add reco-mutil

.github/workflows/ci.yml

@@ -325,6 +325,8 @@ jobs:
           tar xzf clara.tar.gz
           tar xzf coatjava.tar.gz
       - run: ls
+      - name: run mutil
+        run: ./coatjava/bin/reco-mutil -y ./etc/services/data-ai.yaml -t 4 -o rec.hipo ./clas_018779.evio.00001
       - name: run test
         run: ./bin/run-clara -y ./etc/services/data-ai.yaml -t 4 -n 500 -c ./clara -o ./tmp ./clas_018779.evio.00001
       - name: ls tmp

.gitignore

@@ -58,3 +58,6 @@ hs_err_pid*
 
 bin/evio2hipotest
 export.sh
+
+*.txt
+

.gitlab-ci.yml

@@ -175,13 +175,24 @@ clara:
     - run-clara -v -c $CLARA_HOME -t 4 -y ./etc/services/data-ai.yaml -n 30 -o out $EVIOFILE
     - mv out/rec_$EVIOFILE.hipo claroded.hipo
 
+reco-mutil:
+  stage: test
+  needs: [build,download]
+  dependencies: [build,download]
+  script:
+    - tar -xzf coatjava.tar.gz
+    - reco-mutil -t 4 -y ./etc/services/data-ai.yaml -n 30 -o rec_$EVIOFILE.hipo $EVIOFILE
+
 profile:
   extends: .clon
   allow_failure: true
   script:
-    - ./clara/plugins/clas12/libexec/profile -e cpu   -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp1 -t 16 -l $EVIOFILE
-    - ./clara/plugins/clas12/libexec/profile -e alloc -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp2 -t 16 -l $EVIOFILE
-    - ./clara/plugins/clas12/libexec/profile -e lock  -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp3 -t 16 -l $EVIOFILE
+    - ./clara/plugins/clas12/libexec/profile -e cpu   -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp1 -t 16 $EVIOFILE
+    - ./clara/plugins/clas12/libexec/profile -e alloc -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp2 -t 16 $EVIOFILE
+    - ./clara/plugins/clas12/libexec/profile -e lock  -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp3 -t 16 $EVIOFILE
+    - ./clara/plugins/clas12/libexec/profile -e cpu   -o _mutil -- reco-mutil -y ./etc/services/data-ai.yaml -o mutil1.hipo -t 16 $EVIOFILE
+    - ./clara/plugins/clas12/libexec/profile -e alloc -o _mutil -- reco-mutil -y ./etc/services/data-ai.yaml -o mutil2.hipo -t 16 $EVIOFILE
+    - ./clara/plugins/clas12/libexec/profile -e lock  -o _mutil -- reco-mutil -y ./etc/services/data-ai.yaml -o mutil3.hipo -t 16 $EVIOFILE
   artifacts:
     when: always
     expire_in: 1 week

bin/reco-mutil

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+. `dirname $0`/../libexec/env.sh
+
+split_cli $@
+
+export MALLOC_ARENA_MAX=1
+
+#threads=$(get_threads)
+#node=$(((RANDOM % 2)))
+#cpus=$(get_all_numa_cpus $node)
+#cpus=$(get_numa_cpus $node)
+#taskset -c $cpus \
+
+    java ${JAVA_OPTS-} -XX:MaxRAMPercentage=40.0 -Xms10240m ${jvm_options[@]} \
+    -cp ${COATJAVA_CLASSPATH:-''} \
+    org.jlab.clas.reco.RecoMutil \
+    ${class_options[@]}

bin/recon-util

@@ -4,7 +4,7 @@
 
 split_cli $@
 
-export MALLOC_ARENA_MAX=1
+export MALLOC_ARENA_MAX=12
 
 java ${JAVA_OPTS-} -Xmx1536m -Xms1024m -XX:+UseSerialGC ${jvm_options[@]} \
     -cp ${COATJAVA_CLASSPATH:-''} \

common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Writer.java

@@ -5,19 +5,16 @@
 import org.jlab.detector.calib.utils.ConstantsManager;
 import org.jlab.detector.serial.SerialHoncho;
 import org.jlab.detector.serial.Occupancer;
-import org.jlab.jnp.hipo4.data.Bank;
+import org.jlab.io.utils.ParaTrigWriter;
 import org.jlab.jnp.hipo4.data.Event;
-import org.jlab.jnp.hipo4.data.SchemaFactory;
 import org.jlab.jnp.hipo4.io.HipoWriterSorted;
-import org.jlab.jnp.utils.file.FileUtils;
 import org.json.JSONObject;
 
 /**
  * 
  * 1. Copies certain banks on-the-fly to new tag-1 events
  * 2. Caches helicity states, scaler readouts, and unix time
  * 3. Writes HEL::flip, RUN/HEL::scaler, and RUN::unix to new tag-1 events
- * 4. Runs post-processing, writing tag-1 information to all events 
  * 5. Adds .hipo to the output filename, if necessary
  * 6. Outputs a parallel file of select trigger bits with a raw schema
  * @author baltzell
@@ -26,20 +23,14 @@ public class Clas12Writer extends HipoToHipoWriter {
 
     Occupancer occupancer;
     SerialHoncho serial;
-    Bank runConfig;
     ConstantsManager conman;
-    SchemaFactory fullSchema;
-    HipoWriterSorted paraWriter;
-    long paraCount;
+    ParaTrigWriter paraWriter;
     long paraTriggerMask;
     int paraTriggerPrescale;
 
     private void init(JSONObject opts) {
         occupancer = new Occupancer(opts.optLong("occTriggerMask",(long)1<<39),opts.optInt("occEvents",100));
-        fullSchema = new SchemaFactory();
-        fullSchema.initFromDirectory(FileUtils.getEnvironmentPath("CLAS12DIR","etc/bankdefs/hipo4"));
-        serial = new SerialHoncho(fullSchema);
-        runConfig = new Bank(fullSchema.getSchema("RUN::config"));
+        serial = new SerialHoncho();
         conman = new ConstantsManager();
         conman.init("/runcontrol/hwp","/runcontrol/helicity");
         paraTriggerMask = opts.optLong("paraTriggerMask", 0);
@@ -58,8 +49,7 @@ protected HipoWriterSorted createWriter(Path file, JSONObject opts) throws Event
             String basename = file.getFileName().toString();
             if (!basename.endsWith(".hipo")) basename += ".hipo";
             if (paraTriggerMask > 0) {
-                paraWriter = new HipoWriterSorted();
-                paraWriter.getSchemaFactory().copy(fullSchema);
+                paraWriter = new ParaTrigWriter(paraTriggerMask, paraTriggerPrescale);
                 paraWriter.open(dirname + "/tb" + basename.substring(basename.indexOf("_")));
             }
             w.open(dirname + "/" + basename);
@@ -75,16 +65,9 @@ protected void writeEvent(Object event) throws EventWriterException {
         if (!t.isEmpty()) writer.addEvent(t, 1);
         occupancer.process(((Event)event));
         super.writeEvent(event);
-        writeRaw((Event)event, t);
-    }
-
-    void writeRaw(Event physics, Event tagged) {
         if (paraTriggerMask > 0) {
-            physics.read(runConfig);
-            if (runConfig.getRows()>0 && (runConfig.getLong("trigger",0) & paraTriggerMask) != 0)
-                if (paraTriggerPrescale<=0 || (++paraCount % paraTriggerPrescale) == 0)
-                    paraWriter.addEvent(physics);
-            if (!tagged.isEmpty()) paraWriter.addEvent(tagged, tagged.getEventTag());
+            paraWriter.addEvent((Event)event);
+            if (!t.isEmpty()) paraWriter.addEvent(t, t.getEventTag());
         }
     }
 
@@ -95,5 +78,5 @@ protected void closeWriter() {
         serial.clear();
         if (paraTriggerMask > 0) paraWriter.close();
     }
- 
+
 }

common-tools/clas-detector/src/main/java/org/jlab/detector/serial/SerialHoncho.java

@@ -19,6 +19,7 @@
 import org.jlab.jnp.hipo4.data.Schema;
 import org.jlab.jnp.hipo4.data.SchemaFactory;
 import org.jlab.jnp.hipo4.io.HipoWriterSorted;
+import org.jlab.utils.CLASResources;
 
 /**
  *
@@ -33,21 +34,27 @@ public class SerialHoncho {
     Schema recEvent;
     Schema helScaler;
     Schema helicityAdc;
+    Schema runScaler;
+    Schema rawScaler;
+    Schema epics;
     volatile ConstantsManager conman;
     volatile TreeMap<Integer,Integer> eventUnix;
     volatile HelicitySequence helicitySequence;
     volatile TreeSet<HelicityState> helicities;
     volatile DaqScalersSequence scalers;
     int run = 0;
 
-    public SerialHoncho(SchemaFactory schema) {
-        this.schema = schema;
+    public SerialHoncho() {
+        schema = CLASResources.getFullSchema();
         conman = new ConstantsManager();
         conman.init("/runcontrol/hwp","/runcontrol/helicity");
         runConfig = schema.getSchema("RUN::config");
         recEvent = schema.getSchema("REC::Event");
         helicityAdc = schema.getSchema("HEL::adc");
         helScaler = schema.getSchema("HEL::scaler");
+        runScaler = schema.getSchema("RUN::scaler");
+        rawScaler = schema.getSchema("RAW::scaler");
+        epics = schema.getSchema("RAW::epics");
         scalers = new DaqScalersSequence(schema);
         helicities = new TreeSet<>();
         eventUnix = new TreeMap<>();
@@ -56,6 +63,10 @@ public SerialHoncho(SchemaFactory schema) {
             tag1banks[i] = schema.getSchema(TAG1BANKS[i]);
     }
 
+    public boolean containsSerial(Event e) {
+        return e.isEmpty() ? false : e.hasBank(rawScaler) || e.hasBank(epics);
+    }
+
     /**
      * Register an event's serial data and return a (possibly empty) tag-1 event.
      * @param event
@@ -182,16 +193,16 @@ void prune() {
      * @param runConfig
      * @return 
      */
-    Event getUnixEvent(Bank config) {
+    Event getUnixEvent(Bank runConfig) {
         Bank unix = new Bank(schema.getSchema("RUN::unix"), eventUnix.size());
         int row = 0;
         for (int evno : eventUnix.keySet()) {
             unix.putInt("event", row, evno);
-            unix.putInt("unixtime",row, eventUnix.get(evno));
+            unix.putInt("unixtime", row, eventUnix.get(evno));
             row++;
         }
         Event e = new Event();
-        e.write(config);
+        e.write(runConfig);
         e.write(unix);
         return e;
     }

common-tools/clas-io/src/main/java/org/jlab/io/utils/ParaTrigWriter.java

@@ -0,0 +1,45 @@
+package org.jlab.io.utils;
+
+import org.jlab.io.banks.RUN_config;
+import org.jlab.jnp.hipo4.data.Bank;
+import org.jlab.jnp.hipo4.data.Event;
+import org.jlab.jnp.hipo4.data.Schema;
+import org.jlab.jnp.hipo4.data.SchemaFactory;
+import org.jlab.jnp.hipo4.io.HipoWriterSorted;
+import org.jlab.utils.CLASResources;
+
+/**
+ *
+ * @author baltzell
+ */
+public class ParaTrigWriter extends HipoWriterSorted {
+
+    SchemaFactory schema = CLASResources.getFullSchema();
+    Schema runConfig = schema.getSchema("RUN::config");
+
+    long count;
+    long mask;
+    int prescale;
+
+    public ParaTrigWriter(long mask, int prescale) {
+        super();
+        this.mask = mask;
+        this.prescale = prescale;
+        setCompressionType(2);
+        getSchemaFactory().copy(schema);
+    }
+
+    @Override
+    public void addEvent(Event e) {
+        Bank b = new Bank(runConfig,1);
+        e.read(b);
+        if (b.getRows() > 0) {
+            if (mask > 0 && 0 != (b.getLong(RUN_config.trigger,0) & mask)) {
+                if (prescale<=0 || (++count % prescale) == 0) {
+                    super.addEvent(e);
+                }
+            }
+        }
+    }
+
+}

common-tools/clas-reco/src/main/java/org/jlab/clas/reco/EngineProcessor.java

@@ -136,7 +136,7 @@ public void initDefault(){
         String[] names = new String[]{
             "MAGFIELDS",
             "DCCR","DCHB","FTOFHB","EC","HTCC","EBHB",
-            "DCTB","FTOFTB","EBTB","VTX"
+            "DCTB","FTOFTB","EBTB","OCC"
         };
 
         String[] services = new String[]{
@@ -150,7 +150,7 @@ public void initDefault(){
             "org.jlab.service.dc.DCTBEngine",
             "org.jlab.service.ftof.FTOFTBEngine",
             "org.jlab.service.eb.EBTBEngine",
-            "org.jlab.rec.service.vtx.VTXEngine"
+            "org.jlab.calibration.service.OccupanceEngine",
         };
 
         for(int i = 0; i < names.length; i++){
@@ -166,7 +166,7 @@ public void initAll(){
             "CVTFP","CTOF","CND","BAND",
             "HTCC","LTCC","EBHB",
             "DCTB","FMT","FTOFTB","CVT","EBTB",
-            "RICHEB","RTPC","AHDC","ATOF","ALERT", "MC","VTX"
+            "RICHEB","RTPC","AHDC","ATOF","ALERT", "MC","VTX","OCC"
         };
 
         String[] services = new String[]{
@@ -199,7 +199,8 @@ public void initAll(){
             "org.jlab.service.atof.ATOFEngine",
             "org.jlab.service.alert.ALERTEngine",
             "org.jlab.service.mc.TruthMatch",
-            "org.jlab.rec.service.vtx.VTXEngine"
+            "org.jlab.rec.service.vtx.VTXEngine",
+            "org.jlab.calibration.service.OccupanceEngine",
         };
         if(names.length!=services.length)
             LOGGER.log(Level.SEVERE, "initAll : the list of services does not match the list of service names...  ");
@@ -319,6 +320,7 @@ public void processEvent(DataEvent event, HipoDataSync writer) {
         processEvent(event);
         occupancer.process(((HipoDataEvent)event).getHipoEvent());
         removeBanks(event);
+        occupancer.process(((HipoDataEvent)event).getHipoEvent());
         writer.writeEvent(event);
     }
 
@@ -393,24 +395,6 @@ public void show(){
         }
     }
 
-    protected static OptionParser getParser() {
-        OptionParser parser = new OptionParser("recon-util");
-        parser.addRequired("-o","output.hipo");
-        parser.addRequired("-i","input.evio/hipo");
-        parser.setRequiresInputList(false);
-        parser.addOption("-c","0","use default configuration [0 - no, 1 - yes/default, 2 - all services] ");
-        parser.addOption("-s","0","number of events to skip");
-        parser.addOption("-n","0","number of events to process");
-        parser.addOption("-y","0","yaml file");
-        parser.addOption("-u","true","update dictionary from writer ? ");
-        parser.addOption("-S",null,"schema directory");
-        parser.addOption("-B",null,"background file");
-        parser.addOption("-P",null,"preload file for post-processing");
-        parser.addOption("-R","0","rebuild scalers");
-        parser.addOption("-H","0","restream helicity");
-        return parser;
-    }
-
     protected final void init(OptionParser p) {
         p.syncLogLevel(LOGGER);
 
@@ -452,7 +436,20 @@ else if (p.getOption("-c").intValue() > 0) {
     }
 
      public static void main(String[] args) {
-        OptionParser parser = EngineProcessor.getParser();
+        OptionParser parser = new OptionParser("recon-util");
+        parser.addRequired("-o","output.hipo");
+        parser.addRequired("-i","input.evio/hipo");
+        parser.addOption("-c","0","use default configuration [0 - no, 1 - yes/default, 2 - all services] ");
+        parser.addOption("-s","0","number of events to skip");
+        parser.addOption("-n","0","number of events to process");
+        parser.addOption("-y","0","yaml file");
+        parser.addOption("-u","true","update dictionary from writer ? ");
+        parser.addOption("-S",null,"schema directory");
+        parser.addOption("-B",null,"background file");
+        parser.addOption("-P",null,"preload file for post-processing");
+        parser.addOption("-R","0","rebuild scalers");
+        parser.addOption("-H","0","restream helicity");
+        parser.setRequiresInputList(false);
         parser.parse(args);
         EngineProcessor proc = new EngineProcessor(parser);
         proc.processFile(parser.getOption("-i").stringValue(),