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moose import error after manual installation

    • Closed Issue created by Sahil Moza @sahil

    Created by: ChakrapaniNCBS

    After compiling moose,trying to import moose from python and got the following error

    Python 2.7.12 (default, Nov 19 2016, 06:48:10) 
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import moose
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/moose/__init__.py", line 25, in <module>
    from .moose import *
ImportError: No module named moose

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      Activity

      • Sahil Moza
        Sahil Moza @sahil ·
        Author Owner

        Created by: dilawar

        I tried on ubuntu-14.04. Seemed to work just fine.

        Following is the installation log for moose-core subdirectory:

        sudo make install
[sudo] password for dilawars: 
[  3%] Built target intfire
[ 14%] Built target basecode
[ 18%] Built target muparser
[ 21%] Built target msg
[ 25%] Built target shell
[ 32%] Built target randnum
[ 32%] Built target scheduling
[ 50%] Built target biophysics
[ 59%] Built target moose_builtins
[ 62%] Built target utility
[ 67%] Built target mesh
[ 68%] Built target moose_mpi
[ 69%] Built target signeur
[ 77%] Built target ksolve
[ 83%] Built target hsolve
[ 85%] Built target diffusion
[ 86%] Built target device
[ 86%] Built target benchmarks
[ 92%] Built target kinetics
[ 96%] Built target synapse
[ 96%] Built target libmoose
[ 97%] Built target moose.bin
[ 98%] Copying required python files and other files to build directory
[ 98%] Built target copy_python_files
[100%] Built target _moose
Install the project...
-- Install configuration: "Release"
-- Installing: /usr/local/bin/moose.bin
-- Removed runtime path from "/usr/local/bin/moose.bin"
-- Installing: /usr/local/lib/libmoose.so
-- Removed runtime path from "/usr/local/lib/libmoose.so"
-- Installing: /usr/local/bin/moose
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/rdesigneur
copying rdesigneur/rdesigneur.py -> build/lib.linux-x86_64-2.7/rdesigneur
copying rdesigneur/rmoogli.py -> build/lib.linux-x86_64-2.7/rdesigneur
copying rdesigneur/__init__.py -> build/lib.linux-x86_64-2.7/rdesigneur
copying rdesigneur/rdesigneurProtos.py -> build/lib.linux-x86_64-2.7/rdesigneur
creating build/lib.linux-x86_64-2.7/moose
copying moose/hdfutil.py -> build/lib.linux-x86_64-2.7/moose
copying moose/recording.py -> build/lib.linux-x86_64-2.7/moose
copying moose/methods_utils.py -> build/lib.linux-x86_64-2.7/moose
copying moose/merge.py -> build/lib.linux-x86_64-2.7/moose
copying moose/graph_utils.py -> build/lib.linux-x86_64-2.7/moose
copying moose/print_utils.py -> build/lib.linux-x86_64-2.7/moose
copying moose/moose_constants.py -> build/lib.linux-x86_64-2.7/moose
copying moose/verification_utils.py -> build/lib.linux-x86_64-2.7/moose
copying moose/add_Delete_ChemicalSolver.py -> build/lib.linux-x86_64-2.7/moose
copying moose/constants.py -> build/lib.linux-x86_64-2.7/moose
copying moose/moose_config.py -> build/lib.linux-x86_64-2.7/moose
copying moose/graphutil.py -> build/lib.linux-x86_64-2.7/moose
copying moose/plot_utils.py -> build/lib.linux-x86_64-2.7/moose
copying moose/sim_utils.py -> build/lib.linux-x86_64-2.7/moose
copying moose/moose.py -> build/lib.linux-x86_64-2.7/moose
copying moose/__init__.py -> build/lib.linux-x86_64-2.7/moose
copying moose/alternate.py -> build/lib.linux-x86_64-2.7/moose
copying moose/optimizer_interface.py -> build/lib.linux-x86_64-2.7/moose
copying moose/utils.py -> build/lib.linux-x86_64-2.7/moose
creating build/lib.linux-x86_64-2.7/moose/SBML
copying moose/SBML/readSBML.py -> build/lib.linux-x86_64-2.7/moose/SBML
copying moose/SBML/validation.py -> build/lib.linux-x86_64-2.7/moose/SBML
copying moose/SBML/writeSBML.py -> build/lib.linux-x86_64-2.7/moose/SBML
copying moose/SBML/__init__.py -> build/lib.linux-x86_64-2.7/moose/SBML
creating build/lib.linux-x86_64-2.7/moose/neuroml
copying moose/neuroml/ChannelML.py -> build/lib.linux-x86_64-2.7/moose/neuroml
copying moose/neuroml/NeuroML.py -> build/lib.linux-x86_64-2.7/moose/neuroml
copying moose/neuroml/__init__.py -> build/lib.linux-x86_64-2.7/moose/neuroml
copying moose/neuroml/utils.py -> build/lib.linux-x86_64-2.7/moose/neuroml
copying moose/neuroml/MorphML.py -> build/lib.linux-x86_64-2.7/moose/neuroml
copying moose/neuroml/NetworkML.py -> build/lib.linux-x86_64-2.7/moose/neuroml
creating build/lib.linux-x86_64-2.7/moose/genesis
copying moose/genesis/writeKkit.py -> build/lib.linux-x86_64-2.7/moose/genesis
copying moose/genesis/__init__.py -> build/lib.linux-x86_64-2.7/moose/genesis
creating build/lib.linux-x86_64-2.7/moose/chemUtil
copying moose/chemUtil/chemConnectUtil.py -> build/lib.linux-x86_64-2.7/moose/chemUtil
copying moose/chemUtil/graphUtils.py -> build/lib.linux-x86_64-2.7/moose/chemUtil
copying moose/chemUtil/add_Delete_ChemicalSolver.py -> build/lib.linux-x86_64-2.7/moose/chemUtil
copying moose/chemUtil/__init__.py -> build/lib.linux-x86_64-2.7/moose/chemUtil
package init file 'moose/merge/__init__.py' not found (or not a regular file)
creating build/lib.linux-x86_64-2.7/moose/merge
copying moose/merge/mtypes.py -> build/lib.linux-x86_64-2.7/moose/merge
copying moose/merge/merge.py -> build/lib.linux-x86_64-2.7/moose/merge
copying moose/_moose.so -> build/lib.linux-x86_64-2.7/moose
package init file 'moose/merge/__init__.py' not found (or not a regular file)
running install_lib
creating /usr/local/lib/python2.7/dist-packages/rdesigneur
copying build/lib.linux-x86_64-2.7/rdesigneur/rdesigneur.py -> /usr/local/lib/python2.7/dist-packages/rdesigneur
copying build/lib.linux-x86_64-2.7/rdesigneur/rmoogli.py -> /usr/local/lib/python2.7/dist-packages/rdesigneur
copying build/lib.linux-x86_64-2.7/rdesigneur/__init__.py -> /usr/local/lib/python2.7/dist-packages/rdesigneur
copying build/lib.linux-x86_64-2.7/rdesigneur/rdesigneurProtos.py -> /usr/local/lib/python2.7/dist-packages/rdesigneur
creating /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/hdfutil.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/recording.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/methods_utils.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/merge.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/graph_utils.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/print_utils.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/_moose.so -> /usr/local/lib/python2.7/dist-packages/moose
creating /usr/local/lib/python2.7/dist-packages/moose/chemUtil
copying build/lib.linux-x86_64-2.7/moose/chemUtil/chemConnectUtil.py -> /usr/local/lib/python2.7/dist-packages/moose/chemUtil
copying build/lib.linux-x86_64-2.7/moose/chemUtil/graphUtils.py -> /usr/local/lib/python2.7/dist-packages/moose/chemUtil
copying build/lib.linux-x86_64-2.7/moose/chemUtil/add_Delete_ChemicalSolver.py -> /usr/local/lib/python2.7/dist-packages/moose/chemUtil
copying build/lib.linux-x86_64-2.7/moose/chemUtil/__init__.py -> /usr/local/lib/python2.7/dist-packages/moose/chemUtil
copying build/lib.linux-x86_64-2.7/moose/moose_constants.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/verification_utils.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/add_Delete_ChemicalSolver.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/constants.py -> /usr/local/lib/python2.7/dist-packages/moose
creating /usr/local/lib/python2.7/dist-packages/moose/genesis
copying build/lib.linux-x86_64-2.7/moose/genesis/writeKkit.py -> /usr/local/lib/python2.7/dist-packages/moose/genesis
copying build/lib.linux-x86_64-2.7/moose/genesis/__init__.py -> /usr/local/lib/python2.7/dist-packages/moose/genesis
creating /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/neuroml/ChannelML.py -> /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/neuroml/NeuroML.py -> /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/neuroml/__init__.py -> /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/neuroml/utils.py -> /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/neuroml/MorphML.py -> /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/neuroml/NetworkML.py -> /usr/local/lib/python2.7/dist-packages/moose/neuroml
copying build/lib.linux-x86_64-2.7/moose/moose_config.py -> /usr/local/lib/python2.7/dist-packages/moose
creating /usr/local/lib/python2.7/dist-packages/moose/merge
copying build/lib.linux-x86_64-2.7/moose/merge/mtypes.py -> /usr/local/lib/python2.7/dist-packages/moose/merge
copying build/lib.linux-x86_64-2.7/moose/merge/merge.py -> /usr/local/lib/python2.7/dist-packages/moose/merge
copying build/lib.linux-x86_64-2.7/moose/graphutil.py -> /usr/local/lib/python2.7/dist-packages/moose
creating /usr/local/lib/python2.7/dist-packages/moose/SBML
copying build/lib.linux-x86_64-2.7/moose/SBML/readSBML.py -> /usr/local/lib/python2.7/dist-packages/moose/SBML
copying build/lib.linux-x86_64-2.7/moose/SBML/validation.py -> /usr/local/lib/python2.7/dist-packages/moose/SBML
copying build/lib.linux-x86_64-2.7/moose/SBML/writeSBML.py -> /usr/local/lib/python2.7/dist-packages/moose/SBML
copying build/lib.linux-x86_64-2.7/moose/SBML/__init__.py -> /usr/local/lib/python2.7/dist-packages/moose/SBML
copying build/lib.linux-x86_64-2.7/moose/plot_utils.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/sim_utils.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/moose.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/__init__.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/alternate.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/optimizer_interface.py -> /usr/local/lib/python2.7/dist-packages/moose
copying build/lib.linux-x86_64-2.7/moose/utils.py -> /usr/local/lib/python2.7/dist-packages/moose
byte-compiling /usr/local/lib/python2.7/dist-packages/rdesigneur/rdesigneur.py to rdesigneur.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/rdesigneur/rmoogli.py to rmoogli.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/rdesigneur/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/rdesigneur/rdesigneurProtos.py to rdesigneurProtos.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/hdfutil.py to hdfutil.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/recording.py to recording.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/methods_utils.py to methods_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/merge.py to merge.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/graph_utils.py to graph_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/print_utils.py to print_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/chemUtil/chemConnectUtil.py to chemConnectUtil.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/chemUtil/graphUtils.py to graphUtils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/chemUtil/add_Delete_ChemicalSolver.py to add_Delete_ChemicalSolver.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/chemUtil/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/moose_constants.py to moose_constants.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/verification_utils.py to verification_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/add_Delete_ChemicalSolver.py to add_Delete_ChemicalSolver.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/constants.py to constants.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/genesis/writeKkit.py to writeKkit.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/genesis/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/neuroml/ChannelML.py to ChannelML.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/neuroml/NeuroML.py to NeuroML.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/neuroml/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/neuroml/utils.py to utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/neuroml/MorphML.py to MorphML.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/neuroml/NetworkML.py to NetworkML.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/moose_config.py to moose_config.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/merge/mtypes.py to mtypes.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/merge/merge.py to merge.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/graphutil.py to graphutil.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/SBML/readSBML.py to readSBML.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/SBML/validation.py to validation.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/SBML/writeSBML.py to writeSBML.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/SBML/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/plot_utils.py to plot_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/sim_utils.py to sim_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/moose.py to moose.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/alternate.py to alternate.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/optimizer_interface.py to optimizer_interface.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/moose/utils.py to utils.pyc
running install_egg_info
Writing /usr/local/lib/python2.7/dist-packages/moose-3.1.0_358_g07fc0f9-py2.7.egg-info
dilawars@ghevar ~/Work/GITHUB/BhallaLab/moose-core/_build (master) $
unset PYTHONPATH
dilawars@ghevar ~/Work/GITHUB/BhallaLab/moose-core/_build (master) $
python
Python 2.7.6 (default, Oct 26 2016, 20:30:19) 
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
i>>> 
>>> import moose
>>> print moose.__file__
/usr/local/lib/python2.7/dist-packages/moose/__init__.pyc

        I suspect that PYTHONPATH are messed up on this machine or python is not searching /usr/local/lib/python2.7/dist-package .

        I tried it on a fresh virtualbox machine as well. May be you can attach the full installation log.

      • Sahil Moza
        Sahil Moza @sahil ·
        Author Owner

        Created by: ChakrapaniNCBS

        Python looks fine, because other installed modules are importing well. I have python version 2.7.12, Ubuntu 16.04.2 LTS" OS I noticed that, during 'make' there is some error while creating link to ../python/moose/_moose.so Please find the make logs below

        Scanning dependencies of target device [ 81%] Building CXX object device/CMakeFiles/device.dir/PulseGen.cpp.o [ 81%] Building CXX object device/CMakeFiles/device.dir/DiffAmp.cpp.o [ 82%] Building CXX object device/CMakeFiles/device.dir/PIDController.cpp.o [ 82%] Building CXX object device/CMakeFiles/device.dir/RC.cpp.o [ 83%] Linking CXX static library libdevice.a [ 83%] Built target device Scanning dependencies of target benchmarks [ 83%] Building CXX object benchmarks/CMakeFiles/benchmarks.dir/benchmarks.cpp.o [ 84%] Building CXX object benchmarks/CMakeFiles/benchmarks.dir/kineticMarks.cpp.o [ 84%] Linking CXX static library libbenchmarks.a [ 84%] Built target benchmarks Scanning dependencies of target kinetics [ 84%] Building CXX object kinetics/CMakeFiles/kinetics.dir/PoolBase.cpp.o [ 85%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Pool.cpp.o [ 85%] Building CXX object kinetics/CMakeFiles/kinetics.dir/BufPool.cpp.o [ 85%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReacBase.cpp.o [ 86%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Reac.cpp.o [ 86%] Building CXX object kinetics/CMakeFiles/kinetics.dir/EnzBase.cpp.o [ 87%] Building CXX object kinetics/CMakeFiles/kinetics.dir/CplxEnzBase.cpp.o [ 87%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Enz.cpp.o [ 87%] Building CXX object kinetics/CMakeFiles/kinetics.dir/MMenz.cpp.o [ 88%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Species.cpp.o [ 88%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadKkit.cpp.o [ 89%] Building CXX object kinetics/CMakeFiles/kinetics.dir/WriteKkit.cpp.o [ 89%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadCspace.cpp.o [ 90%] Building CXX object kinetics/CMakeFiles/kinetics.dir/lookupVolumeFromMesh.cpp.o [ 90%] Building CXX object kinetics/CMakeFiles/kinetics.dir/testKinetics.cpp.o [ 90%] Linking CXX static library libkinetics.a [ 90%] Built target kinetics Scanning dependencies of target synapse [ 91%] Building CXX object synapse/CMakeFiles/synapse.dir/GraupnerBrunel2012CaPlasticitySynHandler.cpp.o [ 91%] Building CXX object synapse/CMakeFiles/synapse.dir/SimpleSynHandler.cpp.o [ 91%] Building CXX object synapse/CMakeFiles/synapse.dir/testSynapse.cpp.o [ 92%] Building CXX object synapse/CMakeFiles/synapse.dir/SynHandlerBase.cpp.o [ 92%] Building CXX object synapse/CMakeFiles/synapse.dir/RollingMatrix.cpp.o [ 93%] Building CXX object synapse/CMakeFiles/synapse.dir/STDPSynHandler.cpp.o [ 93%] Building CXX object synapse/CMakeFiles/synapse.dir/STDPSynapse.cpp.o [ 93%] Building CXX object synapse/CMakeFiles/synapse.dir/Synapse.cpp.o [ 94%] Building CXX object synapse/CMakeFiles/synapse.dir/SeqSynHandler.cpp.o In file included from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParserStack.h:35:0, from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParserBase.h:39, from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParser.h:32, from /home/bhalla/moose/moose-core/synapse/SeqSynHandler.cpp:17: /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pCallback; ^ In file included from /usr/include/c++/5/memory:81:0, from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParserBase.h:33, from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParser.h:32, from /home/bhalla/moose/moose-core/synapse/SeqSynHandler.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^ In file included from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParser.h:32:0, from /home/bhalla/moose/moose-core/synapse/SeqSynHandler.cpp:17: /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object. ^ In file included from /usr/include/c++/5/memory:81:0, from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParserBase.h:33, from /home/bhalla/moose/moose-core/synapse/../external/muparser/include/muParser.h:32, from /home/bhalla/moose/moose-core/synapse/SeqSynHandler.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^ [ 94%] Linking CXX static library libsynapse.a [ 94%] Built target synapse Scanning dependencies of target libmoose [ 94%] Building CXX object CMakeFiles/libmoose.dir/basecode/main.cpp.o [ 95%] Linking CXX shared library libmoose.so builtins/libmoose_builtins.a(testNSDF.cpp.o): In function testCreateStringDataset()': testNSDF.cpp:(.text+0x6b): warning: the use of tmpnam' is dangerous, better use mkstemp' [ 95%] Built target libmoose Scanning dependencies of target moose.bin [ 95%] Building CXX object CMakeFiles/moose.bin.dir/basecode/main.cpp.o [ 96%] Linking CXX executable moose.bin [ 96%] Built target moose.bin Scanning dependencies of target copy_python_files [ 97%] Copying required python files and other files to build directory [ 97%] Built target copy_python_files Scanning dependencies of target _moose [ 97%] Building CXX object pymoose/CMakeFiles/_moose.dir/moosemodule.cpp.o [ 97%] Building CXX object pymoose/CMakeFiles/_moose.dir/vec.cpp.o [ 98%] Building CXX object pymoose/CMakeFiles/_moose.dir/mfield.cpp.o [ 98%] Building CXX object pymoose/CMakeFiles/_moose.dir/pymooseinit.cpp.o [ 99%] Building CXX object pymoose/CMakeFiles/_moose.dir/melement.cpp.o [ 99%] Building CXX object pymoose/CMakeFiles/_moose.dir/test_moosemodule.cpp.o [ 99%] Building CXX object pymoose/CMakeFiles/_moose.dir/PyRun.cpp.o [100%] Linking CXX shared module ../python/moose/_moose.so ../builtins/libmoose_builtins.a(testNSDF.cpp.o): In function testCreateStringDataset()': testNSDF.cpp:(.text+0x6b): warning: the use of tmpnam' is dangerous, better use mkstemp' [100%] Built target _moose

        • ctest -output-on-failure Test project /home/bhalla/moose/__moose-core_build Start 1: moose.bin-raw-run 1/13 Test #1 (closed): moose.bin-raw-run .................. Passed 0.02 sec Start 2: pymoose-test-synchan 2/13 Test #2 (closed): pymoose-test-synchan ...............***Failed 0.01 sec Start 3: pymoose-test-function 3/13 Test #3 (closed): pymoose-test-function ..............***Failed 0.10 sec Start 4: pymoose-test-vec 4/13 Test #4 (closed): pymoose-test-vec ...................***Failed 0.01 sec Start 5: pymoose-pyrun 5/13 Test #5 (closed): pymoose-pyrun ......................***Failed 0.01 sec Start 6: pymoose-neuroml-reader-test 6/13 Test #6 (closed): pymoose-neuroml-reader-test ........***Failed 0.01 sec Start 7: pymoose-nsdf-sanity-test 7/13 Test #7 (closed): pymoose-nsdf-sanity-test ...........***Failed 0.14 sec Start 8: pymoose-ksolve-test 8/13 Test #8 (closed): pymoose-ksolve-test ................***Failed 0.11 sec Start 9: pymoose-test-basic-sbml-support 9/13 Test #9 (closed): pymoose-test-basic-sbml-support ....***Failed 0.01 sec Start 10: pymoose-test-rng 10/13 Test #10 (closed): pymoose-test-rng ...................***Failed 0.04 sec Start 11: pymoose-test-streamer 11/13 Test #11 (closed): pymoose-test-streamer ..............***Failed 0.01 sec Start 12: pymoose-test-streaming_in_tables 12/13 Test #12 (closed): pymoose-test-streaming_in_tables ...***Failed 0.01 sec Start 13: pymoose-test-kkit 13/13 Test #13 (closed): pymoose-test-kkit ..................***Failed 0.37 sec

        8% tests passed, 12 tests failed out of 13

        Total Test time (real) = 0.85 sec

        The following tests FAILED: 2 - pymoose-test-synchan (Failed) 3 - pymoose-test-function (Failed) 4 - pymoose-test-vec (Failed) 5 - pymoose-pyrun (Failed) 6 - pymoose-neuroml-reader-test (Failed) 7 - pymoose-nsdf-sanity-test (Failed) 8 - pymoose-ksolve-test (Failed) 9 - pymoose-test-basic-sbml-support (Failed) 10 - pymoose-test-rng (Failed) 11 - pymoose-test-streamer (Failed) 12 - pymoose-test-streaming_in_tables (Failed) 13 - pymoose-test-kkit (Failed) Errors while running CTest

        • echo 'Some tests failed' Some tests failed
        • make install [ 4%] Built target intfire [ 14%] Built target basecode [ 18%] Built target msg [ 22%] Built target shell [ 28%] Built target randnum [ 29%] Built target scheduling [ 46%] Built target biophysics [ 55%] Built target moose_builtins [ 59%] Built target utility [ 64%] Built target mesh [ 65%] Built target moose_mpi [ 66%] Built target signeur [ 74%] Built target ksolve [ 79%] Built target hsolve [ 81%] Built target diffusion [ 83%] Built target device [ 84%] Built target benchmarks [ 90%] Built target kinetics [ 94%] Built target synapse [ 95%] Built target libmoose [ 96%] Built target moose.bin [ 97%] Copying required python files and other files to build directory [ 97%] Built target copy_python_files [100%] Built target _moose Install the project... -- Install configuration: "Release" -- Installing: /home/bhalla/moose/__moose-core_install/bin/moose.bin -- Set runtime path of "/home/bhalla/moose/__moose-core_install/bin/moose.bin" to "" -- Installing: /home/bhalla/moose/__moose-core_install/lib/libmoose.so -- Set runtime path of "/home/bhalla/moose/__moose-core_install/lib/libmoose.so" to "" -- Installing: /home/bhalla/moose/__moose-core_install/bin/moose running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/rdesigneur

        Please suggest.

        Thanks, Chakrapani

      • Sahil Moza
        Sahil Moza @sahil ·
        Author Owner

        Created by: dilawar

        I am failing to reproduce this on 16.04 also. Can you post the __moose-core_build/CMakeCache.txt file. It must be in the same folder where you building.

      • Sahil Moza
        Sahil Moza @sahil ·
        Author Owner

        Created by: ChakrapaniNCBS

        File attached. CMakeCache.txt Also there is no error during cmake. file is attached moose-cmake.txt

        Thanks

      • Sahil Moza
        Sahil Moza @sahil ·
        Author Owner

        Created by: dilawar

        I think this has been fixed.

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