[Debichem-devel] Bug#983946: openstructure: ftbfs with -march=x86-64-v3

[Matthias Klose]

Package: src:openstructure
Version: 2.2.0-6
Severity: minor
User: debian-gcc at lists.debian.org
Usertags: ftbfs-x86-64-v3

Starting with LLVM 12 and GCC 11 (and backported to gcc-10 for Debian), 
GCC introduces optimizations for new micro-architecture levels from
the x86-64 psABI.  Filing these bug reports for packages building with
the current level (x86-64), but not with x86-64-v3.

To reproduce these issues, append -march=x86-64-v3 to the compiler
flags (CFLAGS, CXXFLAGS, ...).  You also need hardware supporting these.
The easiest way is to call the dynamic linker in glibc 2.33 like
  /lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 --help
Otherwise look at the flags in /proc/cpuinfo and compare these with
those from table 3.1 in the System V Application Binary Interface doc:
https://gitlab.com/x86-psABIs/x86-64-ABI/-/wikis/x86-64-psABI

Please don't upload a package setting these flags by default.  The
x86-64 baseline is still unchanged.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc10-v3/openstructure_2.2.0-6_unstable_gcc10-v3.log
The last lines of the build log are at the end of this report.

[...]
...s
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Ran 4 tests in 0.002s

OK (skipped=1)
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 97%] Built target test_io_pdb.py_run
make  -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/modules/mol/base/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/mol/base/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/DependInfo.cmake --color=
Scanning dependencies of target ost_mol_tests_run
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 98%] running checks for module mol
cd /<<PKGBUILDDIR>>/modules/mol/base/tests && env OST_ROOT=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/ost_mol_tests
Running 70 test cases...
./modules/mol/base/tests/test_ics.cc(216): error: in "mol_base/ics_settorsion_linear_unbuffered": difference{4} between s.t2.GetAngle(){-2.3561945} and Real(3.14159265358979323846/4){0.785398185} exceeds 0.0001%

*** 1 failure is detected in the test module "ost_mol_base"
make[4]: *** [modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make:80: modules/mol/base/tests/CMakeFiles/ost_mol_tests_run] Error 201
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:5452: modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
.[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_io_sequence_profile.cc
........s
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Ran 10 tests in 0.701s

OK (skipped=1)
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_pir.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_pir.cc
[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o
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[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/tests.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/tests.cc
[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_star_parser.cc
[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o
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[100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_mmcif_info.cc
.
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Ran 2 tests in 22.683s

OK
Could not find CAD score classic executables: ignoring unit tests
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[100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 check ARGS\+=-j4 returned exit code 2
make: *** [debian/rules:4: binary] Error 25
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