[Debichem-devel] Bug#1117752: gpaw: FTBFS: FAILED gpaw/test/test_aeatom.py::test_aeatom - FloatingPointError: invalid va...
Santiago Vila
sanvila at debian.org
Fri Oct 10 17:27:15 BST 2025
Package: src:gpaw
Version: 25.1.0-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202510/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:gpaw, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild --with python3
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py clean
/usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
[... snipped ...]
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/mpa.c -o build/temp.linux-x86_64-cpython-313/c/mpa.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/mpi.c -o build/temp.linux-x86_64-cpython-313/c/mpi.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/operators.c -o build/temp.linux-x86_64-cpython-313/c/operators.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/plane_wave.c -o build/temp.linux-x86_64-cpython-313/c/plane_wave.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/plt.c -o build/temp.linux-x86_64-cpython-313/c/plt.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/point_charges.c -o build/temp.linux-x86_64-cpython-313/c/point_charges.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/spline.c -o build/temp.linux-x86_64-cpython-313/c/spline.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/symmetry.c -o build/temp.linux-x86_64-cpython-313/c/symmetry.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/tetra.c -o build/temp.linux-x86_64-cpython-313/c/tetra.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/transformers.c -o build/temp.linux-x86_64-cpython-313/c/transformers.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/utilities.c -o build/temp.linux-x86_64-cpython-313/c/utilities.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/wigner_seitz.c -o build/temp.linux-x86_64-cpython-313/c/wigner_seitz.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/woperators.c -o build/temp.linux-x86_64-cpython-313/c/woperators.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/ensemble_gga.c -o build/temp.linux-x86_64-cpython-313/c/xc/ensemble_gga.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/libvdwxc.c -o build/temp.linux-x86_64-cpython-313/c/xc/libvdwxc.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/libxc.c -o build/temp.linux-x86_64-cpython-313/c/xc/libxc.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/m06l.c -o build/temp.linux-x86_64-cpython-313/c/xc/m06l.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/pbe.c -o build/temp.linux-x86_64-cpython-313/c/xc/pbe.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/pw91.c -o build/temp.linux-x86_64-cpython-313/c/xc/pw91.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/revtpss.c -o build/temp.linux-x86_64-cpython-313/c/xc/revtpss.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/revtpss_c_pbe.c -o build/temp.linux-x86_64-cpython-313/c/xc/revtpss_c_pbe.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/rpbe.c -o build/temp.linux-x86_64-cpython-313/c/xc/rpbe.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/tpss.c -o build/temp.linux-x86_64-cpython-313/c/xc/tpss.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/vdw.c -o build/temp.linux-x86_64-cpython-313/c/xc/vdw.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/xc.c -o build/temp.linux-x86_64-cpython-313/c/xc/xc.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS -DGPAW_NO_UNDERSCORE_CSCALAPACK -DGPAW_MPI_INPLACE -DPARALLEL -DGPAW_WITH_FFTW -DGPAW_WITH_SL -DGPAW_WITH_ELPA -UNDEBUG -I/usr/include/elpa -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c c/xc/xc_mgga.c -o build/temp.linux-x86_64-cpython-313/c/xc/xc_mgga.o -Wall -Wno-unknown-pragmas -std=c99
mpicc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro [too-long-redacted] cpython-313-x86_64-linux-gnu.so
Build temp: build/temp.linux-x86_64-cpython-313
Build lib: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build
running build_scripts
creating build/scripts-3.13
copying and adjusting tools/gpaw-analyse-basis -> build/scripts-3.13
copying and adjusting tools/gpaw-basis -> build/scripts-3.13
copying and adjusting tools/gpaw-plot-parallel-timings -> build/scripts-3.13
copying and adjusting tools/gpaw-runscript -> build/scripts-3.13
copying and adjusting tools/gpaw-setup -> build/scripts-3.13
copying and adjusting tools/gpaw-upfplot -> build/scripts-3.13
changing mode of build/scripts-3.13/gpaw-analyse-basis from 644 to 755
changing mode of build/scripts-3.13/gpaw-basis from 644 to 755
changing mode of build/scripts-3.13/gpaw-plot-parallel-timings from 644 to 755
changing mode of build/scripts-3.13/gpaw-runscript from 644 to 755
changing mode of build/scripts-3.13/gpaw-setup from 644 to 755
changing mode of build/scripts-3.13/gpaw-upfplot from 644 to 755
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- --test-pytest --test-args="-v -m ci"
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest -v -m ci
============================= test session starts ==============================
platform linux -- Python 3.13.8, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
GPAW MPI rank=0, size=1
Cache directory including gpw files: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/.pytest_cache/d
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build
configfile: pytest.ini
testpaths: gpaw
plugins: typeguard-4.4.4
collecting ... collected 1651 items / 1574 deselected / 77 selected
gpaw/test/ase_features/test_ase3k.py::test_no_cell PASSED [ 1%]
gpaw/test/exx/test_forces_ut.py::test_force PASSED [ 2%]
gpaw/test/fd_ops/test_transformations.py::test_fd_ops_transformations PASSED [ 3%]
gpaw/test/lfc/test_second_derivative.py::test_lfc_second_derivative PASSED [ 5%]
gpaw/test/linalg/test_gemm.py::test_linalg_gemm PASSED [ 6%]
gpaw/test/linalg/test_zher.py::test_linalg_zher PASSED [ 7%]
gpaw/test/parallel/test_mpi.py::test_scalar_reduce PASSED [ 9%]
gpaw/test/poisson/test_poisson.py::test_poisson_poisson PASSED [ 10%]
gpaw/test/pw/test_interpol.py::test_pw_interpol PASSED [ 11%]
gpaw/test/pw/test_lfc.py::test_pw_lfc PASSED [ 12%]
gpaw/test/pw/test_reallfc.py::test_pw_reallfc PASSED [ 14%]
gpaw/test/pw/test_smallanglecell.py::test_pw_smallanglecell PASSED [ 15%]
gpaw/test/radial/test_integral4.py::test_radial_integral4 PASSED [ 16%]
gpaw/test/radial/test_lebedev.py::test_radial_lebedev PASSED [ 18%]
gpaw/test/response/test_gw_si.py::test_small_response_gwsi[all-0] PASSED [ 19%]
gpaw/test/response/test_gw_si.py::test_small_response_gwsi[all-1] PASSED [ 20%]
gpaw/test/response/test_gw_si.py::test_few_freq_response_gwsi PASSED [ 22%]
gpaw/test/response/test_heisenberg.py::test_single_site_magnons PASSED [ 23%]
gpaw/test/response/test_heisenberg.py::test_single_site_magnons_consistency PASSED [ 24%]
gpaw/test/response/test_heisenberg.py::test_fm_random_magnons PASSED [ 25%]
gpaw/test/response/test_heisenberg.py::test_fm_vectorized_magnons PASSED [ 27%]
gpaw/test/response/test_site_kernels.py::test_spherical_kernel PASSED [ 28%]
gpaw/test/response/test_site_kernels.py::test_cylindrical_kernel PASSED [ 29%]
gpaw/test/response/test_site_kernels.py::test_parallelepipedic_kernel PASSED [ 31%]
gpaw/test/response/test_site_kernels.py::test_Co_hcp_site_kernels PASSED [ 32%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[setups0-hello-Na.hello.basis] PASSED [ 33%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[hello-basis1-Na.hello.LDA] PASSED [ 35%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[hello-dzp-Na.hello.dzp.basis] PASSED [ 36%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[hello-sz(dzp)-Na.hello.dzp.basis] PASSED [ 37%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[hello-world.dzp-Na.hello.world.dzp.basis] PASSED [ 38%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[hello-sz(world.dzp)-Na.hello.world.dzp.basis] PASSED [ 40%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[paw-world.dzp-Na.world.dzp.basis] PASSED [ 41%]
gpaw/test/setups/test_setup_basis_spec.py::test_setup_basis_spec[paw-sz(world.dzp)-Na.world.dzp.basis] PASSED [ 42%]
gpaw/test/test_aeatom.py::test_aeatom FAILED [ 44%]
gpaw/test/test_atoms_mismatch.py::test_atoms_mismatch PASSED [ 45%]
gpaw/test/test_fixdensity.py::test_fixdensity PASSED [ 46%]
gpaw/test/test_fixdensity_mgga.py::test_fixdensity PASSED [ 48%]
gpaw/test/test_fuzz.py::test_fuzz[0-pw] PASSED [ 49%]
gpaw/test/test_fuzz.py::test_fuzz[0-lcao] PASSED [ 50%]
gpaw/test/test_fuzz.py::test_fuzz[0-fd] PASSED [ 51%]
gpaw/test/test_fuzz.py::test_fuzz[1-pw] PASSED [ 53%]
gpaw/test/test_fuzz.py::test_fuzz[1-lcao] PASSED [ 54%]
gpaw/test/test_fuzz.py::test_fuzz[1-fd] PASSED [ 55%]
gpaw/test/test_inducedfield_lrtddft.py::test_inducedfield_lrtddft PASSED [ 57%]
gpaw/test/test_inducedfield_td.py::test_inducedfield_td PASSED [ 58%]
gpaw/test/test_libelpa.py::test_libelpa[normal-elpa-float] PASSED [ 59%]
gpaw/test/test_libelpa.py::test_libelpa[normal-elpa-complex] PASSED [ 61%]
gpaw/test/test_libelpa.py::test_libelpa[normal-scalapack-float] PASSED [ 62%]
gpaw/test/test_libelpa.py::test_libelpa[normal-scalapack-complex] PASSED [ 63%]
gpaw/test/test_libelpa.py::test_libelpa[general-elpa-float] PASSED [ 64%]
gpaw/test/test_libelpa.py::test_libelpa[general-elpa-complex] PASSED [ 66%]
gpaw/test/test_libelpa.py::test_libelpa[general-scalapack-float] PASSED [ 67%]
gpaw/test/test_libelpa.py::test_libelpa[general-scalapack-complex] PASSED [ 68%]
gpaw/test/test_multipoletest.py::test_multipole PASSED [ 70%]
gpaw/test/test_new_calculator.py::test_new_calculator PASSED [ 71%]
gpaw/test/test_occupations.py::test_occupations[func0] PASSED [ 72%]
gpaw/test/test_occupations.py::test_occupations[func1] PASSED [ 74%]
gpaw/test/test_occupations.py::test_occupations[func2] PASSED [ 75%]
gpaw/test/test_occupations.py::test_occupations[func3] PASSED [ 76%]
gpaw/test/test_occupations.py::test_occupations[func4] PASSED [ 77%]
gpaw/test/test_occupations.py::test_occupations[func5] PASSED [ 79%]
gpaw/test/test_occupations.py::test_occupations[func6] PASSED [ 80%]
gpaw/test/test_occupations.py::test_occupations[func7] PASSED [ 81%]
gpaw/test/test_occupations.py::test_occupations[func8] PASSED [ 83%]
gpaw/test/test_occupations.py::test_occupations[func9] PASSED [ 84%]
gpaw/test/test_occupations.py::test_occupations[func10] PASSED [ 85%]
gpaw/test/test_occupations.py::test_occupations[func11] PASSED [ 87%]
gpaw/test/test_occupations.py::test_occ_obj[e_kn0-w_k0-2] PASSED [ 88%]
gpaw/test/test_occupations.py::test_occ_obj[e_kn1-w_k1-1.5] PASSED [ 89%]
gpaw/test/test_occupations.py::test_occ_obj[e_kn2-w_k2-2] PASSED [ 90%]
gpaw/test/test_warn_missing_mode.py::test_no_mode_supplied[True] PASSED [ 92%]
gpaw/test/test_warn_missing_mode.py::test_no_mode_supplied[False] PASSED [ 93%]
gpaw/test/utilities/test_wannier_ethylene.py::test_ethylene_energy PASSED [ 94%]
gpaw/test/utilities/test_wannier_ethylene.py::test_wannier_centers PASSED [ 96%]
gpaw/test/utilities/test_wannier_ethylene.py::test_wannier_centers_gpw PASSED [ 97%]
gpaw/test/xc/test_XC2.py::test_xc_XC2 PASSED [ 98%]
gpaw/test/xc/test_xc.py::test_xc_xc PASSED [100%]Memory usage: 839.96 MiB
Date: Fri Oct 10 13:30:21 2025
=================================== FAILURES ===================================
_________________________________ test_aeatom __________________________________
@pytest.mark.ci
@pytest.mark.serial
def test_aeatom():
Z = 79 # gold atom
kwargs = dict(ngpts=5000, alpha2=1000 * Z**2, ngauss=200)
# Test Schroedinger equation:
aea = AllElectronAtom(Z, log=None)
aea.initialize(**kwargs)
errors = []
for channel in aea.channels:
# Basis set of Gaussians:
channel.solve(-Z)
for n in range(7):
e = channel.e_n[n]
e0 = -0.5 * Z**2 / (n + channel.l + 1)**2
errors.append(abs(e / e0 - 1))
# Finite-difference:
channel.solve2(-Z)
for n in range(7):
e = channel.e_n[n]
e0 = -0.5 * Z**2 / (n + channel.l + 1)**2
errors.append(abs(e / e0 - 1))
print(max(errors))
assert max(errors) == pytest.approx(0, abs=2.0e-5)
# Test Dirac equation:
aea = AllElectronAtom(Z, dirac=True, log=None)
> aea.initialize(**kwargs)
gpaw/test/test_aeatom.py:36:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
gpaw/atom/aeatom.py:562: in initialize
basis = GaussianBasis(leff, alpha_B, self.rgd, eps)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <gpaw.atom.aeatom.GaussianBasis object at 0x7fa922f77230>
l = -0.18289639780608224
alpha_B = array([1.00000000e-02, 1.10712653e-02, 1.22572915e-02, 1.35703726e-02,
1.50241195e-02, 1.66336012e-02, 1.841550...3.38899275e+06, 3.75204377e+06, 4.15398720e+06,
4.59898943e+06, 5.09166320e+06, 5.63711540e+06, 6.24100000e+06])
rgd = <gpaw.atom.radialgd.AERadialGridDescriptor object at 0x7fa922ecf9b0>
eps = 1e-07
def __init__(self, l, alpha_B, rgd, eps=1.0e-7):
"""Guassian basis set for spherically symmetric atom.
l: int
Angular momentum quantum number.
alpha_B: ndarray
Exponents.
rgd: GridDescriptor
Grid descriptor.
eps: float
Cutoff for eigenvalues of overlap matrix."""
self.l = l
self.alpha_B = alpha_B
self.rgd = rgd
self.eps = eps
A_BB = np.add.outer(alpha_B, alpha_B)
M_BB = np.multiply.outer(alpha_B, alpha_B)
# Overlap matrix:
S_BB = (2 * M_BB**0.5 / A_BB)**(l + 1.5)
# Kinetic energy matrix:
T_BB = 2**(l + 2.5) * M_BB**(0.5 * l + 0.75) / gamma(l + 1.5) * (
gamma(l + 2.5) * M_BB / A_BB**(l + 2.5) -
0.5 * (l + 1) * gamma(l + 1.5) / A_BB**(l + 0.5) +
0.25 * (l + 1) * (2 * l + 1) * gamma(l + 0.5) / A_BB**(l + 0.5))
# Derivative matrix:
D_BB = 2**(l + 2.5) * M_BB**(0.5 * l + 0.75) / gamma(l + 1.5) * (
0.5 * (l + 1) * gamma(l + 1) / A_BB**(l + 1) -
gamma(l + 2) * alpha_B / A_BB**(l + 2))
# 1/r matrix:
K_BB = 2**(l + 2.5) * M_BB**(0.5 * l + 0.75) / gamma(l + 1.5) * (
0.5 * gamma(l + 1) / A_BB**(l + 1))
# Find set of linearly independent functions.
# We have len(alpha_B) gaussians (index B) and self.nbasis
# linearly independent functions (index b).
s_B, U_BB = eigh(S_BB)
self.nbasis = int((s_B > eps).sum())
Q_Bb = np.dot(U_BB[:, -self.nbasis:],
np.diag(s_B[-self.nbasis:]**-0.5))
self.T_bb = np.dot(np.dot(Q_Bb.T, T_BB), Q_Bb)
self.D_bb = np.dot(np.dot(Q_Bb.T, D_BB), Q_Bb)
self.K_bb = np.dot(np.dot(Q_Bb.T, K_BB), Q_Bb)
r_g = rgd.r_g
with seterr(divide='ignore'):
# Avoid errors in debug mode from division by zero:
gaussians_Bg = np.exp(-np.outer(alpha_B, r_g**2)) * r_g**l
prefactors_B = (2 * (2 * alpha_B)**(l + 1.5) / gamma(l + 1.5))**0.5
> self.basis_bg = np.dot(Q_Bb.T, prefactors_B[:, None] * gaussians_Bg)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E FloatingPointError: invalid value encountered in dot
gpaw/atom/aeatom.py:84: FloatingPointError
----------------------------- Captured stdout call -----------------------------
Z: 79
Name: Gold
Symbol: Au
XC-functional: LDA
Equation: Schrödinger
Grid points: 5000 (0.00000, 0.00002, 0.00004, ..., 41.763, 45.569)
Exponents: 200 (0.010, 0.011, ..., 5637115.398, 6241000.000)
Basis functions: 49, 54, 58, 62 (s, p, d, f)
2.5000917900364072e-06
Z: 79
Name: Gold
Symbol: Au
XC-functional: LDA
Equation: Dirac
Grid points: 5000 (0.00000, 0.00002, 0.00004, ..., 41.763, 45.569)
Exponents: 200 (0.010, 0.011, ..., 5637115.398, 6241000.000)
================================ GPAW-MPI stuff ================================
size: 1
=========================== short test summary info ============================
FAILED gpaw/test/test_aeatom.py::test_aeatom - FloatingPointError: invalid va...
================ 1 failed, 76 passed, 1574 deselected in 51.74s ================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest -v -m ci
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 --test-pytest --test-args="-v -m ci" returned exit code 13
make[1]: *** [debian/rules:10: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
More information about the Debichem-devel
mailing list