Merge pull request #498 from JeffersonLab/development

Merge all updates since 6.3.1 for new production release
JeffersonLab · Mar 7, 2020 · 72578b8 · 72578b8
2 parents a5a59a3 + 423670f
commit 72578b8
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Showing 285 changed files with 11,903 additions and 5,188 deletions.
diff --git a/.gitignore b/.gitignore
@@ -33,4 +33,7 @@ hs_err_pid*
 
 # no log files:
 *.log
+*.evio 
 
+bin/evio2hipotest
+export.sh
diff --git a/.travis.yml b/.travis.yml
@@ -5,13 +5,12 @@ sudo: required
 language: java
 
 jdk:
-  - oraclejdk9
+  - openjdk11
 
-# this affects which java version is used:
 addons:
   apt:
     packages:
-      - oracle-java9-installer
+      - openjfx
 
 before_install:
     - ls -lthra
@@ -32,6 +31,7 @@ script:
   - ./run-eb-tests.sh -100 electrongamma    || travis_terminate 1;
   - ./run-eb-tests.sh -100 electronprotonC  || travis_terminate 1;
   - ./run-eb-tests.sh -100 electronneutronC || travis_terminate 1;
+  - ./run-eb-tests.sh -100 electronFTpion   || travis_terminate 1;
   - cd -
   - echo "finished advanced tests"
 #  - mvn cobertura:cobertura &> /dev/null # for codecov

diff --git a/bin.old/calibration b/bin.old/calibration
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -XX:+UseSerialGC -Xmx2048m -Xms2048m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.calib.services.TOFCalibration $*
diff --git a/bin/clara-rec → bin.old/clara-rec b/bin/clara-rec → bin.old/clara-rec
diff --git a/bin.old/convertor b/bin.old/convertor
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.reco.io.HipoConvertor $*
diff --git a/bin.old/ddr b/bin.old/ddr
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.service.DataDistributionService -type et -host localhost -file /tmp/et_sys_$SESSION
diff --git a/bin.old/decoder-debugger b/bin.old/decoder-debugger
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# This doesn't work in dash (Travis's /bin/sh):
+source `dirname $0`/env.sh 
+
+MALLOC_ARENA_MAX=1; export MALLOC_ARENA_MAX
+
+java -Xmx1536m -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.detector.decode.DetectorDecoderDebug $*
diff --git a/bin.old/decoder3 b/bin.old/decoder3
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source `dirname $0`/env.sh 
+
+MALLOC_ARENA_MAX=1; export MALLOC_ARENA_MAX
+
+java -Xmx1536m -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.detector.decode.CLASDecoder $*
diff --git a/bin.old/grid b/bin.old/grid
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.groot.matrix.SparseGridIO $*
diff --git a/bin.old/hipo-writer b/bin.old/hipo-writer
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.io.utils.Evio2HipoConverter $*
diff --git a/bin.old/hipo3utils b/bin.old/hipo3utils
@@ -0,0 +1,7 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+MALLOC_ARENA_MAX=1; export MALLOC_ARENA_MAX
+
+java -Xmx2048m -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.jnp.hipo.utils.HipoUtilities $*
diff --git a/bin.old/rec-monitor b/bin.old/rec-monitor
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.monitor.eb.ReconstructionMonitor $*
diff --git a/bin.old/studio b/bin.old/studio
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -Xmx2048m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.physics.EventTree $*
diff --git a/bin.old/update b/bin.old/update
@@ -0,0 +1,9 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/utils/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.update.UpdateManager link http://clasweb.jlab.org/clas12maven/org/jlab/coat/coat-libs/3.0-SNAPSHOT/ coat-libs-3.0-SNAPSHOT.jar $CLAS12DIR/lib/clas
+
+java -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/utils/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.update.UpdateManager link https://userweb.jlab.org/~devita/kpp/ KPP-Plots-1.0.jar  $CLAS12DIR/lib/utils
+
+java -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/utils/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.update.UpdateManager link https://userweb.jlab.org/~devita/kpp/ KPP-Monitoring-1.0.jar  $CLAS12DIR/lib/utils
diff --git a/bin.old/x-client b/bin.old/x-client
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.io.hipo.HipoRingSource $*
diff --git a/bin.old/x-client-evio b/bin.old/x-client-evio
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.io.evio.EvioRingSource $*
diff --git a/bin.old/x-server b/bin.old/x-server
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.clas.service.DataDistributionService $*
diff --git a/bin/analyzer b/bin/analyzer
diff --git a/bin/bos2hipo b/bin/bos2hipo
@@ -2,18 +2,4 @@
 
 source `dirname $0`/env.sh 
 
-#CLARA_HOME=`dirname $0`
-#CLARA_SERVICES=`dirname $0`
-#DATAMINING=`dirname $0`
-
-echo +-------------------------------------------------------------------------
-echo "| Starting CLARA-PLATFORM with CLARA_SERVICES = " $CLARA_SERVICES
-echo +-------------------------------------------------------------------------
-echo "\n"
-
-echo "INSTALLATION DIRECTORY = " $CLARA_HOME
-echo "LIBRARY DIRECTORY      = " $DATAMINING/lib/clas/
-
-#java -cp "$DATAMINING/lib/clas/core/*" org.jlab.coda.eventViewer.EventTreeFrame $*
-#java -Xms1024m -cp "$DATAMINING/lib/clas/*:$DATAMINING/lib/plugins/*" org.jlab.io.hipo.HipoDataSync $*
-java -Xms1024m -cp "$DATAMINING/lib/clas/*:$DATAMINING/lib/plugins/*" org.jlab.io.utils.Bos2HipoEventBank $*
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.io.utils.Bos2HipoEventBank $*
diff --git a/bin/browser b/bin/browser
diff --git a/bin/calibration b/bin/calibration
diff --git a/bin/convertor b/bin/convertor
diff --git a/bin/daq-monitor b/bin/daq-monitor
diff --git a/bin/daqEventViewer b/bin/daqEventViewer
@@ -2,17 +2,4 @@
 
 source `dirname $0`/env.sh 
 
-#CLARA_HOME=`dirname $0`
-#CLARA_SERVICES=`dirname $0`
-#DATAMINING=`dirname $0`
-
-echo +-------------------------------------------------------------------------
-echo "| Starting CLARA-PLATFORM with CLARA_SERVICES = " $CLARA_SERVICES
-echo +-------------------------------------------------------------------------
-echo "\n"
-
-echo "INSTALLATION DIRECTORY = " $CLARA_HOME
-echo "LIBRARY DIRECTORY      = " $DATAMINING/lib/clas/
-
-#java -cp "$DATAMINING/lib/clas/core/*" org.jlab.coda.eventViewer.EventTreeFrame $*
-java -Xms1024m -cp "$DATAMINING/lib/clas/*:$DATAMINING/lib/services/*:$DATAMINING/lib/utils/*" org.jlab.detector.examples.RawEventViewer $*
+java -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/services/*:$CLAS12DIR/lib/utils/*" org.jlab.detector.examples.RawEventViewer $*
diff --git a/bin/dclayereffs-ana b/bin/dclayereffs-ana
@@ -0,0 +1,5 @@
+#!/bin/sh -f
+
+source `dirname $0`/env.sh 
+
+java -Dsun.java2d.pmoffscreen=false -Xmx2048m -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/utils/*:$CLAS12DIR/lib/services/*" org.jlab.service.dc.LayerEfficiencyAnalyzer $*
diff --git a/bin/dclayereffs-anal b/bin/dclayereffs-anal
diff --git a/bin/ddr b/bin/ddr
diff --git a/bin/debug_ec.sh b/bin/debug_ec.sh
diff --git a/bin/decoder b/bin/decoder
@@ -5,18 +5,8 @@ source `dirname $0`/env.sh
 
 MALLOC_ARENA_MAX=1; export MALLOC_ARENA_MAX
 
-#CLARA_HOME=`dirname $0`
-#CLARA_SERVICES=`dirname $0`
-#DATAMINING=`dirname $0`
-
 echo +-------------------------------------------------------------------------
 echo "| DECODER GENERATION 4 (using HIPO-4 Library)"
 echo +-------------------------------------------------------------------------
-echo "\n"
-
-echo "INSTALLATION DIRECTORY = " $CLARA_HOME
-echo "LIBRARY DIRECTORY      = " $DATAMINING/lib/clas/
 
-#java -cp "$DATAMINING/lib/clas/core/*" org.jlab.coda.eventViewer.EventTreeFrame $*
-#java -Xms1024m -cp "$DATAMINING/lib/clas/*:$DATAMINING/lib/plugins/*" org.jlab.io.hipo.HipoDataSync $*
-java -Xmx1536m -Xms1024m -cp "$DATAMINING/lib/clas/*:$DATAMINING/lib/plugins/*" org.jlab.detector.decode.CLASDecoder4 $*
+java -Xmx1536m -Xms1024m -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" org.jlab.detector.decode.CLASDecoder4 $*
diff --git a/bin/decoder-debugger b/bin/decoder-debugger
diff --git a/bin/decoder3 b/bin/decoder3