From c8bd3e9c271535cad30de943e391ca6f9e3e59d9 Mon Sep 17 00:00:00 2001
From: karnem <mikhail.karnevskiy@desy.de>
Date: Tue, 11 Jun 2019 12:52:28 +0200
Subject: [PATCH] Add summary job option
---
cal_tools/cal_tools/tools.py | 9 ++++++--
xfel_calibrate/calibrate.py | 42 ++++++++++++++++++++++++++++++++++--
2 files changed, 47 insertions(+), 4 deletions(-)
diff --git a/cal_tools/cal_tools/tools.py b/cal_tools/cal_tools/tools.py
index 904140d10..476a170f7 100644
--- a/cal_tools/cal_tools/tools.py
+++ b/cal_tools/cal_tools/tools.py
@@ -31,9 +31,14 @@ def combine_report(run_path, calibration):
group, name_param, conc_param = "_".join(comps[:-2]), comps[-2], comps[-1]
else:
group, name_param, conc_param = comps[0], "None", "None"
-
+
with open("{}/{}.rst".format(sphinx_path, group), "a") as gfile:
- if conc_param != "None":
+ if conc_param == "summary":
+ title = "{}. {}".format(calibration, "Summary.")
+ gfile.write(title + "\n")
+ gfile.write( "=" *len (title) + "\n")
+ gfile.write("\n")
+ elif conc_param != "None":
title = "{}. {} = {}".format(calibration, name_param, conc_param)
gfile.write(title + "\n")
gfile.write( "=" *len (title) + "\n")
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index a7655aa7b..fff5d3bbf 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -358,9 +358,19 @@ def flatten_list(l):
return "_".join([str(flatten_list(v)) for v in l]) if isinstance(l, list) else l
+def clean_nonfinal_cells(nb):
+ first_cell = False
+ for cell in nb.cells:
+ if not first_cell and cell.cell_type == 'code':
+ first_cell = True
+ continue
+ if '!!!FINAL!!!' not in cell.source:
+ cell.source = ''
+
+
def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
final_job=False, job_list=[], fmtcmd="", cluster_cores=8,
- sequential=False, priority=2):
+ sequential=False, priority=2, dependent=False):
""" Launch a concurrent job on the cluster via SLURM
"""
@@ -376,6 +386,10 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
parms = extract_parameters(nb)
params = parameter_values(parms, **args)
new_nb = replace_definitions(nb, params, execute=False)
+ if dependent:
+ suffix = "summary"
+ clean_nonfinal_cells(new_nb)
+
base_name = nbname.replace(".ipynb", "")
new_name = "{}__{}__{}.ipynb".format(
os.path.basename(base_name), cparm, suffix)
@@ -416,6 +430,12 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
else:
srun_base = []
+ if dependent:
+ srun_dep = "--dependency=afterok"
+ for jobid in job_list:
+ srun_dep += ":{}".format(jobid)
+ srun_base += [srun_dep]
+
srun_base += [os.path.abspath("{}/bin/slurm_calibrate.sh".format(os.path.dirname(__file__))), # path to helper sh
os.path.abspath(nbpath), # path to notebook
python_path, # path to python
@@ -634,15 +654,33 @@ def run():
cvtype = p.type
break
+ run_overall = False
+ for p in parms:
+ if p.name == 'run_overall':
+ run_overall = p.value
+ break
+
for cnum, cval in enumerate(cvals):
jobid = concurrent_run(run_tmp_path, nb, notebook, args,
cvar, [cval, ] if not isinstance(
cval, list) and cvtype is list else cval,
cnum == len(list(cvals)) -
- 1, joblist, fmtcmd,
+ 1 and not run_overall,
+ joblist, fmtcmd,
cluster_cores=cluster_cores, sequential=sequential, priority=priority)
joblist.append(jobid)
+
+ # Run summary job here if needed
+ if run_overall:
+ jobid = concurrent_run(run_tmp_path, nb, os.path.basename(notebook),
+ args,
+ final_job=True, job_list=joblist, fmtcmd=fmtcmd,
+ cluster_cores=cluster_cores,
+ sequential=sequential, priority=priority,
+ dependent=True)
+ joblist.append(jobid)
+
if not all([j is None for j in joblist]):
print("Submitted the following SLURM jobs: {}".format(",".join(joblist)))
--
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