desi_proc_tilenight processes skysub with --laststeps=skysub

py/desispec/scripts/proc_tilenight.py

@@ -70,6 +70,13 @@ def main(args=None, comm=None):
     if comm is not None:
         exptable = comm.bcast(exptable, root=0)
 
+    #- Set the eligible laststep values for different processing steps
+    if args.laststeps is None:
+        prestd_laststeps = ['all', 'fluxcalib', 'skysub']
+        jntpst_laststeps = ['all', 'fluxcalib']
+    else:
+        prestd_laststeps = jntpst_laststeps = args.laststeps
+
     #- Determine expids and cameras for a tile night
     keep  = exptable['OBSTYPE'] == 'science'
     keep &= exptable['TILEID']  == int(args.tileid)
@@ -100,9 +107,9 @@ def main(args=None, comm=None):
             prestd_camwords[expids[i]] = camword
 
         laststep = str(exptable['LASTSTEP'][i]).lower()
-        if laststep in ('all', 'fluxcalib', 'skysub'):
+        if laststep in prestd_laststeps:
             prestdstar_expids.append(expid)
-        if laststep in ('all', 'fluxcalib'):
+        if laststep in jntpst_laststeps:
             stdstar_expids.append(expid)
             poststdstar_expids.append(expid)
 

py/desispec/scripts/submit_night.py

@@ -150,7 +150,8 @@ def submit_night(night, proc_obstypes=None, z_submit_types=None, queue='realtime
 
     ## If laststeps not defined, default is only LASTSTEP=='all' exposures for non-tilenight runs
     if laststeps is None:
-        laststeps = ['all',]
+        if not use_tilenight:
+            laststeps = ['all',]
     else:
         laststep_options = get_last_step_options()
         for laststep in laststeps:
@@ -400,7 +401,8 @@ def submit_night(night, proc_obstypes=None, z_submit_types=None, queue='realtime
                                                     check_for_outputs=check_for_outputs,
                                                     resubmit_partial_complete=resubmit_partial_complete,
                                                     z_submit_types=cur_z_submit_types,
-                                                    system_name=system_name,use_specter=use_specter)
+                                                    system_name=system_name,use_specter=use_specter,
+                                                    laststeps=laststeps)
             else:
                 ## If running redshifts and there is a future exposure of the same tile
                 ## then only run per exposure redshifts until then

py/desispec/workflow/desi_proc_funcs.py

@@ -134,10 +134,17 @@ def add_desi_proc_tilenight_terms(parser):
     """
     parser.add_argument("-t", "--tileid", type=str, help="Tile ID")
     parser.add_argument("-d", "--dryrun", action="store_true", help="show commands only, do not run")
-    parser.add_argument("--laststeps", type=str, default='all',
-                        help="Comma separated list of LASTSTEP's to process "
+    parser.add_argument("--laststeps", type=str, default=None,
+                        help="Comma separated list of LASTSTEP values "
                              + "(e.g. all, skysub, fluxcalib, ignore); "
-                             + "by default we only process 'all'.")
+                             + "by default, exposures with LASTSTEP "
+                             + "'all' and 'fluxcalib' will be processed "
+                             + "to the poststdstar step, and those with "
+                             + "LASTSTEP 'skysub' to the prestdstar step. "
+                             + "If specified, exposures with LASTSTEP "
+                             + "values in the list will be processed to the "
+                             + "poststdstar step, and all others will not "
+                             + "be processed at all.")
 
     return parser
 
@@ -873,7 +880,7 @@ def create_desi_proc_batch_script(night, exp, cameras, jobdesc, queue, runtime=N
 
 def create_desi_proc_tilenight_batch_script(night, exp, tileid, ncameras, queue, runtime=None, batch_opts=None,
                                   system_name=None, mpistdstars=True, use_specter=False,
-                                  no_gpu=False,
+                                  no_gpu=False, laststeps=None
                                   ):
     """
     Generate a SLURM batch script to be submitted to the slurm scheduler to run desi_proc.
@@ -884,6 +891,7 @@ def create_desi_proc_tilenight_batch_script(night, exp, tileid, ncameras, queue,
         tileid: str or int. The tile id for the data.
         ncameras: int. The number of cameras used for joint fitting.
         queue: str. Queue to be used.
+        laststeps (list of str, optional): A list of laststeps to pass as the laststeps argument to tilenight.
 
     Options:
         runtime: str. Timeout wall clock time.
@@ -976,6 +984,9 @@ def create_desi_proc_tilenight_batch_script(night, exp, tileid, ncameras, queue,
         elif use_specter:
             cmd += f' --use-specter'
 
+        if laststeps is not None:
+            cmd += f' --laststeps="{",".join(laststeps)}"'
+
         cmd += f' --timingfile {timingfile}'
 
         fx.write(f'# running a tile-night\n')

py/desispec/workflow/procfuncs.py

@@ -198,7 +198,7 @@ def check_for_outputs_on_disk(prow, resubmit_partial_complete=True):
 
 def create_and_submit(prow, queue='realtime', reservation=None, dry_run=0, joint=False,
                       strictly_successful=False, check_for_outputs=True, resubmit_partial_complete=True,
-                      system_name=None,use_specter=False):
+                      system_name=None,use_specter=False,laststeps=None):
     """
     Wrapper script that takes a processing table row and three modifier keywords, creates a submission script for the
     compute nodes, and then submits that script to the Slurm scheduler with appropriate dependencies.
@@ -225,6 +225,7 @@ def create_and_submit(prow, queue='realtime', reservation=None, dry_run=0, joint
             remaining cameras not found to exist.
         system_name (str): batch system name, e.g. cori-haswell or perlmutter-gpu
         use_specter (bool, optional): Default is False. If True, use specter, otherwise use gpu_specter by default.
+        laststeps (list of str, optional): A list of laststeps to pass as the laststeps argument to tilenight.
 
     Returns:
         Table.Row or dict: The same prow type and keywords as input except with modified values updated to reflect
@@ -241,7 +242,7 @@ def create_and_submit(prow, queue='realtime', reservation=None, dry_run=0, joint
         if prow['STATUS'].upper() == 'COMPLETED':
             return prow
 
-    prow = create_batch_script(prow, queue=queue, dry_run=dry_run, joint=joint, system_name=system_name, use_specter=use_specter)
+    prow = create_batch_script(prow, queue=queue, dry_run=dry_run, joint=joint, system_name=system_name, use_specter=use_specter,laststeps=laststeps)
     prow = submit_batch_script(prow, reservation=reservation, dry_run=dry_run, strictly_successful=strictly_successful)
     ## If resubmitted partial, the PROCCAMWORD and SCRIPTNAME will correspond to the pruned values. But we want to
     ## retain the full job's value, so get those from the old job.
@@ -320,7 +321,7 @@ def desi_proc_joint_fit_command(prow, queue=None):
         cmd += f' -e {expid_str}'
     return cmd
 
-def create_batch_script(prow, queue='realtime', dry_run=0, joint=False, system_name=None, use_specter=False):
+def create_batch_script(prow, queue='realtime', dry_run=0, joint=False, system_name=None, use_specter=False, laststeps=None):
     """
     Wrapper script that takes a processing table row and three modifier keywords and creates a submission script for the
     compute nodes.
@@ -336,6 +337,7 @@ def create_batch_script(prow, queue='realtime', dry_run=0, joint=False, system_n
             run with desi_proc_joint_fit when not using tilenight. Default is False.
         system_name (str): batch system name, e.g. cori-haswell or perlmutter-gpu
         use_specter, bool, optional. Default is False. If True, use specter, otherwise use gpu_specter by default.
+        laststeps (list of str, optional): A list of laststeps to pass as the laststeps argument to tilenight.
 
     Returns:
         Table.Row or dict: The same prow type and keywords as input except with modified values updated values for
@@ -399,7 +401,8 @@ def create_batch_script(prow, queue='realtime', dry_run=0, joint=False, system_n
                                                                queue=queue,
                                                                mpistdstars=True,
                                                                use_specter=use_specter,
-                                                               system_name=system_name)
+                                                               system_name=system_name,
+                                                               laststeps=laststeps)
             else:
                 log.info("Running: {}".format(cmd.split()))
                 scriptpathname = create_desi_proc_batch_script(
@@ -1148,7 +1151,7 @@ def submit_redshifts(ptable, prows, tnight, internal_id, queue, reservation,
 #########################################
 def submit_tilenight(ptable, prows, calibjobs, internal_id, queue, reservation,
               dry_run=0, strictly_successful=False, resubmit_partial_complete=True,
-              system_name=None,use_specter=False):
+              system_name=None,use_specter=False,laststeps=None):
     """
     Given a set of prows, this generates a processing table row, creates a batch script, and submits the appropriate
     tilenight job given by descriptor. The returned ptable has all of these rows added to the
@@ -1175,6 +1178,7 @@ def submit_tilenight(ptable, prows, calibjobs, internal_id, queue, reservation,
             remaining cameras not found to exist.
         system_name (str): batch system name, e.g. cori-haswell or perlmutter-gpu
         use_specter (bool, optional): Default is False. If True, use specter, otherwise use gpu_specter by default.
+        laststeps (list of str, optional): A list of laststeps to pass as the laststeps argument to tilenight.
 
     Returns:
         tuple: A tuple containing:
@@ -1195,7 +1199,7 @@ def submit_tilenight(ptable, prows, calibjobs, internal_id, queue, reservation,
     tnight_prow = create_and_submit(tnight_prow, queue=queue, reservation=reservation, dry_run=dry_run,
                                    strictly_successful=strictly_successful, check_for_outputs=False,
                                    resubmit_partial_complete=resubmit_partial_complete, system_name=system_name,
-                                   use_specter=use_specter)
+                                   use_specter=use_specter,laststeps=laststeps)
     ptable.add_row(tnight_prow)
 
     return ptable, tnight_prow, internal_id
@@ -1520,7 +1524,8 @@ def checkfor_and_submit_joint_job(ptable, arcs, flats, sciences, calibjobs,
 def submit_tilenight_and_redshifts(ptable, sciences, calibjobs, lasttype, internal_id, dry_run=0,
                                   queue='realtime', reservation=None, strictly_successful=False,
                                   check_for_outputs=True, resubmit_partial_complete=True,
-                                  z_submit_types=None, system_name=None,use_specter=False):
+                                  z_submit_types=None, system_name=None,use_specter=False,
+                                  laststeps=None):
     """
     Takes all the state-ful data from daily processing and determines whether a tilenight job needs to be submitted.
 
@@ -1550,7 +1555,7 @@ def submit_tilenight_and_redshifts(ptable, sciences, calibjobs, lasttype, intern
             exposure. If not specified or None, then no redshifts are submitted.
         system_name (str): batch system name, e.g. cori-haswell, cori-knl, permutter-gpu
         use_specter (bool, optional): Default is False. If True, use specter, otherwise use gpu_specter by default.
-
+        laststeps (list of str, optional): A list of laststeps to pass as the laststeps argument to tilenight.
     Returns:
         tuple: A tuple containing:
 
@@ -1565,7 +1570,8 @@ def submit_tilenight_and_redshifts(ptable, sciences, calibjobs, lasttype, intern
                                              queue=queue, reservation=reservation,
                                              dry_run=dry_run, strictly_successful=strictly_successful,
                                              resubmit_partial_complete=resubmit_partial_complete,
-                                             system_name=system_name,use_specter=use_specter
+                                             system_name=system_name,use_specter=use_specter,
+                                             laststeps=laststeps
                                              )
 
     ptable, internal_id = submit_redshifts(ptable, sciences, tnight, internal_id,