Add exec_prefix option

- This adds the option exec_prefix which can be used for overriding
  the sudo command to use when manipulating jobs.
- This defaults to "sudo -E -u {username}" and is appended to every
  command before it is run.
- The condor_q command did not have this, but likely can be used here.
- Closes: #39

Author: rkdarst

batchspawner/batchspawner.py

@@ -90,6 +90,10 @@ class BatchSpawnerBase(Spawner):
     # override default server ip since batch jobs normally running remotely
     ip = Unicode("0.0.0.0", help="Address for singleuser server to listen at").tag(config=True)
 
+    exec_prefix = Unicode('sudo -E -u {username}', \
+        help="Standard executon prefix (e.g. the default sudo -E -u {username})"
+        ).tag(config=True)
+
     # all these req_foo traits will be available as substvars for templated strings
     req_queue = Unicode('', \
         help="Queue name to submit job to resource manager"
@@ -177,7 +181,8 @@ def cmd_formatted_for_batch(self):
     @gen.coroutine
     def submit_batch_script(self):
         subvars = self.get_req_subvars()
-        cmd = self.batch_submit_cmd.format(**subvars)
+        cmd = self.exec_prefix + ' ' + self.batch_submit_cmd
+        cmd = cmd.format(**subvars)
         subvars['cmd'] = self.cmd_formatted_for_batch()
         if hasattr(self, 'user_options'):
             subvars.update(self.user_options)
@@ -207,7 +212,8 @@ def read_job_state(self):
             return self.job_status
         subvars = self.get_req_subvars()
         subvars['job_id'] = self.job_id
-        cmd = self.batch_query_cmd.format(**subvars)
+        cmd = self.exec_prefix + ' ' + self.batch_query_cmd
+        cmd = cmd.format(**subvars)
         self.log.debug('Spawner querying job: ' + cmd)
         try:
             out = yield run_command(cmd)
@@ -226,7 +232,8 @@ def read_job_state(self):
     def cancel_batch_job(self):
         subvars = self.get_req_subvars()
         subvars['job_id'] = self.job_id
-        cmd = self.batch_cancel_cmd.format(**subvars)
+        cmd = self.exec_prefix + ' ' + self.batch_cancel_cmd
+        cmd = cmd.format(**subvars)
         self.log.info('Cancelling job ' + self.job_id + ': ' + cmd)
         yield run_command(cmd)
 
@@ -420,21 +427,21 @@ class TorqueSpawner(BatchSpawnerRegexStates):
 """).tag(config=True)
 
     # outputs job id string
-    batch_submit_cmd = Unicode('sudo -E -u {username} qsub').tag(config=True)
+    batch_submit_cmd = Unicode('qsub').tag(config=True)
     # outputs job data XML string
-    batch_query_cmd = Unicode('sudo -E -u {username} qstat -x {job_id}').tag(config=True)
-    batch_cancel_cmd = Unicode('sudo -E -u {username} qdel {job_id}').tag(config=True)
+    batch_query_cmd = Unicode('qstat -x {job_id}').tag(config=True)
+    batch_cancel_cmd = Unicode('qdel {job_id}').tag(config=True)
     # search XML string for job_state - [QH] = pending, R = running, [CE] = done
     state_pending_re = Unicode(r'<job_state>[QH]</job_state>').tag(config=True)
     state_running_re = Unicode(r'<job_state>R</job_state>').tag(config=True)
     state_exechost_re = Unicode(r'<exec_host>((?:[\w_-]+\.?)+)/\d+').tag(config=True)
 
 class MoabSpawner(TorqueSpawner):
     # outputs job id string
-    batch_submit_cmd = Unicode('sudo -E -u {username} msub').tag(config=True)
+    batch_submit_cmd = Unicode('msub').tag(config=True)
     # outputs job data XML string
-    batch_query_cmd = Unicode('sudo -E -u {username} mdiag -j {job_id} --xml').tag(config=True)
-    batch_cancel_cmd = Unicode('sudo -E -u {username} mjobctl -c {job_id}').tag(config=True)
+    batch_query_cmd = Unicode('mdiag -j {job_id} --xml').tag(config=True)
+    batch_cancel_cmd = Unicode('mjobctl -c {job_id}').tag(config=True)
     state_pending_re = Unicode(r'State="Idle"').tag(config=True)
     state_running_re = Unicode(r'State="Running"').tag(config=True)
     state_exechost_re = Unicode(r'AllocNodeList="([^\r\n\t\f :"]*)').tag(config=True)
@@ -487,10 +494,10 @@ class SlurmSpawner(UserEnvMixin,BatchSpawnerRegexStates):
 {cmd}
 """).tag(config=True)
     # outputs line like "Submitted batch job 209"
-    batch_submit_cmd = Unicode('sudo -E -u {username} sbatch --parsable').tag(config=True)
+    batch_submit_cmd = Unicode('sbatch --parsable').tag(config=True)
     # outputs status and exec node like "RUNNING hostname"
-    batch_query_cmd = Unicode("sudo -E -u {username} squeue -h -j {job_id} -o '%T %B'").tag(config=True) #
-    batch_cancel_cmd = Unicode('sudo -E -u {username} scancel {job_id}').tag(config=True)
+    batch_query_cmd = Unicode("squeue -h -j {job_id} -o '%T %B'").tag(config=True) #
+    batch_cancel_cmd = Unicode('scancel {job_id}').tag(config=True)
     # use long-form states: PENDING,  CONFIGURING = pending
     #  RUNNING,  COMPLETING = running
     state_pending_re = Unicode(r'^(?:PENDING|CONFIGURING)').tag(config=True)
@@ -532,10 +539,10 @@ class GridengineSpawner(BatchSpawnerBase):
 """).tag(config=True)
 
     # outputs job id string
-    batch_submit_cmd = Unicode('sudo -E -u {username} qsub').tag(config=True)
+    batch_submit_cmd = Unicode('qsub').tag(config=True)
     # outputs job data XML string
-    batch_query_cmd = Unicode('sudo -E -u {username} qstat -xml').tag(config=True)
-    batch_cancel_cmd = Unicode('sudo -E -u {username} qdel {job_id}').tag(config=True)
+    batch_query_cmd = Unicode('qstat -xml').tag(config=True)
+    batch_cancel_cmd = Unicode('qdel {job_id}').tag(config=True)
 
     def parse_job_id(self, output):
         return output.split(' ')[2]
@@ -582,10 +589,10 @@ class CondorSpawner(UserEnvMixin,BatchSpawnerRegexStates):
 """).tag(config=True)
 
     # outputs job id string
-    batch_submit_cmd = Unicode('sudo -E -u {username} condor_submit').tag(config=True)
+    batch_submit_cmd = Unicode('condor_submit').tag(config=True)
     # outputs job data XML string
     batch_query_cmd = Unicode('condor_q {job_id} -format "%s, " JobStatus -format "%s" RemoteHost -format "\n" True').tag(config=True)
-    batch_cancel_cmd = Unicode('sudo -E -u {username} condor_rm {job_id}').tag(config=True)
+    batch_cancel_cmd = Unicode('condor_rm {job_id}').tag(config=True)
     # job status: 1 = pending, 2 = running
     state_pending_re = Unicode(r'^1,').tag(config=True)
     state_running_re = Unicode(r'^2,').tag(config=True)
@@ -618,9 +625,9 @@ class LsfSpawner(BatchSpawnerBase):
     ''').tag(config=True)
 
 
-    batch_submit_cmd = Unicode('sudo -E -u {username} bsub').tag(config=True)
-    batch_query_cmd = Unicode('sudo -E -u {username} bjobs -a -noheader -o "STAT EXEC_HOST" {job_id}').tag(config=True)
-    batch_cancel_cmd = Unicode('sudo -E -u {username} bkill {job_id}').tag(config=True)
+    batch_submit_cmd = Unicode('bsub').tag(config=True)
+    batch_query_cmd = Unicode('bjobs -a -noheader -o "STAT EXEC_HOST" {job_id}').tag(config=True)
+    batch_cancel_cmd = Unicode('bkill {job_id}').tag(config=True)
 
     def get_env(self):
         env = super().get_env()

batchspawner/tests/test_spawners.py

@@ -17,6 +17,7 @@
 testjob  = "12345"
 
 class BatchDummy(BatchSpawnerRegexStates):
+    exec_prefix = ''
     batch_submit_cmd = Unicode('cat > /dev/null; echo '+testjob)
     batch_query_cmd = Unicode('echo RUN '+testhost)
     batch_cancel_cmd = Unicode('echo STOP')