[Debichem-devel] Bug#837685: psi4: FTBFS with bindnow and PIE enabled

[Balint Reczey]

Source: psi4
Version: 1.0~rc-3
Severity: important
User: balint at balintreczey.hu
Usertags: pie-bindnow-20160906
Justification: FTBFS on amd64 with extra hardening

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64 with patched GCC and dpkg.

The rebuild tested if packages are ready for a transition
enabling PIE and bindnow for amd64.

For more information about the changes to sid's dpkg and GCC please
visit:
 https://wiki.debian.org/Hardening/PIEByDefaultTransition

Relevant part (hopefully):
...
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[100%] Linking CXX executable ../../../bin/psi4
cd "/<<PKGBUILDDIR>>/builddir/src/bin/psi4" && /usr/bin/cmake -E
cmake_link_script CMakeFiles/psi4.dir/link.txt --verbose=1
/usr/bin/c++   -DRESTRICT=__restrict__ -Xlinker -export-dynamic -fPIC
-std=c++11 -fopenmp -O2 -g -DNDEBUG
CMakeFiles/psi4_objlib.dir/export_psio.cc.o
CMakeFiles/psi4_objlib.dir/export_mints.cc.o
CMakeFiles/psi4_objlib.dir/psi_stop.cc.o
CMakeFiles/psi4_objlib.dir/export_functional.cc.o
CMakeFiles/psi4_objlib.dir/export_oeprop.cc.o
CMakeFiles/psi4_objlib.dir/export_plugins.cc.o
CMakeFiles/psi4_objlib.dir/export_blas_lapack.cc.o
CMakeFiles/psi4_objlib.dir/export_benchmarks.cc.o
CMakeFiles/psi4_objlib.dir/export_efp.cc.o
CMakeFiles/psi4_objlib.dir/export_cubeprop.cc.o
CMakeFiles/psi4_objlib.dir/clean.cc.o
CMakeFiles/psi4_objlib.dir/create_new_plugin.cc.o
CMakeFiles/psi4_objlib.dir/script.cc.o
CMakeFiles/psi4_objlib.dir/set_memory.cc.o
CMakeFiles/psi4_objlib.dir/read_options.cc.o
CMakeFiles/psi4_objlib.dir/export_libparallel.cc.o
CMakeFiles/versioned_code.dir/version.cc.o
CMakeFiles/versioned_code.dir/python.cc.o
CMakeFiles/versioned_code.dir/psi_start.cc.o
CMakeFiles/versioned_code.dir/psi4.cc.o  -o ../../../bin/psi4 -rdynamic
-lutil -lm -lrt -ldl -lpython2.7 -Wl,--whole-archive
../../../lib/libadc.a ../../../lib/libccdensity.a
../../../lib/libccenergy.a ../../../lib/libcceom.a
../../../lib/libcchbar.a ../../../lib/libcclambda.a
../../../lib/libccresponse.a ../../../lib/libccsort.a
../../../lib/libcctransort.a ../../../lib/libcctriples.a
../../../lib/libdcft.a ../../../lib/libderiv_wrapper.a
../../../lib/libdetci.a ../../../lib/libdfmp2.a ../../../lib/libdfocc.a
../../../lib/libefp.a ../../../lib/libfindif.a ../../../lib/libfisapt.a
../../../lib/libfnocc.a ../../../lib/libmcscf.a
../../../lib/libmints_wrapper.a ../../../lib/libmrcc.a
../../../lib/libocc.a ../../../lib/liboptking.a
../../../lib/libpsimrcc.a ../../../lib/libsapt.a ../../../lib/libscf.a
../../../lib/libscfgrad.a ../../../lib/libthermo.a
../../../lib/libtransqt2.a ../../../lib/libdmrg.a
../../../lib/lib3index.a ../../../lib/libciomr.a ../../../lib/libdiis.a
../../../lib/libdisp.a ../../../lib/libdpd.a
../../../lib/libefp_solver.a ../../../lib/libfock.a
../../../lib/libfunctional.a -Wl,--whole-archive ../../../lib/libiwl.a
-Wl,--no-whole-archive ../../../lib/libmints.a ../../../lib/libmoinfo.a
../../../lib/liboptions.a ../../../lib/libparallel.a
../../../lib/libparallel2.a ../../../lib/libplugin.a
../../../lib/libsapt_solver.a ../../../lib/libscf_solver.a
../../../lib/libthce.a ../../../lib/libtrans.a
../../../lib/libpsi4util.a ../../../lib/libpsio.a
../../../lib/libPsiUtil.a ../../../lib/libqt.a
../../../lib/libcubeprop.a ../../../lib/libinterface_libefp.a
-Wl,--no-whole-archive -Wl,-Bstatic -lboost_filesystem -lboost_python
-lboost_regex -lboost_serialization -lboost_system -lboost_timer
-lboost_chrono -lboost_thread -lboost_date_time -lboost_atomic
-Wl,-Bdynamic -lpthread -llapack -lblas -lpython2.7 -lblas -llapack
-lint -lderiv -lutil -ldl -lrt -lm
/usr/lib/x86_64-linux-gnu/libchemps2.so -lchemps2
/usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so -lsz -lz -lpthread
-lm -lpython2.7 -ldl
-Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial/lib /usr/bin/ld:
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libboost_filesystem.a(operations.o):
relocation R_X86_64_32S against symbol
`_ZN5boost6detail15sp_counted_base7destroyEv' can not be used when
making a shared object; recompile with -fPIC
/usr/bin/ld:
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libboost_filesystem.a(path.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when
making a shared object; recompile with -fPIC
...
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
src/bin/psi4/CMakeFiles/psi4.dir/build.make:201: recipe for target
'bin/psi4' failed
make[4]: *** [bin/psi4] Error 1
...

The full build log is available from:
 https://people.debian.org/~rbalint/build-logs/pie-bindnow-20160906/psi4_1.0~rc-3_amd64.build.gz

Linking with boost dynamically would probably fix the problem.

Thanks,
Balint