Changeset 5989

Timestamp:

Aug 19, 2020, 8:19:18 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1259: Add support for Slurm

Implemented support for setting options that go into the sbatch file.

Location:

extensions/net.sf.basedb.opengrid/trunk/src/net/sf/basedb/opengrid

Files:

• config/JobConfig.java (modified) (3 diffs)
• engine/SlurmEngine.java (modified) (3 diffs)

extensions/net.sf.basedb.opengrid/trunk/src/net/sf/basedb/opengrid/config/JobConfig.java

@@ -92 +92 @@
   
   private Map<String, String> qsubOptions;
+  private Map<String, String> sbatchOptions;
   
   /**
@@ -103 +104 @@
     this.nice = null;
     this.qsubOptions = new LinkedHashMap<>();
+    this.sbatchOptions = new LinkedHashMap<>();
   }
 
@@ -254 +256 @@
   }
   
-  /**
-    The priority must be between -1023 and +1024. Other generic qsub
+  
+  /**
+    Set an option for the 'sbatch' command (Slurm). See 
+    https://slurm.schedmd.com/sbatch.html for
+    a lot more information. The options will go into the
+    script file using the #SBATCH prefix. It is not recommended
+    to override options that are automatically set when submitting
+    the job. This is currently: TODO (-terse, -S, -N, -wd, -o, -e 
+    and -p).
+    
+    @param option The name of the option (with or without the hyphen)
+    @param value The value of the option (null will remove it)
+    @since 1.4
+  */
+  public void setSbatchOption(String option, String value)
+  {
+    checkLocked("setSbatchOption(" + option + ")");
+    if (option == null) return;
+    if (option.startsWith("-")) option = option.substring(1); // Remove '-'
+    if (option.startsWith("-")) option = option.substring(1); // Remove '--'
+    if (value == null)
+    {
+      sbatchOptions.remove(option);
+    }
+    else
+    {
+      sbatchOptions.put(option, value);
+    }
+  }
+
+  /**
+    Get the value of a sbatch option.
+    @param option The name of the option (with or without the hyphen)
+    @since 1.4
+  */
+  public String getSbatchOption(String option)
+  {
+    if (option == null) return null;
+    if (option.startsWith("-")) option = option.substring(1); // Remove '-'
+    if (option.startsWith("-")) option = option.substring(1); // Remove '--'
+    return sbatchOptions.get(option);
+  }
+  
+  /**
+    Get all options that has been specified for sbatch so far.
+    @return A read-only map with the sbatch options
+    @since 1.4
+  */
+  public Map<String, String> getSbatchOptions()
+  {
+    return Collections.unmodifiableMap(sbatchOptions);
+  }
+
+  /**
+    Add all sbatch options in this configuration to the script.
+    Each option will create a line:
+    #SBATCH --&lt;option&gt;=&lt;value&gt;
+    or:
+    #SBATCH -&lt;option&gt;=&lt;value&gt;
+  */
+  public void appendSbatchOptionsToScript(StringBuilder script, Set<String> ignore)
+  {
+    for (Map.Entry<String, String> entry : sbatchOptions.entrySet())
+    {
+      String option = entry.getKey();
+      if (ignore == null || !ignore.contains(option))
+      {
+        String prefix = option.length() == 1 ? "-" : "--";
+        script.append("#SBATCH " + prefix + option + "=" + entry.getValue() + "\n");
+      }
+    }
+  }
+  
+  /**
+    The priority must be between -1023 and +1024 and 'nice' must be
+    between -2147483645 and +2147483645. Other generic qsub or sbatch
     options are not checked.
   */

extensions/net.sf.basedb.opengrid/trunk/src/net/sf/basedb/opengrid/engine/SlurmEngine.java

@@ -36 +36 @@
       LoggerFactory.getLogger(SlurmEngine.class);
 
+  private static final Set<String> ignoredSbatchOptions = 
+      new HashSet<>(); // TODO
+
   public SlurmEngine()
   {}
@@ -75 +78 @@
     script.append("#SBATCH --nodes=1\n"); // 1 task on 1 node
     script.append("#SBATCH --ntasks=1\n"); 
-    script.append("#SBATCH --cpus-per-task=2\n"); 
+//    script.append("#SBATCH --cpus-per-task=2\n"); 
     
     if (config.getSlurmNice() != null)
@@ -81 +84 @@
       script.append("#SBATCH --nice=" + config.getSlurmNice() + "\n");
     }
-//    config.appendQsubOptionsToScript(script, ignoredQsubOptions);
+    config.appendSbatchOptionsToScript(script, ignoredSbatchOptions);
     
     script.append("# --- end sbatch options ---\n");