generate canceling script

mcpartools/generator.py

@@ -140,6 +140,9 @@ def run(self):
         # generate submit script
         self.generate_submit_script()
 
+        # generate kill script
+        self.generate_kill_script()
+
         # copy input files
         self.copy_input()
 
@@ -201,6 +204,11 @@ def generate_submit_script(self):
             jobs_no=self.options.jobs_no,
             workspace_dir=self.workspace_dir)
 
+    def generate_kill_script(self):
+        script_path = os.path.join(self.main_dir, self.scheduler.kill_script)
+        logger.debug("Preparation to generate " + script_path)
+        self.scheduler.write_kill_script(script_path)
+
     def copy_input(self):
         indir_name = 'input'
         indir_path = os.path.join(self.main_dir, indir_name)

mcpartools/scheduler/base.py

@@ -25,6 +25,7 @@ def __init__(self, scheduler_options):
 
     submit_script = 'submit.sh'
     main_run_script = 'main_run.sh'
+    kill_script = 'cancel.sh'
 
     def submit_script_body(self, jobs_no, main_dir, workspace_dir):
         from pkg_resources import resource_string
@@ -51,6 +52,12 @@ def main_run_script_body(self, jobs_no, workspace_dir):
                                                           jobs_no=jobs_no)
         return self.main_run_script
 
+    def submit_kill_body(self, ):
+        from pkg_resources import resource_string
+        tpl = resource_string(__name__, self.kill_script_template)
+        self.kill_script = tpl.decode('ascii')
+        return self.kill_script
+
     def write_submit_script(self, main_dir, script_basename, jobs_no, workspace_dir):
         script_path = os.path.join(main_dir, script_basename)
         fd = open(script_path, 'w')
@@ -72,3 +79,10 @@ def write_main_run_script(self, jobs_no, output_dir):
         os.chmod(out_file_path, 0o750)
         logger.debug("Saved main run script: " + out_file_path)
         logger.debug("Output dir " + output_dir)
+
+    def write_kill_script(self, script_path):
+        fd = open(script_path, 'w')
+        fd.write(self.submit_kill_body())
+        fd.close()
+        os.chmod(script_path, 0o750)
+        logger.debug("Saved kill script: " + script_path)

mcpartools/scheduler/data/kill_slurm.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# submit.log is for storing stdout and stderr of submit.sh
+LOGFILE="$(cd $(dirname $0) && pwd)/submit.log"
+
+RE="Job ID: ([0-9]*)"
+
+# no log file. Probably submit.sh not run
+if [ ! -f $LOGFILE ]; then
+    echo "File not found: $LOGFILE"
+    echo "Make sure you run submit script"
+    exit 1
+fi
+
+cat ${LOGFILE} | while read line
+do
+    if [[ ${line} =~ $RE ]];
+    then
+        JOB_ID=${BASH_REMATCH[1]};
+        if [ -n "$JOB_ID" ]
+        then
+            scancel ${JOB_ID}
+            if [ $? -eq 0 ]; then
+                echo "Job with id: $JOB_ID canceled successfully"
+            else
+                echo "Unable to cancel job: $JOB_ID"
+            fi
+        fi
+    fi
+done

mcpartools/scheduler/data/kill_torque.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# submit.log is for storing stdout and stderr of submit.sh
+LOGFILE="$(cd $(dirname $0) && pwd)/submit.log"
+
+RE="Job ID: ([0-9]*\[\])"
+
+# no log file. Probably submit.sh not run
+if [ ! -f $LOGFILE ]; then
+    echo "File not found: $LOGFILE"
+    echo "Make sure you run submit script"
+    exit 1
+fi
+
+cat ${LOGFILE} | while read line
+do
+    if [[ ${line} =~ $RE ]];
+    then
+        JOB_ID=${BASH_REMATCH[1]};
+        if [ -n "$JOB_ID" ]
+        then
+            qdel ${JOB_ID}
+            if [ $? -eq 0 ]; then
+                echo "Job with id: $JOB_ID canceled successfully"
+            else
+                echo "Unable to cancel job: $JOB_ID"
+            fi
+        fi
+    fi
+done

mcpartools/scheduler/slurm.py

@@ -13,3 +13,5 @@ def __init__(self, options_content):
     submit_script_template = os.path.join('data', 'submit_slurm.sh')
 
     main_run_script_template = os.path.join('data', 'run_slurm.sh')
+
+    kill_script_template = os.path.join('data', 'kill_slurm.sh')

mcpartools/scheduler/torque.py

@@ -13,3 +13,5 @@ def __init__(self, options_content):
     submit_script_template = os.path.join('data', 'submit_torque.sh')
 
     main_run_script_template = os.path.join('data', 'run_torque.sh')
+
+    kill_script_template = os.path.join('data', 'kill_torque.sh')