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.