel_opts=$(~/parallel-slurm/parallel_opts.sh)
 module load parallel
@@ -22,6 +21,7 @@ echo "Started SLURM job $SLURM_JOB_ID"
 if [[ n_remaining -eq 0 ]]
 then
     echo "Nothing to run; all $n_sim simulations complete."
+
     echo "Completed SLURM job $SLURM_JOB_ID in $(sacct -nXj $SLURM_JOB_ID -o elapsed)"
     exit 0
 fi

examples/model.py

@@ -38,7 +38,7 @@ def run(index):
                    for param, value in record.items()])))
     value = {'positive': 0.8, 'negative': 0.1, 'control': 0.3}
     result = record['x'] ** record['y'] / value[record['z']]
-    time.sleep(1)
+    time.sleep(5)
     path_result = os.path.join(RESULTS_DIR, '{:02d}.dat'.format(index))
     if not os.path.exists(RESULTS_DIR):
         os.mkdir(RESULTS_DIR)