Bug#1015672: sundials: ftbfs with LTO (link time optimization) enabled

[Matthias Klose]

Package: src:sundials
Version: 5.8.0+dfsg-1
Severity: minor
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-lto

This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled.  For a background
for LTO please see

https://wiki.debian.org/ToolChain/LTO

The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures.  The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.

To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:

export DEB_BUILD_MAINT_OPTIONS = optimize=+lto

Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:

export DEB_BUILD_MAINT_OPTIONS = optimize=-lto

or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/sundials_5.8.0+dfsg-1_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
  268 |  10      vv(i) = vv(i) * pp(i)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
Dependee "/<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_parallel/CMakeFiles/fkinDiagon_kry_p.dir/DependInfo.cmake" is newer than depender "/<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_parallel/CMakeFiles/fkinDiagon_kry_p.dir/depend.internal".
Dependee "/<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_parallel/CMakeFiles/fkinDiagon_kry_p.dir/depend.internal".
Scanning dependencies of target fkinDiagon_kry_p
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make  -f examples/kinsol/fcmix_parallel/CMakeFiles/fkinDiagon_kry_p.dir/build.make examples/kinsol/fcmix_parallel/CMakeFiles/fkinDiagon_kry_p.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/debian/build'
[ 98%] Linking Fortran executable fidaRoberts_dns_pthreads
cd /<<PKGBUILDDIR>>/debian/build/examples/ida/fcmix_pthreads && /usr/bin/cmake -E cmake_link_script CMakeFiles/fidaRoberts_dns_pthreads.dir/link.txt --verbose=1
[ 98%] Building Fortran object examples/kinsol/fcmix_parallel/CMakeFiles/fkinDiagon_kry_p.dir/fkinDiagon_kry_p.f.o
cd /<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_parallel && /usr/bin/mpif90  -I/usr/lib/petscdir/petsc3.16/x86_64-linux-gnu-real/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/debian/build/include -I/<<PKGBUILDDIR>>/src/sundials -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -J../../../fortran -c /<<PKGBUILDDIR>>/examples/kinsol/fcmix_parallel/fkinDiagon_kry_p.f -o CMakeFiles/fkinDiagon_kry_p.dir/fkinDiagon_kry_p.f.o
/usr/bin/gfortran -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong CMakeFiles/fidaRoberts_dns_pthreads.dir/fidaRoberts_dns_pthreads.f.o -o fidaRoberts_dns_pthreads  -Wl,-rpath,/<<PKGBUILDDIR>>/debian/build/src/nvector/pthreads:/<<PKGBUILDDIR>>/debian/build/src/ida ../../../src/ida/fcmix/libsundials_fida.a ../../../src/nvector/pthreads/libsundials_fnvecpthreads.so.5.8.0 -lm /usr/lib/x86_64-linux-gnu/librt.so -lpthread -lm ../../../src/ida/libsundials_ida.so.5.8.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/debian/build/src/nvector/pthreads 
[ 98%] Linking Fortran executable fkinDiagon_kry
cd /<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_serial && /usr/bin/cmake -E cmake_link_script CMakeFiles/fkinDiagon_kry.dir/link.txt --verbose=1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[ 98%] Built target fidaRoberts_dns_openmp
/usr/bin/gfortran -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong CMakeFiles/fkinDiagon_kry.dir/fkinDiagon_kry.f.o -o fkinDiagon_kry  -Wl,-rpath,/<<PKGBUILDDIR>>/debian/build/src/nvector/serial:/<<PKGBUILDDIR>>/debian/build/src/kinsol ../../../src/kinsol/fcmix/libsundials_fkinsol.a ../../../src/nvector/serial/libsundials_fnvecserial.so.5.8.0 -lm /usr/lib/x86_64-linux-gnu/librt.so -lm ../../../src/kinsol/libsundials_kinsol.so.5.8.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/debian/build/src/nvector/serial 
/<<PKGBUILDDIR>>/examples/kinsol/fcmix_parallel/fkinDiagon_kry_p.f:281:72:

  281 |  10      fval(i) = uu(i) * uu(i) - (i + baseadd) * (i + baseadd)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
/<<PKGBUILDDIR>>/examples/kinsol/fcmix_parallel/fkinDiagon_kry_p.f:310:72:

  310 |  10      pp(i) = 0.5d0 / (udata(i) + 5.0d0)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
/<<PKGBUILDDIR>>/examples/kinsol/fcmix_parallel/fkinDiagon_kry_p.f:339:72:

  339 |  10      vv(i) = vv(i) * pp(i)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
/usr/bin/cmake -E cmake_copy_f90_mod examples/arkode/F90_serial/fem.mod examples/arkode/F90_serial/CMakeFiles/ark_bruss1D_FEM_klu.dir/fem.mod.stamp GNU
/usr/bin/cmake -E cmake_copy_f90_mod examples/arkode/F90_serial/quadrature.mod examples/arkode/F90_serial/CMakeFiles/ark_bruss1D_FEM_klu.dir/quadrature.mod.stamp GNU
/usr/bin/cmake -E cmake_copy_f90_mod examples/arkode/F90_serial/userdata.mod examples/arkode/F90_serial/CMakeFiles/ark_bruss1D_FEM_klu.dir/userdata.mod.stamp GNU
/usr/bin/cmake -E touch examples/arkode/F90_serial/CMakeFiles/ark_bruss1D_FEM_klu.dir/ark_bruss1D_FEM_klu.f90.o.provides.build
[ 98%] Linking Fortran executable ark_bruss1D_FEM_klu
cd /<<PKGBUILDDIR>>/debian/build/examples/arkode/F90_serial && /usr/bin/cmake -E cmake_link_script CMakeFiles/ark_bruss1D_FEM_klu.dir/link.txt --verbose=1
/usr/bin/gfortran -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong CMakeFiles/ark_bruss1D_FEM_klu.dir/ark_bruss1D_FEM_klu.f90.o -o ark_bruss1D_FEM_klu  -Wl,-rpath,/<<PKGBUILDDIR>>/debian/build/src/arkode:/<<PKGBUILDDIR>>/debian/build/src/sunlinsol/klu:/<<PKGBUILDDIR>>/debian/build/src/sunmatrix/sparse:/<<PKGBUILDDIR>>/debian/build/src/nvector/serial ../../../src/arkode/fcmix/libsundials_farkode.a ../../../src/arkode/libsundials_arkode.so.4.8.0 -lm /usr/lib/x86_64-linux-gnu/librt.so ../../../src/sunlinsol/klu/libsundials_fsunlinsolklu.so.3.8.0 -lm ../../../src/sunlinsol/klu/libsundials_sunlinsolklu.so.3.8.0 /usr/lib/x86_64-linux-gnu/libklu.so /usr/lib/x86_64-linux-gnu/libklu.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libbtf.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so ../../../src/nvector/serial/libsundials_fnvecserial.so.5.8.0 ../../../src/nvector/serial/libsundials_nvecserial.so.5.8.0 ../../../src/sunmatrix/sparse/libsundials_sunmatrixsparse.so.3.8.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/debian/build/src/sunmatrix/sparse 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[ 98%] Built target fark_diag_kry_bbd_p
/usr/bin/ld: /<<PKGBUILDDIR>>/debian/build/src/nvector/pthreads/libsundials_nvecpthreads.so.5: undefined reference to `pthread_create'
/usr/bin/ld: /<<PKGBUILDDIR>>/debian/build/src/nvector/pthreads/libsundials_nvecpthreads.so.5: undefined reference to `pthread_join'
collect2: error: ld returned 1 exit status
make[3]: *** [examples/ida/fcmix_pthreads/CMakeFiles/fidaRoberts_dns_pthreads.dir/build.make:103: examples/ida/fcmix_pthreads/fidaRoberts_dns_pthreads] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make[2]: *** [CMakeFiles/Makefile2:13961: examples/ida/fcmix_pthreads/CMakeFiles/fidaRoberts_dns_pthreads.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[100%] Linking Fortran executable fkinDiagon_kry_p
cd /<<PKGBUILDDIR>>/debian/build/examples/kinsol/fcmix_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/fkinDiagon_kry_p.dir/link.txt --verbose=1
/usr/bin/mpif90 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong CMakeFiles/fkinDiagon_kry_p.dir/fkinDiagon_kry_p.f.o -o fkinDiagon_kry_p  -Wl,-rpath,/<<PKGBUILDDIR>>/debian/build/src/nvector/parallel:/<<PKGBUILDDIR>>/debian/build/src/kinsol ../../../src/kinsol/fcmix/libsundials_fkinsol.a ../../../src/nvector/parallel/libsundials_fnvecparallel.so.5.8.0 -lm /usr/lib/x86_64-linux-gnu/librt.so -lm ../../../src/kinsol/libsundials_kinsol.so.5.8.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/debian/build/src/nvector/parallel 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[100%] Built target fkinDiagon_kry
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[100%] Built target fkinDiagon_kry_p
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[100%] Linking Fortran executable fidaHeat2D_kry_bbd_p
cd /<<PKGBUILDDIR>>/debian/build/examples/ida/fcmix_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/fidaHeat2D_kry_bbd_p.dir/link.txt --verbose=1
[100%] Built target ark_bruss1D_FEM_klu
/usr/bin/mpif90 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong CMakeFiles/fidaHeat2D_kry_bbd_p.dir/fidaHeat2D_kry_bbd_p.f.o -o fidaHeat2D_kry_bbd_p  -Wl,-rpath,/<<PKGBUILDDIR>>/debian/build/src/nvector/parallel:/<<PKGBUILDDIR>>/debian/build/src/ida ../../../src/ida/fcmix/libsundials_fida.a ../../../src/nvector/parallel/libsundials_fnvecparallel.so.5.8.0 -lm /usr/lib/x86_64-linux-gnu/librt.so -lm ../../../src/ida/libsundials_ida.so.5.8.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/debian/build/src/nvector/parallel 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[100%] Built target fidaHeat2D_kry_bbd_p
make[2]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make[1]: *** [Makefile:149: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
dh_auto_build: error: cd debian/build && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:50: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2