Tumorcode Installation

[LiorEps]

Hello,
I've been trying to install Tumorcode on Ubuntu 18. I get the following error during installation:
$ cmake -DCMAKE_INSTALL_PREFIX=/usr/lib/tumorcode /home/user/tumorcode/
-- Boost version: 1.65.1
no numpy cpp!!!
-- Configuring done
-- Generating done
-- Build files have been written to: /home/lepstein/tumorcode/externalProjects/HDF5-cpp-wrapper
[ 11%] Performing update step for 'HDF5-cpp-wrapper'
Current branch master is up to date.
[ 22%] Performing configure step for 'HDF5-cpp-wrapper'
[ 33%] No build step for 'HDF5-cpp-wrapper'
[ 44%] No install step for 'HDF5-cpp-wrapper'
[ 55%] No test step for 'HDF5-cpp-wrapper'
[ 66%] Completed 'HDF5-cpp-wrapper'
[100%] Built target HDF5-cpp-wrapper
CMAKE_ROOT: /usr/share/cmake-3.10
CMAKE_MODULE_PATH:
CMAKE_MODULE_PATH: /home/lepstein/tumorcode/cmake/modules/;
CMAKE_EXE_LINKER_FLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/lepstein/anaconda3/envs/py2/lib -Wl,-rpath-link,/home/lepstein/anaconda3/envs/py2/lib -L/home/lepstein/anaconda3/envs/py2/lib
USE_PAGMO preprocessor defined
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- program_options
Boost_PROGRAM_OPTIONS_LIBRARY: /home/lepstein/anaconda3/envs/py2/lib/libboost_program_options.so
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- system
Boost_SYSTEM_LIBRARY: /home/lepstein/anaconda3/envs/py2/lib/libboost_system.so
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- serialization
Boost_SERIALIZATION_LIBRARY: /home/lepstein/anaconda3/envs/py2/lib/libboost_serialization.so
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- thread
-- chrono
-- system
-- date_time
-- atomic
Boost_THREAD_LIBRARY: /home/lepstein/anaconda3/envs/py2/lib/libboost_thread.so
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- filesystem
-- system
Boost_FILESYSTEM_LIBRARY: /home/lepstein/anaconda3/envs/py2/lib/libboost_filesystem.so
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- numpy
-- python
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- A library with BLAS API found.
CMake Error at /usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find PNG (missing: PNG_LIBRARY) (found version "1.6.34")
Call Stack (most recent call first):
/usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-3.10/Modules/FindPNG.cmake:144 (find_package_handle_standard_args)
CMakeLists.txt:203 (find_package)

-- Configuring incomplete, errors occurred!
See also "/home/lepstein/tumorcode/CMakeFiles/CMakeOutput.log".
See also "/home/lepstein/tumorcode/CMakeFiles/CMakeError.log".

What could be the issue?
Thank you

[thierry3000]

Dear LiorEps,
there seams to be a problem with your PNG_LIBRARY. Did you install your version via the official ubuntu change (sudo apt-get install libpng-dev)? Did you use the default cmake environment of 18.04?

[LiorEps]

Thank you for the fast response.
libpng-dev is installed and I'm using the default ubuntu 18.04 cmake.

[thierry3000]

please have a look at
#21
and check the problems mentioned there.

[LiorEps]

Thank you for all your help.
Following your suggestion I tryed installing from the dev-fredrich branch.
I successfully installed HDF5 and I have trilinos but when I try to run "make" I get the following errors:
lepstein@lepstein:~/tumorcode-dev_fredrich/build$ make
Scanning dependencies of target numpycpp
[ 1%] Building CXX object externalProjects/numpycpp-build/CMakeFiles/numpycpp.dir/numpy.cpp.o
[ 2%] Linking CXX static library libnumpycpp.a
[ 2%] Built target numpycpp
Scanning dependencies of target demo
[ 3%] Building CXX object externalProjects/numpycpp-build/CMakeFiles/demo.dir/demo.cpp.o
[ 5%] Linking CXX shared library libdemo.so
[ 5%] Built target demo
Scanning dependencies of target mwlib
[ 6%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/any_tree.cpp.o
[ 7%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/drawing.cpp.o
[ 8%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/field.cpp.o
[ 10%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/hdf_wrapper.cpp.o
[ 11%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/hdf_wrapper_array3d.cpp.o
[ 12%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/hdf_wrapper_ptree.cpp.o
[ 13%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/helpers.cpp.o
[ 15%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/histogram.cpp.o
[ 16%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/lattice-data.cpp.o
[ 17%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/mempool.cpp.o
[ 18%] Building CXX object src/mwlib/CMakeFiles/mwlib.dir/ptree_ext.cpp.o
[ 20%] Linking CXX static library lib/libmwlib.a
[ 20%] Built target mwlib
Scanning dependencies of target common
[ 21%] Building CXX object src/common/CMakeFiles/common.dir/bulktissuemodel1_new.cpp.o
[ 22%] Building CXX object src/common/CMakeFiles/common.dir/calcflow.cpp.o
[ 23%] Building CXX object src/common/CMakeFiles/common.dir/calcflow_linsys.cpp.o
[ 25%] Building CXX object src/common/CMakeFiles/common.dir/cell_based_oxygen_update_model.cpp.o
[ 26%] Building CXX object src/common/CMakeFiles/common.dir/common.cpp.o
[ 27%] Building CXX object src/common/CMakeFiles/common.dir/continuum-flow.cpp.o
[ 28%] Building CXX object src/common/CMakeFiles/common.dir/continuum-grid.cpp.o
[ 30%] Building CXX object src/common/CMakeFiles/common.dir/continuum-surfacetension.cpp.o
[ 31%] Building CXX object src/common/CMakeFiles/common.dir/continuum-utils.cpp.o
[ 32%] Building CXX object src/common/CMakeFiles/common.dir/convection_diffusion_solver.cpp.o
[ 33%] Building CXX object src/common/CMakeFiles/common.dir/distancemap.cpp.o
[ 35%] Building CXX object src/common/CMakeFiles/common.dir/glucose_model.cpp.o
[ 36%] Building CXX object src/common/CMakeFiles/common.dir/growthfactor_model.cpp.o
[ 37%] Building CXX object src/common/CMakeFiles/common.dir/hdfio.cpp.o
[ 38%] Building CXX object src/common/CMakeFiles/common.dir/lattice-data-polymorphic.cpp.o
[ 40%] Building CXX object src/common/CMakeFiles/common.dir/levelset.cpp.o
[ 41%] Building CXX object src/common/CMakeFiles/common.dir/shared-object.cpp.o
[ 42%] Building CXX object src/common/CMakeFiles/common.dir/simple_oxygen_model.cpp.o
[ 43%] Building CXX object src/common/CMakeFiles/common.dir/trilinos_helper.cpp.o
[ 45%] Building CXX object src/common/CMakeFiles/common.dir/trilinos_linsys_construction.cpp.o
/home/lepstein/tumorcode-dev_fredrich/src/common/trilinos_linsys_construction.cpp:62:6: warning: #warning "Compiling with MPI Enabled" [-Wcpp]
#warning "Compiling with MPI Enabled"
^~~~~~~
[ 46%] Building CXX object src/common/CMakeFiles/common.dir/vesselmodel1.cpp.o
[ 47%] Building CXX object src/common/CMakeFiles/common.dir/vessels3d_biconnected.cpp.o
[ 48%] Building CXX object src/common/CMakeFiles/common.dir/vessels3d.cpp.o
[ 50%] Linking CXX static library lib/libcommon.a
[ 50%] Built target common
Scanning dependencies of target vesselgenlib
[ 51%] Building CXX object src/common/CMakeFiles/vesselgenlib.dir/vesselgen/remodeler.cpp.o
[ 52%] Building CXX object src/common/CMakeFiles/vesselgenlib.dir/vesselgen/vesselgen_grid.cpp.o
[ 53%] Building CXX object src/common/CMakeFiles/vesselgenlib.dir/vesselgen/vessgen.cpp.o
[ 55%] Building CXX object src/common/CMakeFiles/vesselgenlib.dir/vesselgen/vessgen_support.cpp.o
[ 56%] Linking CXX static library lib/libvesselgenlib.a
[ 56%] Built target vesselgenlib
Scanning dependencies of target krebs_
[ 57%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/mainboost.cpp.o
[ 58%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/pylatticedata.cpp.o
[ 60%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_helpers.cpp.o
[ 61%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/povray_export.cpp.o
[ 62%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/samplevessels.cpp.o
[ 63%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_tumormodel_tests.cpp.o
[ 65%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_numericaltools_tests.cpp.o
[ 66%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_vesselgen.cpp.o
[ 67%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_calcflow.cpp.o
[ 68%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_interpolate_between_vessels.cpp.o
[ 70%] Building CXX object src/python_krebsutils/CMakeFiles/krebs_.dir/python_murray.cpp.o
[ 71%] Linking CXX shared library lib/libkrebs_.so
/home/lepstein/anaconda3/envs/py2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -ltrilinos_belos
/home/lepstein/anaconda3/envs/py2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -ltrilinos_belosepetra
/home/lepstein/anaconda3/envs/py2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -ltrilinos_ml
collect2: error: ld returned 1 exit status
src/python_krebsutils/CMakeFiles/krebs_.dir/build.make:399: recipe for target 'src/python_krebsutils/lib/libkrebs_.so' failed
make[2]: *** [src/python_krebsutils/lib/libkrebs_.so] Error 1
CMakeFiles/Makefile2:372: recipe for target 'src/python_krebsutils/CMakeFiles/krebs_.dir/all' failed
make[1]: *** [src/python_krebsutils/CMakeFiles/krebs_.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

[thierry3000]

Hi
have you cleaned the cache and changed the compiler as instructed in #21?

[asfbar]

Hello,
i'm helping Lior with this issue.

i successfully rebuild and installed the code, but when i executed it with python2 i got the following errors:

base) lepstein@lepstein:/usr/include/tumorcode/bin$ sudo python2 submitVesselgeneration
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Status size changed, may indicate binary incompatibility. Expected 40 from C header, got 48 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Datatype size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Request size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Prequest size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Grequest size changed, may indicate binary incompatibility. Expected 40 from C header, got 48 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Message size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Op size changed, may indicate binary incompatibility. Expected 40 from C header, got 48 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Group size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Info size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Errhandler size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Comm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Intracomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Topocomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Cartcomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Graphcomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Distgraphcomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Intercomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:26: RuntimeWarning: mpi4py.MPI.Win size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from . import _errors
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Status size changed, may indicate binary incompatibility. Expected 40 from C header, got 48 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Datatype size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Request size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Prequest size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Grequest size changed, may indicate binary incompatibility. Expected 40 from C header, got 48 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Message size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Op size changed, may indicate binary incompatibility. Expected 40 from C header, got 48 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Group size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Info size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Errhandler size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Comm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Intracomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Topocomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Cartcomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Graphcomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Distgraphcomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Intercomm size changed, may indicate binary incompatibility. Expected 24 from C header, got 32 from PyObject
from ._conv import register_converters as _register_converters
/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py:36: RuntimeWarning: mpi4py.MPI.Win size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "submitVesselgeneration", line 30, in
import krebsutils
File "/usr/include/tumorcode/py/krebsjobs/../krebsutils/init.py", line 25, in
import h5py
File "/usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/init.py", line 36, in
from ._conv import register_converters as _register_converters
File "h5py/_conv.pyx", line 1, in init h5py._conv
File "h5py/h5r.pyx", line 1, in init h5py.h5r
File "h5py/_objects.pyx", line 1, in init h5py._objects
ImportError: /usr/local/lib/python2.7/dist-packages/h5py-2.9.0-py2.7-linux-x86_64.egg/h5py/defs.so: undefined symbol: H5Pget_dxpl_mpio

Can you please advise?

Thank you.
Assaf.

[thierry3000]

Hi,
and sorry for the late response.
Your call:

lepstein@lepstein:/usr/include/tumorcode/bin$ sudo python2 submitVesselgeneration

seems strange to me:
either use the binary by calling ./submitVesselgeneration in the "bin" folder
or
call the python script by python2 py/krebsjobs/submitVesselgeneration.py

Does this help?