Improve JVM memory setting for run-clara

bin/run-clara

@@ -34,7 +34,6 @@ do
         c) CLARA_HOME=$OPTARG ;;
         t) threads=$OPTARG && echo $threads | grep -q -E '^[0-9]+$' || error "-t must be an integer, threads" ;;
         n) nevents="-e $OPTARG" && echo "$nevents" | grep -q -E '^-e [0-9]+$' || error "-n must be an integer, events" ;;
-        g) memory_gb="-e $OPTARG" && echo "$memory_gb" | grep -q -E '^-e [0-9]+$' || error "-g must be an integer, GB of memory" ;;
         m) merge=1 ;;
         q) quiet=1 ;;
         h) echo -e "\n$usage" && echo -e $info && exit 0 ;;
@@ -43,8 +42,9 @@ done
 shift $((OPTIND-1))
 inputs=$@
 
-# Configure JVM -Xmx memory setting:
-[ -z ${memory_gb+x} ] && memory_gb=$((threads+2))
+# Configure JVM memory settings (overridedable via $JAVA_OPTS):
+gb=$((threads<3?threads+2:2+threads-threads/4))
+java_opts=-Xmx${gb}g
 
 # Check configuration:
 [ $# -lt 1 ] && error "Input data files are required"
@@ -76,11 +76,14 @@ done
 [ $(cat $CLARA_USER_DATA/filelist.txt | wc -l) -gt 0 ] || error "Found no input files"
 
 # Set some JVM options:
-export JAVA_OPTS="$JAVA_OPTS -Xmx${memory_gb}g -XX:+IgnoreUnrecognizedVMOptions"
-export JAVA_OPTS="$JAVA_OPTS -Djava.io.tmpdir=$CLARA_USER_DATA -Dorg.sqlite.tmpdir=$CLARA_USER_DATA"
+JAVA_OPTS="$java_opts $JAVA_OPTS -XX:+IgnoreUnrecognizedVMOptions"
+JAVA_OPTS="$JAVA_OPTS -Djava.io.tmpdir=$CLARA_USER_DATA -Dorg.sqlite.tmpdir=$CLARA_USER_DATA"
+
 # Set verbosity:
 [ -z ${quiet+x} ] && stub=fine || stub=info
-export JAVA_OPTS="$JAVA_OPTS -Djava.util.logging.config.file=$CLAS12DIR/etc/logging/$stub.properties"
+JAVA_OPTS="$JAVA_OPTS -Djava.util.logging.config.file=$CLAS12DIR/etc/logging/$stub.properties"
+
+export JAVA_OPTS
 
 function get_host_ip() {
     if command -v ip >/dev/null 2>&1

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

@@ -0,0 +1,83 @@
+package org.jlab.clas.reco;
+
+import java.util.ArrayList;
+import org.jlab.clara.engine.EngineData;
+import org.jlab.io.base.DataEvent;
+
+/**
+ * A ReconstructionEngine that is a chain of ReconstructionEngines.
+ * 
+ * @author baltzell
+ */
+public abstract class UberEngine extends ReconstructionEngine {
+
+    private final ArrayList<ReconstructionEngine> engines = new ArrayList<>();
+
+    public UberEngine(String name, String author, String version) {
+        super(name,author,version);
+    }
+
+    /**
+     * Add engines to the chain. 
+     * @param e
+     */
+    protected void add(ReconstructionEngine... e) {
+        for (int i=0; i<e.length; ++i) {
+            if (UberEngine.class.isInstance(e[i])) 
+                throw new RuntimeException("UberEngine cannot contain an UberEngine.");
+            engines.add(e[i]);
+        }
+    }
+
+    @Override
+    public boolean processDataEvent(DataEvent event) {
+        throw new RuntimeException("UberEngine does not implement processDataEvent.");
+    }
+
+    /**
+     * Process one event through the chain of engines.
+     * @param event 
+     */
+    @Override
+    public final void filterEvent(DataEvent event) {
+        for (ReconstructionEngine e : engines) 
+            e.filterEvent(event);
+    }
+
+    /**
+     * Run all engines' init methods.
+     * @return
+     */ 
+    @Override
+    public final boolean init() {
+        boolean ret = true;
+        for (ReconstructionEngine e : engines)
+            if (!e.init()) ret = false;
+        return ret;
+    }
+
+    /**
+     * Run all engines' configure methods.
+     * @param ed
+     * @return 
+     */
+    @Override
+    public EngineData configure(EngineData ed) {
+        for (ReconstructionEngine e : engines) { 
+            e.configure(ed);
+        }
+        return ed;
+    }
+
+    /**
+     * Run all engines' execute methods.
+     * @param ed
+     * @return 
+     */
+    @Override
+    public EngineData execute(EngineData ed) {
+        for (ReconstructionEngine e : engines) 
+            ed = e.execute(ed);
+        return ed;
+    }
+}

etc/services/data-ai-uber.yml

@@ -0,0 +1,34 @@
+io-services:
+  reader:
+    class: org.jlab.io.clara.DecoderReader
+    name: DecoderReader
+  writer:
+    class: org.jlab.io.clara.DecoderWriter
+    name: DecoderWriter
+services:
+  - class: org.jlab.service.uber.Uber$First
+    name: 1ST
+  - class: org.jlab.service.uber.Uber$ForwardTagger
+    name: FT
+  - class: org.jlab.service.uber.Uber$Central
+    name: CD
+  - class: org.jlab.service.uber.Uber$HitBased
+    name: HB
+  - class: org.jlab.service.uber.Uber$TimeBased
+    name: TB
+  - class: org.jlab.service.uber.Uber$Last
+    name: NTH
+configuration:
+  global:
+    variation: rgd_fall2023
+  io-services:
+    writer:
+      schema_dir: dst
+  services:
+    1ST:
+      magfieldSolenoidMap: Symm_solenoid_r601_phi1_z1201_13June2018.dat
+      magfieldTorusMap: Full_torus_r251_phi181_z251_25Jan2021.dat
+    HB:
+      run: "6302"
+mime-types:
+  - binary/data-hipo

reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBPostClusterAI.java

@@ -39,6 +39,10 @@ public DCHBPostClusterAI() {
         this.getBanks().init("HitBasedTrkg", "", "AI");
     }
 
+    public DCHBPostClusterAI(String outputBankPrefix) {
+        super("DCHAI");
+        this.getBanks().init("HitBasedTrkg", "", outputBankPrefix);
+    }
 
     @Override
     public void setDropBanks() {

reconstruction/pom.xml

@@ -39,6 +39,7 @@
     <module>postproc</module>
     <module>recoil</module>
     <module>calib</module>
+    <module>uber</module>
   </modules>
 
   <build>

reconstruction/uber/pom.xml

@@ -0,0 +1,114 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <groupId>org.jlab.clas12.detector</groupId>
+  <artifactId>clas12detector-uber</artifactId>
+  <version>13.4.0-SNAPSHOT</version>
+  <packaging>jar</packaging>
+
+  <parent>
+    <groupId>org.jlab.clas12</groupId>
+    <artifactId>reconstruction</artifactId>
+    <version>13.4.0-SNAPSHOT</version>
+  </parent>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.jlab.clas</groupId>
+      <artifactId>clas-reco</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas</groupId>
+      <artifactId>swim-tools</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-dc</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-ec</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-tof</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-htcc</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-ltcc</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-ft</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-cnd</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-band</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-cvt</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-raster</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-vtx</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-calib</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-rtpc</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-rich</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-eb</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-mltn</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.jlab.clas12.detector</groupId>
+      <artifactId>clas12detector-fmt</artifactId>
+      <version>13.4.0-SNAPSHOT</version>
+    </dependency>
+  </dependencies>
+
+ </project>