Merge branch 'AliceO2Group:master' into tpc-cleanup

DATA/common/setenv_calib.sh

@@ -30,6 +30,7 @@ if has_detector_calib FT0 && has_detector_reco FT0; then CAN_DO_CALIB_FT0_TIMEOF
 if has_detector_calib FV0 && has_processing_step FV0_RECO; then CAN_DO_CALIB_FV0_INTEGRATEDCURR=1; else CAN_DO_CALIB_FV0_INTEGRATEDCURR=0; fi
 if has_detector_calib FDD && has_processing_step FDD_RECO; then CAN_DO_CALIB_FDD_INTEGRATEDCURR=1; else CAN_DO_CALIB_FDD_INTEGRATEDCURR=0; fi
 if has_detector_calib ZDC && has_processing_step ZDC_RECO; then CAN_DO_CALIB_ZDC_TDC=1; else CAN_DO_CALIB_ZDC_TDC=0; fi
+if [[ $SYNCMODE == 1 ]] && has_processing_step ENTROPY_ENCODER && [[ ! -z "$WORKFLOW_DETECTORS_CTF" ]] && [[ $WORKFLOW_DETECTORS_CTF != "NONE" ]]; then CAN_DO_CALIB_RCT_UPDATER=1; else CAN_DO_CALIB_RCT_UPDATER=0; fi
 # for async recalibration
 if has_detector_calib EMC && has_detector_reco EMC && [[ $SYNCMODE != 1 ]]; then CAN_DO_CALIB_EMC_ASYNC_RECALIB=1; else CAN_DO_CALIB_EMC_ASYNC_RECALIB=0; fi
 if [[ $SYNCMODE != 1 ]] && has_detector_reco TPC; then CAN_DO_CALIB_ASYNC_EXTRACTTPCCURRENTS=1; else CAN_DO_CALIB_ASYNC_EXTRACTTPCCURRENTS=0; fi
@@ -42,7 +43,7 @@ if [[ ${DISABLE_TRD_PH:-} == 1 ]]; then CAN_DO_CALIB_TRD_T0=0; fi
 : ${CALIB_TPC_SCDCALIB_SLOTLENGTH:=600} # the slot length needs to be known both on the aggregator and the processing nodes, therefore it is defined (in seconds!) here
 : ${CALIB_TPC_SCDCALIB_SENDTRKDATA:=1}  # by default, we want to write the track information in addition to unbinned residuals to allow finer filtering offline
 
-if [[ $BEAMTYPE != "cosmic" ]] || [[ ${FORCECALIBRATIONS:-} == 1 ]] ; then
+if [[ $BEAMTYPE != "cosmic" ]] || [[ ${FORCECALIBRATIONS:-} == 1 ]] ; then # Calibrations enabled in non-COSMIC runs
 
   # here we won't deal with calibrations only for async! e.g. EMC_ASYNC_RECALIB; we want that they are always explicitly enabled
 
@@ -88,26 +89,6 @@ if [[ $BEAMTYPE != "cosmic" ]] || [[ ${FORCECALIBRATIONS:-} == 1 ]] ; then
   if [[ $CAN_DO_CALIB_TPC_VDRIFTTGL == 1 ]]; then
     if [[ -z ${CALIB_TPC_VDRIFTTGL+x} ]]; then CALIB_TPC_VDRIFTTGL=1; fi
   fi
-  # IDCs (by default we enable it for running the synch. reco on the EPNs, but not on staging since we have only 1 calibration node available)
-  if [[ $CAN_DO_CALIB_TPC_IDC == 1 ]]; then
-    if [[ -z ${CALIB_TPC_IDC+x} ]]; then
-      if [[ $EPNSYNCMODE == 1 ]] && [[ "${GEN_TOPO_DEPLOYMENT_TYPE:-}" != "ALICE_STAGING" ]]; then
-        CALIB_TPC_IDC=1;
-      else
-        CALIB_TPC_IDC=0;
-      fi
-    fi
-  fi
-  # SAC (by default we enable it for running the synch. reco on the EPNs)
-  if [[ $CAN_DO_CALIB_TPC_SAC == 1 ]]; then
-    if [[ -z ${CALIB_TPC_SAC+x} ]]; then
-      if [[ $EPNSYNCMODE == 1 ]]; then
-        CALIB_TPC_SAC=1;
-      else
-        CALIB_TPC_SAC=0;
-      fi
-    fi
-  fi
 
   # calibrations for TRD
   if [[ $CAN_DO_CALIB_TRD_VDRIFTEXB == 1 ]] ; then
@@ -170,6 +151,34 @@ if [[ $BEAMTYPE != "cosmic" ]] || [[ ${FORCECALIBRATIONS:-} == 1 ]] ; then
   fi
 fi
 
+# Calibrations irrespective of COSMIC or non-COSMIC run:
+
+# when possible, run RCT updater
+if [[ $CAN_DO_CALIB_RCT_UPDATER == 1 ]]; then
+  if [[ -z ${CALIB_RCT_UPDATER+x} ]]; then CALIB_RCT_UPDATER=1; fi
+fi
+
+# IDCs (by default we enable it for running the synch. reco on the EPNs, but not on staging since we have only 1 calibration node available)
+if [[ $CAN_DO_CALIB_TPC_IDC == 1 ]]; then
+  if [[ -z ${CALIB_TPC_IDC+x} ]]; then
+    if [[ $EPNSYNCMODE == 1 ]] && [[ "${GEN_TOPO_DEPLOYMENT_TYPE:-}" != "ALICE_STAGING" ]]; then
+      CALIB_TPC_IDC=1;
+    else
+      CALIB_TPC_IDC=0;
+    fi
+  fi
+fi
+# SAC (by default we enable it for running the synch. reco on the EPNs)
+if [[ $CAN_DO_CALIB_TPC_SAC == 1 ]]; then
+  if [[ -z ${CALIB_TPC_SAC+x} ]]; then
+    if [[ $EPNSYNCMODE == 1 ]]; then
+      CALIB_TPC_SAC=1;
+    else
+      CALIB_TPC_SAC=0;
+    fi
+  fi
+fi
+
 ( [[ -z ${CALIB_FT0_INTEGRATEDCURR:-} ]] || [[ $CAN_DO_CALIB_FT0_INTEGRATEDCURR == 0 ]] ) && CALIB_FT0_INTEGRATEDCURR=0
 ( [[ -z ${CALIB_FV0_INTEGRATEDCURR:-} ]] || [[ $CAN_DO_CALIB_FV0_INTEGRATEDCURR == 0 ]] ) && CALIB_FV0_INTEGRATEDCURR=0
 ( [[ -z ${CALIB_FDD_INTEGRATEDCURR:-} ]] || [[ $CAN_DO_CALIB_FDD_INTEGRATEDCURR == 0 ]] ) && CALIB_FDD_INTEGRATEDCURR=0
@@ -201,8 +210,8 @@ fi
 ( [[ -z ${CALIB_MFT_DEADMAP_TIME:-} ]] || [[ $CAN_DO_CALIB_MFT_DEADMAP_TIME == 0 ]] ) && CALIB_MFT_DEADMAP_TIME=0
 # for async:
 ( [[ -z ${CALIB_EMC_ASYNC_RECALIB:-} ]] || [[ $CAN_DO_CALIB_EMC_ASYNC_RECALIB == 0 ]] ) && CALIB_EMC_ASYNC_RECALIB=0
-( [[ -z ${CALIB_ASYNC_EXTRACTTPCCURRENTS:-} ]] || [[ $CAN_DO_CALIB_ASYNC_EXTRACTTPCCURRENTS == 0 ]] ) && CALIB_ASYNC_EXTRACTTPCCURRENTS=0 
-( [[ -z ${CALIB_ASYNC_DISABLE3DCURRENTS:-} ]] || [[ $CAN_DO_CALIB_ASYNC_DISABLE3DCURRENTS == 0 ]] ) && CALIB_ASYNC_DISABLE3DCURRENTS=0 
+( [[ -z ${CALIB_ASYNC_EXTRACTTPCCURRENTS:-} ]] || [[ $CAN_DO_CALIB_ASYNC_EXTRACTTPCCURRENTS == 0 ]] ) && CALIB_ASYNC_EXTRACTTPCCURRENTS=0
+( [[ -z ${CALIB_ASYNC_DISABLE3DCURRENTS:-} ]] || [[ $CAN_DO_CALIB_ASYNC_DISABLE3DCURRENTS == 0 ]] ) && CALIB_ASYNC_DISABLE3DCURRENTS=0
 : ${ON_SKIMMED_DATA:=0}
 ( [[ -z ${CALIB_ASYNC_EXTRACTTIMESERIES:-} ]] || [[ $CAN_DO_CALIB_ASYNC_EXTRACTTIMESERIES == 0 ]] ) && CALIB_ASYNC_EXTRACTTIMESERIES=0
 
@@ -241,7 +250,7 @@ fi
 # define spec for proxy for TF-based outputs from BARREL
 if [[ -z ${CALIBDATASPEC_BARREL_TF:-} ]]; then
   # RCT updater
-  if [[ ${CALIB_RCT_UPDATER:-} == 1 ]]; then add_semicolon_separated CALIBDATASPEC_BARREL_TF "calibRCT:CTD/DONE/0"; fi
+  if [[ ${CALIB_RCT_UPDATER:-} == 1 ]]; then add_semicolon_separated CALIBDATASPEC_BARREL_TF "calibRCT:CTF/DONE/0"; fi
   # prim vtx
   if [[ $CALIB_PRIMVTX_MEANVTX == 1 ]]; then add_semicolon_separated CALIBDATASPEC_BARREL_TF "pvtx:GLO/PVTX/0"; fi
 

DATA/production/calib/emc-pedestal-aggregator.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+source common/setenv.sh
+
+# ---------------------------------------------------------------------------------------------------------------------
+# Set general arguments
+source common/getCommonArgs.sh
+
+INPTYPE=""
+  PROXY_INSPEC="A:EMC/PEDDATA/0;eos:***/INFORMATION"
+
+CCDBPATH1="http://o2-ccdb.internal"
+CCDBPATH2="$DCSCCDBSERVER"
+if [[ $RUNTYPE == "SYNTHETIC" || "${GEN_TOPO_DEPLOYMENT_TYPE:-}" == "ALICE_STAGING" || ! -z $ISTEST ]]; then
+  CCDBPATH1="http://ccdb-test.cern.ch:8080"
+  CCDBPATH2="http://ccdb-test.cern.ch:8080"
+fi
+
+QC_CONFIG="/o2/components/qc/ANY/any/emc-pedestal-qc"
+
+WORKFLOW=
+add_W o2-dpl-raw-proxy "--proxy-name emc-pedestal-input-proxy --dataspec \"$PROXY_INSPEC\" --network-interface ib0 --channel-config \"name=emc-pedestal-input-proxy,method=bind,type=pull,rateLogging=1,transport=zeromq\"" "" 0
+add_W o2-calibration-emcal-pedestal-calib-workflow
+add_W o2-calibration-ccdb-populator-workflow "--ccdb-path=\"$CCDBPATH1\" --sspec-min 0 --sspec-max 0"
+add_W o2-calibration-ccdb-populator-workflow "--ccdb-path=\"$CCDBPATH2\" --sspec-min 1 --sspec-max 1 --name-extention dcs"
+add_QC_from_consul "${QC_CONFIG}" "--local --host localhost"
+WORKFLOW+="o2-dpl-run $ARGS_ALL $GLOBALDPLOPT"
+
+if [ $WORKFLOWMODE == "print" ]; then
+  echo Workflow command:
+  echo $WORKFLOW | sed "s/| */|\n/g"
+else
+  # Execute the command we have assembled
+  WORKFLOW+=" --$WORKFLOWMODE ${WORKFLOWMODE_FILE}"
+  eval $WORKFLOW
+fi

DATA/production/calib/emc-pedestal-processing.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+source common/setenv.sh
+
+# ---------------------------------------------------------------------------------------------------------------------
+# Set general arguments
+source common/getCommonArgs.sh
+
+PROXY_INSPEC="A:EMC/RAWDATA;dd:FLP/DISTSUBTIMEFRAME/0;eos:***/INFORMATION"
+
+PROXY_OUTSPEC="downstream:EMC/PEDDATA/0"
+
+[[ -z $NEMCPROCPIPELINES ]] && NEMCPROCPIPELINES=30
+
+WORKFLOW=
+add_W o2-dpl-raw-proxy "--dataspec \"$PROXY_INSPEC\" --inject-missing-data --channel-config \"name=readout-proxy,type=pull,method=connect,address=ipc://@$INRAWCHANNAME,transport=shmem,rateLogging=1\"" "" 0
+add_W o2-calibration-emcal-pedestal-processor-workflow "--pipeline PedestalProcessor:${NEMCPROCPIPELINES}"
+add_W o2-dpl-output-proxy "--dataspec \"$PROXY_OUTSPEC\" --proxy-channel-name emc-pedestal-input-proxy --channel-config \"name=emc-pedestal-input-proxy,method=connect,type=push,transport=zeromq,rateLogging=1\"" "" 0
+WORKFLOW+="o2-dpl-run ${ARGS_ALL} ${GLOBALDPLOPT}"
+
+if [ $WORKFLOWMODE == "print" ]; then
+  echo Workflow command:
+  echo $WORKFLOW | sed "s/| */|\n/g"
+else
+  # Execute the command we have assembled
+  WORKFLOW+=" --$WORKFLOWMODE ${WORKFLOWMODE_FILE}"
+  eval $WORKFLOW
+fi

DATA/production/calib/tpc-pedestal.sh

@@ -39,7 +39,7 @@ WORKFLOW=
 add_W o2-dpl-raw-proxy "--dataspec \"$PROXY_INSPEC\" --inject-missing-data --channel-config \"name=readout-proxy,type=pull,method=connect,address=ipc://@tf-builder-pipe-0,transport=shmem,rateLogging=1\"" "" 0
 add_W o2-tpc-calib-pad-raw "--input-spec \"$CALIB_INSPEC\"  --publish-after-tfs ${publish_after} --max-events ${max_events} --lanes 36" 
 add_W o2-calibration-ccdb-populator-workflow "--ccdb-path \"http://o2-ccdb.internal\" " "" 0
-add_QC_from_consul "${QC_CONFIG}" "--local --host lcoalhost"
+add_QC_from_consul "${QC_CONFIG}" "--local --host localhost"
 
 WORKFLOW+="o2-dpl-run ${ARGS_ALL} ${GLOBALDPLOPT}"
 

DATA/production/calib/tpc-pulser-long.sh

@@ -38,7 +38,7 @@ WORKFLOW=
 add_W o2-dpl-raw-proxy "--dataspec \"$PROXY_INSPEC\" --inject-missing-data --channel-config \"name=readout-proxy,type=pull,method=connect,address=ipc://@tf-builder-pipe-0,transport=shmem,rateLogging=1\"" "" 0
 add_W o2-tpc-calib-pad-raw "--input-spec \"$CALIB_INSPEC\" --calib-type pulser --reset-after-publish --publish-after-tfs ${publish_after} --max-events ${max_events} --lanes 36 --check-calib-infos" 
 add_W o2-calibration-ccdb-populator-workflow "--ccdb-path \"http://o2-ccdb.internal\" " "" 0
-add_QC_from_consul "${QC_CONFIG}" "--local --host lcoalhost"
+add_QC_from_consul "${QC_CONFIG}" "--local --host localhost"
 
 WORKFLOW+="o2-dpl-run ${ARGS_ALL} ${GLOBALDPLOPT}"
 

DATA/production/calib/tpc-pulser.sh

@@ -40,7 +40,7 @@ WORKFLOW=
 add_W o2-dpl-raw-proxy "--dataspec \"$PROXY_INSPEC\" --inject-missing-data --channel-config \"name=readout-proxy,type=pull,method=connect,address=ipc://@tf-builder-pipe-0,transport=shmem,rateLogging=1\"" "" 0
 add_W o2-tpc-calib-pad-raw "--input-spec \"$CALIB_INSPEC\" --calib-type pulser --publish-after-tfs ${publish_after} --max-events ${max_events} --lanes 36 --check-calib-infos" "${CALIB_CONFIG}" 
 add_W o2-calibration-ccdb-populator-workflow "--ccdb-path \"http://o2-ccdb.internal\" " "" 0
-add_QC_from_consul "${QC_CONFIG}" "--local --host lcoalhost"
+add_QC_from_consul "${QC_CONFIG}" "--local --host localhost"
 
 WORKFLOW+="o2-dpl-run ${ARGS_ALL} ${GLOBALDPLOPT}"
 

DATA/production/qc-async/mch-tracks.json

@@ -33,7 +33,7 @@
                 "maxNumberCycles": "-1",
                 "dataSource": {
                     "type": "direct",
-                    "query": "trackMCH:MCH/TRACKS;trackMCHROF:MCH/TRACKROFS;trackMCHTRACKCLUSTERS:MCH/TRACKCLUSTERS;mchtrackdigits:MCH/TRACKDIGITS"
+                    "query": "trackMCH:MCH/TRACKS;trackMCHROF:MCH/TRACKROFS;trackMCHTRACKCLUSTERS:MCH/TRACKCLUSTERS;mchtrackdigits:MCH/CLUSTERDIGITS"
                 },
                 "taskParameters": {
                     "maxTracksPerTF": "600",

DATA/production/standalone-calibration.desc

@@ -1,3 +1,5 @@
+EMC-pedestal-calibration: "O2PDPSuite" reco,1,1,"production/calib/emc-pedestal-processing.sh" calib,1,"production/calib/emc-pedestal-aggregator.sh"
+
 FT0-time-offset-calibration: "O2PDPSuite" reco,5,5,"production/calib/ft0-timeoffset-processing.sh" calib,1,"production/calib/ft0-timeoffset-aggregator.sh"
 
 ITS-noise-calibration: "O2PDPSuite" reco,20,20,"NITSDECTHREADS=4 NITSDECTPIPELINES=6 production/calib/its-noise-processing.sh" calib,20,"NTHREADSACC=4 NTHREADSNORM=16 NITSACCPIPELINES=16 production/calib/its-noise-aggregator.sh"

DATA/testing/detectors/TPC/tpc-laser-raw-filter.sh

@@ -27,7 +27,7 @@ WORKFLOW=
 add_W o2-dpl-raw-proxy "--dataspec \"$PROXY_INSPEC\" --inject-missing-data --channel-config \"name=readout-proxy,type=pull,method=connect,address=ipc://@tf-builder-pipe-0,transport=shmem,rateLogging=1\"" "" 0
 add_W o2-tpc-raw-to-digits-workflow "--ignore-grp --input-spec \"$CALIB_INSPEC\" --remove-duplicates --pipeline tpc-raw-to-digits-0:20"
 add_W o2-tpc-krypton-raw-filter "tpc-raw-to-digits-0:24  --lanes $NLANES --writer-type EPN --meta-output-dir $EPN2EOS_METAFILES_DIR --output-dir $CALIB_DIR --threshold-max 20 --max-tf-per-file 8000 --time-bins-before 20 --max-time-bins 650"
-add_QC_from_consul "${QC_CONFIG_CONSUL}" "--local --host lcoalhost"
+add_QC_from_consul "${QC_CONFIG_CONSUL}" "--local --host localhost"
 
 
 

GRID/utils/grid_submit.sh

@@ -230,6 +230,12 @@ export CONTROLSERVER
 export PRODSPLIT
 [[ $PRODSPLIT -gt 100 ]] && echo "Production split needs to be smaller than 100 for the moment" && exit 1
 
+# check for presence of jq (needed in code path to fetch output files)
+[[ "$FETCHOUTPUT" ]] && { which jq &> /dev/null || { echo "Could not find jq command. Please load or install" && exit 1; }; }
+
+# check if script is actually a valid file and fail early if not
+[[ "${SCRIPT}" ]] && [[ ! -f "${SCRIPT}" ]] && echo "Script file ${SCRIPT} does not exist .. aborting" && exit 1
+
 # analyse options:
 # we should either run with --script or with -c
 [ "${SCRIPT}" ] && [ "$CONTINUE_WORKDIR" ] && echo "Script and continue mode not possible at same time" && exit 1
@@ -411,37 +417,46 @@ EOF
     echo -ne "\b\b\b${spin[$((counter%4))]} ${JOBSTATUS}"
     let counter=counter+1
     if [ ! "${counter}" == "100" ]; then
+      # ensures that we see spinner ... but only check for new job
+      # status every 100 * 0.5 = 50s?
       continue
     fi
-    let counter=0
+    let counter=0 # reset counter
     JOBSTATUS=$(alien.py ps -j ${MY_JOBID} | awk '//{print $4}')
     # echo -ne "Waiting for jobs to return; Last status ${JOBSTATUS}"
-    if [ "$JOBSTATUS" == "D" ]; then
+
+    if [ "${JOBSTATUS}" == "D" ]; then
       echo "Job done"
-      WAITFORALIEN=""
+      WAITFORALIEN=""  # guarantees to go out of outer while loop
 
       if [ "${FETCHOUTPUT}" ]; then
-        SUBJOBIDS=""
-        while [ ! ${SUBJOBIDS} ]; do
-          SUBJOBIDS=($(alien.py ps --trace ${MY_JOBID} | awk '/Subjob submitted/' | sed 's/.*submitted: //' | tr '\n' ' '))
-          sleep 1
-        done
-        # TODO: make this happen in a single alien.py session and with parallel copying
-        echo "Fetching results"
-        for splitcounter in `seq 1 ${PRODSPLIT}`; do
-          # we still need to check if this particular subjob was successful
-          SUBJOBSTATUS=$(alien.py ps -j ${SUBJOBIDS[splitcounter-1]} | awk '//{print $4}')
-          if [ "$SUBJOBSTATUS" == "D" ]; then
-             SPLITOUTDIR=$(printf "%03d" ${splitcounter})
-             [ ! -f ${SPLITOUTDIR} ] && mkdir ${SPLITOUTDIR}
-             echo "Fetching result files for subjob ${splitcounter} into ${PWD}"
-	     CPCMD="alien.py cp ${MY_JOBWORKDIR}/${SPLITOUTDIR}/* file:./${SPLITOUTDIR}"
-	     eval "${CPCMD}" 2> /dev/null
-          else
-	     echo "Not fetching files for subjob ${splitcounter} since job code is ${SUBJOBSTATUS}"
-	  fi
-        done
-        wait
+          SUBJOBIDS=()
+          SUBJOBSTATUSES=()
+          echo "Fetching subjob info"
+          while [ "${#SUBJOBIDS[@]}" == "0" ]; do
+            QUERYRESULT=$(ALIENPY_JSON=true alien.py ps -a -m ${MY_JOBID})
+            SUBJOBIDS=($(echo ${QUERYRESULT} | jq -r '.results[].id' | tr '\n' ' '))
+            SUBJOBSTATUSES=($(echo ${QUERYRESULT} | jq -r '.results[].status' | tr '\n' ' '))
+            # echo "LENGTH SUBJOBS ${#SUBJOBIDS[@]}"
+            sleep 1
+          done
+          # TODO: make this happen with parallel copying
+          echo "Fetching results for ${PRODSPLIT} sub-jobs"
+          for splitcounter in `seq 1 ${PRODSPLIT}`; do
+            let jobindex=splitcounter-1
+            THIS_STATUS=${SUBJOBSTATUSES[jobindex]}
+            THIS_JOB=${SUBJOBIDS[jobindex]}
+            echo "Fetching for job ${THIS_JOB}"
+            if [ "${THIS_STATUS}" == "DONE" ]; then
+               SPLITOUTDIR=$(printf "%03d" ${splitcounter})
+               [ ! -f ${SPLITOUTDIR} ] && mkdir ${SPLITOUTDIR}
+               echo "Fetching result files for subjob ${splitcounter} into ${PWD}"
+	             CPCMD="alien.py cp ${MY_JOBWORKDIR}/${SPLITOUTDIR}/* file:./${SPLITOUTDIR}"
+	             eval "${CPCMD}" 2> /dev/null
+            else
+	            echo "Not fetching files for subjob ${splitcounter} since job code is ${THIS_STATUS}"
+	          fi
+          done
       fi
     fi
     if [[ "${FOO:0:1}" == [EK] ]]; then
@@ -541,13 +556,13 @@ if [ "${ONGRID}" = "1" ]; then
 fi
 
 # ----------- DOWNLOAD ADDITIONAL HELPERS ----------------------------
-curl -o analyse_CPU.py https://raw.githubusercontent.com/sawenzel/AliceO2/swenzel/cpuana/Utilities/Tools/analyse_CPU.py &> /dev/null
-chmod +x analyse_CPU.py
+# curl -o analyse_CPU.py https://raw.githubusercontent.com/sawenzel/AliceO2/swenzel/cpuana/Utilities/Tools/analyse_CPU.py &> /dev/null
+# chmod +x analyse_CPU.py
 export PATH=$PATH:$PWD
-export JOBUTILS_MONITORCPU=ON
-export JOBUTILS_WRAPPER_SLEEP=5
-#export JOBUTILS_JOB_KILLINACTIVE=180 # kill inactive jobs after 3 minutes --> will be the task of pipeline runner? (or make it optional)
-export JOBUTILS_MONITORMEM=ON 
+# export JOBUTILS_MONITORCPU=ON
+# export JOBUTILS_WRAPPER_SLEEP=5
+# export JOBUTILS_JOB_KILLINACTIVE=180 # kill inactive jobs after 3 minutes --> will be the task of pipeline runner? (or make it optional)
+# export JOBUTILS_MONITORMEM=ON 
 
 # ----------- EXECUTE ACTUAL JOB  ------------------------------------ 
 # source the actual job script from the work dir
@@ -558,13 +573,7 @@ chmod +x ./alien_jobscript.sh
 cp alien_log_${ALIEN_PROC_ID:-0}.txt logtmp_${ALIEN_PROC_ID:-0}.txt
 [ "${ALIEN_JOB_OUTPUTDIR}" ] && upload_to_Alien logtmp_${ALIEN_PROC_ID:-0}.txt ${ALIEN_JOB_OUTPUTDIR}/
 
-# MOMENTARILY WE ZIP ALL LOG FILES
-ziparchive=logs_PROCID${ALIEN_PROC_ID:-0}.zip
-find ./ -name "*.log*" -exec zip ${ziparchive} {} ';'
-find ./ -name "*mergerlog*" -exec zip ${ziparchive} {} ';'
-find ./ -name "*serverlog*" -exec zip ${ziparchive} {} ';'
-find ./ -name "*workerlog*" -exec zip ${ziparchive} {} ';'
-find ./ -name "alien_log*.txt" -exec zip ${ziparchive} {} ';'
+echo "Job done"
 
 # We need to exit for the ALIEN JOB HANDLER!
 exit 0

MC/config/PWGLF/xsection/g4config_had_x2.in

@@ -64,10 +64,10 @@
 
 
 # Scale hadronic cross section
-/mcPhysics/setCrossSectionFactor deuteron hadElastic 2.
-/mcPhysics/setCrossSectionFactor anti_deuteron hadElastic 2.
-/mcPhysics/setCrossSectionFactor triton hadElastic 2.
-/mcPhysics/setCrossSectionFactor anti_triton hadElastic 2.
-/mcPhysics/setCrossSectionFactor he3 hadElastic 2.
-/mcPhysics/setCrossSectionFactor anti_he3 hadElastic 2.
+/mcPhysics/setCrossSectionFactor deuteron hadInElastic 2.
+/mcPhysics/setCrossSectionFactor anti_deuteron hadInElastic 2.
+/mcPhysics/setCrossSectionFactor triton hadInElastic 2.
+/mcPhysics/setCrossSectionFactor anti_triton hadInElastic 2.
+/mcPhysics/setCrossSectionFactor he3 hadInElastic 2.
+/mcPhysics/setCrossSectionFactor anti_he3 hadInElastic 2.