From 175e541f7cbc4b9f08cacb3e964c1748a88020ae Mon Sep 17 00:00:00 2001
From: Johannes Schumann <johannes.schumann@fau.de>
Date: Thu, 17 Oct 2019 02:44:19 +0200
Subject: [PATCH] First project components including singularity file for GiBUU
container
---
.gitignore | 6 ++++
Makefile | 36 ++++++++++++++++++++++
README.md | 36 +++++++++++++++++++++-
jobcards/examples/example.job | 56 +++++++++++++++++++++++++++++++++++
km3buu.Singularity | 23 ++++++++++++++
run.sh | 32 ++++++++++++++++++++
6 files changed, 188 insertions(+), 1 deletion(-)
create mode 100644 .gitignore
create mode 100644 Makefile
create mode 100644 jobcards/examples/example.job
create mode 100644 km3buu.Singularity
create mode 100755 run.sh
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..895472b
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+#Singularity
+*.simg
+
+# GiBUU
+*.dat
+output/
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..c7777bd
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,36 @@
+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
+
+
diff --git a/README.md b/README.md
index 4b44b4f..e7b5851 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,37 @@
# 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
diff --git a/jobcards/examples/example.job b/jobcards/examples/example.job
new file mode 100644
index 0000000..f793595
--- /dev/null
+++ b/jobcards/examples/example.job
@@ -0,0 +1,56 @@
+&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
+/
+
diff --git a/km3buu.Singularity b/km3buu.Singularity
new file mode 100644
index 0000000..4a314e8
--- /dev/null
+++ b/km3buu.Singularity
@@ -0,0 +1,23 @@
+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
+
+
+
diff --git a/run.sh b/run.sh
new file mode 100755
index 0000000..1c0fb1f
--- /dev/null
+++ b/run.sh
@@ -0,0 +1,32 @@
+#!/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
--
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