[Espressomd-maintainer] Build failed in Jenkins: master-build-check #441

[Jenkins Demon]

See <http://espressomd.org/jenkins/job/master-build-check/441/changes>

Changes:

[Florian Weik] ...

[Florian Weik] Added tcl comman for cg_dna_baspair IA.

[Florian Weik] Added cg_dna_basepair interaction.

[Florian Weik] Fixed cg_dna bb-interaction for degenerate case.

[Florian Weik] ...

[Florian Weik] ...

[Florian Weik] Fix build w/o CG_DNA.

[Florian Weik] ...

[Florian Weik] cg_dna stacking interaction.

[Florian Weik] Added twisting and stacking force to cg dna model.

[Florian Weik] Added twisting interaction to cg dna model.

[Florian Weik] Some small fixes in the bonded force calculation.

[Florian Weik] cg_dna_stacking debug.

[Florian Weik] Added coulomb-debeye-hueckel-IA.

[Florian Weik] Removed debugg messages.

[Florian Weik] ...

[Florian Weik] Coulomb-debye-hueckel interface code.

[Florian Weik] Added colomb-debye-hueckel potential.

[Florian Weik] Force calculation for coulomb-debye-hueckel potential.

[Florian Weik] Make lj-gen beahave more correctly if cap radius is not set and 
exponents are negative.

[Florian Weik] Fixed sign in Coulomb-Debye-Hueckel IA and correcter parameter 
order for cg_dna_staking interaction.

[Florian Weik] In case of NaN forces, tell which particle caused the error.

[Florian Weik] Fixed misassignment in cg_dna_stacking that caused undefined 
behaviour.

[Florian Weik] cg_dna: Fixed wrong sign of gamma2 in cg_dna_basepair.

[Florian Weik] Fixed force addition for multi-body forces.

[Florian Weik] Fixed several cg_dna_issues.

[Florian Weik] Changed dhc parameters.

[Florian Weik] Added dhc energy calculation.

[Florian Weik] Added cg_dna_stacking energy calculation.

[Florian Weik] cg_dna_basepair energy first part.

[Florian Weik] cg_dna_basepair energy 2nd part.

[Florian Weik] Fixed error cg_dna_basepair interaction.

[Florian Weik] Fixed incorrect handling of pbc in  cg_dna_stacking interaction.

[Florian Weik] Made sqrlen a macro in layerd cell system because it failed to 
inline.

[Florian Weik] Made layered_mi_vector a macro in layerd cell system because it 
failed to inline.

[Florian Weik] Added feature guards.

[Florian Weik] ...

[Florian Weik] Fixed build w/o CG_DNA.

[Florian Weik] Added explicit handling for force and energy calculation of 
contraints of type CONTRAINT_NONE.

[Florian Weik] Handling of CONTRAINT_NONE in collisions.

[Florian Weik] Startet cg_dna doc.

[Florian Weik] Imporoved diagnostics for CG_DNA_DEBUG.

[Florian Weik] More documentation.

[Florian Weik] cg_dna: Fixed reference potential for twist stack interaction.

[Florian Weik] Corrected cdh print command.

[Florian Weik] Fixed scaling error in cg_basepair interaction.

[Florian Weik] ...

[Florian Weik] Fixed Coulomb-Debye-Hueckel IA

[Florian Weik] Fixed build after merge.

[Florian Weik] Renamed cg_dna_stacking to twist_stack in tcl interface.

[Florian Weik] Missing files.

[Florian Weik] Moved twist_stack into separate file.

[Florian Weik] Renamed core functions from cg_dna_stacking* to twist_stack*.

[Florian Weik] Refactoring hydrogen bond.

[Florian Weik] Finished refactoring.

[Florian Weik] Removed spourious files.

[Florian Weik] Update feature defs.

[Florian Weik] Extended Vector class by norm and dot and cross product.

[Florian Weik] Added some actual calculations.

[Florian Weik] Fix small build system error.

[Florian Weik] Fix build with various feature combinations.

[Florian Weik] documentation

[Florian Weik] Change to seperate features for twist-stack and hydrogen-bond IA.

[Florian Weik] Update feature requirements of test cases.

[Florian Weik] Docu

------------------------------------------
[...truncated 324 lines...]
development sources     = yes

Compiler
--------
compiler                = mpic++
linker                  = /usr/x86_64-suse-linux/bin/ld -m elf_x86_64
c++ compiler flags      = -Wall -O3 
c++ preprocessor flags  =  -I/usr/local/cuda/include
linker flags            =  -L/usr/local/cuda/lib64
libraries               = -ltcl8.6 -lcurand -lcublas -lcufft -lcudart -lfftw3  
-lm
using debug flags       = 
using profiling flags   = 

Libraries
---------
FFTW                    = yes
efence                  = no

Cuda
----
CUDA compiler           = /usr/local/cuda/bin/nvcc
CUDA flags              =  --ptxas-options=-v -gencode 
arch=compute_20,code=compute_20

Tcl/Tk
------
Tcl version             = tcl8.6
Tk version              = none

Python
------
python                  = /usr/bin/python -B
build python interface  = 

Other settings
--------------
config                  = myconfig.hpp
installation prefix     = /home/jenkins/Espresso
number of test tasks    = 8
mympiexec               = 
<http://espressomd.org/jenkins/job/master-build-check/ws/mympiexec.sh>
mpiexec                 = /usr/lib64/mpi/gcc/openmpi/bin/mpiexec
pdflatex                = /usr/bin/pdflatex
makeindex               = /usr/bin/makeindex
bibtex                  = /usr/bin/bibtex
doxygen                 = /usr/bin/doxygen
dot                     = /usr/bin/dot

Not building Python interface.
END CONFIGURE
<http://espressomd.org/jenkins/job/master-build-check/ws/>
+ maintainer/jenkins/build.sh
  srcdir=<http://espressomd.org/jenkins/job/master-build-check/ws/>
  builddir=<http://espressomd.org/jenkins/job/master-build-check/ws/>
  insource=true
START BUILD
  myconfig=maxset
  build_procs=1
<http://espressomd.org/jenkins/job/master-build-check/ws/> 
<http://espressomd.org/jenkins/job/master-build-check/ws/>
Copying maxset.hpp to 
<http://espressomd.org/jenkins/job/master-build-check/ws/myconfig.hpp...>
>make -j 1
Making all in config
make[1]: Entering directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/config'>
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/config'>
Making all in src
make[1]: Entering directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src'>
make  all-recursive
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src'>
Making all in core
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src/core'>
  GEN      myconfig-final.hpp <= ../../myconfig.hpp
  GEN      config-features.hpp
make  all-am
make[4]: Entering directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src/core'>
  CXX      config-features.lo
  CXX      cells.lo
  CXX      collision.lo
  CXX      communication.lo
  CXX      comfixed.lo
  CXX      comforce.lo
  CXX      constraint.lo
  CXX      cuda_interface.lo
  CXX      cuda_init.lo
  CXX      debug.lo
  CXX      domain_decomposition.lo
  CXX      electrokinetics_pdb_parse.lo
  CXX      energy.lo
  CXX      external_potential.lo
  CXX      errorhandling.lo
  CXX      fft.lo
  CXX      fft-common.lo
  CXX      fft-dipolar.lo
  CXX      forcecap.lo
  CXX      forces.lo
  CXX      galilei.lo
  CXX      ghosts.lo
  CXX      global.lo
  CXX      grid.lo
  CXX      halo.lo
  CXX      iccp3m.lo
  CXX      imd.lo
  CXX      initialize.lo
  CXX      integrate.lo
  CXX      interaction_data.lo
  CXX      lattice.lo
  CXX      layered.lo
  CXX      lb.lo
lb.cpp: In function 'int lb_lbfluid_load_checkpoint(char*, int)':
lb.cpp:972:64: warning: format '%lf' expects argument of type 'double*', but 
argument 3 has type 'lbForceFloat* {aka float*}' [-Wformat=]
                 fscanf(cpfile, "%lf", &host_checkpoint_force[n]);
                                                                ^
  CXX      lb-boundaries.lo
  CXX      lbgpu.lo
  CXX      lees_edwards.lo
  CXX      lees_edwards_domain_decomposition.lo
  CXX      lees_edwards_comms_manager.lo
  CXX      metadynamics.lo
  CXX      minimize_energy.lo
  CXX      modes.lo
  CXX      molforces.lo
  CXX      mol_cut.lo
  CXX      nemd.lo
  CXX      nsquare.lo
  CXX      particle_data.lo
  CXX      polymer.lo
  CXX      pressure.lo
  CXX      random.lo
  CXX      rattle.lo
  CXX      reaction.lo
  CXX      readpdb.lo
  CXX      rotation.lo
  CXX      RuntimeErrorCollector.lo
  CXX      specfunc.lo
  CXX      statistics.lo
  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
  CXX      thermostat.lo
  CXX      topology.lo
  CXX      tuning.lo
  CXX      uwerr.lo
  CXX      verlet.lo
  CXX      virtual_sites.lo
  CXX      virtual_sites_com.lo
  CXX      virtual_sites_relative.lo
  CXX      vmdsock.lo
  CXX      ghmc.lo
  CXX      integrate_sd.lo
  CXX      EspressoSystemInterface.lo
  CXX      PdbParser.lo
  CXX      bmhtf-nacl.lo
  CXX      buckingham.lo
  CXX      cos2.lo
  CXX      dpd.lo
  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      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      hydrogen_bond.lo
  CXX      twist_stack.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      debye_hueckel.lo
  CXX      elc.lo
  CXX      magnetic_non_p3m_methods.lo
  CXX      mdlc_correction.lo
  CXX      maggs.lo
maggs.cpp: In function 'void maggs_exchange_surface_patch(double*, int, int)':
maggs.cpp:849:5: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(2,1*sizeof(double),2*sizeof(double), MPI_BYTE, &xz_plaq);
     ^
maggs.cpp:849:77: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(2,1*sizeof(double),2*sizeof(double), MPI_BYTE, &xz_plaq);
                                                                             ^
maggs.cpp:853:5: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(surface_patch[2].nblocks, 1, 
dim*surface_patch[2].skip*sizeof(double), oneslice, &xzPlane2D);
     ^
maggs.cpp:853:113: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(surface_patch[2].nblocks, 1, 
dim*surface_patch[2].skip*sizeof(double), oneslice, &xzPlane2D);
                                                                                
                                 ^
  CXX      mmm1d.lo
  CXX      mmm2d.lo
  CXX      mmm-common.lo
  CXX      p3m.lo
  CXX      p3m-common.lo
  CXX      p3m-dipolar.lo
  CXX      reaction_field.lo
  CXX      actor/ActorList.lo
  CXX      actor/HarmonicWell.lo
  CXX      actor/Mmm1dgpuForce.lo
  CXX      actor/EwaldgpuForce.lo
  GEN      config-version.cpp
  CXX      config-version.lo
  NVCC     cuda_init_cuda.lo
  NVCC     cuda_common_cuda.lo
  NVCC     electrokinetics_cuda.lo
electrokinetics_cuda.cu(2054): error: identifier "CUDA_particle_force" is 
undefined

1 error detected in the compilation of 
"/tmp/tmpxft_00006fc5_00000000-6_electrokinetics_cuda.cpp1.ii".
make[4]: *** [electrokinetics_cuda.lo] Error 1
make[4]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src/core'>
make[3]: *** [all] Error 2
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src/core'>
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src'>
make[1]: *** [all] Error 2
make[1]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-build-check/ws/src'>
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