Some tests are sometime infinite or failing
DavidLapous opened this issue · 1 comments
DavidLapous commented
Some tests are (sometimes) failing on my laptop, i.e., I have to rerun ctest multiple times to get a 100% pass.
For these few example below, the behavior is undefined : either pass (~50% times) or segfaults or never finishes.
Typically : ***Exception: Illegal or Subprocess aborted***Exception.
Some test that I've seen fail (may be non exhaustive)
Delaunay_complex_Epeck_dynamic_test_unitWeighted_periodic_alpha_complex_3d_test_unitZero_weighted_alpha_complex_static_test_unitPeriodic_alpha_complex_3d_test_unit
My specs :
- Software
My compiler (clang 15.0.7), boost, tbb, cgal (5.6), python libraries and everything else come from the conda-forge repo. And the c++ compiler used is the c++ compiler provided by thecompilerspackage (what is used to compile every conda-forge package). - Hardware
M1 macbook air, on Ventura 13.5.2
As cgal was recently updated to the 5.6 version, and the error are all linked to alpha triangulation, my first guess would be in that direction.
Not really useful log :
Running 1 test case...
*****************************************************************************************************unknown location:0: fatal error: in "Delaunay_complex_exact_kernel_dynamic_simplices_comparison": memory access violation at address: 0x16b81c000: invalid permissions
gudhi-devel/src/Alpha_complex/test/Delaunay_complex_unit_test.h:37: last checkpoint
Running 1 test case...
*****************************************************************************************************unknown location:0: fatal error: in "Delaunay_complex_exact_kernel_static_simplices_comparison": memory access violation at address: 0x168ea7ff0: invalid permissions
gudhi-devel/src/Alpha_complex/test/Delaunay_complex_unit_test.h:37: last checkpoint
Running 1 test case...
unknown location:0: fatal error: in "Zero_weighted_alpha_complex_static": memory access violation at address: 0x16fd3c000: invalid permissions
gudhi-devel/src/Alpha_complex/test/Zero_weighted_alpha_complex_unit_test.h:41: last checkpoint
The cmake log :
cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_BENCHMARK=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF ..
-- GUDHI version : 3.9.0a1
-- boost include dirs:/Users/dloiseau/micromamba/envs/python/include
-- boost library dirs:/Users/dloiseau/micromamba/envs/python/lib
-- Using header-only CGAL
-- Targeting Unix Makefiles
-- Using /Users/dloiseau/micromamba/envs/python/bin/arm64-apple-darwin20.0.0-clang++ compiler.
-- Running in macOS DARWIN_VERSION=22
-- Boost include dirs: /Users/dloiseau/micromamba/envs/python/include
-- Boost libraries:
-- CGAL version: 5.6.
-- Build type: Release
-- USING CXXFLAGS = '-ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/dloiseau/micromamba/envs/python/include -O3 -DNDEBUG'
-- USING EXEFLAGS = '-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/dloiseau/micromamba/envs/python/lib -L/Users/dloiseau/micromamba/envs/python/lib '
++ TBB version 2021.10.0 found in /Users/dloiseau/micromamba/envs/python/lib - includes in /Users/dloiseau/micromamba/envs/python/include
diff found in /usr/bin/diff
CMake Warning (dev) at src/cmake/modules/GUDHI_third_party_libraries.cmake:130 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:20 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
++ Python module cython - Version 3.0.2 found
++ Python module pytest - Version 7.4.2 found
++ Python module matplotlib - Version 3.7.1 found
++ Python module numpy - Version 1.25.2 found
++ Python module scipy - Version 1.11.2 found
++ Python module sphinx - Version 7.2.6 found
++ Python module sklearn - Version 1.3.0 found
++ Python module ot - Version 0.9.0 found
++ Python module pybind11 - Version 2.11.1 found
++ Python module torch - Version 2.0.0 found
++ Python module pykeops - Version [KeOps] Warning : omp.h header is not in the path, disabling OpenMP. [KeOps] Warning : Cuda libraries were not detected on the system ; using cpu only mode 2.1.2 found
PYTHON_MODULE_NAME = eagerpy
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'eagerpy'
PYTHON_MODULE_NAME = hnswlib
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'hnswlib'
PYTHON_MODULE_NAME = tensorflow
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
AttributeError: module 'tensorflow' has no attribute '__version__'
PYTHON_MODULE_NAME = sphinx_paramlinks
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sphinx_paramlinks'
PYTHON_MODULE_NAME = pydata_sphinx_theme
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pydata_sphinx_theme'
++ Python module networkx - Version 3.1 found
++ Release compilation flags are: -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/dloiseau/micromamba/envs/python/include -Wall -pedantic -O3 -DNDEBUG
++ GUDHI_SUB_DIRECTORIES list is:";test"
++ GudhUI will not be compiled because QGLViewer is not found
++ /Users/dloiseau/micromamba/envs/python/lib/libgmp.dylib => UNIX_LIB_FILE_NAME = gmp
** Add gmp /Users/dloiseau/micromamba/envs/python/lib
++ /Users/dloiseau/micromamba/envs/python/lib/libgmpxx.dylib => UNIX_LIB_FILE_NAME = gmpxx
** Add gmpxx /Users/dloiseau/micromamba/envs/python/lib
++ /Users/dloiseau/micromamba/envs/python/lib/libmpfr.dylib => UNIX_LIB_FILE_NAME = mpfr
** Add mpfr /Users/dloiseau/micromamba/envs/python/lib
++ /Users/dloiseau/micromamba/envs/python/lib/libtbb.12.10.dylib => UNIX_LIB_FILE_NAME = tbb
++ /Users/dloiseau/micromamba/envs/python/lib/libtbbmalloc.2.10.dylib => UNIX_LIB_FILE_NAME = tbbmalloc
** Add tbb /Users/dloiseau/micromamba/envs/python/lib
++ Python documentation module will not be compiled because sphinxcontrib-paramlinks was not found
++ GUDHI_MODULES list is:"common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Collapse;Contraction;Coxeter_triangulation;Cech_complex;Hasse_complex;Persistence_representations;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Toplex_map;Witness_complex;Nerve_GIC;python"
++ GUDHI_MISSING_MODULES list is:"GudhUI;python-documentation;cpp-documentation"
-- Configuring done (5.0s)
-- Generating done (0.2s)
-- Build files have been written to: /Users/dloiseau/Downloads/temp/gudhi-devel/build
mglisse commented
To try to reproduce, I connected to the public machine gcc104.fsffrance.org (cpu M1, MacOSX 12.6), installed mambaforge and a bunch of packages
# Name Version Build Channel
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
boost-cpp 1.78.0 h00df5ed_4 conda-forge
brotli-python 1.1.0 py310h1253130_0 conda-forge
bzip2 1.0.8 h3422bc3_4 conda-forge
c-ares 1.19.1 hb547adb_0 conda-forge
c-compiler 1.6.0 hd291e01_0 conda-forge
ca-certificates 2023.7.22 hf0a4a13_0 conda-forge
cctools 973.0.1 hd1ac623_14 conda-forge
cctools_osx-arm64 973.0.1 h2a25c60_14 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h2399d43_3 conda-forge
cgal-cpp 5.6 hed76ac3_0 conda-forge
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
clang 15.0.7 hce30654_3 conda-forge
clang-15 15.0.7 default_h5dc8d65_3 conda-forge
clang_osx-arm64 15.0.7 h77e971b_3 conda-forge
clangxx 15.0.7 default_h610c423_3 conda-forge
clangxx_osx-arm64 15.0.7 h768a7fd_3 conda-forge
cmake 3.27.5 h1c59155_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
compiler-rt 15.0.7 hf8d1dfb_1 conda-forge
compiler-rt_osx-arm64 15.0.7 hf8d1dfb_1 conda-forge
compilers 1.6.0 hce30654_0 conda-forge
conda 23.7.4 py310hbe9552e_0 conda-forge
conda-libmamba-solver 23.7.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
cryptography 41.0.3 py310hdd3b5e7_0 conda-forge
cxx-compiler 1.6.0 h1995070_0 conda-forge
eigen 3.4.0 h1995070_0 conda-forge
fmt 10.1.1 h1995070_0 conda-forge
fortran-compiler 1.6.0 h5a50232_0 conda-forge
gfortran 12.3.0 h1ca8e4b_1 conda-forge
gfortran_impl_osx-arm64 12.3.0 hbbb9e1e_1 conda-forge
gfortran_osx-arm64 12.3.0 h57527a5_1 conda-forge
gmp 6.2.1 h9f76cd9_0 conda-forge
icu 73.2 hc8870d7_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
isl 0.25 h9a09cb3_0 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py310hbe9552e_2 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
ld64 609 h89fa09d_14 conda-forge
ld64_osx-arm64 609 hc4dc95b_14 conda-forge
libarchive 3.6.2 h82b9b87_1 conda-forge
libclang-cpp15 15.0.7 default_h5dc8d65_3 conda-forge
libcurl 8.3.0 hc52a3a8_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h642e427_1 conda-forge
libexpat 2.5.0 hb7217d7_1 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_1 conda-forge
libgfortran-devel_osx-arm64 12.3.0 hc62be1c_1 conda-forge
libgfortran5 13.2.0 hf226fd6_1 conda-forge
libiconv 1.17 he4db4b2_0 conda-forge
libllvm15 15.0.7 h504e6bf_3 conda-forge
libmamba 1.5.1 h6089622_0 conda-forge
libmambapy 1.5.1 py310ha8cccbf_0 conda-forge
libnghttp2 1.52.0 hae82a92_0 conda-forge
libsolv 0.7.24 ha614eb4_4 conda-forge
libsqlite 3.43.0 hb31c410_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libuv 1.46.0 hb547adb_0 conda-forge
libxml2 2.11.5 h25269f3_1 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 16.0.6 h1c12783_0 conda-forge
llvm-tools 15.0.7 h504e6bf_3 conda-forge
lz4-c 1.9.4 hb7217d7_0 conda-forge
lzo 2.10 h642e427_1000 conda-forge
mamba 1.5.1 py310ha5d4528_0 conda-forge
mpc 1.3.1 h91ba8db_0 conda-forge
mpfr 4.2.0 he09a6ba_0 conda-forge
ncurses 6.4 h7ea286d_0 conda-forge
openssl 3.1.2 h53f4e23_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.4 py310h8e9501a_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.12 h01493a6_0_cpython conda-forge
python_abi 3.10 3_cp310 conda-forge
readline 8.2 h92ec313_1 conda-forge
reproc 14.2.4 h1a8c8d9_0 conda-forge
reproc-cpp 14.2.4 hb7217d7_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rhash 1.4.4 hb547adb_0 conda-forge
ruamel.yaml 0.17.32 py310h2aa6e3c_0 conda-forge
ruamel.yaml.clib 0.2.7 py310h8e9501a_1 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
sigtool 0.1.3 h44b9a77_0 conda-forge
tapi 1100.0.11 he4954df_0 conda-forge
tbb 2021.10.0 h1995070_0 conda-forge
tk 8.6.12 he1e0b03_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml-cpp 0.7.0 hb7217d7_2 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zstandard 0.19.0 py310h8e9501a_0 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
Did a (recursive) git clone of gudhi-devel, created a subdirectory build/, cmake -DCMAKE_BUILD_TYPE=Release .., make -j4, make -j4 test, and all the tests (including the 4 you mention) pass. I re-ran the last command a few times, but the tests always pass. The weighted-periodic one takes ~8s, by far the longest. CMake shows
$ cmake -DCMAKE_BUILD_TYPE=Release ..
-- The C compiler identification is Clang 15.0.7
-- The CXX compiler identification is Clang 15.0.7
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Users/glisse/mambaforge/bin/arm64-apple-darwin20.0.0-clang - 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: /Users/glisse/mambaforge/bin/arm64-apple-darwin20.0.0-clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- GUDHI version : 3.9.0a1
-- boost include dirs:/Users/glisse/mambaforge/include
-- boost library dirs:/Users/glisse/mambaforge/lib
-- Found GMP: /Users/glisse/mambaforge/lib/libgmp.dylib
-- Found GMPXX: /Users/glisse/mambaforge/lib/libgmpxx.dylib
-- Using header-only CGAL
-- Targeting Unix Makefiles
-- Using /Users/glisse/mambaforge/bin/arm64-apple-darwin20.0.0-clang++ compiler.
-- Running in macOS DARWIN_VERSION=21
-- Found MPFR: /Users/glisse/mambaforge/lib/libmpfr.dylib
-- Found Boost: /Users/glisse/mambaforge/lib/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.66")
-- Boost include dirs: /Users/glisse/mambaforge/include
-- Boost libraries:
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- CGAL version: 5.6.
-- Build type: Release
-- USING CXXFLAGS = '-ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/glisse/mambaforge/include -O3 -DNDEBUG'
-- USING EXEFLAGS = '-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/glisse/mambaforge/lib -L/Users/glisse/mambaforge/lib '
-- Could NOT find TBB (missing: TBB_DIR)
-- Found Eigen3: /Users/glisse/mambaforge/include/eigen3 (found suitable version "3.4.0", minimum required is "3.1.0")
diff found in /usr/bin/diff
CMake Warning (dev) at src/cmake/modules/GUDHI_third_party_libraries.cmake:130 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:20 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /Users/glisse/mambaforge/bin/python (found version "3.10.12")
PYTHON_MODULE_NAME = cython
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'cython'
PYTHON_MODULE_NAME = pytest
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pytest'
PYTHON_MODULE_NAME = matplotlib
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'matplotlib'
PYTHON_MODULE_NAME = numpy
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
PYTHON_MODULE_NAME = scipy
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'scipy'
PYTHON_MODULE_NAME = sphinx
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sphinx'
PYTHON_MODULE_NAME = sklearn
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sklearn'
PYTHON_MODULE_NAME = ot
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'ot'
PYTHON_MODULE_NAME = pybind11
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pybind11'
PYTHON_MODULE_NAME = torch
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'torch'
PYTHON_MODULE_NAME = pykeops
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pykeops'
PYTHON_MODULE_NAME = eagerpy
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'eagerpy'
PYTHON_MODULE_NAME = hnswlib
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'hnswlib'
PYTHON_MODULE_NAME = tensorflow
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'tensorflow'
PYTHON_MODULE_NAME = sphinx_paramlinks
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sphinx_paramlinks'
PYTHON_MODULE_NAME = pydata_sphinx_theme
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pydata_sphinx_theme'
PYTHON_MODULE_NAME = networkx
- PYTHON_MODULE_RESULT = 1
- PYTHON_MODULE_VERSION =
- PYTHON_MODULE_ERROR = Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'networkx'
-- Checking to see if CXX compiler accepts flag -Wall
-- Checking to see if CXX compiler accepts flag -Wall - yes
++ Release compilation flags are: -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/glisse/mambaforge/include -Wall -pedantic -O3 -DNDEBUG
++ GUDHI_SUB_DIRECTORIES list is:";test;utilities"
++ GudhUI will not be compiled because Qt5 COMPONENTS Widgets Xml OpenGL are not found
++ Python module will not be compiled because numpy and/or cython and/or pybind11 was/were not found
++ GUDHI_MODULES list is:"common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Collapse;Contraction;Coxeter_triangulation;Cech_complex;Hasse_complex;Persistence_representations;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Toplex_map;Witness_complex;Nerve_GIC"
++ GUDHI_MISSING_MODULES list is:"GudhUI;python;cpp-documentation"
-- Configuring done (1.7s)
-- Generating done (0.3s)
-- Build files have been written to: /Users/glisse/gudhi-devel/build
The OSX version is not the same, and the cmake outputs have a surprising number of seemingly minor differences, but I don't immediately see what may explain the different behavior on your computer.