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pylada / pylada-light

A physics computational framework for python and ipython
GNU General Public License v3.0
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Python 3.6 compatibility problem #22

Closed samtsevich closed 6 years ago

samtsevich commented 6 years ago

I tried to install pylada via pip on different machines (Mac and CentOS). On both of them installed python3.6. For both cases I got:

    [ 37%] Building CXX object crystal/CMakeFiles/cutilities.dir/smith_normal_form.cc.o
    In file included from /private/var/folders/kw/ctt8d34s3cs6y_pg9nq3p3mrbjlb91/T/pip-t4402nwy-build/crystal/smith_normal_form.cc:26:
    In file included from /private/var/folders/kw/ctt8d34s3cs6y_pg9nq3p3mrbjlb91/T/pip-t4402nwy-build/crystal/cutilities.h:4:
    In file included from /private/var/folders/kw/ctt8d34s3cs6y_pg9nq3p3mrbjlb91/T/pip-t4402nwy-build/crystal/types.h:29:
    /usr/local/include/eigen3/Eigen/Core:273:10: fatal error: 'type_traits' file not found
    #include <type_traits>
             ^~~~~~~~~~~~~
    1 error generated.
    make[2]: *** [crystal/CMakeFiles/cutilities.dir/smith_normal_form.cc.o] Error 1
    make[1]: *** [crystal/CMakeFiles/cutilities.dir/all] Error 2
    make: *** [all] Error 2
    error: command '/usr/local/bin/cmake' failed with exit status 2

Any ideas what can be wrong?

mdavezac commented 6 years ago

That's a bit weird, type_traits is a header from the standard C++ library. Do you know what compiler you are using?

samtsevich commented 6 years ago

Just checked. I used c++ compilator from Xcode.

-- 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
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ --version
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Maybe I should specify Intel C compiler because Intel Fortran used for the same compilation of pylada package?

mdavezac commented 6 years ago

I don't think it's Fortran. CMake should pick up which ever Fortran you have. I have used gfortran (from gcc suite) with llvm c++ compilers (!= gcc) in the past. cMore likely, CMake is not picking up or passing on C++11 flags. I can reproduce similar errors on my Mac. I'll take a look.

Do you have CC or cxx line similar to the one you sent above? cc is for C.

mdavezac commented 6 years ago

Sorry, just saw the C++ line you already sent :)

samtsevich commented 6 years ago

Thanks. Actually, have no idea what can go wrong here and why. I hope you can help me or suggest the way how I can solve it myself.

mdavezac commented 6 years ago

I think I've solved the issue on Mac. On centos, do you know what compiler you are using?

mdavezac commented 6 years ago

Please retry installing on mac from the master branch

samtsevich commented 6 years ago

Just tried, but got such kind of error:

cmake .. -DPYTHON_EXECUTABLE:FILEPATH=/opt/intel/intelpython3/bin/python3
-- The C compiler identification is AppleClang 9.0.0.9000039
-- The CXX compiler identification is AppleClang 9.0.0.9000039
-- The Fortran compiler identification is Intel 18.0.1.20171018
-- 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
-- Check for working Fortran compiler: /usr/local/bin/ifort
-- Check for working Fortran compiler: /usr/local/bin/ifort  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/bin/ifort supports Fortran 90
-- Checking whether /usr/local/bin/ifort supports Fortran 90 -- yes
-- [GreatCMakeCookOff] not found. Will attempt to clone it.
-- Found Git: /usr/local/bin/git (found version "2.16.1") 
-- [GreatCMakeCookOff] downloaded to /Users/artem.samtsevich/dev/pylada-light/build/external/src/GreatCMakeCookOff
-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Performing Test has_std_cpp11
-- Performing Test has_std_cpp11 - Success
-- Performing Test has_std_cpp0x
-- Performing Test has_std_cpp0x - Success
-- Found Eigen3
-- Found PythonInterp: /opt/intel/intelpython3/bin/python3 (found version "3.6.3") 
-- Found pytest: /opt/intel/intelpython3/lib/python3.6/site-packages (found version "3.4.0") 
-- Python module runipy could not be found. (missing: runipy_LOCATION) 
-- Will now attempt to install runipy locally
-- Found runipy: /Users/artem.samtsevich/dev/pylada-light/build/external/python/runipy-0.1.5-py3.6.egg/runipy (found version "0.1.5") 
-- Found pytest_bdd: /opt/intel/intelpython3/lib/python3.6/site-packages/pytest_bdd (found version "2.20.0") 
-- Found mpi4py: /opt/intel/intelpython3/lib/python3.6/site-packages/mpi4py (found version "3.0.0") 
-- Found numpy: /opt/intel/intelpython3/lib/python3.6/site-packages/numpy (found version "1.13.3") 
-- Found quantities: /opt/intel/intelpython3/lib/python3.6/site-packages/quantities (found version "0.12.1") 
-- Found f90nml: /opt/intel/intelpython3/lib/python3.6/site-packages/f90nml (found version "1.0.2") 
-- Found six: /opt/intel/intelpython3/lib/python3.6/site-packages (found version "1.10.0") 
-- Found traitlets: /opt/intel/intelpython3/lib/python3.6/site-packages/traitlets (found version "4.3.2") 
-- Found cython: /opt/intel/intelpython3/lib/python3.6/site-packages (found version "0.27.1") 
-- Found NumpyLibrary: /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include (found version "1.13.3") 
-- Python install path (PYTHON_PKG_DIR): /opt/intel/intelpython3/lib/python3.6/site-packages
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/artem.samtsevich/dev/pylada-light/build
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ sudo make
Password:
Scanning dependencies of target lookup_dependencies
[  0%] Built target lookup_dependencies
Scanning dependencies of target pylada_error
[  0%] Built target pylada_error
[  2%] Generating c/c++ source _coordination_shells.pyx with cython ()
Scanning dependencies of target pylada.crystal._coordination_shells-cython
[  5%] Building CXX object crystal/CMakeFiles/pylada.crystal._coordination_shells-cython.dir/cython__coordination_shells.cc.o
[  8%] Linking CXX shared module ../python_package/pylada/crystal/_coordination_shells.so
[  8%] Built target pylada.crystal._coordination_shells-cython
Scanning dependencies of target cutilities
[ 11%] Building CXX object crystal/CMakeFiles/cutilities.dir/smith_normal_form.cc.o
[ 14%] Building CXX object crystal/CMakeFiles/cutilities.dir/gruber.cc.o
[ 17%] Building CXX object crystal/CMakeFiles/cutilities.dir/noopt.cc.o
[ 20%] Linking CXX static library libcutilities.a
[ 20%] Built target cutilities
[ 22%] Generating c/c++ source cutilities.pyx with cython ()
Scanning dependencies of target pylada.crystal.cutilities-cython
[ 25%] Building CXX object crystal/CMakeFiles/pylada.crystal.cutilities-cython.dir/cython_cutilities.cc.o
In file included from /Users/artem.samtsevich/dev/pylada-light/build/crystal/cython_cutilities.cc:531:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1811:
/opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
[ 28%] Linking CXX shared module ../python_package/pylada/crystal/cutilities.so
[ 28%] Built target pylada.crystal.cutilities-cython
[ 31%] Generating c/c++ source _primitive.pyx with cython ()
Scanning dependencies of target pylada.crystal._primitive-cython
[ 34%] Building CXX object crystal/CMakeFiles/pylada.crystal._primitive-cython.dir/cython__primitive.cc.o
[ 37%] Linking CXX shared module ../python_package/pylada/crystal/_primitive.so
[ 37%] Built target pylada.crystal._primitive-cython
[ 40%] Generating c/c++ source _space_group.pyx with cython ()
Scanning dependencies of target pylada.crystal._space_group-cython
[ 42%] Building CXX object crystal/CMakeFiles/pylada.crystal._space_group-cython.dir/cython__space_group.cc.o
In file included from /Users/artem.samtsevich/dev/pylada-light/build/crystal/cython__space_group.cc:531:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1811:
/opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
[ 45%] Linking CXX shared module ../python_package/pylada/crystal/_space_group.so
[ 45%] Built target pylada.crystal._space_group-cython
[ 48%] Generating c/c++ source _map_sites.pyx with cython ()
Scanning dependencies of target pylada.crystal._map_sites-cython
[ 51%] Building CXX object crystal/CMakeFiles/pylada.crystal._map_sites-cython.dir/cython__map_sites.cc.o
[ 54%] Linking CXX shared module ../python_package/pylada/crystal/_map_sites.so
[ 54%] Built target pylada.crystal._map_sites-cython
Scanning dependencies of target pylada.crystal
[ 54%] Built target pylada.crystal
Scanning dependencies of target third_order
[ 57%] Building CXX object crystal/defects/CMakeFiles/third_order.dir/third_order.cc.o
[ 60%] Linking CXX static library libthird_order.a
[ 60%] Built target third_order
[ 62%] Generating c/c++ source cutilities.pyx with cython ()
Scanning dependencies of target pylada.crystal.defects.cutilities-cython
[ 65%] Building CXX object crystal/defects/CMakeFiles/pylada.crystal.defects.cutilities-cython.dir/cython_cutilities.cc.o
[ 68%] Linking CXX shared module ../../python_package/pylada/crystal/defects/cutilities.so
[ 68%] Built target pylada.crystal.defects.cutilities-cython
Scanning dependencies of target pylada.crystal.defects
[ 68%] Built target pylada.crystal.defects
Scanning dependencies of target pylada.crystal.tests
[ 68%] Built target pylada.crystal.tests
Scanning dependencies of target ewaldf90
[ 71%] Building Fortran object ewald/CMakeFiles/ewaldf90.dir/ep_com.f90.o
[ 74%] Building CXX object ewald/CMakeFiles/ewaldf90.dir/erfc.cc.o
[ 77%] Building Fortran object ewald/CMakeFiles/ewaldf90.dir/ewaldf.f90.o
[ 80%] Building CXX object ewald/CMakeFiles/ewaldf90.dir/ewald.cc.o
[ 82%] Linking CXX static library libewaldf90.a
[ 82%] Built target ewaldf90
[ 85%] Generating c/c++ source ewald.pyx with cython ()
Scanning dependencies of target pylada.ewald-cython
[ 88%] Building CXX object ewald/CMakeFiles/pylada.ewald-cython.dir/cython_ewald.cc.o
[ 91%] Linking CXX shared module ../python_package/pylada/ewald.so
[ 91%] Built target pylada.ewald-cython
Scanning dependencies of target pylada
[ 91%] Built target pylada
Scanning dependencies of target pylada.physics
[ 91%] Built target pylada.physics
Scanning dependencies of target pylada.misc
[ 91%] Built target pylada.misc
Scanning dependencies of target pylada.tools
[ 91%] Built target pylada.tools
Scanning dependencies of target pylada.tools.input
[ 91%] Built target pylada.tools.input
Scanning dependencies of target pylada.tools.input.tests
[ 91%] Built target pylada.tools.input.tests
Scanning dependencies of target pylada.tools.tests
[ 91%] Built target pylada.tools.tests
Scanning dependencies of target pylada.ewald.tests
[ 91%] Built target pylada.ewald.tests
[ 94%] Generating c/c++ source _cutilities.pyx with cython ()
Scanning dependencies of target pylada.decorations._cutilities-cython
[ 97%] Building CXX object decorations/CMakeFiles/pylada.decorations._cutilities-cython.dir/cython__cutilities.cc.o
In file included from /Users/artem.samtsevich/dev/pylada-light/build/decorations/cython__cutilities.cc:531:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1811:
/opt/intel/intelpython3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
[100%] Linking CXX shared module ../python_package/pylada/decorations/_cutilities.so
[100%] Built target pylada.decorations._cutilities-cython
Scanning dependencies of target pylada.decorations
[100%] Built target pylada.decorations
Scanning dependencies of target pylada.decorations.tests
[100%] Built target pylada.decorations.tests
Scanning dependencies of target pylada.config
[100%] Built target pylada.config
Scanning dependencies of target pylada.periodic_table
[100%] Built target pylada.periodic_table
Scanning dependencies of target pylada.vasp
[100%] Built target pylada.vasp
Scanning dependencies of target pylada.vasp.incar
[100%] Built target pylada.vasp.incar
Scanning dependencies of target pylada.vasp.incar.tests
[100%] Built target pylada.vasp.incar.tests
Scanning dependencies of target pylada.vasp.extract
[100%] Built target pylada.vasp.extract
Scanning dependencies of target pylada.vasp.extract.tests
[100%] Built target pylada.vasp.extract.tests
Scanning dependencies of target pylada.vasp.nlep
[100%] Built target pylada.vasp.nlep
Scanning dependencies of target pylada.vasp.tests
[100%] Built target pylada.vasp.tests
Scanning dependencies of target pylada.process
[100%] Built target pylada.process
Scanning dependencies of target pylada.process.tests
[100%] Built target pylada.process.tests
Scanning dependencies of target pylada.jobfolder
[100%] Built target pylada.jobfolder
Scanning dependencies of target pylada.jobfolder.tests
[100%] Built target pylada.jobfolder.tests
Scanning dependencies of target pylada.ipython
[100%] Built target pylada.ipython
Scanning dependencies of target pylada.ipython.launch
[100%] Built target pylada.ipython.launch
Scanning dependencies of target pylada.ipython.tests
[100%] Built target pylada.ipython.tests
Scanning dependencies of target pylada.espresso
[100%] Built target pylada.espresso
Scanning dependencies of target pylada.espresso.tests
[100%] Built target pylada.espresso.tests
Scanning dependencies of target pylada.espresso.tests.bdd
[100%] Built target pylada.espresso.tests.bdd
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ 
artem.samtsevich:build$ make test
Running tests...
Test project /Users/artem.samtsevich/dev/pylada-light/build
      Start  1: pylada.crystal.atom
 1/83 Test  #1: pylada.crystal.atom ..........................***Failed    0.56 sec
      Start  2: pylada.crystal.cellinvariants
 2/83 Test  #2: pylada.crystal.cellinvariants ................***Failed    0.49 sec
      Start  3: pylada.crystal.coordination_shells
 3/83 Test  #3: pylada.crystal.coordination_shells ...........***Failed    0.46 sec
      Start  4: pylada.crystal.cutilities
 4/83 Test  #4: pylada.crystal.cutilities ....................***Failed    0.49 sec
      Start  5: pylada.crystal.hart-forcade
 5/83 Test  #5: pylada.crystal.hart-forcade ..................***Failed    0.49 sec
      Start  6: pylada.crystal.map_sites
 6/83 Test  #6: pylada.crystal.map_sites .....................***Failed    0.46 sec
      Start  7: pylada.crystal.neighbors
 7/83 Test  #7: pylada.crystal.neighbors .....................***Failed    0.47 sec
      Start  8: pylada.crystal.primitive
 8/83 Test  #8: pylada.crystal.primitive .....................***Failed    0.47 sec
      Start  9: pylada.crystal.space_group
 9/83 Test  #9: pylada.crystal.space_group ...................***Failed    0.46 sec
      Start 10: pylada.crystal.splitconfigs
10/83 Test #10: pylada.crystal.splitconfigs ..................***Failed    0.47 sec
      Start 11: pylada.crystal.structure
11/83 Test #11: pylada.crystal.structure .....................***Failed    0.48 sec
      Start 12: pylada.crystal.supercell
12/83 Test #12: pylada.crystal.supercell .....................***Failed    0.48 sec
      Start 13: pylada.crystal.third_order
13/83 Test #13: pylada.crystal.third_order ...................***Failed    0.46 sec
      Start 14: pylada.crystal.utilities
14/83 Test #14: pylada.crystal.utilities .....................***Failed    0.46 sec
      Start 15: pylada.crystal.which_site
15/83 Test #15: pylada.crystal.which_site ....................***Failed    0.46 sec
      Start 16: pylada.crystal.write_gulp
16/83 Test #16: pylada.crystal.write_gulp ....................***Failed    0.46 sec
      Start 17: pylada.tools.input.keywords
17/83 Test #17: pylada.tools.input.keywords ..................***Failed    0.48 sec
      Start 18: pylada.tools.input.listblock
18/83 Test #18: pylada.tools.input.listblock .................***Failed    0.47 sec
      Start 19: pylada.tools.input.tree
19/83 Test #19: pylada.tools.input.tree ......................***Failed    0.48 sec
      Start 20: pylada.tools.makeclass
20/83 Test #20: pylada.tools.makeclass .......................***Failed    0.47 sec
      Start 21: pylada.ewald.ewald
21/83 Test #21: pylada.ewald.ewald ...........................***Failed    0.56 sec
      Start 22: pylada.decorations.fciterator
22/83 Test #22: pylada.decorations.fciterator ................***Failed    0.67 sec
      Start 23: pylada.decorations.lexcompare
23/83 Test #23: pylada.decorations.lexcompare ................***Failed    0.59 sec
      Start 24: pylada.decorations.supercells
24/83 Test #24: pylada.decorations.supercells ................***Failed    0.64 sec
      Start 25: pylada.decorations.defects
25/83 Test #25: pylada.decorations.defects ...................***Failed    0.74 sec
      Start 26: pylada.decorations.generator
26/83 Test #26: pylada.decorations.generator .................***Failed    0.55 sec
      Start 27: pylada.decorations.ndimiterator
27/83 Test #27: pylada.decorations.ndimiterator ..............***Failed    0.84 sec
      Start 28: pylada.decorations.transform
28/83 Test #28: pylada.decorations.transform .................***Failed    0.50 sec
      Start 29: pylada.vasp.incar.choices
29/83 Test #29: pylada.vasp.incar.choices ....................***Failed    0.48 sec
      Start 30: pylada.vasp.incar.incar_algo
30/83 Test #30: pylada.vasp.incar.incar_algo .................***Failed    0.81 sec
      Start 31: pylada.vasp.incar.magmom
31/83 Test #31: pylada.vasp.incar.magmom .....................***Failed    0.62 sec
      Start 32: pylada.vasp.incar.nelect
32/83 Test #32: pylada.vasp.incar.nelect .....................***Failed    0.62 sec
      Start 33: pylada.vasp.incar.npar
33/83 Test #33: pylada.vasp.incar.npar .......................***Failed    0.62 sec
      Start 34: pylada.vasp.incar.others
34/83 Test #34: pylada.vasp.incar.others .....................***Failed    0.74 sec
      Start 35: pylada.vasp.incar.relax
35/83 Test #35: pylada.vasp.incar.relax ......................***Failed    0.63 sec
      Start 36: pylada.vasp.incar.restart
36/83 Test #36: pylada.vasp.incar.restart ....................***Failed    0.57 sec
      Start 37: pylada.vasp.incar.smearing
37/83 Test #37: pylada.vasp.incar.smearing ...................***Failed    0.54 sec
      Start 38: pylada.vasp.incar.uparams
38/83 Test #38: pylada.vasp.incar.uparams ....................***Failed    0.50 sec
      Start 39: pylada.vasp.extract.common
39/83 Test #39: pylada.vasp.extract.common ...................***Failed    0.54 sec
      Start 40: pylada.vasp.extract.dft
40/83 Test #40: pylada.vasp.extract.dft ......................***Failed    0.56 sec
      Start 41: pylada.vasp.algo
41/83 Test #41: pylada.vasp.algo .............................***Failed    0.61 sec
      Start 42: pylada.vasp.copyfiles
42/83 Test #42: pylada.vasp.copyfiles ........................***Failed    0.74 sec
      Start 43: pylada.vasp.ediff
43/83 Test #43: pylada.vasp.ediff ............................***Failed    0.59 sec
      Start 44: pylada.vasp.encut
44/83 Test #44: pylada.vasp.encut ............................***Failed    0.54 sec
      Start 45: pylada.vasp.incar
45/83 Test #45: pylada.vasp.incar ............................***Failed    0.55 sec
      Start 46: pylada.vasp.lsorbit
46/83 Test #46: pylada.vasp.lsorbit ..........................***Failed    0.56 sec
      Start 47: pylada.vasp.magmom_attribute
47/83 Test #47: pylada.vasp.magmom_attribute .................***Failed    0.51 sec
      Start 48: pylada.vasp.parse
48/83 Test #48: pylada.vasp.parse ............................***Failed    0.53 sec
      Start 49: pylada.vasp.relax_attribute
49/83 Test #49: pylada.vasp.relax_attribute ..................***Failed    0.52 sec
      Start 50: pylada.vasp.run
50/83 Test #50: pylada.vasp.run ..............................***Failed    0.53 sec
      Start 51: pylada.vasp.runepi
51/83 Test #51: pylada.vasp.runepi ...........................***Failed    0.56 sec
      Start 52: pylada.vasp.runepidoc
52/83 Test #52: pylada.vasp.runepidoc ........................***Failed    0.57 sec
      Start 53: pylada.vasp.runmass
53/83 Test #53: pylada.vasp.runmass ..........................***Failed    0.60 sec
      Start 54: pylada.vasp.runrelax
54/83 Test #54: pylada.vasp.runrelax .........................***Failed    0.68 sec
      Start 55: pylada.vasp.species
55/83 Test #55: pylada.vasp.species ..........................***Failed    0.57 sec
      Start 56: pylada.vasp.system
56/83 Test #56: pylada.vasp.system ...........................***Failed    0.53 sec
      Start 57: pylada.vasp.uparams_attribute
57/83 Test #57: pylada.vasp.uparams_attribute ................***Failed    0.53 sec
      Start 58: pylada.vasp.vasp_keywords
58/83 Test #58: pylada.vasp.vasp_keywords ....................***Failed    0.59 sec
      Start 59: pylada.vasp.vasp_nelect
59/83 Test #59: pylada.vasp.vasp_nelect ......................***Failed    0.54 sec
      Start 60: pylada.vasp.vasp_restart
60/83 Test #60: pylada.vasp.vasp_restart .....................***Failed    0.47 sec
      Start 61: pifunctional
61/83 Test #61: pifunctional .................................***Failed    0.10 sec
      Start 62: pylada.process.call
62/83 Test #62: pylada.process.call ..........................***Failed    0.47 sec
      Start 63: pylada.process.iterator
63/83 Test #63: pylada.process.iterator ......................***Failed    0.46 sec
      Start 64: pylada.process.program
64/83 Test #64: pylada.process.program .......................***Failed    0.46 sec
      Start 65: pylada.process.pool
65/83 Test #65: pylada.process.pool ..........................***Failed    0.52 sec
      Start 66: pylada.process.jobfolder
66/83 Test #66: pylada.process.jobfolder .....................***Failed    0.49 sec
      Start 67: pylada.jobfolder.collect
67/83 Test #67: pylada.jobfolder.collect .....................***Failed    0.49 sec
      Start 68: pylada.jobfolder.forwardingdict
68/83 Test #68: pylada.jobfolder.forwardingdict ..............***Failed    0.47 sec
      Start 69: pylada.jobfolder.jobfolder
69/83 Test #69: pylada.jobfolder.jobfolder ...................***Failed    0.48 sec
      Start 70: pylada.jobfolder.jobparams
70/83 Test #70: pylada.jobfolder.jobparams ...................***Failed    0.50 sec
      Start 71: explore
71/83 Test #71: explore ......................................   Passed    0.76 sec
      Start 72: goto
72/83 Test #72: goto .........................................   Passed    0.64 sec
      Start 73: pylada.espresso.card
73/83 Test #73: pylada.espresso.card .........................***Failed    0.48 sec
      Start 74: pylada.espresso.extract
74/83 Test #74: pylada.espresso.extract ......................***Failed    0.54 sec
      Start 75: pylada.espresso.namelists
75/83 Test #75: pylada.espresso.namelists ....................***Failed    0.48 sec
      Start 76: pylada.espresso.pwscf
76/83 Test #76: pylada.espresso.pwscf ........................***Failed    0.52 sec
      Start 77: pylada.espresso.structure
77/83 Test #77: pylada.espresso.structure ....................***Failed    0.47 sec
      Start 78: pylada.espresso.trait_types
78/83 Test #78: pylada.espresso.trait_types ..................***Failed    0.45 sec
      Start 79: pylada.espresso.tests.bdd.restart
79/83 Test #79: pylada.espresso.tests.bdd.restart ............***Failed    0.46 sec
      Start 80: pylada.espresso.tests.bdd.single_run
80/83 Test #80: pylada.espresso.tests.bdd.single_run .........***Failed    0.49 sec
      Start 81: pylada.espresso.tests.bdd.writing_input
81/83 Test #81: pylada.espresso.tests.bdd.writing_input ......***Failed    0.50 sec
      Start 82: notebook_Creating_a_Job_Folder
82/83 Test #82: notebook_Creating_a_Job_Folder ...............   Passed    5.08 sec
      Start 83: notebook_IPython_high-throughput_interface
83/83 Test #83: notebook_IPython_high-throughput_interface ...   Passed    4.56 sec

5% tests passed, 79 tests failed out of 83

Label Time Summary:
crystal        =   7.62 sec*proc (16 tests)
decorations    =   4.53 sec*proc (7 tests)
espresso       =   4.39 sec*proc (9 tests)
ewald          =   0.56 sec*proc (1 test)
extract        =   1.10 sec*proc (2 tests)
incar          =   6.12 sec*proc (10 tests)
input          =   1.43 sec*proc (3 tests)
ipython        =   1.39 sec*proc (2 tests)
jobfolder      =   2.95 sec*proc (6 tests)
mpi            =   0.10 sec*proc (1 test)
notebook       =   9.64 sec*proc (2 tests)
process        =   2.51 sec*proc (6 tests)
pytest         =  41.88 sec*proc (78 tests)
python         =  53.02 sec*proc (83 tests)
tools          =   1.90 sec*proc (4 tests)
vasp           =  18.54 sec*proc (32 tests)

Total Test time (real) =  53.23 sec

The following tests FAILED:
      1 - pylada.crystal.atom (Failed)
      2 - pylada.crystal.cellinvariants (Failed)
      3 - pylada.crystal.coordination_shells (Failed)
      4 - pylada.crystal.cutilities (Failed)
      5 - pylada.crystal.hart-forcade (Failed)
      6 - pylada.crystal.map_sites (Failed)
      7 - pylada.crystal.neighbors (Failed)
      8 - pylada.crystal.primitive (Failed)
      9 - pylada.crystal.space_group (Failed)
     10 - pylada.crystal.splitconfigs (Failed)
     11 - pylada.crystal.structure (Failed)
     12 - pylada.crystal.supercell (Failed)
     13 - pylada.crystal.third_order (Failed)
     14 - pylada.crystal.utilities (Failed)
     15 - pylada.crystal.which_site (Failed)
     16 - pylada.crystal.write_gulp (Failed)
     17 - pylada.tools.input.keywords (Failed)
     18 - pylada.tools.input.listblock (Failed)
     19 - pylada.tools.input.tree (Failed)
     20 - pylada.tools.makeclass (Failed)
     21 - pylada.ewald.ewald (Failed)
     22 - pylada.decorations.fciterator (Failed)
     23 - pylada.decorations.lexcompare (Failed)
     24 - pylada.decorations.supercells (Failed)
     25 - pylada.decorations.defects (Failed)
     26 - pylada.decorations.generator (Failed)
     27 - pylada.decorations.ndimiterator (Failed)
     28 - pylada.decorations.transform (Failed)
     29 - pylada.vasp.incar.choices (Failed)
     30 - pylada.vasp.incar.incar_algo (Failed)
     31 - pylada.vasp.incar.magmom (Failed)
     32 - pylada.vasp.incar.nelect (Failed)
     33 - pylada.vasp.incar.npar (Failed)
     34 - pylada.vasp.incar.others (Failed)
     35 - pylada.vasp.incar.relax (Failed)
     36 - pylada.vasp.incar.restart (Failed)
     37 - pylada.vasp.incar.smearing (Failed)
     38 - pylada.vasp.incar.uparams (Failed)
     39 - pylada.vasp.extract.common (Failed)
     40 - pylada.vasp.extract.dft (Failed)
     41 - pylada.vasp.algo (Failed)
     42 - pylada.vasp.copyfiles (Failed)
     43 - pylada.vasp.ediff (Failed)
     44 - pylada.vasp.encut (Failed)
     45 - pylada.vasp.incar (Failed)
     46 - pylada.vasp.lsorbit (Failed)
     47 - pylada.vasp.magmom_attribute (Failed)
     48 - pylada.vasp.parse (Failed)
     49 - pylada.vasp.relax_attribute (Failed)
     50 - pylada.vasp.run (Failed)
     51 - pylada.vasp.runepi (Failed)
     52 - pylada.vasp.runepidoc (Failed)
     53 - pylada.vasp.runmass (Failed)
     54 - pylada.vasp.runrelax (Failed)
     55 - pylada.vasp.species (Failed)
     56 - pylada.vasp.system (Failed)
     57 - pylada.vasp.uparams_attribute (Failed)
     58 - pylada.vasp.vasp_keywords (Failed)
     59 - pylada.vasp.vasp_nelect (Failed)
     60 - pylada.vasp.vasp_restart (Failed)
     61 - pifunctional (Failed)
     62 - pylada.process.call (Failed)
     63 - pylada.process.iterator (Failed)
     64 - pylada.process.program (Failed)
     65 - pylada.process.pool (Failed)
     66 - pylada.process.jobfolder (Failed)
     67 - pylada.jobfolder.collect (Failed)
     68 - pylada.jobfolder.forwardingdict (Failed)
     69 - pylada.jobfolder.jobfolder (Failed)
     70 - pylada.jobfolder.jobparams (Failed)
     73 - pylada.espresso.card (Failed)
     74 - pylada.espresso.extract (Failed)
     75 - pylada.espresso.namelists (Failed)
     76 - pylada.espresso.pwscf (Failed)
     77 - pylada.espresso.structure (Failed)
     78 - pylada.espresso.trait_types (Failed)
     79 - pylada.espresso.tests.bdd.restart (Failed)
     80 - pylada.espresso.tests.bdd.single_run (Failed)
     81 - pylada.espresso.tests.bdd.writing_input (Failed)
Errors while running CTest
make: *** [test] Error 8

And it looks very strange. Any ideas?

mdavezac commented 6 years ago

Could you run ctest -V? that should tell us what the error is. I'm guessing some python package is missing.

samtsevich commented 6 years ago

@mdavezac Thanks. Now it passes tests. But, still, I cannot get how I should put pylada into necessary site-packages folder.

I compiled it myself via cmake.

mdavezac commented 6 years ago

If you want to install exactly the stuff in that folder, you could do

python setup.py install

Otherwise, pip install git+https://github.com/pylada/pylada-light should now work.

samtsevich commented 6 years ago

@mdavezac Cool! It works. Thanks a lot