Merge 9fed6b0 into sapling-pr-archive-ehellbar

Author: ehellbar

DATA/production/configurations/asyncReco/setenv_extra.sh

@@ -565,6 +565,9 @@ fi
 # ad-hoc options for GPU reco workflow
 export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+=";GPU_global.dEdxDisableResidualGainMap=1;$TRACKTUNETPC;$VDRIFTPARAMOPTION;"
 
+# if ITS is running on GPU we need to give the workflow most options from ITS reco
+has_detector_gpu ITS && export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+=";$CONFIG_EXTRA_PROCESS_o2_its_reco_workflow;"
+
 [[ ! -z $TPCCLUSTERTIMESHIFT ]] && [[ $ALIEN_JDL_LPMPRODUCTIONTYPE != "MC" ]] && export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+=";GPU_rec_tpc.clustersShiftTimebins=$TPCCLUSTERTIMESHIFT;"
 
 # ad-hoc settings for TOF reco

DATA/tools/parse

@@ -143,6 +143,8 @@ for line in f:
                         command_preopt += ' EPN_NODE_MI100=1 EPN_GLOBAL_SCALING="3/2"'
                         if os.getenv('DISABLE_MI100_SERIALIZATION', '0') == '1':
                             command_preopt += ' DISABLE_MI100_SERIALIZATION=1'
+                        if os.getenv('FULL_MI100_SERIALIZATION', '0') == '1':
+                            command_preopt += ' FULL_MI100_SERIALIZATION=1'
                 if reco_num_nodes_override == 0:
                     command_preopt += ' RECO_NUM_NODES_WORKFLOW=' + wf[1]
                 if is_calib_workflow:

GRID/utils/runGRIDContainerized.sh

@@ -15,11 +15,8 @@ else
     echo "Invalid architecture ${ARCH} detected. Exiting"
     exit 1
 fi
-if [ "$ARCH" == "aarch64" ]; then
-  ISAARCH64="1"
-fi
 # we just use the default singularity container (if not already set)
-APPTAINER_CONTAINER=${APPTAINER_CONTAINER:-/cvmfs/alice.cern.ch/containers/fs/singularity/default${ISAARCH64+"-aarch64"}}
+APPTAINER_CONTAINER=${APPTAINER_CONTAINER:-/cvmfs/alice.cern.ch/containers/fs/apptainer/compat_el9-${ARCH}}
 
 # create workdir if not specified externally
 if [ ! "${WORK_DIR}" ]; then
@@ -47,7 +44,21 @@ cp ${ALIEN_KEYFILE} ${WORK_DIR}/userkey.pem
 
 echo "JALIEN_TOKEN_CERT=/workdir/usercert.pem" > ${WORK_DIR}/envfile
 echo "JALIEN_TOKEN_KEY=/workdir/userkey.pem" >> ${WORK_DIR}/envfile
+if [ "${GRID_CVMFS_PACKAGE}" ]; then
+  echo "GRID_CVMFS_PACKAGE=${GRID_CVMFS_PACKAGE}" >> ${WORK_DIR}/envfile
+fi
+
+# load a CVMFS package if we are asked to do so -- but do it as part of the job
+LOADER='if [ "${GRID_CVMFS_PACKAGE}" ]; then
+  /cvmfs/alice.cern.ch/bin/alienv printenv ${GRID_CVMFS_PACKAGE} > cvmfs_env
+  source cvmfs_env
+fi'
+# Inject the block after the first line (shebang)
+JOBSCRIPT=${WORK_DIR}/job.sh
+awk -v block="$LOADER" 'NR==1 {print; print block; next} 1' "$JOBSCRIPT" > tmpfile && mv tmpfile "$JOBSCRIPT"
+chmod +x "${JOBSCRIPT}"
 
 # launch job = script inside the container in the workdir
-/cvmfs/alice.cern.ch/containers/bin/apptainer/current${ISAARCH64+"-aarch64"}/bin/apptainer exec -C -B /cvmfs:/cvmfs,${WORK_DIR}:/workdir  \
-                                                                    --pwd /workdir --env-file ${WORK_DIR}/envfile ${APPTAINER_CONTAINER} /workdir/job.sh
+APPTAINER_EXEC=${APPTAINER_EXEC:-"/cvmfs/alice.cern.ch/containers/bin/apptainer/${ARCH}/current/bin/apptainer"}
+${APPTAINER_SUDO:+sudo} ${APPTAINER_EXEC} exec -C -B /cvmfs:/cvmfs,${WORK_DIR}:/workdir                 \
+                  --pwd /workdir --env-file ${WORK_DIR}/envfile ${APPTAINER_CONTAINER} bash /workdir/job.sh

MC/bin/o2_dpg_workflow_runner.py

@@ -85,7 +85,8 @@ def setup_logger(name, log_file, level=logging.INFO):
     return logger
 
 # first file logger
-actionlogger = setup_logger('pipeline_action_logger', ('pipeline_action_' + str(os.getpid()) + '.log', args.action_logfile)[args.action_logfile!=None], level=logging.DEBUG)
+actionlogger_file = ('pipeline_action_' + str(os.getpid()) + '.log', args.action_logfile)[args.action_logfile!=None]
+actionlogger = setup_logger('pipeline_action_logger', actionlogger_file, level=logging.DEBUG)
 
 # second file logger
 metriclogger = setup_logger('pipeline_metric_logger', ('pipeline_metric_' + str(os.getpid()) + '.log', args.action_logfile)[args.action_logfile!=None])
@@ -1808,5 +1809,46 @@ def speedup_ROOT_Init():
         exit(code)
     actionlogger.info("Running in cgroup")
 
-executor=WorkflowExecutor(args.workflowfile,jmax=int(args.maxjobs),args=args)
-exit (executor.execute())
+
+# This starts the fanotify fileaccess monitoring process
+# if asked for
+o2dpg_filegraph_exec = os.getenv("O2DPG_PRODUCE_FILEGRAPH") # switches filegraph monitoring on and contains the executable name
+if o2dpg_filegraph_exec:
+    env = os.environ.copy()
+    env["FILEACCESS_MON_ROOTPATH"] = os.getcwd()
+    env["MAXMOTHERPID"] = f"{os.getpid()}"
+
+    fileaccess_log_file_name = f"pipeline_fileaccess_{os.getpid()}.log"
+    fileaccess_log_file = open(fileaccess_log_file_name, "w")
+    fileaccess_monitor_proc = subprocess.Popen(
+        [o2dpg_filegraph_exec],
+        stdout=fileaccess_log_file,
+        stderr=subprocess.STDOUT,
+        env=env)
+else:
+    fileaccess_monitor_proc = None
+
+try:
+    # This is core workflow runner invocation
+    executor=WorkflowExecutor(args.workflowfile,jmax=int(args.maxjobs),args=args)
+    rc = executor.execute()
+finally:
+    if fileaccess_monitor_proc:
+        fileaccess_monitor_proc.terminate()  # sends SIGTERM
+        try:
+            fileaccess_monitor_proc.wait(timeout=5)
+        except subprocess.TimeoutExpired:
+            fileaccess_monitor_proc.kill()   # force kill if not stopping
+        # now produce the final filegraph output
+        o2dpg_root = os.getenv("O2DPG_ROOT")
+        analyse_cmd = [
+                sys.executable,  # runs with same Python interpreter
+                f"{o2dpg_root}/UTILS/FileIOGraph/analyse_FileIO.py",
+                "--actionFile", actionlogger_file,
+                "--monitorFile", fileaccess_log_file_name,
+                "-o", f"pipeline_fileaccess_report_{os.getpid()}.json",
+                "--basedir", os.getcwd() ]
+        print (f"Producing FileIOGraph with command {analyse_cmd}")
+        subprocess.run(analyse_cmd, check=True)
+
+sys.exit(rc)

MC/bin/o2dpg_sim_workflow.py

@@ -276,6 +276,18 @@ def load_external_config(configfile):
 for det in activeDetectors:
     activate_detector(det)
 
+# function to finalize detector source lists based on activeDetectors
+# detector source lists are comma separated lists of DET1, DET2, DET1-DET2, ...
+def cleanDetectorInputList(inputlist):
+   sources_list = inputlist.split(",")
+   # Filter the sources
+   filtered_sources = [
+      src for src in sources_list
+      if all(isActive(part) for part in src.split("-"))
+   ]
+   # Recompose into a comma-separated string
+   return ",".join(filtered_sources)
+
 if not args.with_ZDC:
    # deactivate to be able to use isActive consistently for ZDC
    deactivate_detector('ZDC')
@@ -1071,6 +1083,7 @@ def createRestDigiTask(name, det='ALLSMALLER'):
          t['cmd'] = ('','ln -nfs ../bkg_Hits*.root . ;')[doembedding]
          detlist = ''
          detlist = ','.join(smallsensorlist)
+         detlist = cleanDetectorInputList(detlist)
          t['cmd'] += commondigicmd + ' --onlyDet ' + detlist
          t['cmd'] += ' --ccdb-tof-sa --forceSelectedDets '
          t['cmd'] += (' --combine-devices ','')[args.no_combine_dpl_devices]
@@ -1292,7 +1305,7 @@ def getDigiTaskName(det):
    #<--------- TRD global tracking 
    # FIXME This is so far a workaround to avoud a race condition for trdcalibratedtracklets.root
    TRDTRACKINGtask2 = createTask(name='trdreco2_'+str(tf), needs=[TRDTRACKINGtask['name']], tf=tf, cwd=timeframeworkdir, lab=["RECO"], cpu='1', mem='2000')
-   trd_track_sources = dpl_option_from_config(anchorConfig, 'o2-trd-global-tracking', 'track-sources', default_value='TPC,ITS-TPC')
+   trd_track_sources = cleanDetectorInputList(dpl_option_from_config(anchorConfig, 'o2-trd-global-tracking', 'track-sources', default_value='TPC,ITS-TPC'))
    TRDTRACKINGtask2['cmd'] = task_finalizer([
       '${O2_ROOT}/bin/o2-trd-global-tracking',
       getDPL_global_options(bigshm=True), 
@@ -1445,7 +1458,8 @@ def getDigiTaskName(det):
       getDPL_global_options(), 
       putConfigValues(), 
       ('',' --disable-mc')[args.no_mc_labels]])
-   workflow['stages'].append(PHSRECOtask)
+   if isActive("PHS"):
+      workflow['stages'].append(PHSRECOtask)
 
    #<--------- CPV reco workflow
    CPVRECOtask = createTask(name='cpvreco_'+str(tf), needs=[getDigiTaskName("CPV")], tf=tf, cwd=timeframeworkdir, lab=["RECO"], mem='1500')
@@ -1454,7 +1468,8 @@ def getDigiTaskName(det):
        getDPL_global_options(), 
        putConfigValues(), 
        ('',' --disable-mc')[args.no_mc_labels]])
-   workflow['stages'].append(CPVRECOtask)
+   if isActive("CPV"):
+      workflow['stages'].append(CPVRECOtask)
 
    #<--------- ZDC reco workflow
    ZDCRECOtask = createTask(name='zdcreco_'+str(tf), needs=[getDigiTaskName("ZDC")], tf=tf, cwd=timeframeworkdir, lab=["RECO", "ZDC"])
@@ -1463,7 +1478,8 @@ def getDigiTaskName(det):
        getDPL_global_options(), 
        putConfigValues(), 
        ('',' --disable-mc')[args.no_mc_labels]])
-   workflow['stages'].append(ZDCRECOtask)
+   if isActive("ZDC"):
+      workflow['stages'].append(ZDCRECOtask)
 
    ## forward matching
    #<--------- MCH-MID forward matching
@@ -1509,7 +1525,7 @@ def getDigiTaskName(det):
 
    #<--------- HMP forward matching
    hmpmatchneeds = [HMPRECOtask['name'], ITSTPCMATCHtask['name'], TOFTPCMATCHERtask['name'], TRDTRACKINGtask2['name']]
-   hmp_match_sources = dpl_option_from_config(anchorConfig, 'o2-hmpid-matcher-workflow', 'track-sources', default_value='ITS-TPC,ITS-TPC-TRD,TPC-TRD')
+   hmp_match_sources = cleanDetectorInputList(dpl_option_from_config(anchorConfig, 'o2-hmpid-matcher-workflow', 'track-sources', default_value='ITS-TPC,ITS-TPC-TRD,TPC-TRD'))
    HMPMATCHtask = createTask(name='hmpmatch_'+str(tf), needs=hmpmatchneeds, tf=tf, cwd=timeframeworkdir, lab=["RECO"], mem='1000')
    HMPMATCHtask['cmd'] = task_finalizer(
       ['${O2_ROOT}/bin/o2-hmpid-matcher-workflow',
@@ -1524,24 +1540,29 @@ def getDigiTaskName(det):
                                              'o2-primary-vertexing-workflow',
                                              'vertexing-sources',
                                              default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,FDD,HMP,FV0,TRD,MCH,CTP')
+   pvfinder_sources = cleanDetectorInputList(pvfinder_sources)
+
    pvfinder_matching_sources = dpl_option_from_config(anchorConfig,
                                                       'o2-primary-vertexing-workflow',
                                                       'vertex-track-matching-sources',
                                                       default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,FDD,HMP,FV0,TRD,MCH,CTP')
-   pvfinderneeds = [TRDTRACKINGtask2['name'], 
-                    FT0RECOtask['name'], 
-                    FV0RECOtask['name'], 
-                    EMCRECOtask['name'], 
-                    PHSRECOtask['name'], 
-                    CPVRECOtask['name'], 
-                    FDDRECOtask['name'], 
-                    ZDCRECOtask['name'], 
-                    HMPMATCHtask['name'], 
-                    HMPMATCHtask['name'], 
-                    ITSTPCMATCHtask['name'], 
-                    TOFTPCMATCHERtask['name'], 
-                    MFTMCHMATCHtask['name'], 
+   pvfinder_matching_sources = cleanDetectorInputList(pvfinder_matching_sources)
+
+   pvfinderneeds = [TRDTRACKINGtask2['name'],
+                    FT0RECOtask['name'],
+                    FV0RECOtask['name'],
+                    EMCRECOtask['name'],
+                    PHSRECOtask['name'] if isActive("PHS") else None,
+                    CPVRECOtask['name'] if isActive("CPV") else None,
+                    FDDRECOtask['name'],
+                    ZDCRECOtask['name'] if isActive("ZDC") else None,
+                    HMPMATCHtask['name'],
+                    HMPMATCHtask['name'],
+                    ITSTPCMATCHtask['name'],
+                    TOFTPCMATCHERtask['name'],
+                    MFTMCHMATCHtask['name'],
                     MCHMIDMATCHtask['name']]
+   pvfinderneeds = [ p for p in pvfinderneeds if p != None ]
 
    PVFINDERtask = createTask(name='pvfinder_'+str(tf), needs=pvfinderneeds, tf=tf, cwd=timeframeworkdir, lab=["RECO"], cpu=NWORKERS_TF, mem='4000')
    PVFINDERtask['cmd'] = task_finalizer(
@@ -1572,6 +1593,7 @@ def getDigiTaskName(det):
                           'o2-primary-vertexing-workflow',
                           'vertex-track-matching-sources',
                           default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,ZDC,FDD,HMP,FV0,TRD,MCH,CTP')
+   svfinder_sources = cleanDetectorInputList(svfinder_sources)
    SVFINDERtask = createTask(name='svfinder_'+str(tf), needs=[PVFINDERtask['name'], FT0FV0EMCCTPDIGItask['name']], tf=tf, cwd=timeframeworkdir, lab=["RECO"], cpu=svfinder_cpu, mem='5000')   
    SVFINDERtask['cmd'] = task_finalizer(
    [ '${O2_ROOT}/bin/o2-secondary-vertexing-workflow', 
@@ -1591,6 +1613,7 @@ def getDigiTaskName(det):
    # TODO This needs further refinement, sources and dependencies should be constructed dynamically
    aod_info_souces_default = 'ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,ZDC,FDD,HMP,FV0,TRD,MCH,CTP'
    aodinfosources = dpl_option_from_config(anchorConfig, 'o2-aod-producer-workflow', 'info-sources', default_value=aod_info_souces_default)
+   aodinfosources = cleanDetectorInputList(aodinfosources)
    aodneeds = [PVFINDERtask['name'], SVFINDERtask['name']]
 
    if usebkgcache:
@@ -1644,20 +1667,20 @@ def getDigiTaskName(det):
       print ("Adding TPC residuals extraction and aggregation")
 
       #<------------- TPC residuals extraction
-      scdcalib_vertex_sources = dpl_option_from_config(anchorConfig,
+      scdcalib_vertex_sources = cleanDetectorInputList(dpl_option_from_config(anchorConfig,
                                                        'o2-tpc-scdcalib-interpolation-workflow',
                                                        'vtx-sources',
-                                                       default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,FDD,HMP,FV0,TRD,MCH,CTP')
+                                                       default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,FDD,HMP,FV0,TRD,MCH,CTP'))
 
-      scdcalib_track_sources = dpl_option_from_config(anchorConfig,
+      scdcalib_track_sources = cleanDetectorInputList(dpl_option_from_config(anchorConfig,
                                                       'o2-tpc-scdcalib-interpolation-workflow',
                                                       'tracking-sources',
-                                                      default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,FDD,HMP,FV0,TRD,MCH,CTP')
+                                                      default_value='ITS-TPC,TPC-TRD,ITS-TPC-TRD,TPC-TOF,ITS-TPC-TOF,TPC-TRD-TOF,ITS-TPC-TRD-TOF,MFT-MCH,MCH-MID,ITS,MFT,TPC,TOF,FT0,MID,EMC,PHS,CPV,FDD,HMP,FV0,TRD,MCH,CTP'))
 
-      scdcalib_track_extraction = dpl_option_from_config(anchorConfig,
+      scdcalib_track_extraction = cleanDetectorInputList(dpl_option_from_config(anchorConfig,
                                                          'o2-tpc-scdcalib-interpolation-workflow',
                                                          'tracking-sources-map-extraction',
-                                                         default_value='ITS-TPC')
+                                                         default_value='ITS-TPC'))
 
       SCDCALIBtask = createTask(name='scdcalib_'+str(tf), needs=[PVFINDERtask['name']], tf=tf, cwd=timeframeworkdir, lab=["CALIB"], mem='4000')
       SCDCALIBtask['cmd'] = task_finalizer(

MC/config/PWGDQ/external/generator/GeneratorCocktailPromptCharmoniaToMuonEvtGen_pp5TeV.C

@@ -133,11 +133,17 @@ class O2_GeneratorParamPsi : public GeneratorTGenerator
   static Double_t YPsipp5TeV(const Double_t* py, const Double_t* /*dummy*/)
   {
     // psi2s y in pp at 5.02 TeV, tuned on https://www.hepdata.net/record/ins1935680
+    // WARNING! The shape extracted from data provide wired rapidity shape (low stat.), the J/psi one is used 
     Double_t y = *py;
     Float_t p0, p1, p2;
+    // Extracted from Psi(2S) Run 2 data
+    //p0 = 1;
+    //p1 = -17.4857;
+    //p2 = 2.98887;
+    // Same parametrization as J/psi
     p0 = 1;
-    p1 = -17.4857;
-    p2 = 2.98887;
+    p1 = 0.0338222;
+    p2 = 2.96748;
     return p0 * TMath::Exp(-(1. / 2.) * TMath::Power(((y - p1) / p2), 2));
   }