Bug#904669: xmds2: autopkgtest times out since 2018-07-19

[Paul Gevers]

Source: xmds2
Version: 2.2.3+dfsg-10
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: timeout

Dear maintainers,

Since 2018-07-19 the autopkgtest of your package times out (after 2:47h)
on ci.debian.net. I have copied the output below.

Could you please make your autopkgtest robust against this? The
autpkgtest used to pass in around 13 minutes, so something really
changed. (gcc-8 was introduced as default around that time if I am correct).

Don't hesitate to ask for help for the Debian CI team² if you need help
solving this issue.

I will blacklist this package on the ci.debian.net infrastructure and
will remove the blacklist once this bug is fixed.

Paul

https://ci.debian.net/data/autopkgtest/unstable/amd64/x/xmds2/667396/log.gz

autopkgtest [12:59:22]: test run-tests: [-----------------------
Checking for 'g++' (c++ compiler)        : /usr/bin/g++
Checking whether the compiler works      : yes
Checking that we have a C++ compiler     : yes
Checking whether we are cross-compiling  : no
Checking whether we can link to only static libraries : no (will use
dynamic libraries)
Trying to make compiler optimise for this machine     : yes
Trying to make compiler tune for this machine         : yes
Checking for compiler flags -O3                       : yes
Checking for compiler flags -ffast-math               : yes
Checking for compiler flags -funroll-all-loops        : yes
Checking for compiler flags -fomit-frame-pointer      : yes
Checking for compiler flags -falign-loops             : yes
Checking for compiler flags -fstrict-aliasing         : yes
Checking for compiler flags -momit-leaf-frame-pointer : yes
Checking for cautious math flags                      : yes
Checking for Autovectorisation                        : yes
Checking for OpenMP                                   : yes
Checking for pthreads                                 : yes
Checking for compiler debug flags                     : yes
Checking for srandomdev                               : not found
Checking for /dev/urandom                             : yes
Checking for program h5cc                             : /usr/bin/h5cc
Checking for HDF5 (static library)                    : yes
Checking for HDF5 High-level library (static library) : yes
Checking for function H5Lexists                       : yes
Checking for libxmds (static library)                 : no (will try
dynamic library instead)
Checking for libxmds (dynamic library)                : no (it's
optional anyway)
Checking for Intel's Vector Math Library (static library) : no (will try
dynamic library instead)
Checking for Intel's Vector Math Library (dynamic library) : no (it's
optional anyway)
Checking aggressive dSFMT compile flags                    : yes
Checking for Intel's Math Kernel Library (static library)  : no (will
try dynamic library instead)
Checking for Intel's Math Kernel Library (dynamic library) : no (it's
optional anyway)
Checking for ATLAS's CBLAS. (static library)               : no (will
try dynamic library instead)
Checking for ATLAS's CBLAS. (dynamic library)              : yes
Checking for GSL (static library)                          : yes
Checking for FFTW3 (static library)                        : yes
Checking for single-precision FFTW3 (static library)       : yes
Checking for threading support in FFTW3 (static library)   : yes
Checking for OpenMP support in FFTW3 (static library)      : yes
Checking for threading support in single-precision FFTW3 (static
library) : yes
Checking for OpenMP support in single-precision FFTW3 (static library)
 : yes
Checking for program mpic++
 : /usr/bin/mpic++
Checking for 'g++' (c++ compiler)
 : /usr/bin/mpic++
Checking whether the compiler works
 : yes
Checking that we have a C++ compiler
 : yes
Checking whether we are cross-compiling
 : no
Checking whether we can link to only static libraries
 : no (will use dynamic libraries)
Trying to make compiler optimise for this machine
 : yes
Trying to make compiler tune for this machine
 : yes
Checking for compiler flags -O3
 : yes
Checking for compiler flags -ffast-math
 : yes
Checking for compiler flags -funroll-all-loops
 : yes
Checking for compiler flags -fomit-frame-pointer
 : yes
Checking for compiler flags -falign-loops
 : yes
Checking for compiler flags -fstrict-aliasing
 : yes
Checking for compiler flags -momit-leaf-frame-pointer
 : yes
Checking for cautious math flags
 : yes
Checking for Autovectorisation
 : yes
Checking for OpenMP
 : yes
Checking for pthreads
 : yes
Checking for compiler debug flags
 : yes
Checking for srandomdev
 : not found
Checking for /dev/urandom
 : yes
Checking for program h5cc
 : /usr/bin/h5cc
Checking for HDF5 (static library)
 : yes
Checking for HDF5 High-level library (static library)
 : yes
Checking for function H5Lexists
 : yes
Checking for libxmds (static library)
 : no (will try dynamic library instead)
Checking for libxmds (dynamic library)
 : no (it's optional anyway)
Checking for Intel's Vector Math Library (static library)
 : no (will try dynamic library instead)
Checking for Intel's Vector Math Library (dynamic library)
 : no (it's optional anyway)
Checking aggressive dSFMT compile flags
 : yes
Checking for Intel's Math Kernel Library (static library)
 : no (will try dynamic library instead)
Checking for Intel's Math Kernel Library (dynamic library)
 : no (it's optional anyway)
Checking for ATLAS's CBLAS. (static library)
 : no (will try dynamic library instead)
Checking for ATLAS's CBLAS. (dynamic library)
 : yes
Checking for GSL (static library)
 : yes
Checking for FFTW3 (static library)
 : yes
Checking for single-precision FFTW3 (static library)
 : yes
Checking for threading support in FFTW3 (static library)
 : yes
Checking for OpenMP support in FFTW3 (static library)
 : yes
Checking for threading support in single-precision FFTW3 (static
library) : yes
Checking for OpenMP support in single-precision FFTW3 (static library)
 : yes
Checking for FFTW3 with MPI (static library)
 : yes
Checking for single-precision FFTW3 with MPI (static library)
 : yes
xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-10)
Copyright 2000-2014 Graham Dennis, Joseph Hope, Mattias Johnsson
                    and the xmds team

Configuring for single-process scripts...

Configuring for MPI scripts...
Config log saved to
/tmp/autopkgtest-lxc.svx_k37p/downtmp/build.pTE/src/debian/xmds-user-data/waf_configure/config.log
test_bug_adaptive_timestep_hang (__main__.ScriptTestCase)
integrators/bug_adaptive_timestep_hang.xmds ...
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning:
Conversion of the second argument of issubdtype from `float` to
`np.floating` is deprecated. In future, it will be treated as
`np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
ok
test_vibstring_ark45 (__main__.ScriptTestCase)
integrators/vibstring_ark45.xmds ... ok
test_vibstring_ark89 (__main__.ScriptTestCase)
integrators/vibstring_ark89.xmds ... ok
test_vibstring_rk4 (__main__.ScriptTestCase)
integrators/vibstring_rk4.xmds ... ok
test_vibstring_rk45 (__main__.ScriptTestCase)
integrators/vibstring_rk45.xmds ... ok
test_vibstring_rk89 (__main__.ScriptTestCase)
integrators/vibstring_rk89.xmds ... ok
test_vibstring_rk9 (__main__.ScriptTestCase)
integrators/vibstring_rk9.xmds ... ok
test_vibstring_si (__main__.ScriptTestCase)
integrators/vibstring_si.xmds ... ok
test_vibstring_mm (__main__.ScriptTestCase)
integrators/richardson_extrapolation/vibstring_mm.xmds ... ok
test_vibstring_re (__main__.ScriptTestCase)
integrators/richardson_extrapolation/vibstring_re.xmds ... ok
test_vibstring_mm (__main__.ScriptTestCase)
integrators/richardson_extrapolation/vibstring_mm.xmds ... ok
test_vibstring_re (__main__.ScriptTestCase)
integrators/richardson_extrapolation/vibstring_re.xmds ... ok
test_RbGSdipoles (__main__.ScriptTestCase)
fast/RbGSdipoles.xmds ... ok
test_anharmonic_oscillator_wigner_mpi (__main__.ScriptTestCase)
fast/anharmonic_oscillator_wigner_mpi.xmds ... skipped 'Skipping test as
XMDS1 is required and not installed'
test_anharmonic_oscillator_wigner_mpi_parsing (__main__.ScriptTestCase)
fast/anharmonic_oscillator_wigner_mpi_parsing.xmds ... skipped 'Skipping
test as XMDS1 is required and not installed'
test_bessel_cosine_evolution (__main__.ScriptTestCase)
fast/bessel_cosine_evolution.xmds ... ok
test_bessel_cosine_groundstate (__main__.ScriptTestCase)
fast/bessel_cosine_groundstate.xmds ... ok
test_cpc_example4 (__main__.ScriptTestCase)
fast/cpc_example4.xmds ... ok
test_eigenvalues (__main__.ScriptTestCase)
fast/eigenvalues.xmds ... ok
test_groundstate (__main__.ScriptTestCase)
fast/groundstate.xmds ... ok
test_lorenz (__main__.ScriptTestCase)
fast/lorenz.xmds ... ok
test_tla (__main__.ScriptTestCase)
fast/tla.xmds ... ok
test_transverse_integration_in_vector_initialisation
(__main__.ScriptTestCase)
fast/transverse_integration_in_vector_initialisation.xmds ... ok
test_vibstring_circle_spectral (__main__.ScriptTestCase)
fast/vibstring_circle_spectral.xmds ... ok
test_arguments (__main__.ScriptTestCase)
features/arguments.xmds ... ok
test_arguments_append_args_to_output_filename (__main__.ScriptTestCase)
features/arguments_append_args_to_output_filename.xmds ... ok
test_arguments_with_similar_names (__main__.ScriptTestCase)
features/arguments_with_similar_names.xmds ... ok
test_error_check_multipath (__main__.ScriptTestCase)
features/error_check_multipath.xmds ... ok
test_halt_non_finite (__main__.ScriptTestCase)
features/halt_non_finite.xmds ... ./run_tests.py:64: RuntimeWarning:
invalid value encountered in less_equal
  return numpy.logical_or(numpy.logical_or(numpy.abs(diff) <= 0.5 *
relTol * (numpy.abs(array2) + numpy.abs(array1)), numpy.abs(diff) <=
absTol), numpy.isnan(array2)).all()
ok
test_hermitegauss_transform_2d_chunked_breakpoints (__main__.ScriptTestCase)
features/hermitegauss_transform_2d_chunked_breakpoints.xmds ... ok
test_hermitegauss_transform_2d_chunked_breakpoints_hdf5
(__main__.ScriptTestCase)
features/hermitegauss_transform_2d_chunked_breakpoints_hdf5.xmds ... ok
test_realistic_Rb_and_fields (__main__.ScriptTestCase)
features/realistic_Rb_and_fields.xmds ... ok
test_runtime_paths (__main__.ScriptTestCase)
features/runtime_paths.xmds ... ok
test_space in filename (__main__.ScriptTestCase)
features/space in filename.xmds ... ok
test_integer_dimensions (__main__.ScriptTestCase)
geometry/integer_dimensions.xmds ... ok
test_integer_dimensions_reordered (__main__.ScriptTestCase)
geometry/integer_dimensions_reordered.xmds ... ok
test_nonlocal_access_multiple_components (__main__.ScriptTestCase)
geometry/nonlocal_access_multiple_components.xmds ... ok
test_nonlocal_edge_uniform_access (__main__.ScriptTestCase)
geometry/nonlocal_edge_uniform_access.xmds ... ok
test_nonlocal_index_access (__main__.ScriptTestCase)
geometry/nonlocal_index_access.xmds ... ok
test_nonlocal_negative_uniform_access (__main__.ScriptTestCase)
geometry/nonlocal_negative_uniform_access.xmds ... ok
test_nonlocal_split_uniform_access (__main__.ScriptTestCase)
geometry/nonlocal_split_uniform_access.xmds ... ok
test_bessel_cosine_groundstate (__main__.ScriptTestCase)
openmp/bessel_cosine_groundstate.xmds ... ok
test_diffusion_openmp (__main__.ScriptTestCase)
openmp/diffusion_openmp.xmds ... ok
test_diffusion_openmp_chunked (__main__.ScriptTestCase)
openmp/diffusion_openmp_chunked.xmds ... ok
test_eigenvalues (__main__.ScriptTestCase)
openmp/eigenvalues.xmds ... ok
test_hermitegauss_transform_2d_openmp (__main__.ScriptTestCase)
openmp/hermitegauss_transform_2d_openmp.xmds ... ok
test_hermitegauss_transform_2d_openmp_small (__main__.ScriptTestCase)
openmp/hermitegauss_transform_2d_openmp_small.xmds ... ok
test_kubo_integer_dimensions_openmp (__main__.ScriptTestCase)
openmp/kubo_integer_dimensions_openmp.xmds ... ok
test_lorenz_openmp (__main__.ScriptTestCase)
openmp/lorenz_openmp.xmds ... ok
test_openmp_dft (__main__.ScriptTestCase)
openmp/openmp_dft.xmds ... ok
test_openmp_dft_hdf5 (__main__.ScriptTestCase)
openmp/openmp_dft_hdf5.xmds ... ok
test_openmp_dft_small (__main__.ScriptTestCase)
openmp/openmp_dft_small.xmds ... ok
test_openmp_highdimcrossprop (__main__.ScriptTestCase)
openmp/openmp_highdimcrossprop.xmds ... ok
test_partial_integration_computed_vector (__main__.ScriptTestCase)
openmp/partial_integration_computed_vector.xmds ... ok
test_vibstring_dst_openmp (__main__.ScriptTestCase)
openmp/vibstring_dst_openmp.xmds ... ok
test_vibstring_dst_openmp_chunked (__main__.ScriptTestCase)
openmp/vibstring_dst_openmp_chunked.xmds ... ok
test_breakpoints_hdf5 (__main__.ScriptTestCase)
runtime_lattice/breakpoints_hdf5.xmds ... ok
test_integer_dimensions (__main__.ScriptTestCase)
runtime_lattice/integer_dimensions.xmds ... ok
test_integer_dimensions_with_fixed_lattice (__main__.ScriptTestCase)
runtime_lattice/integer_dimensions_with_fixed_lattice.xmds ... ok
test_integer_dimensions_with_runtime_lattice (__main__.ScriptTestCase)
runtime_lattice/integer_dimensions_with_runtime_lattice.xmds ... ok
test_runtime_lattice_diffusion_dst (__main__.ScriptTestCase)
runtime_lattice/runtime_lattice_diffusion_dst.xmds ... ok
test_runtime_lattice_initialisation_order (__main__.ScriptTestCase)
runtime_lattice/runtime_lattice_initialisation_order.xmds ... ok
test_runtime_lattice_mpi_dft_small (__main__.ScriptTestCase)
runtime_lattice/runtime_lattice_mpi_dft_small.xmds ... ok
test_runtime_lattice_nonlocal_split_uniform_access (__main__.ScriptTestCase)
runtime_lattice/runtime_lattice_nonlocal_split_uniform_access.xmds ... ok
test_runtime_lattice_vibstring_ark89 (__main__.ScriptTestCase)
runtime_lattice/runtime_lattice_vibstring_ark89.xmds ... ok
test_runtime_lattice_xsilloading_hdf5_loose2 (__main__.ScriptTestCase)
runtime_lattice/runtime_lattice_xsilloading_hdf5_loose2.xmds ... ok
test_breakpoints (__main__.ScriptTestCase)
io/breakpoints.xmds ... ok
test_breakpoints_hdf5 (__main__.ScriptTestCase)
io/breakpoints_hdf5.xmds ... ok
test_mpi_xsilloading (__main__.ScriptTestCase)
io/mpi_xsilloading.xmds ... skipped 'Skipping test as XMDS1 is required
and not installed'
test_mpi_xsilloading_hdf5 (__main__.ScriptTestCase)
io/mpi_xsilloading_hdf5.xmds ... ok
test_mpi_xsilloading_hdf5_loose (__main__.ScriptTestCase)
io/mpi_xsilloading_hdf5_loose.xmds ... ok
test_mpi_xsilloading_hdf5_loose2 (__main__.ScriptTestCase)
io/mpi_xsilloading_hdf5_loose2.xmds ... ok
test_mpi_xsilloading_loose (__main__.ScriptTestCase)
io/mpi_xsilloading_loose.xmds ... skipped 'Skipping test as XMDS1 is
required and not installed'
test_mpi_xsilloading_loose2 (__main__.ScriptTestCase)
io/mpi_xsilloading_loose2.xmds ... skipped 'Skipping test as XMDS1 is
required and not installed'
test_nlse_sampling (__main__.ScriptTestCase)
io/nlse_sampling.xmds ... ok
test_xsilloading (__main__.ScriptTestCase)
io/xsilloading.xmds ... skipped 'Skipping test as XMDS1 is required and
not installed'
test_xsilloading_hdf5 (__main__.ScriptTestCase)
io/xsilloading_hdf5.xmds ... ok
test_xsilloading_hdf5_loose (__main__.ScriptTestCase)
io/xsilloading_hdf5_loose.xmds ... ok
test_xsilloading_hdf5_loose2 (__main__.ScriptTestCase)
io/xsilloading_hdf5_loose2.xmds ... ok
test_xsilloading_loose (__main__.ScriptTestCase)
io/xsilloading_loose.xmds ... skipped 'Skipping test as XMDS1 is
required and not installed'
test_xsilloading_loose2 (__main__.ScriptTestCase)
io/xsilloading_loose2.xmds ... skipped 'Skipping test as XMDS1 is
required and not installed'
test_diffusion_mpi (__main__.ScriptTestCase)
mpi/diffusion_mpi.xmds ... FAIL
test_diffusion_mpi_chunked (__main__.ScriptTestCase)
mpi/diffusion_mpi_chunked.xmds ... FAIL
test_eigenvalues (__main__.ScriptTestCase)
mpi/eigenvalues.xmds ... ok
test_fibre_integer_dimensions_mpi (__main__.ScriptTestCase)
mpi/fibre_integer_dimensions_mpi.xmds ... ok
test_hermitegauss_transform_2d_mpi (__main__.ScriptTestCase)
mpi/hermitegauss_transform_2d_mpi.xmds ... ok
test_hermitegauss_transform_2d_mpi_small (__main__.ScriptTestCase)
mpi/hermitegauss_transform_2d_mpi_small.xmds ... ok
test_kubo_adaptive_mpi_paths (__main__.ScriptTestCase)
mpi/kubo_adaptive_mpi_paths.xmds ... ok
test_kubo_integer_dimensions_mpi (__main__.ScriptTestCase)
mpi/kubo_integer_dimensions_mpi.xmds ... ok
test_kubo_mpi_paths (__main__.ScriptTestCase)
mpi/kubo_mpi_paths.xmds ... ok
test_lorenz_mpi (__main__.ScriptTestCase)
mpi/lorenz_mpi.xmds ... ok
test_mpi_dft (__main__.ScriptTestCase)
mpi/mpi_dft.xmds ... ok
test_mpi_dft_hdf5 (__main__.ScriptTestCase)
mpi/mpi_dft_hdf5.xmds ... ok
test_mpi_dft_small (__main__.ScriptTestCase)
mpi/mpi_dft_small.xmds ... ok
test_mpi_highdimcrossprop (__main__.ScriptTestCase)
mpi/mpi_highdimcrossprop.xmds ... FAIL
test_partial_integration_computed_vector (__main__.ScriptTestCase)
mpi/partial_integration_computed_vector.xmds ... ok
test_vibstring_dst_mpi (__main__.ScriptTestCase)
mpi/vibstring_dst_mpi.xmds ... autopkgtest [15:46:02]: ERROR: timed out
on command "su -s /bin/bash debci -c set -e; export USER=`id -nu`; .
/etc/profile >/dev/null 2>&1 || true;  . ~/.profile >/dev/null 2>&1 ||
true; buildtree="/tmp/autopkgtest-lxc.svx_k37p/downtmp/build.pTE/src";
mkdir -p -m 1777 --
"/tmp/autopkgtest-lxc.svx_k37p/downtmp/run-tests-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.svx_k37p/downtmp/run-tests-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.svx_k37p/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.svx_k37p/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=2; unset LANGUAGE
LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE   LC_MONETARY LC_MESSAGES
LC_PAPER LC_NAME LC_ADDRESS   LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo
$$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f
/tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; chmod
+x
/tmp/autopkgtest-lxc.svx_k37p/downtmp/build.pTE/src/debian/tests/run-tests;
touch /tmp/autopkgtest-lxc.svx_k37p/downtmp/run-tests-stdout
/tmp/autopkgtest-lxc.svx_k37p/downtmp/run-tests-stderr;
/tmp/autopkgtest-lxc.svx_k37p/downtmp/build.pTE/src/debian/tests/run-tests
2> >(tee -a /tmp/autopkgtest-lxc.svx_k37p/downtmp/run-tests-stderr >&2)
> >(tee -a /tmp/autopkgtest-lxc.svx_k37p/downtmp/run-tests-stdout);"
(kind: test)
autopkgtest [15:46:02]: test run-tests: -----------------------]

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