Open LiorEps opened 4 years ago
thierry3000
commented
4 years ago 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
commented
4 years ago Thank you for the fast response. libpng-dev is installed and I'm using the default ubuntu 18.04 cmake.
thierry3000
commented
4 years ago please have a look at
and check the problems mentioned there.
LiorEps
commented
4 years ago 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]
^~~~~~~[ 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/vessgensupport.cpp.o [ 56%] Linking CXX static library lib/libvesselgenlib.a [ 56%] Built target vesselgenlib Scanning dependencies of target krebs [ 57%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/mainboost.cpp.o [ 58%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/pylatticedata.cpp.o [ 60%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/python_helpers.cpp.o [ 61%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/povray_export.cpp.o [ 62%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/samplevessels.cpp.o [ 63%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/python_tumormodel_tests.cpp.o [ 65%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/python_numericaltools_tests.cpp.o [ 66%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/python_vesselgen.cpp.o [ 67%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/python_calcflow.cpp.o [ 68%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/python_interpolate_between_vessels.cpp.o [ 70%] Building CXX object src/pythonkrebsutils/CMakeFiles/krebs.dir/pythonmurray.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/pythonkrebsutils/CMakeFiles/krebs.dir/build.make:399: recipe for target 'src/pythonkrebsutils/lib/libkrebs.so' failed make[2]: [src/pythonkrebsutils/lib/libkrebs.so] Error 1 CMakeFiles/Makefile2:372: recipe for target 'src/pythonkrebsutils/CMakeFiles/krebs.dir/all' failed make[1]: [src/pythonkrebsutils/CMakeFiles/krebs.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2
thierry3000
commented
4 years ago Hi have you cleaned the cache and changed the compiler as instructed in #21?
asfbar
commented
4 years ago 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
Can you please advise?
Thank you. Assaf.
thierry3000
commented
4 years ago 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?
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