Your message dated Sun, 13 Jan 2019 10:32:08 +0100
with message-id <[email protected]>
and subject line Re: Bug#904669: xmds2: autopkgtest times out since 2018-07-19
has caused the Debian Bug report #904669,
regarding xmds2: autopkgtest times out since 2018-07-19
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
904669: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=904669
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: xmds2
Version: 2.2.3+dfsg-10
X-Debbugs-CC: [email protected]
User: [email protected]
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: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Control: fixed -1 2.2.3+dfsg-12
* Paul Gevers <[email protected]> [2019-01-13 10:19]:
It already is.
https://ci.debian.net/status/blacklist/
Great, thanks!
I am hereby closing this bug report.
Best,
Rafael
--- End Message ---
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