automatically find date, which, bash, env etc. using shutil.which()

binarycpython/utils/condor.py

@@ -216,7 +216,7 @@ class condor():
 
             # build the grid command
             grid_command = [
-                os.path.join("/usr","bin","env"),
+                str(self.grid_options['condor_env']),
                 sys.executable,
                 pyscriptpath,
             ] + sys.argv[1:] + [

binarycpython/utils/grid_options_defaults.py

@@ -15,6 +15,7 @@ All the options starting with _ should not be changed by the user except when yo
 
 import datetime
 import os
+import shutil
 import sys
 
 from binarycpython.utils.custom_logging_functions import temp_dir
@@ -207,9 +208,10 @@ class grid_options_defaults():
             "slurm_extra_settings": {},  # Dictionary of extra settings for Slurm to put in its launch script.
             "slurm_sbatch": "sbatch", # sbatch command
             "slurm_restart_dir" : None, # restart Slurm jobs from this directory
-            "slurm_bash" : "/bin/bash", # bash location for Slurm
-            "slurm_pwd" : "/usr/bin/pwd", # pwd command location for Slurm
-            "slurm_date" : "/usr/bin/date", # bash location for Slurm
+            "slurm_env" : shutil.which("env"), # env location for Slurm
+            "slurm_bash" : shutil.which("bash"), # bash location for Slurm
+            "slurm_pwd" : shutil.which("pwd"), # pwd command location for Slurm
+            "slurm_date" : shutil.which("date"), # bash location for Slurm
 
             ########################################
             # Condor stuff
@@ -239,10 +241,10 @@ class grid_options_defaults():
             'condor_save_joined_file':0, # if 1 then results/joined contains the results
             # (useful for debugging, otherwise a lot of work)
             'condor_requirements':'', # job requirements
-            'condor_usr_bin_env' : '/usr/bin/env', # /usr/bin/env location
-            'condor_bash' : '/bin/bash', # bash executable location
-            "condor_pwd" : "/usr/bin/pwd", # pwd command location for Condor
-            "condor_date" : "/usr/bin/date", # bash location for Condor
+            'condor_usr_bin_env' : shutil.which("env"), # /usr/bin/env location
+            'condor_bash' : shutil.which("bash"), # bash executable location
+            "condor_pwd" : shutil.which("pwd"), # pwd command location for Condor
+            "condor_date" : shutil.which("date"), # bash location for Condor
             "condor_array_max_jobs" : None, # override for the max number of concurrent array jobs
             "condor_initial_dir" : None, # directory from which condor is run, if None is the directory in which your script is run
             "condor_submit" : "condor_submit", # the condor_submit command

binarycpython/utils/slurm.py

@@ -175,19 +175,19 @@ class slurm():
             # run a grid of stars only, leaving the results
             # in the appropriate outfile
             return False
-        
+
         elif self.grid_options['slurm'] == 3:
             # joining : set the evolution type to "join" and return
             # False to continue
             self.grid_options['evolution_type'] = 'join'
             return False
-        
+
         elif self.grid_options['slurm'] == 1:
             # if slurm=1,  we should have no evolution type, we
             # set up the Slurm scripts and get them evolving
             # in a Slurm array
             self.grid_options['evolution_type'] = None
-            
+
             # make dirs
             self.make_slurm_dirs()
 
@@ -219,7 +219,7 @@ class slurm():
 
             # build the grid command
             grid_command = [
-                os.path.join("/usr","bin","env"),
+                str(grid_options['slurm_env'])
                 sys.executable,
                 str(lib_programname.get_path_executed_script()),
             ] + sys.argv[1:] + [
@@ -351,4 +351,3 @@ echo {slurm_dir}/results/$SLURM_ARRAY_JOB_ID.$SLURM_ARRAY_TASK_ID.gz >> {slurm_d
 
         # return True so we exit immediately
         return True
-