invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] #252

sophiehourihane · 2024-08-05T20:43:38Z

Hi, I am trying to load my python bindings but I keep getting these errors, is there something wrong with what I am doing?

(bw_cpp_env_080524_raw) dhcp-123-144:bayeswave-cpp sophie$ python
Python 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:11:10) [Clang 16.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from bayeswavecpp_bindings import autoload_cppyy 
(Re-)building pre-compiled headers (options: -O2 -march=native); this may take a minute ...
ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
Invoking:
  LC_ALL=C clang-14  -O2 -DNDEBUG -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.*include/,${' -e '/^ \/.*++/p' -e '}'
Results was:
With exit code 0
In file included from input_line_3:38:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/cassert:19:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assertion_handler:13:
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__config:48:8: warning: "Libc++ only supports Clang 16 and later" [-W#warnings]
#      warning "Libc++ only supports Clang 16 and later"
       ^
In file included from input_line_3:38:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/cassert:19:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assertion_handler:14:
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__verbose_abort:20:1: error: expected identifier or '{'
_LIBCPP_BEGIN_NAMESPACE_STD
^
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__config:884:81: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#  define _LIBCPP_BEGIN_NAMESPACE_STD namespace _LIBCPP_TYPE_VISIBILITY_DEFAULT std {                                  \
                                                                                ^
In file included from input_line_3:38:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/cassert:19:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assertion_handler:14:
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__verbose_abort:20:1: error: C++ requires a type specifier for all declarations
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__config:884:81: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#  define _LIBCPP_BEGIN_NAMESPACE_STD namespace _LIBCPP_TYPE_VISIBILITY_DEFAULT std {                                  \
                                                                                ^
In file included from input_line_3:38:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/cassert:19:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assertion_handler:14:
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__verbose_abort:20:1: error: expected expression
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__config:885:32: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
                               inline namespace _LIBCPP_ABI_NAMESPACE {
                               ^
In file included from input_line_3:38:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/cassert:19:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__assertion_handler:14:
/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/bin/../include/c++/v1/__verbose_abort:51:26: error: expected ';' after top level declarator
_LIBCPP_END_NAMESPACE_STD
                         ^
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/bayeswavecpp_bindings/__init__.py", line 17, in <module>
    from .autoload_cppyy import *
  File "/Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/bayeswavecpp_bindings/autoload_cppyy.py", line 2, in <module>
    load_cppyy.load_library_for_cppyy('/Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/build')
  File "/Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/bayeswavecpp_bindings/load_cppyy.py", line 45, in load_library_for_cppyy
    cppyy.load_library('libbayeswavecpp')
  File "/Users/sophie/mambaforge/envs/bw_cpp_env_080524_raw/lib/python3.12/site-packages/cppyy/__init__.py", line 281, in load_library
    sc = gSystem.Load(name)
         ^^^^^^^^^^^^^^^^^^
cppyy.gbl.std.invalid_argument: int CppyyLegacy::TSystem::Load(const char* module, const char* entry = "", CppyyLegacy::Bool_t system = kFALSE) =>
    invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] of the machine's allowed thread counts; to construct a ThreadCount, provide a value within that interval

The text was updated successfully, but these errors were encountered:

wlav · 2024-08-06T05:03:20Z

Mismatch between installed compiler (clang-14) and installed standard lib (it states warning "Libc++ only supports Clang 16 and later"). Note that cppyy still uses clang-13; work is underway on 17.

Not sure how you both got a newer version of libc++ but an older version of clang in the same environment? And in particular the output of the command above (LC_ALL=C clang-14 -O2 -DNDEBUG -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.*include/,${' -e '/^ \/.*++/p' -e '}') indicates that clang-14 can't find any headers suitable for its own use?

sophiehourihane · 2024-08-06T17:13:25Z

Hm ok, it seems that that dependency is not in the conda version. I made the env with this .yaml file:

channels:
- conda-forge
dependencies:
- c-compiler
- cxx-compiler
- cppyy
- clang
- clang-tools
- catch2
- cmake
- doxygen
- make
- h5py
- llvm-openmp
- ezdag
- eigen
- autodiff
- pkg-config
- fftw * nompi*
- gsl
- gwpy
- liblal
- liblalframe
- liblalinference
- liblalsimulation
- lalsimulation
- pandas
- pytables
- python
- python-clang
- rapidjson
- matplotlib
- numpy
- scipy
- bilby
name: bayeswave-cpp

Is there a way (or a recommendation) of how I should specify the clang (and python clang?) versions?

sophiehourihane · 2024-08-06T17:53:48Z

Also, when I try to specify an older version of clang like so:

channels:
- conda-forge
dependencies:
- c-compiler
- cxx-compiler
- clang <= 14
- clang-tools <= 14
- cppyy
- catch2
- cmake
- doxygen
- make
- h5py
- llvm-openmp
- ezdag
- eigen
- autodiff
- pkg-config
- fftw * nompi*
- gsl
- gwpy
- liblal
- liblalframe
- liblalinference
- liblalsimulation
- lalsimulation
- pandas
- pytables
- python
- python-clang <= 14
- rapidjson
- matplotlib
- numpy
- scipy
- bilby
name: bayeswave-cpp

I get compiler errors saying:


(bw_cpp_env_080624_clangleq14) Sophies-MacBook-Pro-4:bayeswave-cpp sophie$ cmake --build build --target main create_data -j8
-- GIT_PROJECT_REMOTE_ORIGIN_URL is [email protected]:sophie.hourihane/bayeswave-cpp.git
-- CMAKE_CURRENT_LIST_DIR : /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src
[  0%] Built target version
[  1%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/builders/injection_data_builder.cpp.o
[  1%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/builders/cached_data_builder.cpp.o
[  3%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/builders/lal_data_builder.cpp.o
[  5%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/builders/run_builder.cpp.o
[  5%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/builders/state_injector.cpp.o
[  6%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/chains/chain_collection_updaters.cpp.o
[  8%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/chains/chain_swappers.cpp.o
[  8%] Building CXX object src/CMakeFiles/bayeswavecpp.dir/chains/chain_collection.cpp.o
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/run_builder.cpp:23:
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/run_builder.hpp:26:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/memory:921:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assertion_handler:13:
/Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__config:48:8: warning: "Libc++ only supports Clang 16 and later" [-W#warnings]
#      warning "Libc++ only supports Clang 16 and later"
      ^
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/state_injector.cpp:23:
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/state_injector.hpp:26:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/filesystem:536:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assertion_handler:13:
/Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__config:48:8: warning: "Libc++ only supports Clang 16 and later" [-W#warnings]
#      warning "Libc++ only supports Clang 16 and later"
      ^
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/run_builder.cpp:23:
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/run_builder.hpp:26:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/memory:921:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assertion_handler:14:
/Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__verbose_abort:20:1: error: expected identifier or '{'
_LIBCPP_BEGIN_NAMESPACE_STD
^
/Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__config:884:81: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#  define _LIBCPP_BEGIN_NAMESPACE_STD namespace _LIBCPP_TYPE_VISIBILITY_DEFAULT std {                                  \
                                                                               ^
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/state_injector.cpp:23:
In file included from /Users/sophie/src/BayesWave_Cpp/bayeswave-cpp/src/builders/state_injector.hpp:26:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/filesystem:536:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assert:13:
In file included from /Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__assertion_handler:14:
/Users/sophie/mambaforge/envs/bw_cpp_env_080624_clangleq14/bin/../include/c++/v1/__verbose_abort:20:1: error: expected identifier or '{'
_LIBCPP_BEGIN_NAMESPACE_STD
^
...

sophiehourihane · 2024-08-27T22:53:28Z

Also, when I try to install cppyy with nothing else in my environment, the specs that you described are not respected and clang 16 etc are installed

(base) Sophies-MacBook-Pro-4:~ sophie$ mamba create -n bw_cpp_env_082724 cppyy

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.4.1) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['cppyy']

warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
pkgs/main/noarch                                   874.9kB @   1.5MB/s  0.9s
pkgs/r/osx-64                                      820.9kB @   1.3MB/s  1.0s
pkgs/r/noarch                                        2.3MB @   2.0MB/s  1.6s
pkgs/main/osx-64                                     6.9MB @   2.8MB/s  3.3s
conda-forge/noarch                                  18.7MB @   3.1MB/s  6.6s
conda-forge/osx-64                                  38.6MB @   4.1MB/s 12.5s
Transaction

  Prefix: /Users/sophie/mambaforge/envs/bw_cpp_env_082724

  Updating specs:

   - cppyy


  Package                  Version  Build                Channel                  Size
────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────

  + bzip2                    1.0.8  h6c40b1e_6           pkgs/main/osx-64        155kB
  + c-compiler               1.7.0  h282daa2_1           conda-forge/osx-64     Cached
  + ca-certificates       2024.7.2  hecd8cb5_0           pkgs/main/osx-64       Cached
  + cctools                    986  h40f6528_3           conda-forge/osx-64     Cached
  + cctools_osx-64             986  h303a5ab_3           conda-forge/osx-64     Cached
  + clang                   16.0.6  default_h179603d_11  conda-forge/osx-64     Cached
  + clang-16                16.0.6  default_h0c94c6a_11  conda-forge/osx-64     Cached
  + clang_impl_osx-64       16.0.6  h8787910_19          conda-forge/osx-64       18kB
  + clang_osx-64            16.0.6  hb91bd55_19          conda-forge/osx-64       21kB
  + clangxx                 16.0.6  default_h179603d_11  conda-forge/osx-64     Cached
  + clangxx_impl_osx-64     16.0.6  h6d92fbe_19          conda-forge/osx-64       18kB
  + clangxx_osx-64          16.0.6  hb91bd55_19          conda-forge/osx-64       19kB
  + compiler-rt             16.0.6  ha38d28d_2           conda-forge/osx-64     Cached
  + compiler-rt_osx-64      16.0.6  ha38d28d_2           conda-forge/noarch     Cached
  + cppyy                    3.1.2  py312h3204919_2      conda-forge/osx-64     Cached
  + cppyy-backend           1.15.2  py312h9230928_1      conda-forge/osx-64     Cached
  + cppyy-cling             6.30.0  py312h99981ff_3      conda-forge/osx-64      119MB
  + cpycppyy               1.12.16  py312h9230928_1      conda-forge/osx-64     Cached
  + cxx-compiler             1.7.0  h7728843_1           conda-forge/osx-64     Cached
  + icu                       75.1  h120a0e1_0           conda-forge/osx-64     Cached
  + ld64                       711  ha02d983_3           conda-forge/osx-64     Cached
  + ld64_osx-64                711  h04ffbf3_3           conda-forge/osx-64     Cached
  + libclang-cpp16          16.0.6  default_h0c94c6a_11  conda-forge/osx-64     Cached
  + libcxx                  18.1.8  hd876a4e_6           conda-forge/osx-64        1MB
  + libexpat                 2.6.2  h73e2aa4_0           conda-forge/osx-64     Cached
  + libffi                   3.4.4  hecd8cb5_1           pkgs/main/osx-64        132kB
  + libiconv                  1.17  hd75f5a5_2           conda-forge/osx-64     Cached
  + libllvm16               16.0.6  hbedff68_3           conda-forge/osx-64     Cached
  + libsqlite               3.46.0  h1b8f9f3_0           conda-forge/osx-64     Cached
  + libxml2                 2.12.7  heaf3512_4           conda-forge/osx-64     Cached
  + libzlib                  1.3.1  h87427d6_1           conda-forge/osx-64     Cached
  + llvm-openmp             14.0.6  h0dcd299_0           pkgs/main/osx-64       Cached
  + llvm-tools              16.0.6  hbedff68_3           conda-forge/osx-64     Cached
  + ncurses                    6.5  hf036a51_1           conda-forge/osx-64      822kB
  + openssl                  3.3.1  hd23fc13_3           conda-forge/osx-64        3MB
  + pip                       24.2  py312hecd8cb5_0      pkgs/main/osx-64          3MB
  + python                  3.12.5  h37a9e06_0_cpython   conda-forge/osx-64       12MB
  + python_abi                3.12  5_cp312              conda-forge/osx-64        6kB
  + readline                   8.2  hca72f7f_0           pkgs/main/osx-64       Cached
  + setuptools              72.1.0  py312hecd8cb5_0      pkgs/main/osx-64          3MB
  + sigtool                  0.1.3  h88f4db0_0           conda-forge/osx-64     Cached
  + tapi                 1100.0.11  h1527ee5_1           pkgs/main/osx-64        186kB
  + tk                      8.6.13  h1abcd95_1           conda-forge/osx-64     Cached
  + tzdata                   2024a  h04d1e81_0           pkgs/main/noarch       Cached
  + wheel                   0.43.0  py312hecd8cb5_0      pkgs/main/osx-64        143kB
  + xz                       5.4.6  h6c40b1e_1           pkgs/main/osx-64        380kB
  + zstd                     1.5.6  h915ae27_0           conda-forge/osx-64     Cached

  Summary:

  Install: 47 packages

  Total download: 143MB

wlav · 2024-08-28T04:31:42Z

Yes, it's a conda thing on Mac. The pip install should not suffer from it. Looks like this is being fixed, though: conda-forge/cppyy-cling-feedstock#62
However, what is really needed is an upgrade of LLVM to have full support on Mac again. I'm working on LLVM16 (upstream has this released in production) and soon on LLVM18 (upstream claims they are almost done porting to that version). I was hoping to wait for the latter, but this Mac problem is forcing the issue.

StasJ · 2024-10-31T01:23:56Z

I have the same issue. If I install the latest version of CPPYY on macOS (cppyy=3.1.2 cppyy-cling=6.30.0), clang-16 gets installed along with it. When attempting to import any code, I get an error cling cannot extract standard library include paths from clang-14 which is not installed.

sophiehourihane changed the title ~~invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0]~~ invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] Aug 5, 2024

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invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] #252

invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] #252

sophiehourihane commented Aug 5, 2024

wlav commented Aug 6, 2024

sophiehourihane commented Aug 6, 2024

sophiehourihane commented Aug 6, 2024

sophiehourihane commented Aug 27, 2024

wlav commented Aug 28, 2024

StasJ commented Oct 31, 2024

invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] #252

invalid_argument: Attempted to construct a ThreadCount with a value (1) that falls outside the interval [0, 0] #252

Comments

sophiehourihane commented Aug 5, 2024

wlav commented Aug 6, 2024

sophiehourihane commented Aug 6, 2024

sophiehourihane commented Aug 6, 2024

sophiehourihane commented Aug 27, 2024

wlav commented Aug 28, 2024

StasJ commented Oct 31, 2024