SLURM batch script generator

Do you ever get tired of having to create your SLURM scripts by hand, even though most everything in them is the same, except for that one line command?

This script takes a job name and your command in quotes and then creates the script for you (and runs it for you).

sbatch_run jobname 'ls'

WIll create the following script and run it for you:

    #!/bin/env bash
    #SBATCH -J jobname.sbatch
    #SBATCH -o jobname.sbatch.o_%j
    #SBATCH -e jobname.sbatch.e_%j
    #SBATCH --partition c14,general,HighMem
    #SBATCH --mem 5G
    #SBATCH --cpus-per-task 1
    #SBATCH --nodes 1
    #SBATCH --time 2-0

    ls

sbatch_run

@@ -0,0 +1,114 @@
+#!/bin/env perl6
+
+# Default for memory is 5GB of RAM
+# Default maximum run time is two day (i.e. 48 hours)
+
+constant $DEFAULT_TIME        = '2-0'; # 2 days
+constant $DEFAULT_MEM         = '5G';  # WARNING this will need to be higher for many jobs
+constant $DEFAULT_JOBNAME     = time;
+constant $DEFAULT_PARTITION   = 'c14,general,HighMem';
+constant $DEFAULT_CPUs        = 1;
+
+# job and wrap as positional parameters
+multi MAIN (
+    $job,
+    $wrap,
+
+    :$cpu=$DEFAULT_CPUs,
+Str :$mem=$DEFAULT_MEM,
+    :$time=$DEFAULT_TIME,
+    :$partition=$DEFAULT_PARTITION,
+    :$run=True,
+)
+{
+    MAIN( :$wrap, :$cpu, :$mem, :$job, :$time, :$partition, :$run);
+}
+
+# wrap as a positional parameter
+multi MAIN (
+    $wrap,
+    :$cpu=$DEFAULT_CPUs,
+Str :$mem=$DEFAULT_MEM,
+    :$job=$DEFAULT_JOBNAME,
+    :$time=$DEFAULT_TIME,
+    :$partition=$DEFAULT_PARTITION,
+    :$run=True,
+)
+{
+    MAIN( :$wrap, :$cpu, :$mem, :$job, :$time, :$partition, :$run);
+}
+
+# wrap as a named parameter
+multi MAIN (
+    :$wrap,
+    :$cpu=$DEFAULT_CPUs,
+Str :$mem=$DEFAULT_MEM,
+    :$job=$DEFAULT_JOBNAME,
+    :$time=$DEFAULT_TIME,
+    :$partition=$DEFAULT_PARTITION,
+    :$run=True,
+)
+{
+    my $job_script_name = job_script_name_for($job);
+    my $batch_code      = batch_code(:$mem, :$cpu, :$wrap, :job($job_script_name), :$time, :$partition);
+
+    # Write batch file
+    spurt($job_script_name, $batch_code);
+
+    if ( $run )
+    {
+        # Run batch file
+        run("sbatch", $job_script_name);
+    }
+}
+
+# Create the text for a batch script
+sub batch_code ( :$wrap, :$cpu, :$mem, :$job, :$time, :$partition)
+{
+    # Create batch header
+    my $header = batch_header( :$cpu, :$mem, :$job, :$time, :$partition);
+
+    # Add body to code
+    my $code = "$header\n$wrap";
+
+    return $code;
+}
+
+sub batch_header ( :$cpu, :$mem, :$job, :$time, :$partition)
+{
+    return qq:heredoc/END/;
+    #!/bin/env bash
+    #SBATCH -J $job
+    #SBATCH -o $job.o_%j
+    #SBATCH -e $job.e_%j
+    #SBATCH --partition $partition
+    #SBATCH --mem $mem
+    #SBATCH --cpus-per-task $cpu
+    #SBATCH --nodes 1
+    #SBATCH --time $time
+    END
+}
+
+sub replace_nonword_characters ( $name is copy)  # copies can be modified within a subroutine
+{
+    $name ~~ s:g/\W/_/; # Search globally and replace nonword characters with underscore
+    return $name;
+}
+
+# Create script name based on the job name
+# If needed, make the scriptname versioned to avoid overwriting previous batch files
+sub job_script_name_for ( $job )
+{
+    my $job_name    = replace_nonword_characters($job);
+    my $version     = 0;
+    my $script_name = "$job_name.sbatch";
+
+    # Increment the version number until a unique script name is created
+    while ( $script_name.IO ~~ :e)
+    {
+        $version++;
+        $script_name        = "$job_name.sbatch.$version";
+    }
+
+    return $script_name;
+}