Add multi-threaded recon-util

.github/workflows/ci.yml

@@ -224,20 +224,15 @@ jobs:
             clas_018779.evio.00001
       - name: untar build
         run: |
-          tar xzvf clara.tar.gz
           tar xzvf coatjava.tar.gz
       - run: ls
       - name: run test
-        run: ./bin/run-clara -y ./etc/services/rgd-clarode.yml -t 4 -n 500 -c ./clara -o ./tmp ./clas_018779.evio.00001
-      - name: ls tmp
-        run: ls -lhtr tmp
-      - name: rename
-        run: mv -v tmp/rec_clas_018779.evio.00001.hipo rec.hipo
+        run: ./coatjava/bin/recon-mutil -t 4 -n 500 -y etc/services/rgd-clarode.yml -o rec_clas_018779.evio.00001.hipo -i clas_018779.evio.00001
       - uses: actions/upload-artifact@v7
         with:
           name: test_clara_result
           retention-days: 1
-          path: rec.hipo
+          path: rec_clas_018779.evio.00001.hipo
 
   test_coatjava:
     needs: [ build ]

bin/postprocess2

@@ -6,5 +6,5 @@ export MALLOC_ARENA_MAX=1
 
 java ${JAVA_OPTS-} -Xmx768m -Xms768m -XX:+UseSerialGC \
     -cp ${COATJAVA_CLASSPATH:-''} \
-    org.jlab.analysis.postprocess.Processor \
+    org.jlab.detector.serial.PostProcessor \
     $*

bin/recon-mutil

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+. `dirname $0`/../libexec/env.sh
+
+split_cli $@
+
+export MALLOC_ARENA_MAX=1
+
+java ${JAVA_OPTS-} -Xms10240m -XX:+UseParallelGC ${jvm_options[@]} \
+    -cp ${COATJAVA_CLASSPATH:-''} \
+    org.jlab.clas.reco.ReconMutil \
+    ${class_options[@]}

common-tools/clara-io/pom.xml

@@ -48,12 +48,6 @@
       <version>14.2.0-SNAPSHOT</version>
     </dependency>
 
-    <dependency>
-      <groupId>org.jlab.clas</groupId>
-      <artifactId>clas-analysis</artifactId>
-      <version>14.2.0-SNAPSHOT</version>
-    </dependency> 
-
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>

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

@@ -3,16 +3,11 @@
 import java.io.File;
 import java.nio.file.Path;
 import java.util.List;
-import java.util.TreeMap;
-import java.util.TreeSet;
-import org.jlab.analysis.postprocess.Processor;
 import org.jlab.clara.std.services.EventWriterException;
 import org.jlab.detector.calib.utils.ConstantsManager;
-import org.jlab.detector.decode.CLASDecoder4;
-import org.jlab.detector.helicity.HelicitySequence;
 import org.jlab.detector.helicity.HelicitySequenceDelayed;
-import org.jlab.detector.helicity.HelicityState;
-import org.jlab.detector.scalers.DaqScalersSequence;
+import org.jlab.detector.serial.PostProcessor;
+import org.jlab.detector.serial.SerialHoncho;
 import org.jlab.jnp.hipo4.data.Bank;
 import org.jlab.jnp.hipo4.data.Event;
 import org.jlab.jnp.hipo4.data.SchemaFactory;
@@ -33,34 +28,22 @@
  */
 public class Clas12Writer extends HipoToHipoWriter {
 
-    static final String[] TAG1BANKS = {"RUN::scaler","HEL::scaler","RAW::scaler","RAW::epics","HEL::flip","COAT::config"};
-
-    Bank[] tag1banks;
+    SerialHoncho serial;
     Bank runConfig;
-    Bank helicityAdc;
     ConstantsManager conman;
-    TreeMap<Integer,Integer> eventUnix;
-    TreeSet<HelicityState> helicities;
-    DaqScalersSequence scalers;
     SchemaFactory fullSchema;
     boolean postprocess;
 
     private void init(JSONObject opts) {
         fullSchema = new SchemaFactory();
         fullSchema.initFromDirectory(FileUtils.getEnvironmentPath("CLAS12DIR","etc/bankdefs/hipo4"));
+        serial = new SerialHoncho(fullSchema);
         runConfig = new Bank(fullSchema.getSchema("RUN::config"));
-        helicityAdc = new Bank(fullSchema.getSchema("HEL::adc"));
-        helicities = new TreeSet<>();
-        scalers = new DaqScalersSequence(fullSchema);
         conman = new ConstantsManager();
-        eventUnix = new TreeMap<>();
         conman.init("/runcontrol/hwp","/runcontrol/helicity");
         postprocess = opts.optBoolean("postprocess", false);
         if (opts.has("variation")) conman.setVariation(opts.getString("variation"));
         if (opts.has("timestamp")) conman.setTimeStamp(opts.getString("timestamp"));
-        tag1banks = new Bank[TAG1BANKS.length];
-        for (int i=0; i<tag1banks.length; ++i)
-            tag1banks[i] = new Bank(fullSchema.getSchema(TAG1BANKS[i]));
     }
 
     @Override
@@ -78,29 +61,17 @@ protected HipoWriterSorted createWriter(Path file, JSONObject opts) throws Event
 
     @Override
     protected void writeEvent(Object event) throws EventWriterException {
-        scalers.add((Event)event);
-        ((Event)event).read(runConfig);
-        ((Event)event).read(helicityAdc);
-        if (runConfig.getRows() > 0) {
-            int unix = runConfig.getInt("unixtime",0);
-            int evno = runConfig.getInt("event",0);
-            if (unix > 0 && evno > 0) eventUnix.put(evno, unix);
-        }
-        helicities.add(HelicityState.createFromFadcBank(helicityAdc, runConfig, conman));
-        Event t = CLASDecoder4.createTaggedEvent((Event)event, runConfig, tag1banks);
-        if (!t.isEmpty()) writer.addEvent(t, 1);
+        Event tagged = serial.read(((Event)event));
+        if (!tagged.isEmpty()) writer.addEvent(tagged, 1);
         super.writeEvent(event);
     }
 
     @Override
     protected void closeWriter() {
-        HelicitySequence.writeFlips(fullSchema, writer, helicities);
-        writer.addEvent(getUnixEvent(runConfig),1);
+        serial.finish(writer);
         super.closeWriter();
         if (postprocess) postprocess();
-        // keep the latest helicity/scaler reading for the next file:
-        while (helicities.size() > 60) helicities.pollFirst();
-        scalers.clear(10);
+        serial.clear();
     }
 
     /**
@@ -120,35 +91,14 @@ private int getRunNumber() {
         return 0;
     }
 
-    /**
-     * Get a new event with a RUN::unix bank containing event-timestamp mapping,
-     * and the latest RUN::config bank.
-     * @param config
-     * @return 
-     */
-    private Event getUnixEvent(Bank config) {
-        Bank unix = new Bank(fullSchema.getSchema("RUN::unix"));
-        unix.setRows(eventUnix.size());
-        int row = 0;
-        for (int evno : eventUnix.keySet()) {
-            unix.putInt("event", row, evno);
-            unix.putInt("unixtime",row, eventUnix.get(evno));
-            row++;
-        }
-        Event e = new Event();
-        e.write(config);
-        e.write(unix);
-        return e;
-    }
-
     /**
      * Copy helicity/charge tag-1 information to all events.
      */
     private void postprocess() {
         int d = conman.getConstants(getRunNumber(), "/runcontrol/helicity").getIntValue("delay",0,0,0);
         HelicitySequenceDelayed helicity = new HelicitySequenceDelayed(d);
-        helicity.addStream(helicities);
-        Processor p = new Processor(List.of(filename), fullSchema, helicity, scalers);
+        helicity.addStream(serial.getHelicities());
+        PostProcessor p = new PostProcessor(List.of(filename), fullSchema, helicity, serial.getScalers());
         HipoReader r = new HipoReader();
         r.open(filename);
         Event e = new Event();

common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/RebuildScalers.java

@@ -9,6 +9,7 @@
 import org.jlab.detector.scalers.DaqScalers;
 import org.jlab.detector.helicity.HelicitySequenceManager;
 import org.jlab.detector.scalers.DaqScalersSequence;
+import org.jlab.detector.serial.SerialUtil;
 import org.jlab.jnp.hipo4.data.Bank;
 import org.jlab.jnp.hipo4.data.Event;
 import org.jlab.jnp.hipo4.io.HipoReader;
@@ -122,7 +123,7 @@ else if (seq != null) {
                     runScalerBank = ds.createRunBank(writer.getSchemaFactory());
                     helScalerBank = ds.createHelicityBank(writer.getSchemaFactory());
 
-                    Util.assignScalerHelicity(event, helScalerBank, helSeq);
+                    SerialUtil.assignScalerHelicity(event, helScalerBank, helSeq);
 
                     // put modified HEL/RUN::scaler back in the event:
                     event.write(runScalerBank);

common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java

@@ -1,5 +1,6 @@
 package org.jlab.analysis.postprocess;
 
+import org.jlab.detector.serial.PostProcessor;
 import java.util.TreeMap;
 import java.util.logging.Logger;
 import org.jlab.clas.reco.ReconstructionEngine;
@@ -13,6 +14,7 @@
 import org.jlab.detector.scalers.DaqScalersSequence;
 import org.jlab.detector.helicity.HelicityBit;
 import org.jlab.detector.helicity.HelicitySequenceDelayed;
+import org.jlab.detector.serial.SerialUtil;
 import org.jlab.jnp.hipo4.data.SchemaFactory;
 import org.jlab.utils.groups.IndexedTable;
 import org.jlab.utils.options.OptionParser;
@@ -81,7 +83,7 @@ public static void main(String[] args) {
             LOGGER.info("\n>>> Initializing helicity configuration from CCDB ...\n");
             ConstantsManager conman = new ConstantsManager();
             conman.init("/runcontrol/hwp","/runcontrol/helicity");
-            final int run = Util.getRunNumber(parser.getInputList().get(0));
+            final int run = SerialUtil.getRunNumber(parser.getInputList().get(0));
             IndexedTable helTable = conman.getConstants(run, "/runcontrol/helicity");
 
             // Initialize the scaler sequence from tag-1 events:
@@ -102,7 +104,7 @@ public static void main(String[] args) {
             }
 
             // Initialize the unix-event map:
-            TreeMap<Integer,Integer> eventUnix = Processor.getEventUnixMap(schema, parser.getInputList());
+            TreeMap<Integer,Integer> eventUnix = PostProcessor.getEventUnixMap(schema, parser.getInputList());
 
             // Loop over the input HIPO files:
             LOGGER.info("\n>>> Starting post-processing ...\n");
@@ -138,7 +140,7 @@ public static void main(String[] args) {
                     if (doHelicityDelay) {
                         recEventBank.putByte("helicity",0,hb.value());
                         recEventBank.putByte("helicityRaw",0,hbraw.value());
-                        Util.assignScalerHelicity(runConfigBank.getLong("timestamp",0), helScalerBank, helSeq);
+                        SerialUtil.assignScalerHelicity(runConfigBank.getLong("timestamp",0), helScalerBank, helSeq);
                     }
 
                     // Write beam charge to REC::Event:
@@ -169,7 +171,7 @@ public static void main(String[] args) {
                     writer.addEvent(event, event.getEventTag());
 
                     // Copy config banks to new, tag-1 events:
-                    Util.createTag1Events(writer, event, configEvent, configBanks);
+                    SerialUtil.createTag1Events(writer, event, configEvent, configBanks);
                 }
 
                 reader.close();

common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Processor.java → common-tools/clas-detector/src/main/java/org/jlab/detector/serial/PostProcessor.java

@@ -1,30 +1,30 @@
-package org.jlab.analysis.postprocess;
+package org.jlab.detector.serial;
 
 import java.util.List;
 import java.util.TreeMap;
 
+import org.jlab.io.base.DataBank;
+import org.jlab.io.base.DataEvent;
+import org.jlab.io.hipo.HipoDataBank;
 import org.jlab.jnp.hipo4.data.Bank;
 import org.jlab.jnp.hipo4.data.Event;
 import org.jlab.jnp.hipo4.data.SchemaFactory;
 import org.jlab.jnp.hipo4.io.HipoReader;
-import org.jlab.io.base.DataBank;
-import org.jlab.io.base.DataEvent;
-import org.jlab.io.hipo.HipoDataBank;
+import org.jlab.jnp.hipo4.io.HipoWriterSorted;
 
-import org.jlab.detector.calib.utils.ConstantsManager;
 import org.jlab.detector.scalers.DaqScalers;
 import org.jlab.detector.scalers.DaqScalersSequence;
 import org.jlab.detector.helicity.HelicityBit;
 import org.jlab.detector.helicity.HelicitySequenceDelayed;
-import org.jlab.jnp.hipo4.io.HipoWriterSorted;
+import org.jlab.detector.calib.utils.ConstantsManager;
 import org.jlab.utils.options.OptionParser;
 import org.jlab.utils.system.ClasUtilsFile;
 
 /**
  *
  * @author baltzell
  */
-public class Processor {
+public class PostProcessor {
 
     public static final String CCDB_TABLES[] = {"/runcontrol/fcup","/runcontrol/slm",
         "/runcontrol/helicity","/daq/config/scalers/dsc1","/runcontrol/hwp"};
@@ -37,7 +37,7 @@ public class Processor {
     private HelicitySequenceDelayed helicitySequence = null;
     private TreeMap<Integer,Integer> eventUnix = null;
 
-    public Processor(List<String> files, boolean restream, boolean rebuild) {
+    public PostProcessor(List<String> files, boolean restream, boolean rebuild) {
         HipoReader r = new HipoReader();
         r.open(files.get(0));
         schemaFactory = r.getSchemaFactory();
@@ -46,13 +46,13 @@ public Processor(List<String> files, boolean restream, boolean rebuild) {
         recEvent = new Bank(schemaFactory.getSchema("REC::Event"));
         conman = new ConstantsManager();
         conman.init(CCDB_TABLES);
-        helicitySequence = Util.getHelicity(files, schemaFactory, restream, conman);
+        helicitySequence = SerialUtil.getHelicity(files, schemaFactory, restream, conman);
         if (rebuild) chargeSequence = DaqScalersSequence.rebuildSequence(1, conman, files);
         else chargeSequence = DaqScalersSequence.readSequence(files);
         eventUnix = getEventUnixMap(schemaFactory, files); 
     }
 
-    public Processor(List<String> files, SchemaFactory schema, HelicitySequenceDelayed h, DaqScalersSequence s) {
+    public PostProcessor(List<String> files, SchemaFactory schema, HelicitySequenceDelayed h, DaqScalersSequence s) {
         schemaFactory = schema;
         helicitySequence = h;
         chargeSequence = s;
@@ -102,7 +102,7 @@ private void processEventHelicity(DataEvent event, DataBank runcfg, DataBank rec
         DataBank helScaler = event.getBank("HEL::scaler");
         if (helScaler.rows()>0) {
             event.removeBank("HEL::scaler");
-            Util.assignScalerHelicity(runcfg.getLong("timestamp",0), ((HipoDataBank)helScaler).getBank(), helicitySequence);
+            SerialUtil.assignScalerHelicity(runcfg.getLong("timestamp",0), ((HipoDataBank)helScaler).getBank(), helicitySequence);
             event.appendBank(helScaler);
         }
     }
@@ -122,7 +122,7 @@ private void processEventHelicity(Event event, Bank runcfg, Bank recevt) {
         event.read(helScaler);
         if (helScaler.getRows()>0) {
             event.remove(schemaFactory.getSchema("HEL::scaler"));
-            Util.assignScalerHelicity(runcfg.getLong("timestamp",0), helScaler, helicitySequence);
+            SerialUtil.assignScalerHelicity(runcfg.getLong("timestamp",0), helScaler, helicitySequence);
             event.write(helScaler);
         }
     }
@@ -247,7 +247,7 @@ public static void main(String args[]) {
         boolean restream = !o.getOption("-f").isDefault();
         boolean rebuild = !o.getOption("-c").isDefault();
 
-        Processor post = new Processor(o.getInputList(), restream, rebuild);
+        PostProcessor post = new PostProcessor(o.getInputList(), restream, rebuild);
 
         HipoWriterSorted writer = null;
 
@@ -274,4 +274,20 @@ public static void main(String args[]) {
         if (writer != null) writer.close();
     }
 
+    public void postprocess(int run, String input, SerialHoncho serial, HipoWriterSorted writer, List<Bank> banks) {
+        int d = serial.getConstantsManager().getConstants(run, "/runcontrol/helicity").getIntValue("delay",0,0,0);
+        HelicitySequenceDelayed helicity = new HelicitySequenceDelayed(d);
+        helicity.addStream(serial.getHelicities());
+        PostProcessor p = new PostProcessor(List.of(input), serial.getSchemaFactory(), helicity, serial.getScalers());
+        HipoReader r = new HipoReader();
+        r.open(input);
+        Event e = new Event();
+        while (r.hasNext()) {
+            r.nextEvent(e);
+            p.processEvent(e);
+            int tag = e.getEventTag();
+            if (tag==1 || banks.isEmpty()) writer.addEvent(e,tag);
+            else writer.addEvent(e.reduceEvent(banks),tag);
+        }
+    }
 }