[Espressomd-maintainer] Build failed in Jenkins: master-nightly-distcheck #220

[Jenkins Demon]

See <http://espressomd.org/jenkins/job/master-nightly-distcheck/220/changes>

Changes:

[Owen Hickey] removed unused variable

[Owen Hickey] added momentum to cython, compiles untested

[Owen Hickey] analyze_linear_momentum now works in Cython

[Owen Hickey] added calc_rg, calc_rh, and calc_re to python, cleaned up c side 
a bit too

[Owen Hickey] analyze rg rh re in cython seems to be working

[Owen Hickey] added documentation for python interface analyze linear momentum 
and calculate rg/rh/re

[Florian Weik] Autopep8.

[Florian Weik] Autopep.

[Florian Weik] Autopep8.

------------------------------------------
[...truncated 219 lines...]
checking for libcufft... yes
checking for libcublas... yes
checking for cublas_v2.h... yes
checking for libcurand... yes
checking whether CUDA compiles... yes
checking whether CUDA runs... yes
checking whether the compiler accepts -stdlib=libstdc++... no
checking whether to use MAGMA... guess
checking for library containing magma_init... no
configure: WARNING: MAGMA not found. Some features will not be available!
checking whether to use ARPACK... guess
checking for libarpack... no
configure: WARNING: could not find ARPACK library. Some features will not be 
available!
configure: WARNING: ARPACK not found. Some features will not be available!
****************************************************************
*                  Checking for Python                         *
****************************************************************
checking for a Python interpreter with version >= 2.5... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... 
${exec_prefix}/lib64/python2.7/site-packages
checking whether python -B works... yes
checking whether the python interface is wanted... no
****************************************************************
*                  Checking for Tcl/Tk                         *
****************************************************************
checking whether to build the Tcl interface... yes
checking for libtcl8.6... yes
checking for tcl.h... yes
checking whether to use Tk... yes
****************************************************************
*                          h5md                                *
****************************************************************
checking whether to build with h5md support... yes
checking for libhdf5... yes
checking for hdf5.h... yes
****************************************************************
*                   Other settings                             *
****************************************************************
checking whether to use efence... no
checking whether the variable MYCONFIG is set... no
checking the number of available CPUs... 8 
****************************************************************
*                   Creating output files                      *
****************************************************************
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config/Makefile
config.status: creating config/myconfig-sample-header.hpp
config.status: creating src/Makefile
config.status: creating src/core/Makefile
config.status: creating src/tcl/Makefile
config.status: creating src/python/espressomd/Makefile
config.status: creating tools/Makefile
config.status: creating scripts/Makefile
config.status: creating testsuite/Makefile
config.status: creating doc/Makefile
config.status: creating doc/logo/Makefile
config.status: creating doc/ug/Makefile
config.status: creating doc/dg/Makefile
config.status: creating doc/doxygen/Makefile
config.status: creating doc/tutorials/Makefile
config.status: creating doc/tutorials/01-lennard_jones/Makefile
config.status: creating doc/tutorials/02-charged_system/Makefile
config.status: creating doc/tutorials/03-object_in_fluid/Makefile
config.status: creating doc/latexit.sh
config.status: creating testsuite/runtest.sh
config.status: creating tools/es_mpiexec
config.status: creating src/python/pypresso
config.status: creating src/acconfig.hpp
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing myconfig-sample.hpp commands
****************************************************************
*                   Configuration summary                      *
****************************************************************
platform detected       = x86_64-suse-linux-gnu
package version         = 3.4-dev-962-g9594f16
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               = -lhdf5 -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-nightly-distcheck/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-nightly-distcheck/ws/>
+ maintainer/jenkins/distcheck.sh
19329 (process ID) old priority 0, new priority 5
  srcdir=<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/>
  builddir=<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/>
  insource=true
  distcheck_flags=
<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/> 
<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/>
START DISTCHECK
>make distcheck DISTCHECK_CONFIGURE_FLAGS=""
make  dist-xz dist-gzip am__post_remove_distdir='@:'
make[1]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/'>
cd .; sh config/genversion.sh -rd > 
<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/version.txt>
if test -d "espresso-3.4-dev-962-g9594f16"; then find 
"espresso-3.4-dev-962-g9594f16" -type d ! -perm -200 -exec chmod u+w {} ';' && 
rm -rf "espresso-3.4-dev-962-g9594f16" || { sleep 5 && rm -rf 
"espresso-3.4-dev-962-g9594f16"; }; else :; fi
test -d "espresso-3.4-dev-962-g9594f16" || mkdir "espresso-3.4-dev-962-g9594f16"
 (cd config && make  top_distdir=../espresso-3.4-dev-962-g9594f16 
distdir=../espresso-3.4-dev-962-g9594f16/config \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/config'>
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/config'>
 (cd src && make  top_distdir=../espresso-3.4-dev-962-g9594f16 
distdir=../espresso-3.4-dev-962-g9594f16/src \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src'>
 (cd core && make  top_distdir=../../espresso-3.4-dev-962-g9594f16 
distdir=../../espresso-3.4-dev-962-g9594f16/src/core \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src/core'>
  GEN      config-features.cpp
  GEN      config-version.cpp
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src/core'>
 (cd tcl && make  top_distdir=../../espresso-3.4-dev-962-g9594f16 
distdir=../../espresso-3.4-dev-962-g9594f16/src/tcl \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src/tcl'>
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src/tcl'>
 (cd python/espressomd && make  
top_distdir=../../../espresso-3.4-dev-962-g9594f16 
distdir=../../../espresso-3.4-dev-962-g9594f16/src/python/espressomd \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src/python/espressomd'>
Makefile:732: target `electrostatics.cpp' given more than once in the same rule.
Makefile:735: target `electrostatics.la' given more than once in the same rule.
Makefile:739: target `electrostatics.so' given more than once in the same rule.
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src/python/espressomd'>
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/src'>
 (cd scripts && make  top_distdir=../espresso-3.4-dev-962-g9594f16 
distdir=../espresso-3.4-dev-962-g9594f16/scripts \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/scripts'>
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/scripts'>
 (cd tools && make  top_distdir=../espresso-3.4-dev-962-g9594f16 
distdir=../espresso-3.4-dev-962-g9594f16/tools \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/tools'>
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/tools'>
 (cd testsuite && make  top_distdir=../espresso-3.4-dev-962-g9594f16 
distdir=../espresso-3.4-dev-962-g9594f16/testsuite \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/testsuite'>
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/testsuite'>
 (cd doc && make  top_distdir=../espresso-3.4-dev-962-g9594f16 
distdir=../espresso-3.4-dev-962-g9594f16/doc \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc'>
 (cd logo && make  top_distdir=../../espresso-3.4-dev-962-g9594f16 
distdir=../../espresso-3.4-dev-962-g9594f16/doc/logo \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/logo'>
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/logo'>
 (cd doxygen && make  top_distdir=../../espresso-3.4-dev-962-g9594f16 
distdir=../../espresso-3.4-dev-962-g9594f16/doc/doxygen \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/doxygen'>
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/doxygen'>
 (cd dg && make  top_distdir=../../espresso-3.4-dev-962-g9594f16 
distdir=../../espresso-3.4-dev-962-g9594f16/doc/dg \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/dg'>
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/dg'>
 (cd ug && make  top_distdir=../../espresso-3.4-dev-962-g9594f16 
distdir=../../espresso-3.4-dev-962-g9594f16/doc/ug \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/ug'>
make  \
  top_distdir="../../espresso-3.4-dev-962-g9594f16" 
distdir="../../espresso-3.4-dev-962-g9594f16/doc/ug" \
  dist-hook
make[4]: Entering directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/ug'>
Assembling quickref.inp..
Running LaTeX..
sh ../latexit.sh . ug-dist 1
TEXINPUTS=.:.:<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc>:
ESPRESSO_VERSION=3.4-dev-962-g9594f16
Running LaTeX stage 1...
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/TeX Live for SUSE 
Linux)
 restricted \write18 enabled.
entering extended mode
ERROR: LaTeX stage 1 failed.
These are the last 20 lines of ug-dist.log:
--------------------------------------------
.................................................
. LaTeX info: "xparse/define-command"
. 
. Defining document command \property with arg. spec. 'mmm' on line 750.
.................................................
! Undefined control sequence.
<inserted text> ...arg {system},\par chain\_start 
                                                  = \arg {int},\par n\_chain...
l.760   }
          
Here is how much of TeX's memory you used:
 24096 strings out of 493315
 422503 string characters out of 6145892
 529668 words of memory out of 5000000
 26699 multiletter control sequences out of 15000+600000
 20902 words of font info for 76 fonts, out of 8000000 for 9000
 957 hyphenation exceptions out of 8191
 77i,16n,77p,549b,518s stack positions out of 5000i,500n,10000p,200000b,80000s

!  ==> Fatal error occurred, no output PDF file produced!
--------------------------------------------
make[4]: *** [ug-dist.pdf] Error 1
make[4]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/ug'>
make[3]: *** [distdir] Error 2
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc/ug'>
make[2]: *** [distdir] Error 1
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/doc'>
make[1]: *** [distdir] Error 1
make[1]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-nightly-distcheck/ws/'>
make: *** [dist] Error 2
+ exit 1
Build step 'Execute shell' marked build as failure
[WARNINGS] Skipping publisher since build result is FAILURE
Archiving artifacts