optional hawc2_path in HAWC2PBSFile,

wetb/hawc2/hawc2_pbs_file.py

@@ -5,15 +5,7 @@ from wetb.utils.cluster_tools.os_path import pjoin, relpath, abspath,\
 
 template = Template("""
 
-#===============================================================================
-echo copy hawc2 to scratch
-#===============================================================================
-(flock -x 200
-unzip -u -o -q [hawc2_path]/*.zip -d /scratch/$USER/$PBS_JOBID/hawc2/
-find [hawc2_path]/* ! -name *.zip -exec cp -u -t /scratch/$USER/$PBS_JOBID/hawc2/ {} +
-) 200>/scratch/$USER/$PBS_JOBID/lock_file_hawc2
-mkdir -p /scratch/$USER/$PBS_JOBID/[model_name]/run_[jobname]/[rel_exe_dir]
-cp /scratch/$USER/$PBS_JOBID/hawc2/* /scratch/$USER/$PBS_JOBID/[model_name]/run_[jobname]/[rel_exe_dir]
+[copy_hawc2]
 
 #===============================================================================
 echo copy input
@@ -91,7 +83,7 @@ class HAWC2PBSFile(PBSFile):
     def commands(self):
         rel_exe_dir = relpath(self.exe_dir, self.model_path)
         copy_input_to_scratch, copy_input_to_exe_dir = self.copy_input()
-        return template(hawc2_path=os.path.dirname(cluster_path(self.hawc2_path)),
+        return template(copy_hawc2=self.copy_hawc2(),
                         exe_dir=cluster_path(self.exe_dir),
                         copy_input_to_scratch=copy_input_to_scratch,
                         copy_input_to_exe_dir=copy_input_to_exe_dir,
@@ -103,6 +95,21 @@ class HAWC2PBSFile(PBSFile):
                         model_path=cluster_path(self.model_path),
                         model_name=self.model_name)
 
+    def copy_hawc2(self):
+        copy_hawc2 = Template("""#===============================================================================
+echo copy hawc2 to scratch
+#===============================================================================
+(flock -x 200
+unzip -u -o -q [hawc2_path]/*.zip -d /scratch/$USER/$PBS_JOBID/hawc2/
+find [hawc2_path]/* ! -name *.zip -exec cp -u -t /scratch/$USER/$PBS_JOBID/hawc2/ {} +
+) 200>/scratch/$USER/$PBS_JOBID/lock_file_hawc2
+mkdir -p /scratch/$USER/$PBS_JOBID/[model_name]/run_[jobname]/[rel_exe_dir]
+cp /scratch/$USER/$PBS_JOBID/hawc2/* /scratch/$USER/$PBS_JOBID/[model_name]/run_[jobname]/[rel_exe_dir]""")
+        if self.hawc2_path is None:
+            return ""
+        else:
+            return copy_hawc2(hawc2_path=os.path.dirname(cluster_path(self.hawc2_path)))
+
     def copy_input(self):
         rel_input_files = [relpath(f, self.model_path) for f in self.input_files]
 

wetb/hawc2/htc_file_set.py

@@ -23,17 +23,17 @@ class HTCFileSet():
                 for filename in glob.iglob(htc_path, recursive=True):
                     self.htc_files.append(filename)
 
-    def pbs_files(self, hawc2_path, hawc2_cmd, htc_lst="**/*.htc", queue='workq',
+    def pbs_files(self, hawc2_path, hawc2_cmd, queue='workq', walltime=None,
                   input_files=None, output_files=None, copy_turb=(True, True)):
 
-        return [HTCFile(htc).pbs_file(hawc2_path, hawc2_cmd, queue=queue,
+        return (HTCFile(htc).pbs_file(hawc2_path, hawc2_cmd, queue=queue, walltime=walltime,
                                       input_files=copy.copy(input_files),
                                       output_files=copy.copy(output_files),
-                                      copy_turb=copy_turb) for htc in self.htc_files]
+                                      copy_turb=copy_turb) for htc in self.htc_files)
 
-    def save_pbs_files(self, hawc2_path, hawc2_cmd, htc_lst="**/*.htc", queue='workq',
+    def save_pbs_files(self, hawc2_path=None, hawc2_cmd=JESS_WINE32_HAWC2MB, queue='workq', walltime=None,
                        input_files=None, output_files=None, copy_turb=(True, True)):
-        for pbs in self.pbs_files(hawc2_path, hawc2_cmd, htc_lst, queue=queue,
+        for pbs in self.pbs_files(hawc2_path, hawc2_cmd, queue=queue, walltime=walltime,
                                   input_files=input_files, output_files=output_files,
                                   copy_turb=copy_turb):
             pbs.save(self.model_path)

wetb/utils/cluster_tools/pbsfile.py

@@ -33,6 +33,7 @@ pbs_template = Template('''### Jobid
 #PBS -q [queue]
 cd [workdir]
 mkdir -p stdout
+if [ -z "$PBS_JOBID" ]; then echo "Run using qsub"; exit ; fi
 pwd
 [commands]
 exit

wetb/utils/tests/test_pbs_file.py

@@ -33,6 +33,7 @@ def test_pbs_file_str():
 #PBS -q workq
 cd /home/user/tmp
 mkdir -p stdout
+if [ -z "$PBS_JOBID" ]; then echo "Run using qsub"; exit ; fi
 pwd
 python -c "print('hello world')"
 exit
@@ -83,6 +84,7 @@ def test_pbs_multirunner():
 #PBS -q workq
 cd /home/user/tmp
 mkdir -p stdout
+if [ -z "$PBS_JOBID" ]; then echo "Run using qsub"; exit ; fi
 pwd
 echo "import os
 import glob