First project components including singularity file for GiBUU container

.gitignore

+#Singularity
+*.simg
+
+# GiBUU
+*.dat
+output/

Makefile

+export REPO_OUTPUT_DIR := output
+export REPO_JOBCARDS_DIR := jobcards
+export CONTAINER_OUTPUT_DIR := /opt/output
+export CONTAINER_JOBCARD_DIR := /opt/jobcards
+
+default: run
+
+build: km3buu.Singularity
+	sudo singularity build GiBUU.simg km3buu.Singularity 
+
+
+run: GiBUU.simg
+	@if [ ! -d "jobcards/${CARDSET}" ];then \
+	    exit 1; \
+        fi;
+	@if [ -d "${REPO_OUTPUT_DIR}/${CARDSET}" ];then \
+	    echo "Output directory for this cardset already exists; remove and go on [y/n]";\
+	    read REPLY; \
+	    if [ ! $$REPLY = "y" ];then \
+		exit 2;\
+	    fi;\
+	fi;
+	rm -rf ${REPO_OUTPUT_DIR}/${CARDSET};
+	mkdir -p ${REPO_OUTPUT_DIR}/${CARDSET};
+	singularity exec -B ${REPO_JOBCARDS_DIR}/${CARDSET}:$$CONTAINER_JOBCARD_DIR\
+			 -B ${REPO_OUTPUT_DIR}/${CARDSET}:$$CONTAINER_OUTPUT_DIR\
+			 GiBUU.simg\
+			 /bin/sh run.sh $$CONTAINER_JOBCARD_DIR $$CONTAINER_OUTPUT_DIR 
+
+lyon:
+	@echo "TO DO"
+
+clean:
+	@rm -rf output
+
+

README.md

 # KM3BUU
 
-This project contains software and data related to the GiBUU studies done for KM3NeT.
\ No newline at end of file
+The KM3BUU project is an integrated environment for the GiBUU studies within the KM3NeT experiment. The execution is mainly based on 
+
+## Installation
+The project is based on images using `singularity`, for which version 3 or higher (e.g. [v3.4](https://sylabs.io/guides/3.4/user-guide/)) is required. This is done due to the intention to provide a comparable installation on all systems and thus make the results 
+easily reproducible. The main project control is based on `make`.
+In order to apply installation commands presented within this section, clone this repository and change to the project directory:
+```
+git clone https://git.km3net.de/jschumann/km3buu
+cd km3buu
+```
+
+
+### Local Machine
+By "Local Machine" a computer where are root (administrative) privileges are available is 
+meant. These root privileges are required to build the singularity image by yourself. To start the build run following `make` command:
+```
+make build
+```
+
+### Compute Cluster
+In order to make this project also usable in a non-root environment, binaries will be provided. Within KM3NeT computing infrastructure this is the case for the lyon compute cluster, thus this case is customised for this environment.
+
+This part is currently under development, so it is time to say: Coming soon ... ;-)
+
+
+## Structure & Usage
+
+The used GiBUU jobcards are located in a sub-folder within the jobcards folder.
+Each sub-folder represents a set of jobcards, which can be processed by:
+
+```
+make run CARDSET=examples
+```
+
+This command runs all jobcards within the `jobcards/examples` folder and writes the output it to the folder `output`. The folder structure is applied from the `jobcards`folder.
\ No newline at end of file

jobcards/examples/example.job

+&neutrino_induced
+	process_ID = -2 		! 2:CC, 3:NC, -2:antiCC, -3:antiNC
+	flavor_ID = 2 		! 1:electron, 2:muon, 3:tau
+	nuXsectionMode = 6 	! 6: dSigmaMC
+	includeDIS = .true. 	! enables DIS events
+	printAbsorptionXS = T
+/
+
+&target
+	target_Z=1
+	target_A=1
+/
+
+&input
+	numEnsembles = 1000	! for H: 100000,
+				! for O: 6400
+				! decrease it if there are
+				! problems with memory or
+				! for heavier nuclei
+	eventtype = 5 		! 5=neutrino
+				! of a given particle
+	numTimeSteps = 0	! the distance numTimeSteps*delta_T
+				! should significantly
+				! exceed the radius
+				! of the target nucleus
+				! for H this must be 0
+				! numTimeSteps=0 gives inclusive
+				! X-sections
+	delta_T = 0.2		! timestep for hadron propagation
+	localEnsemble = .true.	! sets fullEnsemble = True
+	num_runs_SameEnergy = 1	! increase these if you want to 
+				! increase statistics 
+				! (= number of generated events)
+	LRF_equals_CALC_frame = .true.	! if .false.: 
+					! no offshelltransport
+					! possible
+	path_to_input = '/opt/buuinput2019' 	! needs to be
+					! changed to actual path
+/
+
+&nl_SigmaMC
+	enu = 4.0		!energy of the initial neutrino
+/
+
+
+&neutrinoAnalysis
+	outputEvents = .true	! output list of events and
+				! all outgoing particles in
+				! each event to the file 
+				! FinalEvents.dat
+/
+
+&pythia
+	PARP(91)=0.44
+/
+

km3buu.Singularity

+Bootstrap: docker
+From: debian:stretch
+
+%post
+    apt-get update -qq 
+    apt-get install -qq -y neovim
+    apt-get install -qq -y gfortran make libbz2-dev
+    apt-get install -qq -y wget
+    cd /opt && \
+    wget https://gibuu.hepforge.org/downloads?f=buuinput2019.tar.gz && \
+    tar xvzf downloads?f=buuinput2019.tar.gz && \
+    wget https://gibuu.hepforge.org/downloads?f=release2019.tar.gz && \
+    tar xvzf downloads?f=release2019.tar.gz && \
+    ls -ahl && \
+    cd release2019 && \
+    make -j withROOT=0
+    rm -rf /opt/*.tar.gz 
+
+%environment
+    export CONTAINER_GIBUU_EXEC=/opt/release2019/objects/GiBUU.x
+
+
+

run.sh

+#!/bin/bash
+
+if [ -z "$CONTAINER_GIBUU_EXEC+x" ];
+then 
+    echo "No GIBUU executable provided via CONTAINER_GIBUU_EXEC";
+    exit 1
+fi;
+
+if [ $# -eq 0 ];
+then
+    echo "No paths provided!";
+    exit 1;
+elif [ $# -eq 1 ];
+then
+    echo "No output directory within the container given!";
+    exit 1;
+fi;
+
+CONTAINER_JOBCARD_DIR=$1
+CONTAINER_OUTPUT_DIR=$2
+
+JOBCARDS=$(find $CONTAINER_JOBCARD_DIR -name "*.job")
+
+cd $CONTAINER_OUTPUT_DIR
+
+for filepath in $JOBCARDS; do
+    filename=$(basename -- $filepath)
+    foldername="${filename%.*}"
+    mkdir $foldername; cd $foldername
+    $CONTAINER_GIBUU_EXEC < $filepath;
+    cd ..
+done