[Espressomd-maintainer] Build failed in Jenkins: master-nightly-mac #60

[Jenkins Demon]

See <http://espressomd.org/jenkins/job/master-nightly-mac/60/changes>

Changes:

[Florian Weik] Added class to keep running average and variance.

[Florian Weik] Added new class to build system.

------------------------------------------
[...truncated 587 lines...]
                                                                         ^
1 warning generated.
  CXX      statistics_chain.lo
  CXX      statistics_cluster.lo
  CXX      statistics_correlation.lo
  CXX      statistics_fluid.lo
  CXX      statistics_molecule.lo
  CXX      statistics_observable.lo
  CXX      statistics_wallstuff.lo
In file included from statistics_observable.cpp:24:
In file included from ./pressure.hpp:32:
In file included from ./forces_inline.hpp:31:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
1  CXX      thermostat.lo
 warning generated.
  CXX      topology.lo
statistics_observable.cpp:576:9: warning: unused variable 'pdata_' 
[-Wunused-variable]
  void* pdata_ = self->container;
        ^
statistics_observable.cpp:577:16: warning: unused variable 'n_A' 
[-Wunused-variable]
  unsigned int n_A = self->n;
               ^
  CXX      tuning.lo
  CXX      uwerr.lo
  CXX      verlet.lo
  CXX      virtual_sites.lo
3 warnings generated.
  CXX      virtual_sites_com.lo
  CXX      virtual_sites_relative.lo
  CXX      vmdsock.lo
In file included from verlet.cpp:35:
In file included from ./forces.hpp:33:
In file included from ./actor/Actor.hpp:22:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
  CXX      ghmc.lo
In file included from virtual_sites.cpp:23:
In file included from ./pressure.hpp:32:
In file included from ./forces_inline.hpp:31:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
1 warning generated.
  CXX      integrate_sd.lo
In file included from ghmc.cpp:34:
In file included from ./energy.hpp:43:
In file included from ./actor/ActorList.hpp:23:
In file included from ./actor/Actor.hpp:22:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
  CXX      EspressoSystemInterface.lo
1 warning generated.
  CXX      PdbParser.lo
In file included from integrate_sd.cpp:47:
In file included from ./pressure.hpp:32:
In file included from ./forces_inline.hpp:31:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
In file included from EspressoSystemInterface.cpp:19:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
1 warning generated.
  CXX      RunningAverage.lo
  CXX      bmhtf-nacl.lo
1 warning generated.
  CXX      buckingham.lo
  CXX      cos2.lo
  CXX      dpd.lo
1 warning generated.
  CXX      gaussian.lo
  CXX      gb.lo
  CXX      hat.lo
  CXX      hertzian.lo
  CXX      lj.lo
  CXX      ljangle.lo
  CXX      ljcos.lo
  CXX      ljcos2.lo
  CXX      ljgen.lo
  CXX      morse.lo
  CXX      soft_sphere.lo
  CXX      steppot.lo
  CXX      tab.lo
  CXX      tunable_slip.lo
  CXX      angle.lo
  CXX      angle_harmonic.lo
  CXX      angle_cosine.lo
  CXX      angle_cossquare.lo
  CXX      angledist.lo
  CXX      dihedral.lo
  CXX      endangledist.lo
  CXX      fene.lo
  CXX      harmonic_dumbbell.lo
  CXX      harmonic.lo
  CXX      quartic.lo
  CXX      overlap.lo
  CXX      umbrella.lo
  CXX      bonded_coulomb.lo
  CXX      subt_lj.lo
  CXX      hydrogen_bond.lo
  CXX      twist_stack.lo
  CXX      debye_hueckel.lo
  CXX      elc.lo
  CXX      magnetic_non_p3m_methods.lo
  CXX      mdlc_correction.lo
In file included from elc.cpp:34:
In file included from ./pressure.hpp:32:
In file included from ./forces_inline.hpp  CXX      maggs.lo
:31:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
  CXX      mmm1d.lo
  CXX      mmm2d.lo
1 warning generated.
  CXX      mmm-common.lo
  CXX      p3m.lo
  CXX      p3m-common.lo
  CXX      p3m-dipolar.lo
  CXX      reaction_field.lo
  GEN      config-version.cpp
  CXX      object-in-fluid/area_force_local.lo
  CXX      object-in-fluid/area_force_global.lo
  CXX      object-in-fluid/bending_force.lo
  CXX      object-in-fluid/stretching_force.lo
  CXX      object-in-fluid/stretchlin_force.lo
  CXX      object-in-fluid/volume_force.lo
  CXX      immersed_boundary/ibm_main.lo
  CXX      immersed_boundary/ibm_triel.lo
  CXX      immersed_boundary/ibm_volume_conservation.lo
  CXX      immersed_boundary/ibm_tribend.lo
  CXX      immersed_boundary/ibm_cuda_interface.lo
  CXX      actor/ActorList.lo
  CXX      actor/HarmonicWell.lo
  CXX      actor/HarmonicOrientationWell.lo
  CXX      actor/Mmm1dgpuForce.lo
In file included from actor/ActorList.cpp:20:
In file included from actor/ActorList.hpp:23:
In file included from actor/Actor.hpp:22:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
In file included from actor/HarmonicWell.cpp:20:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
1 warning generated.
  CXX      actor/EwaldgpuForce.lo
In file included from actor/HarmonicOrientationWell.cpp:20:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
  CXX      actor/DipolarDirectSum.lo
In file included from actor/Mmm1dgpuForce.cpp:2:
In file included from ./EspressoSystemInterface.hpp:24:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
1 warning generated.
  CXX      config-version.lo
1 warning generated.
  CXX      mpifake/mpi.lo
1 warning generated.
In file included from actor/DipolarDirectSum.cpp:5:
In file included from ./forces.hpp:33:
In file included from ./actor/Actor.hpp:22:
./SystemInterface.hpp:29:74: warning: field 'm_needsQuatu' will be initialized 
after field 'm_needsDip' [-Wreorder]
  SystemInterface() : m_needsR(false), m_needsV(false), m_needsQ(false), 
m_needsQuatu(false), m_needsDip(false), m_needsRGpu(false), m_needsVGpu(false), 
m_needsQGpu(false), m_needsQuatuGpu(false), m_needsDipGpu(false) {};
                                                                         ^
1 warning generated.
  CXXLD    libEspresso.la
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(cuda_interface.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(cuda_init.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(electrokinetics_pdb_parse.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(lbgpu.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(lees_edwards_domain_decomposition.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(lees_edwards_comms_manager.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(metadynamics.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(mol_cut.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(virtual_sites_com.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(RunningAverage.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(cos2.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(tunable_slip.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(angle.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(umbrella.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_main.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_triel.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_volume_conservation.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_tribend.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_cuda_interface.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(HarmonicWell.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(HarmonicOrientationWell.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(Mmm1dgpuForce.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(EwaldgpuForce.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(DipolarDirectSum.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(cuda_interface.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(cuda_init.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(electrokinetics_pdb_parse.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(lbgpu.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(lees_edwards_domain_decomposition.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(lees_edwards_comms_manager.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(metadynamics.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(mol_cut.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(virtual_sites_com.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(RunningAverage.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(cos2.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(tunable_slip.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(angle.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(umbrella.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_main.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_triel.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_volume_conservation.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_tribend.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(ibm_cuda_interface.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(HarmonicWell.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(HarmonicOrientationWell.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(Mmm1dgpuForce.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(EwaldgpuForce.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
 file: .libs/libEspresso.a(DipolarDirectSum.o) has no symbols
Making all in tcl
  CXX      bin_tcl.lo
  CXX      blockfile_tcl.lo
  CXX      binary_file_tcl.lo
  CXX      h5mdfile_tcl.lo
h5mdfile_tcl.cpp:13:10: fatal error: 'hdf5.h' file not found
#include "hdf5.h"
         ^
1 error generated.
make[3]: *** [h5mdfile_tcl.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
+ exit 1
Build step 'Execute shell' marked build as failure
[WARNINGS] Skipping publisher since build result is FAILURE
Archiving artifacts