Merge branch 'development' into development

JeffersonLab · Dec 10, 2024 · 9abc31a · 9abc31a
2 parents 506e888 + a2711f3
commit 9abc31a
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diff --git a/.containers/coatjava.Dockerfile b/.containers/coatjava.Dockerfile
@@ -0,0 +1,25 @@
+#syntax=docker/dockerfile:1
+
+FROM ubuntu:noble
+
+LABEL name="coatjava"
+LABEL maintainer="Whitney Armstrong <[email protected]>"
+LABEL architecture="amd64"
+
+USER root
+
+
+RUN apt update && apt upgrade -y
+RUN apt install cmake vim maven groovy git ca-certificates wget curl python-is-python3 \
+                openjdk-17-jdk openjdk-17-jre openjdk-17-jdk-headless openjdk-17-jre-headless \
+                python3-sqlalchemy -y && update-ca-certificates
+
+# CA certificates
+ADD https://pki.jlab.org/JLabCA.crt /etc/ssl/certs/JLabCA.crt 
+#RUN trust anchor --store /image/JLabCA.crt
+
+ARG REF_NAME=development 
+# build coatjava 
+RUN java --version && cd /opt && \
+    git clone https://code.jlab.org/hallb/alert/coatjava.git && cd coatjava && \
+    git fetch origin && git checkout ${REF_NAME} && ./build-coatjava.sh --nomaps
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,31 @@
+workflow:
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+    - if: '$CI_PIPELINE_SOURCE == "web"'
+    - if: '$CI_PIPELINE_SOURCE == "webide"'
+    - if: '$CI_COMMIT_BRANCH == "master"'
+    - if: '$CI_COMMIT_BRANCH == "development"'
+    - if: '$CI_COMMIT_TAG'
+
+default:
+  image: ubuntu:noble
+  retry: 2
+
+coatjava_build:
+  image: gcr.io/kaniko-project/executor:debug
+  script:
+    - echo "${CI_COMMIT_REF_NAME}"
+    - >-
+      /kaniko/executor
+      --context     $CI_PROJECT_DIR/docker
+      --dockerfile  $CI_PROJECT_DIR/.containers/coatjava.Dockerfile
+      --destination $CI_REGISTRY_IMAGE/coatjava:${CI_COMMIT_REF_NAME}
+      --build-arg REF_NAME=${CI_COMMIT_REF_NAME}
+    
+alert_testing:
+  needs: ["coatjava_build"]
+  variables:
+    REF_NAME: "$CI_COMMIT_REF_NAME"
+  trigger:
+    project: hallb/alert/c12
+    strategy: depend
diff --git a/bin/hipo-multi-merge b/bin/hipo-multi-merge
@@ -0,0 +1,107 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'ostruct'
+require 'fileutils'
+
+def print_log(name, val)
+  puts name.rjust(30) + " = #{val}"
+end
+
+# user options
+@args = OpenStruct.new
+@args.inputs     = nil
+@args.output_dir = nil
+@args.prefix     = nil
+@args.num_merge  = nil
+@args.use_batch  = false
+@args.dry_run    = false
+OptionParser.new do |o|
+  o.banner = '''
+  This tool merges a set of input HIPO files to a set of output HIPO files,
+  where you may control the number of input files per output file; for example,
+  use this tool if you have 1000 small HIPO files but would rather have 10
+  large HIPO files.
+  '''
+  o.separator "USAGE: #{$0} [OPTIONS]..."
+  o.separator ''
+  o.separator 'REQUIRED OPTIONS:'
+  o.on('-i', '--input INPUTS', 'input directory or file glob;', 'surround file glob in quotes') { |a| @args.inputs = a }
+  o.on('-o', '--output OUTPUT_DIR', 'output directory') { |a| @args.output_dir = a }
+  o.on('-p', '--prefix OUTPUT_PREFIX', 'output filename prefix; names will be:', ' [OUTPUT_DIR]/[OUTPUT_PREFIX]_#####.hipo') { |a| @args.prefix = a }
+  o.on('-n', '--num NUM_FILES', 'number of files per output merged file') { |a| @args.num_merge = a.to_i }
+  o.separator ''
+  o.separator 'OPTIONAL OPTIONS:'
+  o.on('-b', '--batch', 'submit jobs to Slurm', '(default is sequential jobs)') { |a| @args.use_batch = true }
+  o.on('-d', '--dry-run', 'just print what would be done') { |a| @args.dry_run = true }
+  o.on_tail('-h', '--help', 'show this message') do
+    puts o
+    exit
+  end
+end.parse! ARGV.empty? ? ['--help'] : ARGV
+
+# check required options
+if [@args.inputs, @args.output_dir, @args.prefix, @args.num_merge].include? nil
+  raise 'missing required option(s;) re-run with "--help" for guidance.'
+end
+raise 'option "--num" must be greater than zero' unless @args.num_merge > 0
+
+# glob inputs
+input_glob = File.expand_path @args.inputs
+input_glob = File.join input_glob, "*.hipo" if File.directory? input_glob
+print_log 'input glob', input_glob
+print_log 'output dir', @args.output_dir
+print_log 'output prefix', @args.prefix
+print_log 'num files per output', @args.num_merge
+
+# chunks
+input_files = Dir.glob input_glob
+raise "no input files found with glob '#{input_glob}'" if input_files.empty?
+input_chunks = input_files.each_slice(@args.num_merge).to_a
+print_log 'num input files', input_files.size
+print_log 'num output files', input_chunks.size
+raise 'option "--num" >= num input files, therefore there is nothing to do' if input_chunks.size == 1
+
+# build commands
+puts "="*82
+merge_cmds = input_chunks.each_with_index.map do |input_chunk, chunk_num|
+  out_name = File.join @args.output_dir, "#{@args.prefix}_#{chunk_num.to_s.rjust(5, '0')}.hipo"
+  raise "output file #{out_name} already exists; cannot overwrite! delete it or choose another path/name" if File.exist? out_name
+  [ 'hipo-utils', '-merge', '-o', out_name, *input_chunk ].join ' '
+end
+
+# sbatch commands
+if @args.use_batch
+  sbatch_args = {
+    'job-name'      => "hipo_multi_merge___#{@args.prefix}",
+    'account'       => 'clas12',
+    'partition'     => 'production',
+    'mem-per-cpu'   => 500,
+    'time'          => '1:00:00',
+    'ntasks'        => 1,
+    'cpus-per-task' => 1,
+  }.map{ |opt, val| "--#{opt}=#{val.to_s}" }
+  exe_cmds = merge_cmds.each_with_index.map do |merge_cmd, job_num|
+    log_name = "/farm_out/%u/%x_#{job_num.to_s.rjust(5, '0')}"
+    [
+      'sbatch',
+      *sbatch_args,
+      "--output=#{log_name}.out",
+      "--error=#{log_name}.err",
+      "--wrap='#{merge_cmd}'",
+    ].join ' '
+  end
+else
+  exe_cmds = merge_cmds
+end
+
+# execute
+if @args.dry_run
+  puts 'THIS IS JUST A DRY RUN. Here are the commands which would be executed:'
+  puts "="*82
+  puts "mkdir -p #{@args.output_dir}"
+  exe_cmds.each do |cmd| puts cmd end
+else
+  FileUtils.mkdir_p @args.output_dir
+  exe_cmds.each do |cmd| system cmd end
+end
diff --git a/bin/run-clara b/bin/run-clara
@@ -34,7 +34,7 @@ do
         p) prefix=$OPTARG ;;
         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" ;;
+        n) nevents="-e $OPTARG" && echo "$nevents" | grep -q -E '^-e [0-9]+$' || error "-n must be an integer, events" ;;
         m) merge=1 ;;
         h) echo -e "\n$usage" && echo -e $info && exit 0 ;;
     esac

diff --git a/common-tools/clara-io/pom.xml b/common-tools/clara-io/pom.xml
@@ -3,14 +3,14 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clara-io</artifactId>
-  <version>11.0.3-SNAPSHOT</version>
+  <version>11.0.5-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.0.3-SNAPSHOT</version>
+    <version>11.0.5-SNAPSHOT</version>
   </parent>
 
   <dependencies>

diff --git a/common-tools/clas-analysis/pom.xml b/common-tools/clas-analysis/pom.xml
@@ -3,63 +3,63 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-analysis</artifactId>
-  <version>11.0.3-SNAPSHOT</version>
+  <version>11.0.5-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.0.3-SNAPSHOT</version>
+    <version>11.0.5-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-physics</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-jcsg</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>swim-tools</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-detector</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-reco</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
   </dependencies>
 

diff --git a/common-tools/clas-detector/pom.xml b/common-tools/clas-detector/pom.xml
@@ -3,21 +3,21 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-detector</artifactId>
-  <version>11.0.3-SNAPSHOT</version>
+  <version>11.0.5-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.0.3-SNAPSHOT</version>
+    <version>11.0.5-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
@@ -29,13 +29,13 @@
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
   </dependencies>
 

diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorType.java b/common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorType.java
@@ -29,6 +29,8 @@ public enum DetectorType {
     BAND      (21, "BAND"),
     RASTER    (22, "RASTER"),
     URWELL    (23, "URWELL"),
+    AHDC      (24, "AHDC"),
+    ATOF      (25, "ATOF"),
     TARGET    (100, "TARGET"),
     MAGNETS   (101, "MAGNETS"),
     ECIN      (110, "ECIN"),