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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
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Build fails with LTO due to ODR violations #395

Closed eli-schwartz closed 3 weeks ago

eli-schwartz commented 3 weeks ago

I tried to build with the following *FLAGS to optimize the build: -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing

Link-Time Optimization is a massively global compiler optimization pass which is pretty handy for producing faster executables. It also has the interesting property that because the compiler does whole-program analysis using bytecode, it can save type information and perform error checks that it normally doesn’t have enough insight for. In particular, checking for ODR issues and checking function type signature mismatches.

Note that all the -Werror=* flags are used to help detect cases where the compiler tries to optimize by assuming UB cannot exist in the source code -- if it does exist, ordinarily the code would be miscompiled, and this says to make the miscompilation a fatal error.

I got this error:

2024-09-04 17:32:02,648 root INFO x86_64-pc-linux-gnu-g++ -pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security -std=c++17 -DNDEBUG -shared -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Werror=int-conversion -Werror=incompatible-pointer-types -DNDEBUG /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/build/generated/ShaderText.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o 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/var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o 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/var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVContext.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVHeap.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVHeapArray.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVLexicon.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVOneToAny.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVOneToOne.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVRandom.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/ov_utility.o -L/usr/lib64 -L/usr/lib -L/usr/lib64 -lpng -lfreetype -lxml2 -lGL -lGLEW -lnetcdf -o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/lib.linux-x86_64-cpython-312/pymol/_cmd.cpython-312-x86_64-linux-gnu.so -fopenmp
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:62:16: error: type ‘struct parm’ violates the C++ One Definition Rule [-Werror=odr]
   62 | typedef struct parm {
      |                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:59:16: note: a different type is defined in another translation unit
   59 | typedef struct parm {
      |                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:63:8: note: the first difference of corresponding definitions is field ‘title’
   63 |   char title[85];
      |        ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:60:17: note: a field with different name is defined in another translation unit
   60 |         char    ititl[81];
      |                 ^
contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:33:3: error: type ‘struct parmdata’ violates the C++ One Definition Rule [-Werror=odr]
   33 | } parmdata;
      |   ^
contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:32:3: note: a different type is defined in another translation unit
   32 | } parmdata;
      |   ^
contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:28:15: note: the first difference of corresponding definitions is field ‘prm’
   28 |   parmstruct *prm;
      |               ^
contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:28:13: note: a field with different name is defined in another translation unit
   28 |   ReadPARM *rp;
      |             ^
layer0/Isosurf.cpp:47:16: error: type ‘struct PointType’ violates the C++ One Definition Rule [-Werror=odr]
   47 | typedef struct PointType {
      |                ^
layer0/Tetsurf.cpp:46:3: note: a different type is defined in another translation unit
   46 | } PointType;
      |   ^
layer0/Isosurf.cpp:49:7: note: the first difference of corresponding definitions is field ‘NLink’
   49 |   int NLink;
      |       ^
layer0/Tetsurf.cpp:43:9: note: a field with different name is defined in another translation unit
   43 |   float Normal[3];
      |         ^
ov/src/OVOneToAny.cpp:15:3: error: type ‘struct up_element’ violates the C++ One Definition Rule [-Werror=odr]
   15 | } up_element;
      |   ^
ov/src/OVOneToOne.cpp:15:3: note: a different type is defined in another translation unit
   15 | } up_element;
      |   ^
ov/src/OVOneToOne.cpp:14:25: note: the first difference of corresponding definitions is field ‘reverse_next’
   14 |   ov_size forward_next, reverse_next;
      |                         ^
ov/src/OVOneToOne.cpp:15:3: note: a type with different number of fields is defined in another translation unit
   15 | } up_element;
      |   ^
lto1: some warnings being treated as errors
lto-wrapper: fatal error: /usr/bin/x86_64-pc-linux-gnu-g++ returned 1 exit status
compilation terminated.
/usr/libexec/gcc/x86_64-pc-linux-gnu/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
error: command '/usr/bin/x86_64-pc-linux-gnu-g++' failed with exit code 1
 * ERROR: sci-chemistry/pymol-3.0.0::gentoo failed (compile phase):

Originally reported downstream: https://bugs.gentoo.org/933235 Full build log: build.log

eli-schwartz commented 3 weeks ago

From a quick look, e.g. parm vs parm7 define similar types using the same name.

JarrettSJohnson commented 3 weeks ago

Thanks for the report. Should be resolved now.

eli-schwartz commented 3 weeks ago

Thank you for the fast response! :)

(I have not tested the change as the approach to building the package seems to have changed quite a bit in git master, so I'm going to wait until the maintainer of the distro package upgrades to the next version.)