Hello
It seems as if there is a problem with the file loading in testElectronPairProduction.py
Here is the error output:

usr@pc:/path/to/CrPropa3/test/python$ python testElectronPairProduction.py
Traceback (most recent call last):
File "testElectronPairProduction.py", line 39, in
compare(getDataPath('pair_rate_CMB.txt'), CMB, 'ElectronPairProduction_CMB.png')
File "testElectronPairProduction.py", line 9, in compare
A = genfromtxt(dataFileName, comments="#", unpack=True)
File "/[...]/anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py", line 1364, in genfromtxt
fhd = iter(np.lib._datasource.open(fname, 'rbU'))
File "/[...]/anaconda/lib/python2.7/site-packages/numpy/lib/_datasource.py", line 151, in open
return ds.open(path, mode)
File "/[...]/anaconda/lib/python2.7/site-packages/numpy/lib/_datasource.py", line 501, in open
raise IOError("%s not found." % path)
IOError: /[...]/CrPropa3/share/crpropa/pair_rate_CMB.txt not found.

Best regards, Lukas

Sometimes I have an issue in which running simulation (for example benchmark scenario) stops without apparent reason and without any additional output. It looks like it's running but there is no advancement of progress bar or anything. Behaviour seems random and I cannot locate the cause.

The same problem is having Stefan who has sent me an e-mail in which he writes:

I've been doing some CRPropa runs using the updated version, the ouput is as expected, so everything seems to work fine. There's only one problem: some runs are terminated before they are finished (most times after he already did >90% of the work...). The output data we need has to be of roughly the same size for comparison, so we cannot use these runs and, as ~ every 5th run is terminated too early, much computation time is lost.

The last status output of CRPropa is something like:

Started Mon Jul 20 20:32:55 2015 : [=========>] 91% Finish in: 01:18:55

it prints this for every completed 1%, so he doesn't tell me any reason why it was terminated, nor does he even tell me, that it was terminated. (Usually, when I terminate a run manually, these lines appear much faster until he reached 100% so the status output is like that of a successful run. Here instead he just stops calculating so the status output stops at some point.)

and more...

Well, the frequency of that error is pretty unstable, so it's hard to tell how often it happens (I didn't count the errors).
I do runs with 10^7 particles per run and in the single thread case I got 4 runs without errors but the fifth broke after 60%-70%.
For the other runs, I sometimes loose runs pretty fast (e.g. run is lost, the next is good, but the over-next is lost again), but then sometimes I get 10 runs in a row, but I guess every fifth run is a good guess.

I cannot remember any such issues when I was using the old version. Back then I mostly produced runs with 10^5 or 10^6 particles and only 5 with 10^7, so maybe that can make a difference. Apart from that I do nothing different.

First I thought that it has something to do with multi-threading when it encounters some thread conflicts, but apparently the same problem occurs in single-thread (even I still need to confirm this).

Another possibility is that the problem lies PhotoPionProduction module because when it's skipped there is no evidence of these sudden stops of simulations.

I'll try to further investigate the issue myself but I'm wondering if anyone else has experienced the bug?

The method returns a swig object and not a list of modules as expected

ParticleMapsContainer::addParticlesFromFile is incompatible with the new TextOutput format.

I cannot import detected particles into ParticleMapContainer with addParticlesFromFile method because it differs from TextOutput(). I've got an empty list without any error message.

When running a 1D simulation with secondary gamma (DINT) the code crashes.
The module is called this way:

phot1 = PhotonDINT1D('test-dint.txt')
...
m.add(Observer1D())
m.add(EventOutput1D(OutputName))
m.add(phot1)

I tried:

• running crpropa with only one thread
• calling prop_second() in PhotoDINT1D.cpp with #pragma omp critical
  The problem always persists. Sometimes the run lasts a bit longer and I get some photon output, but not in general.

The full error message can be seen here:
http://pastebin.com/jHCwGZS3

Constructor

SimplePropagation(double minStep = 0, double maxStep = 10 * Mpc)

with SWIG_BUILTIN = off

s = SimplePropagation()
s.getDescription()
>>> 'Simple Propagation: Step size = 0 - 3.24078e-22 Mpc'

with SWIG_BUILTIN = on

s = SimplePropagation()
s.getDescription()
>>> 'Simple Propagation: Step size = 0 - 10 Mpc'

This breaks our notebook-examples as they do not terminate in reasonable time.

Vector3d is not printed correctly in python.
For example:
t = Vector3d(1, 2, 3)
print t returns Vector3d(1.0, 1.0, 1.0)
t.x, t.y, and t.z display the correct values of the components. Operations such as t.dot or t.cross are also correct.

I'm trying to install CRPropa 3 on my Mac (Mac OS X Yosemite 10.10.4) at the moment. When running "cmake ..", "make" and "sudo make install" I get a bunch of warnings but no errors. However, when running "make test" test 11 (testMagneticLensPythonInterface) fails. And when I try to import crpropa in python it gives a segmentation violation. I've pasted the output of "cmake ..", "make" and "python; from crpropa import *" below.

I thought this might be due to a problem with linking to python, so I tried "cmake .. -DPYTHON_EXECUTABLE=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h -DPYTHON_LIBRARIES=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib" but then I get these error messages:

Arjens-MacBook-Pro:build avanvliet$ cmake .. -DPYTHON_EXECUTABLE=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h -DPYTHON_LIBRARIES=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Build Type: Release
-- CRPropa version: -128-NOTFOUND
Using provided EIGEN
-- ROOT: Found!
-- CFlags: -pthread -stdlib=libc++ -std=c++11 -m64 -I/Users/avanvliet/Documents/Werk/software/root-6.04.02/include
-- Libs: -L/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -Wl,-rpath,/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -stdlib=libc++ -lm -ldl
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
-- Google perftools: NOT Found!
-- Include: GOOGLE_PERFTOOLS_INCLUDE_DIR-NOTFOUND
-- FFTW3 with single precision (FFTW3F): Found!
-- Include: /usr/local/include
-- Library: /usr/local/lib/libfftw3f.a
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- CFITSIO: NOT Found!
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- Library: CFITSIO_LIBRARY-NOTFOUND
-- Quimby: NOT Found!
-- Include: QUIMBY_INCLUDE_DIR-NOTFOUND
-- Library: QUIMBY_LIBRARY-NOTFOUND
-- SAGA: NOT Found!
-- Include: SAGA_INCLUDE_DIR-NOTFOUND
-- Library: SAGA_LIBRARY-NOTFOUND
-- SQLite3: NOT Found!
-- Include: /usr/include
-- Library: SQLITE3_LIBRARY-NOTFOUND
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
-- muParser: NOT Found!
-- Include: MUPARSER_INCLUDE_DIR-NOTFOUND
-- Library: MUPARSER_LIBRARY-NOTFOUND

Searching for data archive
File found: /Users/avanvliet/Documents/Werk/software/CRPropa3/build/data.tar.gz
MD5sum matching

-- Using user provided Python library: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib
-- Python: Found!
-- Version: ./
-- Executeable: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h
-- Include:
-- Library: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib
-- Site-package directory:
-- Numpy not found.
CMake Error at CMakeLists.txt:379 (install):
install DIRECTORY given no DESTINATION!

-- Configuring incomplete, errors occurred!
See also "/Users/avanvliet/Documents/Werk/software/CRPropa3/build/CMakeFiles/CMakeOutput.log".
See also "/Users/avanvliet/Documents/Werk/software/CRPropa3/build/CMakeFiles/CMakeError.log".

Arjens-MacBook-Pro:build avanvliet$ cmake ..
-- The Fortran compiler identification is GNU 5.1.0
-- The C compiler identification is AppleClang 6.1.0.6020053
-- The CXX compiler identification is AppleClang 6.1.0.6020053
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Check for working Fortran compiler: /usr/local/bin/gfortran
-- Check for working Fortran compiler: /usr/local/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/bin/gfortran supports Fortran 90
-- Checking whether /usr/local/bin/gfortran supports Fortran 90 -- yes
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Build Type: Release
-- CRPropa version: -128-NOTFOUND
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
Using provided EIGEN
-- ROOT: Found!
-- CFlags: -pthread -stdlib=libc++ -std=c++11 -m64 -I/Users/avanvliet/Documents/Werk/software/root-6.04.02/include
-- Libs: -L/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -Wl,-rpath,/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -stdlib=libc++ -lm -ldl
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP Fortran flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
-- Google perftools: NOT Found!
-- Include: GOOGLE_PERFTOOLS_INCLUDE_DIR-NOTFOUND
-- FFTW3 with single precision (FFTW3F): Found!
-- Include: /usr/local/include
-- Library: /usr/local/lib/libfftw3f.a
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- CFITSIO: NOT Found!
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- Library: CFITSIO_LIBRARY-NOTFOUND
-- Quimby: NOT Found!
-- Include: QUIMBY_INCLUDE_DIR-NOTFOUND
-- Library: QUIMBY_LIBRARY-NOTFOUND
-- SAGA: NOT Found!
-- Include: SAGA_INCLUDE_DIR-NOTFOUND
-- Library: SAGA_LIBRARY-NOTFOUND
-- SQLite3: NOT Found!
-- Include: /usr/include
-- Library: SQLITE3_LIBRARY-NOTFOUND
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
-- muParser: NOT Found!
-- Include: MUPARSER_INCLUDE_DIR-NOTFOUND
-- Library: MUPARSER_LIBRARY-NOTFOUND
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5")

Searching for data archive
File not found: data.tar.gz
Downloading from crpropa.desy.de ~ 60 MB
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 30.8M 100 30.8M 0 0 4150k 0 0:00:07 0:00:07 --:--:-- 4908k
Unpacking to CRPropa3/data

-- Found SWIG: /usr/local/bin/swig (found version "3.0.6")
-- Running on Mac OS X < 10.9: Linking to Python as framework
INFOLooking for python framework as on apple system
-- Python: Found!
-- Version: 2.7/27
-- Executeable: /Users/avanvliet/Library/Enthought/Canopy_64bit/User/bin/python
-- Include: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7
-- Library: -framework Python
-- Site-package directory: /usr/local/lib/python2.7/site-packages
-- Found numpy headers in /Users/avanvliet/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/core/include
-- Configuring done
CMake Warning (dev):
Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake
--help-policy CMP0042" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

crpropa

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /Users/avanvliet/Documents/Werk/software/CRPropa3/build

Arjens-MacBook-Pro:build avanvliet$ make
Scanning dependencies of target healpix_base
[ 0%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/error_handling.cc.o
[ 1%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/geom_utils.cc.o
[ 2%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/healpix_base.cc.o
[ 3%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/healpix_tables.cc.o
[ 3%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/pointing.cc.o
[ 4%] Linking CXX static library libhealpix_base.a
[ 4%] Built target healpix_base
Scanning dependencies of target sophia
[ 5%] Building Fortran object libs/sophia/CMakeFiles/sophia.dir/sophia_interface.f.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/sophia/sophia_interface.f:1827:72: Warning: Deleted feature: PAUSE statement at (1)
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/sophia/sophia_interface.f:16396:72: Warning: Deleted feature: PAUSE statement at (1)
[ 6%] Linking Fortran static library libsophia.a
[ 6%] Built target sophia
Scanning dependencies of target HepPID
[ 6%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/ParticleIDMethods.cc.o
[ 7%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/ParticleName.cc.o
[ 8%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/Version.cc.o
[ 9%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateEvtGen.cc.o
[ 9%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateGeanttoPDT.cc.o
[ 10%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateHerwig.cc.o
[ 11%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateIsajet.cc.o
[ 12%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePDG.cc.o
[ 12%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePDTtoGeant.cc.o
[ 13%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePythia.cc.o
[ 14%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateQQ.cc.o
[ 15%] Linking CXX static library libHepPID.a
[ 15%] Built target HepPID
Scanning dependencies of target eleca
[ 16%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Common.cpp.o
In file included from /Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/Common.cpp:1:
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/include/EleCa/Common.h:20:31: warning: use of right-shift operator ('>>') in template argument will require parentheses
in C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
1 warning generated.
[ 17%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/EnergyLoss.cpp.o
In file included from /Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/EnergyLoss.cpp:6:
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/include/EleCa/Common.h:20:31: warning: use of right-shift operator ('>>') in template argument will require parentheses
in C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/EnergyLoss.cpp:464:3: warning: control may reach end of non-void function [-Wreturn-type]
}
^
2 warnings generated.
[ 17%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Particle.cpp.o
[ 18%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Process.cpp.o
[ 19%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Propagation.cpp.o
In file included from /Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/Propagation.cpp:4:
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/include/EleCa/Common.h:20:31: warning: use of right-shift operator ('>>') in template argument will require parentheses
in C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
1 warning generated.
[ 20%] Linking CXX static library libeleca.a
[ 20%] Built target eleca
Scanning dependencies of target kiss
[ 21%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/logger.cpp.o
[ 22%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/path.cpp.o
[ 22%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/string.cpp.o
[ 23%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/uuid.cpp.o
[ 24%] Linking CXX static library libkiss.a
[ 24%] Built target kiss
Scanning dependencies of target pugixml
[ 25%] Building CXX object libs/pugixml/CMakeFiles/pugixml.dir/pugixml.cpp.o
[ 25%] Linking CXX static library libpugixml.a
[ 25%] Built target pugixml
Scanning dependencies of target dint
[ 26%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/advance.cpp.o
[ 27%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/background.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/dint/src/background.cpp:9:31: warning: use of right-shift operator ('>>') in template argument will require parentheses in
C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
1 warning generated.
[ 27%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/binfread.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/dint/src/binfread.cpp:58:73: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long')
[-Wformat]
fprintf(stderr,"DINT / binfread : Strange member size = %d. Exit",size);
~~ ^~~~
%lu
1 warning generated.
[ 28%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/check.cpp.o
[ 29%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/cvector.cpp.o
[ 30%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/decay.cpp.o
[ 30%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/deriv.cpp.o
[ 31%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/error.cpp.o
[ 32%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/final.cpp.o
[ 33%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/fold.cpp.o
[ 33%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/frag.cpp.o
[ 34%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/gauleg.cpp.o
[ 35%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/inject.cpp.o
[ 36%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/io_util.cpp.o
[ 36%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/load.cpp.o
[ 37%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/math_util.cpp.o
[ 38%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/prepare.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/dint/src/prepare.cpp:235:15: warning: format specifies type 'double ' but the argument has type 'int *' [-Wformat]
scanf("%lf", pTauNeutrinoMassSwitch);
~~~ ^~~~~~~~~~~~~~~~~~~~~~
%d
1 warning generated.
[ 39%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/prop_second.cpp.o
[ 39%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/rate.cpp.o
[ 40%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/spectrum.cpp.o
[ 41%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/sync.cpp.o
[ 42%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/vector.cpp.o
[ 42%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/DintEMCascade.cpp.o
[ 43%] Linking CXX static library libdint.a
[ 43%] Built target dint
Scanning dependencies of target crpropa
[ 43%] Building CXX object CMakeFiles/crpropa.dir/src/Random.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:228:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 s1;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:288:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = 1;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:289:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 j = 0;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:290:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int k = (N > seedLength ? N : seedLength);
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:325:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *s = bigSeed;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:326:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:327:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register bool success = true;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:342:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *s = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:343:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *r = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:344:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = 1;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:353:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *p = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:354:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:383:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *sa = saveArray;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:384:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register const uint32 *s = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:385:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:392:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *s = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:393:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *la = loadArray;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:394:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:402:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register const Random::uint32 *s = mtrand.state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:403:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = mtrand.N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:410:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register Random::uint32 *s = mtrand.state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:411:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = mtrand.N;
^~~~~~~~~
22 warnings generated.
[ 44%] Building CXX object CMakeFiles/crpropa.dir/src/Clock.cpp.o
[ 45%] Building CXX object CMakeFiles/crpropa.dir/src/ModuleList.cpp.o
[ 46%] Building CXX object CMakeFiles/crpropa.dir/src/Module.cpp.o
[ 46%] Building CXX object CMakeFiles/crpropa.dir/src/Candidate.cpp.o
[ 47%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleState.cpp.o
[ 48%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleID.cpp.o
[ 49%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleMass.cpp.o
[ 49%] Building CXX object CMakeFiles/crpropa.dir/src/ProgressBar.cpp.o
[ 50%] Building CXX object CMakeFiles/crpropa.dir/src/Cosmology.cpp.o
[ 51%] Building CXX object CMakeFiles/crpropa.dir/src/Source.cpp.o
[ 52%] Building CXX object CMakeFiles/crpropa.dir/src/Common.cpp.o
[ 52%] Building CXX object CMakeFiles/crpropa.dir/src/PhotonBackground.cpp.o
[ 53%] Building CXX object CMakeFiles/crpropa.dir/src/PhotonPropagation.cpp.o
[ 54%] Building CXX object CMakeFiles/crpropa.dir/src/GridTools.cpp.o
[ 55%] Building CXX object CMakeFiles/crpropa.dir/src/XmlExecute.cpp.o
[ 55%] Building CXX object CMakeFiles/crpropa.dir/src/module/BreakCondition.cpp.o
[ 56%] Building CXX object CMakeFiles/crpropa.dir/src/module/Boundary.cpp.o
[ 57%] Building CXX object CMakeFiles/crpropa.dir/src/module/Observer.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/module/Observer.cpp:215:11: warning: using floating point absolute value function 'fabs' when argument is of integer type
[-Wabsolute-value]
int id = fabs(c->current.getId());
^
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/module/Observer.cpp:215:11: note: use function 'std::abs' instead
int id = fabs(c->current.getId());
^~~~
std::abs
1 warning generated.
[ 58%] Building CXX object CMakeFiles/crpropa.dir/src/module/SimplePropagation.cpp.o
[ 58%] Building CXX object CMakeFiles/crpropa.dir/src/module/PropagationCK.cpp.o
[ 59%] Building CXX object CMakeFiles/crpropa.dir/src/module/ElectronPairProduction.cpp.o
[ 60%] Building CXX object CMakeFiles/crpropa.dir/src/module/NuclearDecay.cpp.o
[ 61%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotoPionProduction.cpp.o
[ 61%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotoDisintegration.cpp.o
[ 62%] Building CXX object CMakeFiles/crpropa.dir/src/module/Redshift.cpp.o
[ 63%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputTXT.cpp.o
[ 64%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputShell.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/module/OutputShell.cpp:48:8: warning: expression result unused [-Wunused-value]
for (i; i != c->properties.end(); i++) {
^
1 warning generated.
[ 64%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputROOT.cpp.o
[ 65%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputCRPropa2.cpp.o
[ 66%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonOutput1D.cpp.o
[ 67%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonDINT.cpp.o
[ 67%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonDINT1D.cpp.o
[ 68%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonEleCa.cpp.o
[ 69%] Building CXX object CMakeFiles/crpropa.dir/src/module/Tools.cpp.o
[ 70%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/MagneticField.cpp.o
[ 70%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/MagneticFieldGrid.cpp.o
[ 71%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/TurbulentMagneticField.cpp.o
[ 72%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/JF12Field.cpp.o
[ 73%] Building CXX object CMakeFiles/crpropa.dir/src/Version.cpp.o
[ 73%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/MagneticLens.cpp.o
[ 74%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/ModelMatrix.cpp.o
[ 75%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/Pixelization.cpp.o
[ 76%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/ParticleMapsContainer.cpp.o
[ 76%] Linking CXX shared library libcrpropa.dylib
clang: warning: argument unused during compilation: '-pthread'
ld: warning: could not create compact unwind for lushow: stack subq instruction is too different from dwarf stack size
[ 76%] Built target crpropa
[ 77%] Generating crpropa_wrap.cxx
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:172: Warning 361: operator! ignored
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/module/PropagationCK.h:46: Warning 325: Nested class not currently supported (Y ignored)
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:124: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:129: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:124: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:129: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:158: Warning 503: Can't wrap 'operator crpropa::Grid< crpropa::Vector3< float > >' unless renamed to a valid identifier.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:158: Warning 503: Can't wrap 'operator crpropa::Grid< float >*' unless renamed to a valid identifier.
Scanning dependencies of target crpropa-swig
[ 78%] Building CXX object CMakeFiles/crpropa-swig.dir/crpropa_wrap.cxx.o
[ 79%] Linking CXX shared module _crpropa.so
clang: warning: argument unused during compilation: '-pthread'
[ 79%] Built target crpropa-swig
Scanning dependencies of target crpropa-xmlrun
[ 79%] Building CXX object CMakeFiles/crpropa-xmlrun.dir/src/main.cpp.o
[ 80%] Linking CXX executable crpropa-xmlrun
clang: warning: argument unused during compilation: '-pthread'
[ 80%] Built target crpropa-xmlrun
Scanning dependencies of target gtest
[ 80%] Building CXX object libs/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 81%] Linking CXX static library libgtest.a
[ 81%] Built target gtest
Scanning dependencies of target gtest_main
[ 82%] Building CXX object libs/gtest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 83%] Linking CXX static library libgtest_main.a
[ 83%] Built target gtest_main
Scanning dependencies of target testBreakCondition
[ 84%] Building CXX object CMakeFiles/testBreakCondition.dir/test/testBreakCondition.cpp.o
[ 84%] Linking CXX executable testBreakCondition
clang: warning: argument unused during compilation: '-pthread'
[ 84%] Built target testBreakCondition
Scanning dependencies of target testCore
[ 85%] Building CXX object CMakeFiles/testCore.dir/test/testCore.cpp.o
[ 86%] Linking CXX executable testCore
clang: warning: argument unused during compilation: '-pthread'
[ 86%] Built target testCore
Scanning dependencies of target testDINT
[ 87%] Building CXX object CMakeFiles/testDINT.dir/test/testDINT.cpp.o
[ 87%] Linking CXX executable testDINT
clang: warning: argument unused during compilation: '-pthread'
[ 87%] Built target testDINT
Scanning dependencies of target testGalacticMagneticLens
[ 88%] Building CXX object CMakeFiles/testGalacticMagneticLens.dir/test/testMagneticLens.cpp.o
[ 89%] Linking CXX executable testGalacticMagneticLens
clang: warning: argument unused during compilation: '-pthread'
[ 89%] Built target testGalacticMagneticLens
Scanning dependencies of target testInteraction
[ 90%] Building CXX object CMakeFiles/testInteraction.dir/test/testInteraction.cpp.o
[ 90%] Linking CXX executable testInteraction
clang: warning: argument unused during compilation: '-pthread'
[ 90%] Built target testInteraction
Scanning dependencies of target testMagneticField
[ 91%] Building CXX object CMakeFiles/testMagneticField.dir/test/testMagneticField.cpp.o
[ 92%] Linking CXX executable testMagneticField
clang: warning: argument unused during compilation: '-pthread'
[ 92%] Built target testMagneticField
Scanning dependencies of target testModuleList
[ 93%] Building CXX object CMakeFiles/testModuleList.dir/test/testModuleList.cpp.o
[ 93%] Linking CXX executable testModuleList
clang: warning: argument unused during compilation: '-pthread'
[ 93%] Built target testModuleList
Scanning dependencies of target testPropagation
[ 94%] Building CXX object CMakeFiles/testPropagation.dir/test/testPropagation.cpp.o
[ 95%] Linking CXX executable testPropagation
clang: warning: argument unused during compilation: '-pthread'
[ 95%] Built target testPropagation
Scanning dependencies of target testSource
[ 96%] Building CXX object CMakeFiles/testSource.dir/test/testSource.cpp.o
[ 96%] Linking CXX executable testSource
clang: warning: argument unused during compilation: '-pthread'
[ 96%] Built target testSource
Scanning dependencies of target testVector3
[ 97%] Building CXX object CMakeFiles/testVector3.dir/test/testVector3.cpp.o
[ 98%] Linking CXX executable testVector3
clang: warning: argument unused during compilation: '-pthread'
[ 98%] Built target testVector3
Scanning dependencies of target test_uuid
[ 99%] Building CXX object libs/kiss/CMakeFiles/test_uuid.dir/test/test_uuid.cpp.o
[100%] Linking CXX executable test_uuid
[100%] Built target test_uuid

Arjens-MacBook-Pro:build avanvliet$ python
Enthought Canopy Python 2.7.9 | 64-bit | (default, Jun 30 2015, 19:41:21)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.6)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

from crpropa import *

*** Break *** segmentation violation
Generating stack trace...
0x00000001039f3c77 in 0x00000001039f3c77 (in Python) + 50
0x0000000101908a72 in init_crpropa (in crpropa.so) + 66
0x00000001000c29ca in PyImport_LoadDynamicModule (in Python) + 170
0x00000001000bf4a5 in imp_load_module (in Python) + 341
0x00000001000a8fab in PyEval_EvalFrameEx (in Python) + 17995
0x00000001000ac3b3 in fast_function (in Python) + 179
0x00000001000a905d in PyEval_EvalFrameEx (in Python) + 18173
0x00000001000ac273 in PyEval_EvalCodeEx (in Python) + 2083
0x00000001000ac2f6 in PyEval_EvalCode (in Python) + 54
0x00000001000bfc53 in PyImport_ExecCodeModuleEx (in Python) + 243
0x00000001000c0257 in load_source_module (in Python) + 1351
0x00000001000c1147 in import_submodule (in Python) + 327
0x00000001000c134b in load_next (in Python) + 251
0x00000001000c2192 in PyImport_ImportModuleLevel (in Python) + 1170
0x000000010009f364 in builtin___import (in Python) + 132
0x000000010000f2b1 in PyObject_Call (in Python) + 97
0x00000001000a3d64 in PyEval_CallObjectWithKeywords (in Python) + 180
0x00000001000aad3b in PyEval_EvalFrameEx (in Python) + 25563
0x00000001000ac273 in PyEval_EvalCodeEx (in Python) + 2083
0x00000001000ac2f6 in PyEval_EvalCode (in Python) + 54
0x00000001000cc292 in PyRun_InteractiveOneFlags (in Python) + 578
0x00000001000cc3ee in PyRun_InteractiveLoopFlags (in Python) + 222
0x00000001000cc497 in PyRun_AnyFileExFlags (in Python) + 119
0x00000001000dfc7b in Py_Main (in Python) + 3435
0x000000010000281f in from /Users/avanvliet/Library/Enthought/Canopy_64bit/User/Resources/Python.app/Contents/MacOS/Python
0x0000000100001f94 in from /Users/avanvliet/Library/Enthought/Canopy_64bit/User/Resources/Python.app/Contents/MacOS/Python
0x0000000000000001 in

The Secondaries example on the wiki uses SophiaPhotoPionProduction, but it does not seem to be part of the crpropa package when imported in Python.

Using:

m.add(ElectronPairProduction(CMB_IRB))

results via:

this = _crpropa.new_ElectronPairProduction(*args)

in:

RuntimeError: ElectronPairProduction: unknown photon background

Could this problem be related to:

%run generate_epairTable.py

generating the mistake:

xKneiske, yKneiske = genfromtxt('KneiskeIRB_z0.txt', unpack=1)

31.10. use of randBin to simplify several SourceProperties

I get the following output:

Building CXX object CMakeFiles/crpropa.dir/src/module/Observer.cpp.o
[ 57%] /afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Random.cpp: In function ‘size_t crpropa::randBin(const std::vector<double, std::allocator >&)’:
/afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Random.cpp:126: error: ‘lower_bound’ is not a member of ‘std’
/afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Random.cpp:127: error: ‘rand’ was not declared in this scope
Building CXX object CMakeFiles/crpropa.dir/src/module/SimplePropagation.cpp.o
[ 58%] make[2]: *** [CMakeFiles/crpropa.dir/src/Random.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Building CXX object CMakeFiles/crpropa.dir/src/module/DeflectionCK.cpp.o
/afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Source.cpp: In member function ‘virtual void crpropa::SourceDensityGrid::prepare(crpropa::ParticleState&) const’:
/afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Source.cpp:217: error: no matching function for call to ‘crpropa::Random::randBin(std::vector<float, std::allocator >&)’
/afs/desy.de/group/pheno/software/SL6/CRPropa3/include/crpropa/Random.h:136: note: candidates are: size_t crpropa::Random::randBin(const std::vector<double, std::allocator >&)
/afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Source.cpp: In member function ‘virtual void crpropa::SourceDensityGrid1D::prepare(crpropa::ParticleState&) const’:
/afs/desy.de/group/pheno/software/SL6/CRPropa3/src/Source.cpp:247: error: no matching function for call to ‘crpropa::Random::randBin(std::vector<float, std::allocator >&)’
/afs/desy.de/group/pheno/software/SL6/CRPropa3/include/crpropa/Random.h:136: note: candidates are: size_t crpropa::Random::randBin(const std::vector<double, std::allocator >&)

When using three observers only the one last added to the mode produces output.
Example:

obs1 = Observer()
obs1.add(ObserverSmallSphere(position, size1))
obs1.onDetection(TextOutput(out1))
obs2 = Observer()
obs2.add(ObserverSmallSphere(position, size2))
obs2.onDetection(TextOutput(out2))
...
m.add(obs1)
m.add(obs2)

Only out2 has non-zero size, even if the observers are identical.

This might be related to the default option makeInactive=True, which renders a candidate inactive when crossing the sphere. Manually hard-coding Observer::Observer() : makeInactive(false) solves the problem, but is not elegant. Maybe a function to control it more easily should be implemented. In principle, the deprecated ConditionalOutput module would fix this, since outputs would be written depending on the flag.

add missing initial direction
make ROOT accept more than 14 branches

void ROOTEventOutput3D::process(Candidate *c) const {
if (not (c->hasProperty("Detected")))
return;

c->removeProperty("Detected");

TThread::Lock();

pragma omp critical

{
   Ntuple->Fill(c->getTrajectoryLength() / Mpc,   // TrajectoryLength_Mpc
           c->current.getId(),                    // Particle_Type
           c->source.getId(),                     // Initial_Type
           c->current.getEnergy() / EeV,          // Momentum_E_EeV
           c->source.getEnergy() / EeV,           // Initial_Momentum_E_EeV
           c->current.getPosition().x / Mpc, // Position_X_Mpc
           c->current.getPosition().y / Mpc, // Position_Y_Mpc
           c->current.getPosition().z / Mpc, // Position_Z_Mpc
           c->source.getPosition().x / Mpc,  // Initial_Position_X_Mpc
           c->source.getPosition().y / Mpc,  // Initial_Position_Y_Mpc
           c->source.getPosition().z / Mpc,  // Initial_Position_Z_Mpc
           c->current.getDirection().x,      // Direction_X_Mpc
           c->current.getDirection().y,      // Direction_Y_Mpc
           c->current.getDirection().z);      // Direction_Z_Mpc

// c->source.getDirection().x, // Initial_Direction_X_Mpc
// c->source.getDirection().y, // Initial_Direction_Y_Mpc
// c->source.getDirection().z); // Initial_Direction_Z_Mpc
}
TThread::UnLock();
}

From the following code:

observer

obs = Observer()
obs.add( ObserverPoint() )
sim.add( obs )

output

output_txt = TextOutput(outfile[:-4] + "txt")
obs.onDetection(output_txt)
output_root = ROOTEventOutput1D(outfile)
obs.onDetection(output_root)

I would expect the same output in both files. Currently, the output is only recorded in one file.

For some reason, I'm getting the following error when testing the AMR support of CRPropa:

File "../test/test-SAGA_CRPropa.py", line 20, in
bField = AMRMagneticField(field, cL, cD, cB)
TypeError: in method 'new_AMRMagneticField', argument 1 of type 'saga::ref_ptr< saga::MagneticField >'

When I compile WITHOUT the -builtin option, it works as it did in the past.

This is one more thing that was previously okay and stopped working after the builtin option became default. Is there an actual advantage in using it? As far as I see, it has been causing problems, and I don't see a significant performance improvement. Is this option really useful/needed? If not, I would suggest to switch back to the previous version, without builtin.

Currently the tabulated spectra from CRPropa 2 are used.
These should be recalculated using e.g. Kelner & Aharonian 2008 http://link.aps.org/doi/10.1103/PhysRevD.78.034013

Description: A method for removing already added modules in ModuleList.
User case: Sometimes I would like to re-run the simulation but with different modules parameters while I don't want to reload the whole thing (i.e. making a new ModuleList and reading out all tables and fields which costs time), hence removing the module and re-adding it seems like a useful feature. (Possible blocker: initialization of every module is done on run(), so there is no benefit in terms of skipping re-loading tables and fields)

Examples of extending CRPropa given here are leading to segmentation faults when used in Python interactive shell.

Steps to reproduce:

1. run python shell (tried python 2.7.9 and 2.6.6)
2. import crpropa: from crpropa import *
3. paste an example to shell:

class MyModule(Module):
    """ Reduces the cosmic ray energy by 10% in each step """
    def process(self, c):
        c.current.setEnergy(c.current.getEnergy() * 0.9)

m = ModuleList()
m.add(MyModule())

c = Candidate()
c.current.setEnergy(10)
m.process(c)

1. segmentation fault, trace:

 *** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x0000003b320c7eea in waitpid () from /lib64/libc.so.6
#1  0x0000003b32043a4b in do_system () from /lib64/libc.so.6
#2  0x0000003b3446dff2 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so.5.34
#3  0x0000003b3447025c in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so.5.34
#4  <signal handler called>
#5  0x0000003b3208a9da in strlen () from /lib64/libc.so.6
#6  0x0000003b3e491f7f in PyString_FromFormatV () from /lib64/libpython2.7.so.1.0
#7  0x0000003b3e4ec01c in PyErr_Format () from /lib64/libpython2.7.so.1.0
#8  0x0000003b3e4862e5 in PyObject_GetAttr () from /lib64/libpython2.7.so.1.0
#9  0x0000003b3e486534 in PyObject_GetAttrString () from /lib64/libpython2.7.so.1.0
#10 0x0000003b3e44aead in PyObject_CallMethod () from /lib64/libpython2.7.so.1.0
#11 0x00007f49655a96a3 in SwigDirector_Module::process (this=0x1d5f660, candidate=0x1d90da0) at /home/a/crpropa_virtenv/crpropa3_build/build/crpropa_wrap.cxx:6968
#12 0x00007f4964f0553b in crpropa::ModuleList::process (this=0x1a258b0, candidate=0x1d90da0) at /home/a/crpropa_virtenv/crpropa3_build/src/ModuleList.cpp:47
#13 0x00007f496566d5ad in _wrap_ModuleList_process (self=0x7f496c31a1f0, args=0x7f496c312610) at /home/a/crpropa_virtenv/crpropa3_build/build/crpropa_wrap.cxx:62139
#14 0x0000003b3e4e290e in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0
#15 0x0000003b3e4e3704 in PyEval_EvalCodeEx () from /lib64/libpython2.7.so.1.0
#16 0x0000003b3e4e3829 in PyEval_EvalCode () from /lib64/libpython2.7.so.1.0
#17 0x0000003b3e4fcb5f in run_mod () from /lib64/libpython2.7.so.1.0
#18 0x0000003b3e4febba in PyRun_InteractiveOneFlags () from /lib64/libpython2.7.so.1.0
#19 0x0000003b3e4fed9e in PyRun_InteractiveLoopFlags () from /lib64/libpython2.7.so.1.0
#20 0x0000003b3e4ff42e in PyRun_AnyFileExFlags () from /lib64/libpython2.7.so.1.0
#21 0x0000003b3e511141 in Py_Main () from /lib64/libpython2.7.so.1.0
#22 0x0000003b32020790 in __libc_start_main () from /lib64/libc.so.6
#23 0x0000000000400729 in _start ()
===========================================================

The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x0000003b3208a9da in strlen () from /lib64/libc.so.6
#6  0x0000003b3e491f7f in PyString_FromFormatV () from /lib64/libpython2.7.so.1.0
#7  0x0000003b3e4ec01c in PyErr_Format () from /lib64/libpython2.7.so.1.0
#8  0x0000003b3e4862e5 in PyObject_GetAttr () from /lib64/libpython2.7.so.1.0
#9  0x0000003b3e486534 in PyObject_GetAttrString () from /lib64/libpython2.7.so.1.0
#10 0x0000003b3e44aead in PyObject_CallMethod () from /lib64/libpython2.7.so.1.0
#11 0x00007f49655a96a3 in SwigDirector_Module::process (this=0x1d5f660, candidate=0x1d90da0) at /home/a/crpropa_virtenv/crpropa3_build/build/crpropa_wrap.cxx:6968
#12 0x00007f4964f0553b in crpropa::ModuleList::process (this=0x1a258b0, candidate=0x1d90da0) at /home/a/crpropa_virtenv/crpropa3_build/src/ModuleList.cpp:47
#13 0x00007f496566d5ad in _wrap_ModuleList_process (self=0x7f496c31a1f0, args=0x7f496c312610) at /home/a/crpropa_virtenv/crpropa3_build/build/crpropa_wrap.cxx:62139
#14 0x0000003b3e4e290e in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0
#15 0x0000003b3e4e3704 in PyEval_EvalCodeEx () from /lib64/libpython2.7.so.1.0
#16 0x0000003b3e4e3829 in PyEval_EvalCode () from /lib64/libpython2.7.so.1.0
#17 0x0000003b3e4fcb5f in run_mod () from /lib64/libpython2.7.so.1.0
#18 0x0000003b3e4febba in PyRun_InteractiveOneFlags () from /lib64/libpython2.7.so.1.0
#19 0x0000003b3e4fed9e in PyRun_InteractiveLoopFlags () from /lib64/libpython2.7.so.1.0
#20 0x0000003b3e4ff42e in PyRun_AnyFileExFlags () from /lib64/libpython2.7.so.1.0
#21 0x0000003b3e511141 in Py_Main () from /lib64/libpython2.7.so.1.0
#22 0x0000003b32020790 in __libc_start_main () from /lib64/libc.so.6
#23 0x0000000000400729 in _start ()
===========================================================

Segmentation fault (core dumped)

It seems that every call to a method which is doing something with object crafted in Python leads to segfault: .process(), getCandidate() and so on.

Code doesn't compile with a user defined python (e.g. Enthought / Canopy) in Mac OS X.
Not possible to set PYTHON_LIBRARIES (system framework default is read).

28.10. SourceMultiplePositions: speed improvement and test

Tests 8 and 9 fail in this revision.

bash-4.1$ make test
Running tests...
Test project /afs/desy.de/group/pheno/software/SL6/CRPropa3/build
Start 1: testCore
1/9 Test #1: testCore ......................... Passed 0.95 sec
Start 2: testVector3
2/9 Test #2: testVector3 ...................... Passed 0.51 sec
Start 3: testModuleList
3/9 Test #3: testModuleList ................... Passed 0.55 sec
Start 4: testMagneticField
4/9 Test #4: testMagneticField ................ Passed 3.03 sec
Start 5: testPropagation
5/9 Test #5: testPropagation .................. Passed 0.52 sec
Start 6: testBreakCondition
6/9 Test #6: testBreakCondition ............... Passed 0.52 sec
Start 7: testOutput
7/9 Test #7: testOutput ....................... Passed 0.53 sec
Start 8: testInteraction
8/9 Test #8: testInteraction .................._Failed 9.13 sec
Start 9: testSource
9/9 Test #9: testSource ......................._Failed 0.53 sec

The energy distribution of electrons from beta decay is given by (Basdevant, eq 4.92)
p(E_e) ~ F(Z',E_e) E_e \sqrt{E_e^2 - m_e^2 c^4} (\Delta m c^2 - E_e)^2

Currently beta energies are generated according to the free neutron decay (Delta m = m_n - m_p, F=1) and then approximatively scaled to the given nuclear decay.
Implementing the correct treatment would be straightforward however.

When doing print grid.get(i, j, k) in python, I get:

<Swig Object of type 'float *' at 0x109f21750>

I've tested this with a ScalarGrid.

Probably crpropa.i needs some modifying to dereference this SWIG float reference.

I had to apply some hacks to get CRPropa running on my system with a Homebrew installed Python.

It showed the correct paths to the /usr/local version of Python during cmake ..
However, when doing ccmake .. it used the wrong Python Headers:

PYTHON_EXECUTABLE   /usr/local/bin/python
PYTHON_H_FOUND      /System/Library/Frameworks/Python.framework/Headers

I had to manually set the Python headers location to the homebrew version:

/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Headers/Python.h

Then I proceeded with make && make test, which passed 100%, then make install.
Which also went fine, but importing crpropa resulted in Python crashing.
I found wrong links to python:

otool -L /usr/local/lib/python2.7/site-packages/_crpropa.so

And had to change it to the correct one:

install_name_tool -change /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/Python /usr/local/lib/python2.7/site-packages/_crpropa.so

After which running the example worked.

A minimal example:

from crpropa import *
c = Candidate()
bar = ''
c.setProperty( "foo", "bar" )
c.getProperty( "foo", bar )
print bar

returns:

TypeError: in method 'Candidate_getProperty', argument 3 of type 'std::string &'

In SWIG interface we should somehow bypass the second argument in Candidate::getProperty so that we can return the property's value to string, but even if we wrap the third argument as a reference to std:string I'm not sure if it's possible to return the value because in Python strings are immutable.

So I suppose the only way to solve this is to change the function so that it returns value instead of "true/false". Am I right?

Dear devels,

I am looking at

PhotoDisintegration::setPhotonField()

and wonder why the interaction rates and branching ratios are not consistent for some options. For instance, for the Stecker05 model, the interaction rate is using the Stecker05 table, but the branching ratios are from Kneiske04:

    case IRB_Stecker05:
        setDescription("PhotoDisintegration: IRB Stecker '05");
        initRate(getDataPath("pd_IRB_Stecker05.txt"));
        initBranching(getDataPath("pd_branching_IRB_Kneiske04.txt"));

Same for IRB_Kneiske10 and IRB_Franceschini08. Is this a cut-and-paste bug, or is there a deeper reason for this?

Cheers,
Michael

on Ubuntu 12.04:

cmake -DCMAKE_INSTALL_PREFIX=/home/user/install/CRPropa3_280114 ..
-- The Fortran compiler identification is GNU
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working Fortran compiler: /usr/bin/f95
-- Check for working Fortran compiler: /usr/bin/f95  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/f95 supports Fortran 90
-- Checking whether /usr/bin/f95 supports Fortran 90 -- yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Looking for include files CMAKE_HAVE_PTHREAD_H
-- Looking for include files CMAKE_HAVE_PTHREAD_H - found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp 
-- FFTW3 with single precision (FFTW3F): Found!
--   Include:     /usr/include
--   Library:     /usr/lib/libfftw3f.so
-- Quimby: NOT Found!
--   Include:     QUIMBY_INCLUDE_DIR-NOTFOUND
--   Library:     QUIMBY_LIBRARY-NOTFOUND
-- ROOT: Found!
--   CFlags:      -pthread -m64 -I/home/user/install/root_v5p34p09/include/root
--   Libs:        -L/home/user/install/root_v5p34p09/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic
-- Google perftools: NOT Found!
--   Include: GOOGLE_PERFTOOLS_INCLUDE_DIR-NOTFOUND
-- Python: Found!
--   Version:     2.7/27
--   Executeable: /usr/bin/python
--   Include:     /usr/include/python2.7
--   Library:     /usr/lib/libpython2.7.so
--   Site-package directory: /home/user/install/CRPropa3_280114/lib/python2.7/site-packages
-- Configuring done
-- Generating done
-- Build files have been written to: /home/user/software/CRPropa3_280114/CRPropa3/build

make
Scanning dependencies of target kiss
[  1%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/logger.cpp.o
[  2%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/path.cpp.o
[  3%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/string.cpp.o
[  4%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/uuid.cpp.o
Linking CXX static library libkiss.a
[  4%] Built target kiss
Scanning dependencies of target dint
[  5%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/advance.cpp.o
[  6%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/background.cpp.o
[  7%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/binfread.cpp.o
/home/user/software/CRPropa3_280114/CRPropa3/libs/dint/src/binfread.cpp: In Funktion »size_t binfread(void*, size_t, size_t, FILE*)«:
/home/user/software/CRPropa3_280114/CRPropa3/libs/dint/src/binfread.cpp:58:77: Warnung: Format »%d« erwartet Argumenttyp »int«, aber Argument 3 hat Typ »size_t {aka long unsigned int}« [-Wformat]
[  8%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/check.cpp.o
[  9%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/cvector.cpp.o
[ 10%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/decay.cpp.o
[ 12%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/deriv.cpp.o
[ 13%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/error.cpp.o
[ 14%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/final.cpp.o
[ 15%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/fold.cpp.o
[ 16%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/frag.cpp.o
[ 17%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/gauleg.cpp.o
[ 18%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/inject.cpp.o
[ 19%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/io_util.cpp.o
[ 20%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/load.cpp.o
[ 21%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/math_util.cpp.o
[ 23%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/prepare.cpp.o
/home/user/software/CRPropa3_280114/CRPropa3/libs/dint/src/prepare.cpp: In Funktion »void InteractionParameterInput(FILE*, int, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)«:
/home/user/software/CRPropa3_280114/CRPropa3/libs/dint/src/prepare.cpp:235:37: Warnung: Format »%lf« erwartet Argumenttyp »double*«, aber Argument 2 hat Typ »int*« [-Wformat]
[ 24%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/prop_second.cpp.o
[ 25%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/rate.cpp.o
[ 26%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/spectrum.cpp.o
[ 27%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/sync.cpp.o
[ 28%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/vector.cpp.o
Linking CXX static library libdint.a
[ 28%] Built target dint
Scanning dependencies of target sophia
[ 29%] Building Fortran object libs/sophia/CMakeFiles/sophia.dir/sophia_interface.f.o
/home/user/software/CRPropa3_280114/CRPropa3/libs/sophia/sophia_interface.f:1827.72:

            PAUSE                                                       
                                                                        1
Warnung: Gelöschte Funktion: PAUSE-Anweisung bei (1)
/home/user/software/CRPropa3_280114/CRPropa3/libs/sophia/sophia_interface.f:16396.72:

        pause                                                           
                                                                        1
Warnung: Gelöschte Funktion: PAUSE-Anweisung bei (1)
Linking Fortran static library libsophia.a
[ 29%] Built target sophia
Scanning dependencies of target pugixml
[ 30%] Building CXX object libs/pugixml/CMakeFiles/pugixml.dir/pugixml.cpp.o
Linking CXX static library libpugixml.a
[ 30%] Built target pugixml
Scanning dependencies of target HepPID
[ 31%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/ParticleIDMethods.cc.o
[ 32%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/ParticleName.cc.o
[ 34%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/Version.cc.o
[ 35%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateEvtGen.cc.o
[ 36%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateGeanttoPDT.cc.o
[ 37%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateHerwig.cc.o
[ 38%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateIsajet.cc.o
[ 39%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePDG.cc.o
[ 40%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePDTtoGeant.cc.o
[ 41%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePythia.cc.o
[ 42%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateQQ.cc.o
Linking CXX static library libHepPID.a
[ 42%] Built target HepPID
Scanning dependencies of target crpropa
[ 43%] Building CXX object CMakeFiles/crpropa.dir/src/Random.cpp.o
[ 45%] Building CXX object CMakeFiles/crpropa.dir/src/Clock.cpp.o
[ 46%] Building CXX object CMakeFiles/crpropa.dir/src/ModuleList.cpp.o
[ 47%] Building CXX object CMakeFiles/crpropa.dir/src/Module.cpp.o
[ 48%] Building CXX object CMakeFiles/crpropa.dir/src/Candidate.cpp.o
[ 49%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleState.cpp.o
[ 50%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleID.cpp.o
[ 51%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleMass.cpp.o
[ 52%] Building CXX object CMakeFiles/crpropa.dir/src/Cosmology.cpp.o
[ 53%] Building CXX object CMakeFiles/crpropa.dir/src/Source.cpp.o
[ 54%] Building CXX object CMakeFiles/crpropa.dir/src/Common.cpp.o
[ 56%] Building CXX object CMakeFiles/crpropa.dir/src/PhotonBackground.cpp.o
[ 57%] Building CXX object CMakeFiles/crpropa.dir/src/GridTools.cpp.o
[ 58%] Building CXX object CMakeFiles/crpropa.dir/src/XmlExecute.cpp.o
[ 59%] Building CXX object CMakeFiles/crpropa.dir/src/module/BreakCondition.cpp.o
[ 60%] Building CXX object CMakeFiles/crpropa.dir/src/module/Boundary.cpp.o
[ 61%] Building CXX object CMakeFiles/crpropa.dir/src/module/Observer.cpp.o
[ 62%] Building CXX object CMakeFiles/crpropa.dir/src/module/SimplePropagation.cpp.o
[ 63%] Building CXX object CMakeFiles/crpropa.dir/src/module/DeflectionCK.cpp.o
[ 64%] Building CXX object CMakeFiles/crpropa.dir/src/module/ElectronPairProduction.cpp.o
[ 65%] Building CXX object CMakeFiles/crpropa.dir/src/module/NuclearDecay.cpp.o
[ 67%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotoPionProduction.cpp.o
[ 68%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotoDisintegration.cpp.o
[ 69%] Building CXX object CMakeFiles/crpropa.dir/src/module/Redshift.cpp.o
[ 70%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputTXT.cpp.o
[ 71%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputShell.cpp.o
[ 72%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputROOT.cpp.o
[ 73%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputCRPropa2.cpp.o
[ 74%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonDINT.cpp.o
[ 75%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonDINT1D.cpp.o
[ 76%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonEleCa.cpp.o
[ 78%] Building CXX object CMakeFiles/crpropa.dir/src/module/Tools.cpp.o
[ 79%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/MagneticField.cpp.o
[ 80%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/MagneticFieldGrid.cpp.o
[ 81%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/TurbulentMagneticField.cpp.o
[ 82%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/JF12Field.cpp.o
Linking CXX shared library libcrpropa.so
[ 82%] Built target crpropa
[ 83%] Generating crpropa_wrap.cxx
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:172: Warning 361: operator! ignored
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/ExplicitRungeKutta.h:18: Warning 325: Nested class not currently supported (F ignored)
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Grid.h:124: Warning 508: previous declaration of 'get'.
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Grid.h:129: Warning 508: previous declaration of 'get'.
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Grid.h:124: Warning 508: previous declaration of 'get'.
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Grid.h:129: Warning 508: previous declaration of 'get'.
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:158: Warning 503: Can't wrap 'operator crpropa::Grid< crpropa::Vector3< float > >*' unless renamed to a valid identifier.
/home/user/software/CRPropa3_280114/CRPropa3/include/crpropa/Referenced.h:158: Warning 503: Can't wrap 'operator crpropa::Grid< float >*' unless renamed to a valid identifier.
Scanning dependencies of target crpropa-swig
[ 84%] Building CXX object CMakeFiles/crpropa-swig.dir/crpropa_wrap.cxx.o
Linking CXX shared module _crpropa.so
[ 84%] Built target crpropa-swig
Scanning dependencies of target crpropa-xmlrun
[ 85%] Building CXX object CMakeFiles/crpropa-xmlrun.dir/src/main.cpp.o
Linking CXX executable crpropa-xmlrun
libcrpropa.so: undefined reference to `TFile::TFile(char const*, char const*, char const*, int)'
libcrpropa.so: undefined reference to `TStorage::ObjectAlloc(unsigned long)'
libcrpropa.so: undefined reference to `TVersionCheck::TVersionCheck(int)'
libcrpropa.so: undefined reference to `TThread::UnLock()'
libcrpropa.so: undefined reference to `TObject::operator delete(void*)'
libcrpropa.so: undefined reference to `TNtuple::TNtuple(char const*, char const*, char const*, int)'
libcrpropa.so: undefined reference to `TThread::Lock()'
collect2: ld gab 1 als Ende-Status zurück
make[2]: *** [crpropa-xmlrun] Fehler 1
make[1]: *** [CMakeFiles/crpropa-xmlrun.dir/all] Fehler 2
make: *** [all] Fehler 2

It would be beneficial if a common naming would logically group the functions together, as it is currently done with SourceXXX and ObserverXXX.

e.g.

from crpropa import *
v1 = coordinates_galactic(124, -32, degree=True)  # 3-vector in galactic coordinates, |v1| = 1
v2 = coordinates_gal2sgal(v1)  # the same vector in supergalactic coordinates
v2 = coordinates_gal2eq(v1)  # the same vector in equatorial coordinates
...

There seem to be some type-conversion errors in the generated file crpropa_wrap.cxx. Any idea which source file could be causing them? Thanks!

Error report:
...
[ 98%] Built target testModuleList
Scanning dependencies of target testSource
[ 99%] Building CXX object CMakeFiles/testSource.dir/test/testSource.cpp.o
Linking CXX executable testOutput
[ 99%] Built target testOutput
Scanning dependencies of target testVector3
[100%] Building CXX object CMakeFiles/testVector3.dir/test/testVector3.cpp.o
Linking CXX executable testPropagation
[100%] Built target testPropagation
/CRPropa3/build/crpropa_wrap.cxx:6810:27: error:
non-constant-expression cannot be narrowed from type 'size_t'
(aka 'unsigned long') to 'npy_intp' (aka 'long') in initializer list
[-Wc++11-narrowing]
npy_intp dims[1] = {npix};
^~~~
/CRPropa3/build/crpropa_wrap.cxx:6810:27: note:
insert an explicit cast to silence this issue
npy_intp dims[1] = {npix};
^~~~
static_cast<npy_intp>( )
/CRPropa3/build/crpropa_wrap.cxx:6815:24: error:
non-constant-expression cannot be narrowed from type 'size_type'
(aka 'unsigned long') to 'npy_intp' (aka 'long') in initializer list
[-Wc++11-narrowing]
npy_intp size = {v.size()};
^~~~~~~~
/CRPropa3/build/crpropa_wrap.cxx:6815:24: note:
insert an explicit cast to silence this issue
npy_intp size = {v.size()};
^~~~~~~~
static_cast<npy_intp>( )
/CRPropa3/build/crpropa_wrap.cxx:6822:24: error:
non-constant-expression cannot be narrowed from type 'size_type'
(aka 'unsigned long') to 'npy_intp' (aka 'long') in initializer list
[-Wc++11-narrowing]
npy_intp size = {v.size()};
^~~~~~~~
/CRPropa3/build/crpropa_wrap.cxx:6822:24: note:
insert an explicit cast to silence this issue
npy_intp size = {v.size()};
^~~~~~~~
static_cast<npy_intp>( )
/CRPropa3/build/crpropa_wrap.cxx:6835:24: error:
non-constant-expression cannot be narrowed from type 'size_t'
(aka 'unsigned long') to 'npy_intp' (aka 'long') in initializer list
[-Wc++11-narrowing]
npy_intp size = {N};
^
/CRPropa3/build/crpropa_wrap.cxx:6835:24: note:
insert an explicit cast to silence this issue
npy_intp size = {N};
^
static_cast<npy_intp>( )
Linking CXX executable testSource
Linking CXX executable testVector3
[100%] Built target testSource
[100%] Built target testVector3
4 errors generated.
make[2]: *** [CMakeFiles/crpropa-swig.dir/crpropa_wrap.cxx.o] Error 1
make[1]: *** [CMakeFiles/crpropa-swig.dir/all] Error
make: *** [all] Error 2

v = Vector3d(1,1,1)

# working
v *= 1
v /= 1
v += 1 
v -= 1
v + 1
v - 1
v * 1

# not working
v / 1.
TypeError: unsupported operand type(s) for /: 'crpropa.Vector3d' and 'float'
v / 1
TypeError: unsupported operand type(s) for /: 'crpropa.Vector3d' and 'int'

same for Vector3f

make test fails.
Error occurs both in Mac and Linux.
CRPropa works correctly, except for this.
Both numpy and python are working properly.

Running tests...
Test project /Users/rogerio/CRPropa3/build
      Start  1: testCore
 1/12 Test  #1: testCore ..........................   Passed    0.99 sec
      Start  2: testVector3
 2/12 Test  #2: testVector3 .......................   Passed    0.15 sec
      Start  3: testModuleList
 3/12 Test  #3: testModuleList ....................   Passed    0.21 sec
      Start  4: testMagneticField
 4/12 Test  #4: testMagneticField .................   Passed    0.82 sec
      Start  5: testDINT
 5/12 Test  #5: testDINT ..........................   Passed    0.77 sec
      Start  6: testPropagation
 6/12 Test  #6: testPropagation ...................   Passed    0.33 sec
      Start  7: testBreakCondition
 7/12 Test  #7: testBreakCondition ................   Passed    0.16 sec
      Start  8: testInteraction
 8/12 Test  #8: testInteraction ...................   Passed   12.26 sec
      Start  9: testSource
 9/12 Test  #9: testSource ........................   Passed    0.21 sec
      Start 10: testGalacticMagneticLens
10/12 Test #10: testGalacticMagneticLens ..........   Passed    0.33 sec
      Start 11: testMagneticLensPythonInterface
11/12 Test #11: testMagneticLensPythonInterface ...***Failed   11.74 sec
      Start 12: testSimulationExecution
12/12 Test #12: testSimulationExecution ...........   Passed    2.07 sec

92% tests passed, 1 tests failed out of 12

Total Test time (real) =  30.08 sec

The following tests FAILED:
     11 - testMagneticLensPythonInterface (Failed)
Errors while running CTest
make: *** [test] Error 8

how to set the crpropa simulation to get secondary gamma-rays?

The new advanced TextOutput class has the possibility to choose the length scale for the outout file. Is there a similar option for the ConditionalOutput which I do not see? Or maybe the other way round: Is it possible to use the TextOutput with a condition argument?
Best regards, Lukas

txt output modules obsolet and not up-to-date. E.g. 1D example in wiki does not work (ObserverOutput1D). Should be fixed before release.

Running main() from gtest_main.cc
[==========] Running 6 tests from 6 test cases.
[----------] Global test environment set-up.
[----------] 1 test from ConditionalOutput
[ RUN ] ConditionalOutput.removeProperty
[ OK ] ConditionalOutput.removeProperty (0 ms)
[----------] 1 test from ConditionalOutput (0 ms total)

[----------] 1 test from EventOutput1D
[ RUN ] EventOutput1D.removeProperty
[ OK ] EventOutput1D.removeProperty (0 ms)
[----------] 1 test from EventOutput1D (0 ms total)

[----------] 1 test from CRPropa2EventOutput3D
[ RUN ] CRPropa2EventOutput3D.removeProperty
[ OK ] CRPropa2EventOutput3D.removeProperty (0 ms)
[----------] 1 test from CRPropa2EventOutput3D (0 ms total)

[----------] 1 test from CRPropa2EventOutput1D
[ RUN ] CRPropa2EventOutput1D.removeProperty
[ OK ] CRPropa2EventOutput1D.removeProperty (0 ms)
[----------] 1 test from CRPropa2EventOutput1D (0 ms total)

[----------] 1 test from CRPropa2ROOTEventOutput3D
[ RUN ] CRPropa2ROOTEventOutput3D.removeProperty
Error in TFile::TFile: file name is not specified
Warning in TFile::Write: file not opened in write mode
[ OK ] CRPropa2ROOTEventOutput3D.removeProperty (12 ms)
[----------] 1 test from CRPropa2ROOTEventOutput3D (12 ms total)

[----------] 1 test from CRPropa2ROOTEventOutput1D
[ RUN ] CRPropa2ROOTEventOutput1D.removeProperty
Error in TFile::TFile: file name is not specified
Warning in TFile::Write: file not opened in write mode
[ OK ] CRPropa2ROOTEventOutput1D.removeProperty (0 ms)
[----------] 1 test from CRPropa2ROOTEventOutput1D (0 ms total)

[----------] Global test environment tear-down
[==========] 6 tests from 6 test cases ran. (12 ms total)
[ PASSED ] 6 tests.

The lines
"
M = crpropa.ParticleMapsContainer()
wexp = -1
M.addParticlesFromFile("crpropa_output.txt", wexp)
"
do not work for the default 3D output, only if you use the TextOutput(file, "3D events") format.
It would be good if the addParticlesFromFile() function actually reads the default output or, even better, could read all outputs.

from crpropa import *
class Test(Module):
   def __init__ (self):
      pass

m = ModuleList()
m.add(Test())

TypeError: in method 'ModuleList_add', argument 2 of type 'crpropa::Module *'

Input:
from crpropa import *
lens = MagneticLens('pathto/lens.cfg')

Output:
ERROR READING LINE:
... line skipped!

TALYS computes cross sections for channels where the nucleus stays intact (xs000000.tot)
as well as channels where the residual nucleus is in an excited state (eg. xs010000.L01) and elastic scattering.
This information can be used to implement secondary photons from photo-nuclear interactions.

for

• ElectronPairProduction
• PhotoPionProduction
• PhotoDisintegration

The 'data/' folder is in CRPropa3/data and all the files are in place. When running test/python/testBoundaries.py (or any other test) I get the error:

terminate called after throwing an instance of 'std::runtime_error'
what(): crpropa: could not open file data/nuclear_mass.txt

It works normally when calling the test script from the CRPropa3/ folder.
Using XML inputs the program runs normally.

Our random number generator is absed on 32Bit random numbers. 64Bit may sometimes be needed, e.g. for the random distribution in healpix pixels. The current 64Bit Random capability is a hack that use 32Bit seed for a XORSHIFT algorithm which might be very predictable.

We should probably update to a 64Bit Mersenne Twister.

The view of README.md needs to be fixed

I tried to write a source code NeutrinoOutput1D.cpp similar as PhotonOutput1D.cpp (also NeutrinoOutput1D.h) to calculate secondary neutrinos. I changed "if ((pid != 22) and (abs(pid) != 11))" to "if ((abs(pid) != 12) and (abs(pid) != 14))", then recompile the code, but it seems doesn't work.

Dear CRPropa3 devels,

I think at the end NuclearDecay::betaDecay() instead of

    if (haveElectrons)
    // add electron/positron boosted to lab frame
        candidate->addSecondary(electronId, gamma * E * (1 + p * cosTheta));

it should be

    if (haveElectrons)
        // add electron/positron boosted to lab frame
        candidate->addSecondary(electronId, gamma * (E + p * cosTheta));

(wrong Lorentztransformation, even units don't make sense).

Similar for neutrinos, where you currently have

    candidate->addSecondary(neutrinoId, gamma * (Q - E) * (1 - p * cosTheta));

please change the Lorentz transformation. Moreover, I would not use p_e but T_nu for the momentum and finally (Q-E) is not the neutrino kinetic energy, but (Q- T), since Q here is m_n - m_p - m_e:

        candidate->addSecondary(neutrinoId, gamma * (Q - T) * (1 - cosTheta));

Makes quite some difference :)

The bug would probably have been spotted earlier if you did not silently ignore negative energies in ParticleState::setEnergy() where

        energy = std::max(0., newEnergy); // prevent negative energies

Maybe you should add a warning output here?

Cheers,
Michael