diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000000000000000000000000000000000..ac6e7e293f675117f535fe87cbb70707fcfbfe22
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "externals/km3net-dataformat"]
+ path = externals/km3net-dataformat
+ url = git@git.km3net.de:common/km3net-dataformat.git
diff --git a/Dockerfile b/Dockerfile
index e3792bdfd213432560028727341581b9bfe366a6..d434257f37bb2bb4452bceb447c0a67d9245d7b8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,27 +1,9 @@
-FROM debian:stretch
+FROM docker.km3net.de/base/centos7-bundle:2021.03.01
-RUN apt-get update -qq && \
- apt-get upgrade -qq -y
-RUN apt-get install -qq -y gfortran make cmake libbz2-dev wget g++ git && \
- apt-get install -qq -y python3-dev python3-pip python3-tk python3-lxml python3-six
+RUN yum install -y -e 0 devtoolset-10
-
-RUN cd /opt && \
- mkdir -p cmake-3.18 && wget -qO- "https://cmake.org/files/v3.18/cmake-3.18.2-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C cmake-3.18
-
-RUN cd /opt && \
- wget https://root.cern.ch/download/root_v6.20.04.source.tar.gz && \
- tar xvzf root_v6.20.04.source.tar.gz
-
-RUN export PATH=/opt/cmake-3.18/bin:$PATH && \
- cd /opt/root-6.20.04 && \
- mkdir -p obj && \
- cd obj && \
- cmake -DCMAKE_INSTALL_PREFIX=/usr/local -Dpyroot=OFF -Dpyroot_experimental=OFF -Dx11=OFF -Dxft=OFF .. && \
- make -j4; make install && \
- rm -rf /opt/root-6.20.04*
-
-RUN cd /opt && \
+RUN source /opt/rh/devtoolset-10/enable && \
+ cd /opt && \
wget http://www.hepforge.org/archive/roottuple/RootTuple-1.0.0.tar.gz && \
tar -xzvf RootTuple-1.0.0.tar.gz && \
cd RootTuple-1.0.0 && \
@@ -31,7 +13,8 @@ RUN cd /opt && \
cmake -DCMAKE_INSTALL_PREFIX=/usr/local .. && \
make; make install
-RUN cd /opt && \
+RUN source /opt/rh/devtoolset-10/enable && \
+ cd /opt && \
wget https://gibuu.hepforge.org/downloads?f=buuinput2021.tar.gz && \
tar xvzf downloads?f=buuinput2021.tar.gz && \
wget https://gibuu.hepforge.org/downloads?f=release2021.tar.gz && \
@@ -43,5 +26,15 @@ RUN cd /opt && \
make -j withROOT=1 && \
rm -rf /opt/*.tar.gz
+ADD . /km3buu
+
+RUN cd /km3buu && \
+ pip3 install setuptools-scm && \
+ pip3 install pytest-runner && \
+ pip3 install -e .
+
+RUN cd /km3buu/externals/km3net-dataformat/ && \
+ make
+ENV KM3NET_LIB=/km3buu/externals/km3net-dataformat/lib
ENV CONTAINER_GIBUU_EXEC=/opt/release2021/objects/GiBUU.x
ENV LD_LIBRARY_PATH="/usr/local/lib:${LD_LIBRARY_PATH}"
diff --git a/config/MediaComposition.xml b/config/MediaComposition.xml
new file mode 100644
index 0000000000000000000000000000000000000000..11bc934fd242298e4d66dcd974d16b9af744e874
--- /dev/null
+++ b/config/MediaComposition.xml
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+
+<media_comp>
+
+<!--
+Definition of the interaction media composition
+
+-->
+
+<!--
+ // media composition: SeaWater, Rock, Mantle, Core
+-->
+
+ <param_set media="SeaWater" density="1.03975">
+ <param name="O"> 0.8584 </param>
+ <param name="H"> 0.1082 </param>
+ <param name="Cl"> 1.94E-2 </param>
+ <param name="Na"> 1.08E-2 </param>
+ <param name="Mg"> 0.1292E-2 </param>
+ <param name="S"> 0.091E-2 </param>
+ <param name="Ca"> 0.04E-2 </param>
+ <param name="K"> 0.04E-2 </param>
+ <param name="Br"> 0.0067E-2 </param>
+ <param name="C"> 0.0028E-2 </param>
+ </param_set>
+
+
+ <param_set media="Rock" density="2.65">
+ <param name="O"> 0.463 </param>
+ <param name="Si"> 0.282 </param>
+ <param name="Al"> 0.0823 </param>
+ <param name="Fe"> 0.0563 </param>
+ <param name="Ca"> 0.0415 </param>
+ <param name="Na"> 0.0236 </param>
+ <param name="Mg"> 0.0233 </param>
+ <param name="K"> 0.0209 </param>
+ <param name="Ti"> 0.0057 </param>
+ <param name="H"> 0.0014 </param>
+ </param_set>
+
+
+ <param_set media="Mantle">
+ <param name="O"> 0.4522 </param>
+ <param name="Mg"> 0.2283 </param>
+ <param name="Si"> 0.2149 </param>
+ <param name="Fe"> 0.0597 </param>
+ <param name="Al"> 0.0225 </param>
+ <param name="Ca"> 0.0224 </param>
+ </param_set>
+
+
+ <param_set media="Core">
+ <param name="Fe"> 0.9 </param>
+ <param name="Ni"> 0.1 </param>
+ </param_set>
+
+</media_comp>
+
diff --git a/externals/km3net-dataformat b/externals/km3net-dataformat
new file mode 160000
index 0000000000000000000000000000000000000000..59d2e2bc4de69fb5497cdf09a0146d0090913933
--- /dev/null
+++ b/externals/km3net-dataformat
@@ -0,0 +1 @@
+Subproject commit 59d2e2bc4de69fb5497cdf09a0146d0090913933
diff --git a/km3buu/config.py b/km3buu/config.py
index 083f953659c876350f4fdc1a803a21ee6b74c939..25279ce20f4210c4563af4ffda9475decbd41c10 100644
--- a/km3buu/config.py
+++ b/km3buu/config.py
@@ -159,5 +159,10 @@ def read_media_compositions(filename):
def read_default_media_compositions():
cfg = Config()
- fpath = join(cfg.gseagen_path, "dat", GSEAGEN_MEDIA_COMPOSITION_FILE)
+ try:
+ fpath = join(cfg.gseagen_path, "dat", GSEAGEN_MEDIA_COMPOSITION_FILE)
+ except:
+ fpath = abspath(
+ join(dirname(__file__), "../config/",
+ GSEAGEN_MEDIA_COMPOSITION_FILE))
return read_media_compositions(fpath)
diff --git a/km3buu/ctrl.py b/km3buu/ctrl.py
index d696530dec1c1f3c5c18be24d1c0fa55c9c94af3..d0dfe4b1b00e49bd29bfd7940480c5e5a14030dd 100644
--- a/km3buu/ctrl.py
+++ b/km3buu/ctrl.py
@@ -13,7 +13,9 @@ __email__ = "jschumann@km3net.de"
__status__ = "Development"
from shutil import copy
+import subprocess
from spython.main import Client
+import os
from os.path import join, abspath, basename, isdir, isfile
from tempfile import NamedTemporaryFile, TemporaryDirectory
from thepipe.logger import get_logger
@@ -21,15 +23,10 @@ from thepipe.logger import get_logger
from . import IMAGE_NAME
from .config import Config
from .jobcard import Jobcard, read_jobcard
-from .environment import is_singularity_version_greater, MIN_SINGULARITY_VERSION
+from .environment import check_singularity_version
log = get_logger(basename(__file__))
-if not is_singularity_version_greater(
- MIN_SINGULARITY_VERSION): # pragma: no cover
- log.error("Singularity version lower than %s" % MIN_SINGULARITY_VERSION)
- raise OSError("Singularity version below %s" % MIN_SINGULARITY_VERSION)
-
GIBUU_SHELL = """
#!/bin/bash
@@ -47,7 +44,7 @@ $CONTAINER_GIBUU_EXEC < {1};
"""
-def run_jobcard(jobcard, outdir):
+def run_jobcard(jobcard, outdir, container=False):
"""
Method for run
@@ -58,6 +55,8 @@ def run_jobcard(jobcard, outdir):
of a jobcard object or a path to a jobcard
outdir: str
The path to the directory the output should be written to.
+ container: boolean
+ Call GiBUU inside container environment
"""
input_dir = TemporaryDirectory()
outdir = abspath(outdir)
@@ -80,23 +79,31 @@ def run_jobcard(jobcard, outdir):
jobcard["neutrino_induced"]["FileNameflux"] = tmp_fluxfile
with open(jobcard_fpath, "w") as f:
f.write(str(jobcard))
- log.info("Create temporary file for associated runscript")
- script_fpath = join(input_dir.name, "run.sh")
- with open(script_fpath, "w") as f:
- ctnt = GIBUU_SHELL.format(outdir, jobcard_fpath)
- f.write(ctnt)
- output = Client.execute(
- Config().gibuu_image_path,
- ["/bin/sh", script_fpath],
- bind=[outdir, input_dir.name],
- return_result=True,
- )
with open(join(outdir, jobcard.filename), "w") as f:
f.write(str(jobcard))
- msg = output["message"]
- if isinstance(msg, str):
- log.info("GiBUU output:\n %s" % msg)
+ if container:
+ check_singularity_version()
+ log.info("Create temporary file for associated runscript")
+ script_fpath = join(input_dir.name, "run.sh")
+ with open(script_fpath, "w") as f:
+ ctnt = GIBUU_SHELL.format(outdir, jobcard_fpath)
+ f.write(ctnt)
+ output = Client.execute(
+ Config().gibuu_image_path,
+ ["/bin/sh", script_fpath],
+ bind=[outdir, input_dir.name],
+ return_result=True,
+ )
+ msg = output["message"]
+ if isinstance(msg, str):
+ log.info("GiBUU output:\n %s" % msg)
+ else:
+ log.info("GiBUU output:\n %s" % msg[0])
+ log.error("GiBUU stacktrace:\n%s" % msg[1])
+ return output["return_code"]
else:
- log.info("GiBUU output:\n %s" % msg[0])
- log.error("GiBUU stacktrace:\n%s" % msg[1])
- return output["return_code"]
+ p = subprocess.Popen(
+ "%s < %s" % (os.environ["CONTAINER_GIBUU_EXEC"], jobcard_fpath),
+ shell=True,
+ cwd=outdir)
+ return p.wait()
diff --git a/km3buu/environment.py b/km3buu/environment.py
index 8a4c3f03f4b9b05b6263086e16d244a657719cdc..5bed27339de93906a8eadce3912a8a3a39dfa780 100644
--- a/km3buu/environment.py
+++ b/km3buu/environment.py
@@ -26,6 +26,13 @@ log = get_logger(basename(__file__))
MIN_SINGULARITY_VERSION = "3.3"
+def check_singularity_version(): # pragma: no cover
+ if not is_singularity_version_greater(MIN_SINGULARITY_VERSION):
+ log.error("Singularity version lower than %s" %
+ MIN_SINGULARITY_VERSION)
+ raise OSError("Singularity version below %s" % MIN_SINGULARITY_VERSION)
+
+
def is_singularity_version_greater(min_version): # pragma: no cover
singularity_version = LooseVersion(get_singularity_version().split()[-1])
retval = singularity_version > LooseVersion(MIN_SINGULARITY_VERSION)
diff --git a/km3buu/jobcard.py b/km3buu/jobcard.py
index 3db1c675329b6df9adecda4003bc7a6ada2c48b8..14013d9eac9933658691b5d8a92b275078d82d58 100644
--- a/km3buu/jobcard.py
+++ b/km3buu/jobcard.py
@@ -89,6 +89,11 @@ def read_jobcard(filepath):
return Jobcard(f90nml.read(filepath), filename=basename(filepath))
+def write_jobcard(jobcard, filepath):
+ with open(filepath, 'w') as nml_file:
+ f90nml.write(jobcard, nml_file)
+
+
def generate_neutrino_jobcard(events,
process,
flavour,
diff --git a/km3buu/tests/test_ctrl.py b/km3buu/tests/test_ctrl.py
index 6d310997f9ed47d15bc61544adde20dc6a1e0700..34d4faa8e300471b005b04c82637d8099384ca06 100644
--- a/km3buu/tests/test_ctrl.py
+++ b/km3buu/tests/test_ctrl.py
@@ -35,7 +35,7 @@ class TestCTRLbyJobcardFile(unittest.TestCase):
writer.writerows(zip(ene, np.power(ene, -1)))
jc = read_jobcard(self.filename)
jc["neutrino_induced"]["FileNameFlux"] = self.flux_file.name
- self.retval = run_jobcard(jc, self.output_dir.name)
+ self.retval = run_jobcard(jc, self.output_dir.name, container=True)
log = get_logger("ctrl.py")
log.setLevel("INFO")
@@ -78,7 +78,9 @@ class TestCTRLbyJobcardObject(unittest.TestCase):
self.test_jobcard["neutrinoAnalysis"]["outputEvents"] = True
self.test_jobcard["pythia"]["PARP(91)"] = 0.44
self.output_dir = TemporaryDirectory()
- self.retval = run_jobcard(self.test_jobcard, self.output_dir.name)
+ self.retval = run_jobcard(self.test_jobcard,
+ self.output_dir.name,
+ container=True)
# raise Exception(self.test_jobcard)
def test_output(self):
diff --git a/notebooks/create_jobcard.py b/notebooks/create_jobcard.py
new file mode 100644
index 0000000000000000000000000000000000000000..e1445718fee00ebaf18ae1482aa3c57f96286c27
--- /dev/null
+++ b/notebooks/create_jobcard.py
@@ -0,0 +1,16 @@
+#!/usr/bin/python3
+
+from km3buu.jobcard import generate_neutrino_jobcard
+from km3buu.jobcard import write_jobcard
+from km3buu.jobcard import XSECTIONMODE_LOOKUP, PROCESS_LOOKUP, FLAVOR_LOOKUP
+
+events = 1000
+energy_min = 0.1
+energy_max = 50
+interaction = "cc"
+flavor = "electron"
+target_z = 8
+target_a = 16
+fluxfile = None
+jc = generate_neutrino_jobcard(events, interaction, flavor, (energy_min,energy_max), (target_z,target_a),fluxfile=fluxfile)
+write_jobcard(jc,"./job.job")