Support for 2tag anchoredMC

MC/bin/o2_dpg_workflow_runner.py

@@ -470,8 +470,44 @@ def update_resource_estimates(workflow, resource_json):
 # a python dictionary
 def get_alienv_software_environment(packagestring):
     """
-    packagestring is something like O2::v202298081-1,O2Physics::xxx
+    packagestring is something like O2::v202298081-1,O2Physics::xxx representing packages
+    published on CVMFS ... or ... a file containing directly the software environment to apply
     """
+
+    # the trivial cases do nothing
+    if packagestring == None or packagestring == "" or packagestring == "None":
+        return {}
+
+    def load_env_file(env_file):
+        """Transform an environment file generated with 'export > env.txt' into a python dictionary."""
+        env_vars = {}
+        with open(env_file, "r") as f:
+          for line in f:
+            line = line.strip()
+
+            # Ignore empty lines or comments
+            if not line or line.startswith("#"):
+                continue
+
+            # Remove 'declare -x ' if present
+            if line.startswith("declare -x "):
+                line = line.replace("declare -x ", "", 1)
+
+            # Handle case: "FOO" without "=" (assign empty string)
+            if "=" not in line:
+                key, value = line.strip(), ""
+            else:
+                key, value = line.split("=", 1)
+                value = value.strip('"')  # Remove surrounding quotes if present
+
+            env_vars[key.strip()] = value
+        return env_vars
+
+    # see if this is a file
+    if os.path.exists(packagestring) and os.path.isfile(packagestring):
+       actionlogger.info("Taking software environment from file " + packagestring)
+       return load_env_file(packagestring)
+
     # alienv printenv packagestring --> dictionary
     # for the moment this works with CVMFS only
     cmd="/cvmfs/alice.cern.ch/bin/alienv printenv " + packagestring
@@ -1089,19 +1125,28 @@ def submit(self, tid, nice):
           return subprocess.Popen(['/bin/bash','-c',drycommand], cwd=workdir)
 
       taskenv = os.environ.copy()
-      # add task specific environment
-      if self.workflowspec['stages'][tid].get('env')!=None:
-          taskenv.update(self.workflowspec['stages'][tid]['env'])
-
       # apply specific (non-default) software version, if any
       # (this was setup earlier)
       alternative_env = self.alternative_envs.get(tid, None)
-      if alternative_env != None:
+      if alternative_env != None and len(alternative_env) > 0:
           actionlogger.info('Applying alternative software environment to task ' + self.idtotask[tid])
-          for entry in alternative_env:
+          if alternative_env.get('TERM') != None:
+              # the environment is a complete environment
+              taskenv = {}
+              taskenv = alternative_env
+          else:
+            for entry in alternative_env:
               # overwrite what is present in default
               taskenv[entry] = alternative_env[entry]
 
+      # add task specific environment
+      if self.workflowspec['stages'][tid].get('env')!=None:
+          taskenv.update(self.workflowspec['stages'][tid]['env'])
+
+      # envfilename = "taskenv_" + str(tid) + ".json"
+      # with open(envfilename, "w") as file:
+      #    json.dump(taskenv, file, indent=2)
+
       p = psutil.Popen(['/bin/bash','-c',c], cwd=workdir, env=taskenv)
       try:
           p.nice(nice)
@@ -1406,7 +1451,7 @@ def get_tar_command(dir='./', flags='cf', findtype='f', filename='checkpoint.tar
 
     def init_alternative_software_environments(self):
         """
-        Initiatialises alternative software environments for specific tasks, if there
+        Initialises alternative software environments for specific tasks, if there
         is an annotation in the workflow specificiation.
         """
 

MC/bin/o2dpg_sim_config.py

@@ -180,7 +180,7 @@ def parse_dpl_help_output(executable, envfile):
 
         # the DEVNULL is important for o2-dpl workflows not to hang on non-interactive missing tty environments
         # it is cleaner that the echo | trick
-        output = subprocess.check_output([executable, "--help", "full"], env=env, text=True, stdin=subprocess.DEVNULL, timeout = 10)
+        output = subprocess.check_output([executable, "--help", "full"], env=env, text=True, stdin=subprocess.DEVNULL, timeout = 100)
     except subprocess.CalledProcessError:
         return {}, {}
 
@@ -211,6 +211,5 @@ def get_dpl_options_for_executable(executable, envfile):
 
 def option_if_available(executable, option, envfile = None):
     """Checks if an option is available for a given executable and returns it as a string. Otherwise empty string"""
-    # _, inverse_lookup = get_dpl_options_for_executable(executable, envfile)
-    # return ' ' + option if option in inverse_lookup else ''
-    return option
+    _, inverse_lookup = get_dpl_options_for_executable(executable, envfile)
+    return ' ' + option if option in inverse_lookup else ''

MC/bin/o2dpg_sim_workflow.py

@@ -1603,6 +1603,7 @@ def addQCPerTF(taskName, needs, readerCommand, configFilePath, objectsFile=''):
    AOD_merge_task['cmd'] += ' o2-aod-merger --input aodmerge_input.txt --output AO2D.root'
    # produce MonaLisa event stat file
    AOD_merge_task['cmd'] += ' ; ${O2DPG_ROOT}/MC/bin/o2dpg_determine_eventstat.py'
+   AOD_merge_task['alternative_alienv_package'] = "None" # we want latest software for this step
    workflow['stages'].append(AOD_merge_task)
 
    job_merging = False

MC/bin/o2dpg_sim_workflow_anchored.py

@@ -14,6 +14,8 @@
 import json
 import math
 import pandas as pd
+import subprocess
+import shlex
 
 # Creates a time anchored MC workflow; positioned within a given run-number (as function of production size etc)
 
@@ -542,7 +544,14 @@ def main():
       print ("TIMESTAMP IS EXCLUDED IN RUN")
     else:
       print ("Creating time-anchored workflow...")
-      os.system(cmd)
+      print ("Executing: " + cmd)
+      # os.system(cmd)
+      try:
+        cmd_list = shlex.split(os.path.expandvars(cmd))
+        output = subprocess.check_output(cmd_list, text=True, stdin=subprocess.DEVNULL, timeout = 120)
+      except subprocess.CalledProcessError:
+        return {}, {}
+
 
 if __name__ == "__main__":
   sys.exit(main())

MC/bin/o2dpg_workflow_utils.py

@@ -307,7 +307,8 @@ def matches_or_inherits_label(taskid, label, cache):
     for taskid in range(len(workflowspec['stages'])):
         if (matches_or_inherits_label(taskid, "RECO", matches_label)):
            # now we do the final adjust (as annotation) in the workflow itself
-           workflowspec['stages'][taskid]["alternative_alienv_package"] = package
+           if workflowspec['stages'][taskid].get("alternative_alienv_package") == None:
+              workflowspec['stages'][taskid]["alternative_alienv_package"] = package
 
 def merge_dicts(dict1, dict2):
     """

MC/run/ANCHOR/anchorMC.sh

@@ -282,7 +282,9 @@ remainingargs="${remainingargs} -productionTag ${ALIEN_JDL_LPMPRODUCTIONTAG:-ali
 # since the last passed argument wins, e.g. -productionTag cannot be overwritten by the user
 remainingargs="${ALIEN_JDL_ANCHOR_SIM_OPTIONS} ${remainingargs} --anchor-config config-json.json"
 # apply software tagging choice
-remainingargs="${remainingargs} ${ALIEN_JDL_O2DPG_ASYNC_RECO_TAG:+--alternative-reco-software ${ALIEN_JDL_O2DPG_ASYNC_RECO_TAG}}"
+# remainingargs="${remainingargs} ${ALIEN_JDL_O2DPG_ASYNC_RECO_TAG:+--alternative-reco-software ${ALIEN_JDL_O2DPG_ASYNC_RECO_TAG}}"
+remainingargs="${remainingargs} ${ALIEN_JDL_O2DPG_ASYNC_RECO_TAG:+--alternative-reco-software ${PWD}/env_async.env}"
+
 
 echo_info "baseargs passed to o2dpg_sim_workflow_anchored.py: ${baseargs}"
 echo_info "remainingargs forwarded to o2dpg_sim_workflow.py: ${remainingargs}"