Rebase Compair2 on geant_11.2

.gitignore

@@ -10,6 +10,17 @@ bin/realta
 bin/revan
 bin/sivan
 bin/spectralyze
+bin/AspectOptimizerStep1
+bin/CompareHistograms
+bin/DistanceOptimizerForEventClusterizer
+bin/SimBinaryConverter
+bin/TH1_summer_cpp
+bin/ThresholdCalculation
+bin/TraMerger
+bin/UTARMFitter
+bin/UTCosimaInputSpectra
+bin/photopeak_depth_distribution
+bin/xyscanner
 
 BackgroundMixer
 ConvertACTtools
@@ -75,6 +86,7 @@ configure_lastgoodoptions
 source-megalib.sh
 SetupOptions.txt
 new-source-megalib.sh
+config/Configuration.txt
 
 # doc directory:
 Peoples.txt
@@ -102,4 +114,5 @@ External
 callgrind.*
 *.rsp
 *.erm
+*.swp
 

CodeOfConduct.md

@@ -0,0 +1,133 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[email protected].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

Contribute.md

@@ -0,0 +1,59 @@
+# Contributor Guide
+
+Welcome to the MEGAlib contributor guide! We're excited to have you interested in contributing to our project. This guide will help you get started, understand our workflow, and know what to expect when contributing.
+How to Contribute
+
+We use a fork and pull request workflow for contributions. Here’s a step-by-step guide to help you get started:
+
+## Fork the Repository
+Go to our GitHub repository and click the "Fork" button at the top right corner of the page. This will create a copy of the repository under your GitHub account.
+
+## Clone Your Fork
+
+Clone your fork to your local machine using the following command:
+
+```
+git clone https://github.com/zoglauer/MEGAlib.git
+cd MEGAlib
+```
+
+## Create a Branch
+Create a new branch for your feature or bug fix. Use a descriptive name for your branch:
+
+```
+git checkout -b feature/your-feature-name
+```
+
+## Make Your Changes
+Make your changes in your local repository. Be sure to follow the same coding standards as in the rest of MEGAlib.
+
+## Commit Your Changes
+Commit your changes with a clear and concise commit message:
+
+```
+git add .
+git commit -m "Add feature: your feature name"
+```
+
+## Push to Your Fork
+Push your changes to your forked repository on GitHub:
+
+```
+git push origin feature/your-feature-name
+```
+
+## Open a Pull Request
+Go to your forked repository on GitHub and click the "New pull request" button. Select the branch you created and make sure the base repository is set to the original repository. Provide a clear and descriptive title and description for your pull request.
+
+## Respond to Feedback
+Your pull request will be reviewed by the project maintainers. Be prepared to make additional changes based on their feedback. Engage in constructive discussions to refine your contribution.
+
+## Merge Your Pull Request
+
+Once your pull request is approved, it will be merged into the main repository. Congratulations on your contribution!
+
+## Final words
+
+If you need help or have questions, feel free to open an issue or discussion on GitHub.
+
+

bin/mmaxmem

@@ -0,0 +1,77 @@
+#! /bin/bash
+
+echo ""
+echo "mmaxmem - MEGAlib's memory monitor"
+echo ""
+
+
+
+help() {
+  echo ""
+  echo "mmaxmem - script for MEGAlib";
+  echo "(C) by Andreas Zoglauer"
+  echo "";
+  echo "This script keeps track of the maximum memory used by a process."
+  echo "";
+  echo "Usage:";
+  echo "    mmaxmem [program name] [optional command line arguments]";
+  echo "";
+  echo "Example:";
+  echo "    mmaxmem mimrec";
+  echo "";
+}
+
+
+# Make sure there's at least one argument
+if [ $# -lt 1 ]; then
+  help
+  exit 1
+fi
+
+# Check for help flag
+if [[ "$1" == "*-h*" ]]; then
+  help
+  exit 0
+fi
+
+OS=$(uname)
+
+RSS_KB=0
+MAX_RSS_KB=0
+
+# Start the command in the background
+"$@" &> /dev/null &
+APPPID=$!
+APPNAME=$*
+sleep 0.2
+
+echo "Monitoring memory usage of program ${APPNAME} with ${APPPID} ..."
+echo ""
+
+while true; do
+  if ps -p "${APPPID}" > /dev/null 2>&1; then
+    if [[ "${OS}" == *inux* ]]; then
+      RSS_KB=$(awk '/VmRSS/ {print $2}' /proc/${APPPID}/status 2>/dev/null)
+    elif [[ "${OS}" == *arwin* ]]; then
+      RSS_KB=$(ps -o rss= -p "${APPPID}" | awk '{print $1}')
+    else
+      echo "Unsupported OS: \"${OS}\""
+      exit 1
+    fi
+
+    if [[ "${RSS_KB}" =~ ^[0-9]+$ ]]; then
+      if [ "${RSS_KB}" -gt "${MAX_RSS_KB}" ]; then
+        MAX_RSS_KB=${RSS_KB}
+      fi
+      CURRENT_MB=$(awk "BEGIN {printf \"%.2f\", ${RSS_KB}/1024}")
+      MAX_MB=$(awk "BEGIN {printf \"%.2f\", ${MAX_RSS_KB}/1024}")
+      echo -ne "Current: ${CURRENT_MB} MB\tMax: ${MAX_MB} MB\r"
+    fi
+    sleep 1.0
+  else
+    echo -e "\nProcess ${APPPID} has exited."
+    MAX_MB=$(awk "BEGIN {printf \"%.2f\", ${MAX_RSS_KB}/1024}")
+    echo "Maximum RSS memory used: ${MAX_MB} MB"
+    break
+  fi
+done

bin/mwait

@@ -13,8 +13,9 @@ commandhelp() {
   echo "  --instances=[integer or \"cores\", \"threads\"]: Maximum number of instances or \"cores\"/\"threads\" for the number of available cores or threads (default: 1)"
   echo "  --load=[integer or \"cores\", \"threads\"]: Maximum system load as integer or \"cores\"/\"threads\" for the number of available cores or threads (default: threads + 3)"
   echo "  --program=[name]: The main program to wait for"
-  #echo "  --auxprogram=[name]: Other programs to wait for"
+  echo "  --auxprogram=[name]: Other programs to wait for"
   echo "  --memory: Make sure we have enough free memory, if more than one instance is running"
+  echo "  --delay=[integer]: The delay time"
   echo "  --quiet: No text output"
   echo ""
   echo "Examples:"
@@ -29,10 +30,11 @@ commandhelp() {
 # Defaults
 INSTANCES="cores"
 LOAD="10000"
-PROGAM=""
+PROGRAM=""
 AUXPROGRAMS=()
 MEMORY=false
 QUIET=false
+DELAY=5
 
 # Store command line as array
 CMD=( "$@" )
@@ -54,8 +56,10 @@ for C in "${CMD[@]}"; do
     LOAD=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-p*=* ]]; then
     PROGRAM=`echo ${C} | awk -F"=" '{ print $2 }'`
-  elif [[ ${C} == *-c*=* ]]; then
-    AUXPROGRAMS+=`echo ${C} | awk -F"=" '{ print $2 }'`
+  elif [[ ${C} == *-a*=* ]]; then
+    AUXPROGRAMS+=( `echo ${C} | awk -F"=" '{ print $2 }'` )
+  elif [[ ${C} == *-d*=* ]]; then
+    DELAY=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-m* ]]; then
     MEMORY=true
   elif [[ ${C} == *-q* ]]; then
@@ -122,7 +126,11 @@ while [[ ${WAIT} == true ]]; do
   # We exclude this process itself in the listing
   # sed -> don't remember
   RUNNINGTHREADS=0
-  RUNNINGTHREADS=$(( RUNNINGTHREADS + $(ps -Af | grep "[ ]${PROGRAM}" | grep -v "mwait ${PROGRAM}" | grep -v "bash -c " | grep -v "timeout " | wc -l | sed 's/^ *//g') ))
+  RUNNINGTHREADS=$(( RUNNINGTHREADS + $(ps -Af | grep -e "[ ]${PROGRAM}" -e "/${PROGRAM}" | grep -v "mwait ${PROGRAM}" | grep -v "bash -c " | grep -v "timeout " | grep -v "grep" | wc -l | sed 's/^ *//g') ))
+  for A in "${AUXPROGRAMS[@]}"; do
+    RUNNINGTHREADS=$(( RUNNINGTHREADS + $(ps -Af | grep -e "[ ]${A}" -e "/${A}" | grep -v "mwait ${A}" | grep -v "bash -c " | grep -v "timeout " | grep -v "grep" | wc -l | sed 's/^ *//g') ))
+  done
+
 
   #echo "mwait: ${MAXTHREADS} vs. ${RUNNINGTHREADS}"
 
@@ -131,7 +139,7 @@ while [[ ${WAIT} == true ]]; do
     if [[ ${QUIET} == false ]]; then
       echo "Waiting for a free slot: Running ${RUNNINGTHREADS} of ${MAXTHREADS} allowed instances of ${PROGRAM}"
     fi
-    sleep 5
+    sleep ${DELAY}
     continue
   fi
 
@@ -159,7 +167,7 @@ while [[ ${WAIT} == true ]]; do
             echo "Waiting till all programs (n=${RUNNINGTHREADS}) reach memory saturation (now: ${TOTALMEMORY}), last: ${LASTTOTALMEMORY} )..."
           fi
         fi
-        sleep 1
+        sleep ${DELAY}
       else
         break
       fi
@@ -177,7 +185,7 @@ while [[ ${WAIT} == true ]]; do
       if [[ ${QUIET} == false ]]; then
         echo "Waiting until we have enough free memory (required: ${REQUIREDMEMORY}, available: ${AVAILABLEMEMORY})..."
       fi
-      sleep 5
+      sleep ${DELAY}
       continue
     fi
   fi
@@ -195,7 +203,7 @@ while [[ ${WAIT} == true ]]; do
     if [[ ${QUIET} == false ]]; then
       echo "Waiting until the system load falls below the threshold (threshold: ${MAXLOAD}, current:  ${CURRENTLOAD})..."
     fi
-    sleep 5
+    sleep ${DELAY}
     continue  
   fi
 

config/AllowedGeant4Versions.txt

@@ -1 +1 @@
-102
+112

config/AllowedROOTVersions.txt

@@ -1 +1 @@
-628 
+628 634