Build fails with GCC 11 on Linux

[awvwgk]

Trying to build molassembler against Nauty 2.7.2 fails with

[21/81] Building CXX object src/CMakeFiles/molassembler_obj.dir/Molassembler/Graph/Canonicalization.cpp.o
FAILED: src/CMakeFiles/molassembler_obj.dir/Molassembler/Graph/Canonicalization.cpp.o 
/home/abt-grimme/opt/conda/envs/gcc/bin/x86_64-conda-linux-gnu-c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DEIGEN_USE_BLAS -DEIGEN_USE_MKL_ALL -I/tmp1/ehlert/scine/molassembler/src -I/tmp1/ehlert/scine/molassembler/_build/src -I/software/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.6.324/linux/mkl/include -I/tmp1/ehlert/scine/molassembler/_build/RingDecomposerLib/src/RingDecomposerLib -isystem /home/abt-grimme/opt/conda/envs/scine/include -isystem /tmp1/ehlert/scine/molassembler/_build -isystem /home/abt-grimme/opt/conda/envs/scine/include/eigen3 -isystem /home/abt-grimme/opt/conda/envs/scine/include/Scine -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/abt-grimme/opt/conda/envs/gcc/include -g -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -Wall -Wextra -Wshadow -Wpedantic -Wduplicated-cond -Wlogical-op -Wold-style-cast -Wuseless-cast -Wdouble-promotion -Wno-maybe-uninitialized -std=gnu++14 -MD -MT src/CMakeFiles/molassembler_obj.dir/Molassembler/Graph/Canonicalization.cpp.o -MF src/CMakeFiles/molassembler_obj.dir/Molassembler/Graph/Canonicalization.cpp.o.d -o src/CMakeFiles/molassembler_obj.dir/Molassembler/Graph/Canonicalization.cpp.o -c /tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp
In file included from /home/abt-grimme/opt/conda/envs/scine/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/property_map/property_map.hpp:602,
                 from /home/abt-grimme/opt/conda/envs/scine/include/boost/graph/adjacency_list.hpp:27,
                 from /tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/PrivateGraph.h:11,
                 from /tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:15:
/home/abt-grimme/opt/conda/envs/scine/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use <iterator> instead.'
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/abt-grimme/opt/conda/envs/scine/include/nauty/nausparse.h:26,
                 from /tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:24:
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp: In function 'void molassembler_nauty_canonicalize(int, size_t, size_t*, int*, int*, size_t, size_t, size_t, int*, int*)':
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:51:3: error: '_Thread_local' does not name a type; did you mean 'thread_local'?
   51 |   DYNALLSTAT(int, orbits, orbits_sz);
      |   ^~~~~~~~~~
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:51:3: error: '_Thread_local' does not name a type; did you mean 'thread_local'?
   51 |   DYNALLSTAT(int, orbits, orbits_sz);
      |   ^~~~~~~~~~
In file included from /home/abt-grimme/opt/conda/envs/scine/include/nauty/nausparse.h:26,
                 from /tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:24:
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:52:26: error: 'orbits_sz' was not declared in this scope
   52 |   DYNALLOC1(int, orbits, orbits_sz, nv, "malloc");
      |                          ^~~~~~~~~
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:52:18: error: 'orbits' was not declared in this scope
   52 |   DYNALLOC1(int, orbits, orbits_sz, nv, "malloc");
      |                  ^~~~~~
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:52:18: error: 'orbits' was not declared in this scope
   52 |   DYNALLOC1(int, orbits, orbits_sz, nv, "malloc");
      |                  ^~~~~~
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:58:34: error: 'orbits' was not declared in this scope
   58 |   sparsenauty(&source, lab, ptn, orbits, &options, &stats, &canong);
      |                                  ^~~~~~
In file included from /home/abt-grimme/opt/conda/envs/scine/include/nauty/nausparse.h:26,
                 from /tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:24:
/tmp1/ehlert/scine/molassembler/src/Molassembler/Graph/Canonicalization.cpp:66:19: error: 'orbits_sz' was not declared in this scope
   66 |   DYNFREE(orbits, orbits_sz);
      |                   ^~~~~~~~~

cmake

❯ cmake -B _build -G Ninja -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DSCINE_MARCH=""
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/abt-grimme/opt/conda/envs/gcc/bin/x86_64-conda-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/abt-grimme/opt/conda/envs/gcc/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Setting build type to default 'Debug'
-- Scine::UtilsOS found locally at /home/abt-grimme/opt/conda/envs/scine/lib/cmake/ScineUtilsOS
-- Enabling GCC specific warning flags
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found LAPACKE for use with Eigen3
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Configuring done
CMake Warning at test/CMakeLists.txt:16 (add_executable):
  Cannot generate a safe runtime search path for target MolassemblerTests
  because files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libgomp.so.1] in /home/abt-grimme/opt/conda/envs/gcc/lib may be hidden by files in:
      /home/abt-grimme/opt/conda/envs/scine/lib

  Some of these libraries may not be found correctly.


-- Generating done
-- Build files have been written to: /tmp1/ehlert/scine/molassembler/_build

mamba info

     active environment : scine
    active env location : /home/abt-grimme/opt/conda/envs/scine
            shell level : 3
       user config file : /home/ehlert/.condarc
 populated config files : /home/abt-grimme/opt/conda/.condarc
                          /home/ehlert/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.10.final.0
       virtual packages : __linux=4.12.14=0
                          __glibc=2.26=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/abt-grimme/opt/conda  (writable)
      conda av data dir : /home/abt-grimme/opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/abt-grimme/opt/conda/pkgs
                          /home/ehlert/.conda/pkgs
       envs directories : /home/abt-grimme/opt/conda/envs
                          /home/ehlert/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.10 Linux/4.12.14-lp151.28.13-default opensuse-leap/15.1 glibc/2.26
                UID:GID : 1748:1001
             netrc file : None
           offline mode : False

mamba list

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
abseil-cpp                20211102.0           h27087fc_1    conda-forge
boost-cpp                 1.74.0               h75c5d50_8    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.6.15            ha878542_0    conda-forge
cyrus-sasl                2.1.27               h7604b24_5    conda-forge
docutils                  0.19            py310hff52083_0    conda-forge
eigen                     3.4.0                h4bd325d_0    conda-forge
gitdb                     4.0.9              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.27             pyhd8ed1ab_0    conda-forge
gmock                     1.11.0               h924138e_0    conda-forge
gtest                     1.11.0               h924138e_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.19.3               h08a2579_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libblas                   3.9.0           15_linux64_openblas    conda-forge
libbson                   1.21.2               h27087fc_0    conda-forge
libcblas                  3.9.0           15_linux64_openblas    conda-forge
libcurl                   7.83.1               h2283fc2_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
liblapack                 3.9.0           15_linux64_openblas    conda-forge
libmongoc                 1.21.2               h0506597_0    conda-forge
libmongocxx               3.6.7                h6e2fe03_0    conda-forge
libnghttp2                1.47.0               he49606f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libntlm                   1.4               h7f98852_1002    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_0    conda-forge
libssh2                   1.10.0               ha35d2d1_2    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libzlib                   1.2.12               h166bdaf_1    conda-forge
llvm-openmp               14.0.4               he0ac6c6_0    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
mctc-lib                  0.3.0                hc3ea6d6_0    conda-forge
mkl                       2022.1.0           h84fe81f_915    conda-forge
mongodb                   5.1.1                h0e13805_3    conda-forge
nauty                     2.7.2                h7f98852_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nlohmann_json             3.10.5               h27087fc_1    conda-forge
numpy                     1.23.0          py310h53a5b5f_0    conda-forge
openssl                   3.0.5                h166bdaf_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pip                       22.1.2             pyhd8ed1ab_0    conda-forge
psutil                    5.9.1           py310h5764c6d_0    conda-forge
pybind11                  2.9.2           py310hbf28c38_1    conda-forge
pybind11-global           2.9.2           py310hbf28c38_1    conda-forge
python                    3.10.5          ha86cf86_0_cpython    conda-forge
python-daemon             2.3.0              pyhd8ed1ab_1    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pyyaml                    6.0             py310h5764c6d_4    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
ringdecomposerlib         1.1.3                h166bdaf_1    conda-forge
scine-core                4.0.1                h6e2fe03_0    conda-forge
scine-database            1.0.0                    pypi_0    pypi
scine-puffin              1.0.0                    pypi_0    pypi
scine-readuct             4.0.0                he3004b7_0    conda-forge
scine-sparrow             3.0.1                he3004b7_1    conda-forge
scine-utilsos             5.0.0                h99171d1_0    conda-forge
scine-xtb                 1.0.1                h886c582_1    conda-forge
scipy                     1.8.1           py310h7612f91_0    conda-forge
setproctitle              1.2.3           py310h5764c6d_0    conda-forge
setuptools                63.1.0          py310hff52083_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snappy                    1.1.9                hbd366e4_1    conda-forge
sqlite                    3.39.0               h4ff8645_0    conda-forge
tbb                       2021.5.0             h924138e_1    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xtb                       6.5.0                h9d67668_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.7.0                h27087fc_1    conda-forge
zlib                      1.2.12               h166bdaf_1    conda-forge
zstd                      1.5.2                h8a70e8d_2    conda-forge

[weymutht]

Did this issue resolve now that you sorted out the problem with having multiple versions of nauty on your system?

If it persists, I recommend you use an older version of GCC. We tested Molassembler successfully up to GCC 10.

[awvwgk]

No the issue is unfortunately not due to multiple nauty versions but due to non-portable C++ usage which is flagged only in GCC 11 and above.

Edit: Also happens with GCC 10

[awvwgk]

This seems to be solvable by this somewhat hacky patch

diff --git a/src/Molassembler/Graph/Canonicalization.cpp b/src/Molassembler/Graph/Canonicalization.cpp
index dcf244bc..0ac57edf 100644
--- a/src/Molassembler/Graph/Canonicalization.cpp
+++ b/src/Molassembler/Graph/Canonicalization.cpp
@@ -21,6 +21,7 @@
 #include "Molassembler/Temple/Functional.h"
 
 extern "C" {
+#define _Thread_local thread_local
 #include "nauty/nausparse.h"
 
 /*!

[jan-grimo]

I don't much want to include this patch in molassembler; this seems like an upstream issue, no? _Thread_local seems to have been substituted into your nauty/nausparse.h header file by nauty's configure script:

Line 5429: for ax_tls_keyword in _Thread_local __thread '__declspec(thread)' none; do

Fixing that by including a preprocessor redefinition in molassembler strikes me as the wrong way of fixing your issue.