flexibility in camb,ngenic,gadget2 param filenames in lenstools.submi…

…ssion

lenstools/pipeline/simulation.py

@@ -761,7 +761,7 @@ def getModel(self,cosmo_id):
 	##########################################Job submission scripts###########################################################################
 	###########################################################################################################################################
 
-	def writeCAMBSubmission(self,realization_list,job_settings,job_handler,chunks=1,**kwargs):
+	def writeCAMBSubmission(self,realization_list,job_settings,job_handler,config_file="camb.param",chunks=1,**kwargs):
 
 		"""
 		Writes CAMB submission script
@@ -778,6 +778,9 @@ def writeCAMBSubmission(self,realization_list,job_settings,job_handler,chunks=1,
 		:param job_handler: handler of the cluster specific features (job scheduler, architecture, etc...)
 		:type job_handler: JobHandler
 
+		:param config_file: name of the CAMB configuration file
+		:type config_file: str.
+
 		:param kwargs: you can set one_script=True to include all the executables sequentially in a single script
 		:type kwargs: dict.
 
@@ -829,7 +832,7 @@ def writeCAMBSubmission(self,realization_list,job_settings,job_handler,chunks=1,
 				box_size = float(box_size) * model.Mpc_over_h
 				collection = model.getCollection(box_size=box_size,nside=nside)
 
-				parameter_file = os.path.join(collection.home_subdir,"camb.param")
+				parameter_file = os.path.join(collection.home_subdir,config_file)
 				if not(self.syshandler.exists(parameter_file)):
 					raise IOError("CAMB parameter file at {0} does not exist yet!".format(parameter_file))
 
@@ -867,7 +870,7 @@ def writeCAMBSubmission(self,realization_list,job_settings,job_handler,chunks=1,
 
 	############################################################################################################################################
 
-	def writeNGenICSubmission(self,realization_list,job_settings,job_handler,chunks=1,**kwargs):
+	def writeNGenICSubmission(self,realization_list,job_settings,job_handler,config_file="ngenic.param",chunks=1,**kwargs):
 
 		"""
 		Writes NGenIC submission script
@@ -884,6 +887,9 @@ def writeNGenICSubmission(self,realization_list,job_settings,job_handler,chunks=
 		:param job_handler: handler of the cluster specific features (job scheduler, architecture, etc...)
 		:type job_handler: JobHandler
 
+		:param config_file: name of the NGenIC config file
+		:type config_file: str.
+
 		:param kwargs: you can set one_script=True to include all the executables sequentially in a single script
 		:type kwargs: dict.
 
@@ -930,7 +936,7 @@ def writeNGenICSubmission(self,realization_list,job_settings,job_handler,chunks=
 
 				r = collection.getRealization(int(ic_number.strip("ic")))
 
-				parameter_file = os.path.join(r.home_subdir,"ngenic.param")
+				parameter_file = os.path.join(r.home_subdir,config_file)
 				if not(self.syshandler.exists(parameter_file)):
 					raise IOError("NGenIC parameter file at {0} does not exist yet!".format(parameter_file))
 
@@ -973,7 +979,7 @@ def writeNGenICSubmission(self,realization_list,job_settings,job_handler,chunks=
 	############################################################################################################################################
 
 
-	def writeNbodySubmission(self,realization_list,job_settings,job_handler,chunks=1,**kwargs):
+	def writeNbodySubmission(self,realization_list,job_settings,job_handler,config_file="gadget2.param",chunks=1,**kwargs):
 
 		"""
 		Writes N-body simulation submission script
@@ -990,6 +996,9 @@ def writeNbodySubmission(self,realization_list,job_settings,job_handler,chunks=1
 		:param job_handler: handler of the cluster specific features (job scheduler, architecture, etc...)
 		:type job_handler: JobHandler
 
+		:param config_file: name of the Nbody configuration file
+		:type config_file: str.
+
 		:param kwargs: you can set one_script=True to include all the executables sequentially in a single script
 		:type kwargs: dict.
 
@@ -1046,7 +1055,7 @@ def writeNbodySubmission(self,realization_list,job_settings,job_handler,chunks=1
 
 				r = collection.getRealization(int(ic_number.strip("ic")))
 
-				parameter_file = os.path.join(r.home_subdir,"gadget2.param")
+				parameter_file = os.path.join(r.home_subdir,config_file)
 				if not(self.syshandler.exists(parameter_file)):
 					raise IOError("Gadget2 parameter file at {0} does not exist yet!".format(parameter_file))
 

scripts/lenstools.submission

@@ -36,7 +36,7 @@ system2handler = {
 #Parse command line options
 parser = argparse.ArgumentParser()
 parser.add_argument("-e","--environment",dest="env_file",action="store",type=str,default=lensData("environment_default.ini"),help="environment option file")
-parser.add_argument("-o","--options",dest="exec_options",action="store",type=str,default=lensData("lens_default.ini"),help="configuration file to pass to the executable (planes or raytracing)")
+parser.add_argument("-o","--options",dest="exec_options",action="store",type=str,default=None,help="name of the configuration file to pass to the executable")
 parser.add_argument("-O","--one",dest="one_script",action="store_true",default=False,help="Use to collapse all the lens planes and raytracing executables in a single job script")
 parser.add_argument("-j","--job",dest="job_options_file",action="store",type=str,default=lensData("job_default.ini"),help="job specifications file")
 parser.add_argument("-t","--type",dest="job_type",action="store",type=str,default=None,help="type of job submission (Gadget,NGenIC,etc...)")
@@ -102,23 +102,39 @@ if job_type=="camb":
 	print("[+] Generating CAMB submission script")
 	print("[*] Reading job specifications from {0} section {1}".format(cmd_args.job_options_file,section))
 	job_settings = JobSettings.read(cmd_args.job_options_file,section)
-	batch.writeCAMBSubmission(realizations,job_settings,job_handler,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+
+	#Write script
+	if cmd_args.exec_options is not None:
+		batch.writeCAMBSubmission(realizations,job_settings,job_handler,config_file=cmd_args.exec_options,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+	else:
+		batch.writeCAMBSubmission(realizations,job_settings,job_handler,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
 
 elif job_type=="ngenic":
 
 	section = type2section[job_type]
 	print("[+] Generating N-GenIC submission script")
 	print("[*] Reading job specifications from {0} section {1}".format(cmd_args.job_options_file,section))
 	job_settings = JobSettings.read(cmd_args.job_options_file,section)
-	batch.writeNGenICSubmission(realizations,job_settings,job_handler,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+
+	#Write script
+	if cmd_args.exec_options is not None:
+		batch.writeNGenICSubmission(realizations,job_settings,job_handler,config_file=cmd_args.exec_options,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+	else:
+		batch.writeNGenICSubmission(realizations,job_settings,job_handler,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+
 
 elif job_type in ["nbody","gadget2"]:
 
 	section = type2section[job_type]
 	print("[+] Generating Gadget2 submission script")
 	print("[*] Reading job specifications from {0} section {1}".format(cmd_args.job_options_file,section))
 	job_settings = JobSettings.read(cmd_args.job_options_file,section)
-	batch.writeNbodySubmission(realizations,job_settings,job_handler,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+
+	#Write script
+	if cmd_args.exec_options is not None:
+		batch.writeNbodySubmission(realizations,job_settings,job_handler,config_file=cmd_args.exec_options,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
+	else:
+		batch.writeNbodySubmission(realizations,job_settings,job_handler,chunks=cmd_args.chunks,one_script=cmd_args.one_script)
 
 elif job_type=="planes":