add example for parallel execution with GNU parallel

.gitignore

@@ -138,6 +138,7 @@ examples/*.ech
 examples/*.inp
 examples/*.html
 examples/*.sel
+examples/log/
 
 # IDL
 dump.bin

examples/parallel.py

@@ -0,0 +1,79 @@
+# -*- coding: utf-8 -*-
+"""
+Example of a parallel execution script
+
+The script is called with command line parameters that are
+then used to modify the runs. Here those are Teff, logg, and [M/H], but they
+can be anything, e.g. names of different input spectra.
+
+Here we simply synthesize different spectra for different input paramters,
+but it can also be used to analyse different spectra, etc.
+"""
+import sys
+from os import makedirs
+from os.path import dirname, join, realpath
+
+from pysme import sme as SME
+from pysme import util
+from pysme.gui import plot_plotly
+from pysme.synthesize import synthesize_spectrum
+
+if __name__ == "__main__":
+
+    # Read the command line parameters
+    # the first parameter is always the command used to call this script
+    # i.e. the name of this file, thus we ignore it
+    # The expected number of parameters is then 1 + 3 = 4
+    if len(sys.argv) == 4:
+        # Here we parse the input parameters
+        # since they are supposed to be numbers, we convert them from strings
+        teff, logg, monh = sys.argv[1], sys.argv[2], sys.argv[3]
+        teff = float(teff)
+        logg = float(logg)
+        monh = float(monh)
+    else:
+        print(
+            "No (or the wrong number of) command line "
+            "parameters passed to the script"
+        )
+        raise RuntimeError
+
+    # Define the location of all your files
+    # here we use different directories for the different
+    # products
+    target = f"sun_{teff}_{logg}_{monh}"
+    examples_dir = dirname(realpath(__file__))
+    in_file = join(examples_dir, "sun_6440_grid.inp")
+    out_file = join(examples_dir, f"out/{target}.sme")
+    plot_file = join(examples_dir, f"plot/{target}.html")
+    log_file = join(examples_dir, f"log/{target}.log")
+
+    # Start the logging to the file
+    makedirs(dirname(log_file), exist_ok=True)
+    util.start_logging(log_file)
+
+    # Load your existing SME structure or create your own
+    sme = SME.SME_Structure.load(in_file)
+
+    # Change parameters if your want
+    sme.vrad = 0.35
+    sme.vrad_flag = "whole"
+    sme.cscale_flag = "linear"
+    sme.cscale_type = "match"
+
+    # Apply the parameters set via the command line
+    sme.teff = teff
+    sme.logg = logg
+    sme.monh = monh
+
+    # Start SME solver
+    sme = synthesize_spectrum(sme)
+
+    # Save results
+    makedirs(dirname(out_file), exist_ok=True)
+    sme.save(out_file)
+
+    # Plot results
+    makedirs(dirname(plot_file), exist_ok=True)
+    fig = plot_plotly.FinalPlot(sme)
+    fig.save(filename=plot_file)

examples/parallel.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+# Run GNU parallel using the parallel.py script in this folder
+# by passing 3 parameters to it (teff, logg, monh)
+# For each parameter there are three values, resulting in
+# a total of 27 different runs
+
+# Format for the call is:
+# parallel cmd ::: p1 ::: p2
+# where cmd is the command to be executed (here calling the python script with
+# three command line parameters), and p1 and p2 are the parameters to pass to the script
+# With keywords:
+# --bar : show a progress bar
+# --joblog parallel.log : save runtime data about the runs in parallel.log
+# --header : : the first value of each parameter list is its header, which is not used otherwise
+# --results ./log : save the stdout and stderr of each run to logfiles in the log folder.
+#                   These logfiles are seperate from the regular logfiles created by PySME,
+#
+# The "normal" stdout is passed to dev/null, since we don't need it and only want the progress bar
+#
+# For the full documentation on GNU parallel see https://www.gnu.org/software/parallel/parallel.html
+
+parallel --bar --joblog parallel.log --header : --results log/ "python parallel.py {teff} {logg} {monh}" ::: teff 5000 5500 6000 ::: logg 4 4.2 4.4 ::: monh -0.5 0 0.5 > /dev/null