Compilation failing on RH8 with GCC 11.3.0

[orliac]

Hello,
I'm failing to compile arcae on a RH8 box using GCC 11.3.0 (using Spack 0.20.0). Here is the log:

==> Installing py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja
==> No binary for py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja found: installing from source
==> Ran patch() for py-arcae
==> py-arcae: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
    '/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.10.4-tl3vrz4pgbao3vfzuyldkj5bn7qpic4g/bin/python3.10' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja' '.'

144 errors found in build log:
     266      -- Detecting C compile features - done
     267      -- Found PkgConfig: /work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/bin/pkg-config (found version "1.9.5")
     268      -- Checking for module 'casacore'
     269      --   Found casacore, version 3.5.0
     270      -- Found PythonInterp: /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.10.4-tl3vrz4pgbao3vfzuyldkj5bn7qpic4g/bin/python3
            .10 (found version "3.10.4")
     271      -- Found PythonLibs: /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.10.4-tl3vrz4pgbao3vfzuyldkj5bn7qpic4g/lib/libpython
            3.10.so (found version "3.10.4")
  >> 272    <string>:2: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternati
            ves                                                                                                                                                                
  >> 273      <string>:2: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
     274      -- Found Cython: /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-cython-0.29.33-ocv6lqlck5nqwelih2edoa6jltp3em4n/bin/cython
     275      CYTHON table /tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/_skbuild/linux-x86_64-3.10/cmake-build/arcae/arrow_tab
            les.cxx
     276      -- Performing Test Weak Link MODULE -> SHARED (gnu_ld_ignore) - Success
     277      _modinit_prefix:PyInit_
     278      Linking arrow_tables against arrow_python
     279      Linking arrow_tables against arrow

     ...

     298      [4/11] Building CXX object cpp/CMakeFiles/arcae.dir/casa_visitors.cpp.o
     299      [5/11] Building CXX object cpp/CMakeFiles/arcae.dir/safe_table_proxy.cpp.o
     300      [6/11] Building CXX object cpp/CMakeFiles/arcae.dir/column_convert_visitor.cpp.o
     301      [7/11] Linking CXX shared library cpp/libarcae.so
     302      [8/11] Generating CXX source arcae/arrow_tables.cxx
     303      [9/11] Building CXX object arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o
  >> 304    FAILED: arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o
     305      /work/backup/ska/orliac/spack_0200/lib/spack/env/gcc/g++ -Darrow_tables_EXPORTS -I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3
            cnja/spack-src/arcae/PkgConfig::casacore -I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyf
            xmxdpzjy7t/lib/python3.10/site-packages/pyarrow/include -I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-numpy-1.24.3-a24j2n7xq
            pnc4qlygxwkatwvmpbbbwxm/lib/python3.10/site-packages/numpy/core/include -I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack
            -src/cpp -I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.10.4-tl3vrz4pgbao3vfzuyldkj5bn7qpic4g/include/python3.10 -I/tmp
            /orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/cpp/PkgConfig::casacore -isystem /tmp/orliac/spack-stage/spack-stage-py-a
            rcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/vcpkg/installed/x64-linux-dynamic-cxx17-abi0-rel/lib/pkgconfig/../../include -O3 -DNDEBUG -std=c++17 -fPIC -D
            _GLIBCXX_USE_CXX11_ABI=0 -MD -MT arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o -MF arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o.d -o arcae/CMakeFil
            es/arrow_tables.dir/arrow_tables.cxx.o -c /tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/_skbuild/linux-x86_64-3.10/
            cmake-build/arcae/arrow_tables.cxx
     306      In file included from /tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/_skbuild/linux-x86_64-3.10/cmake-build/arcae/
            arrow_tables.cxx:786:
  >> 307      /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyfxmxdpzjy7t/lib/python3.10/site-packages/p
            yarrow/src/arrow/python/datetime.h:50:8: error: 'PyDateTime_CAPI' does not name a type; did you mean 'PyDateTimeAPI'?                                              
     308         50 | extern PyDateTime_CAPI* datetime_api;
     309            |        ^~~~~~~~~~~~~~~
     310            |        PyDateTimeAPI
     311      /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyfxmxdpzjy7t/lib/python3.10/site-packages/p
            yarrow/src/arrow/python/datetime.h: In function 'int64_t arrow::py::internal::PyTime_to_us(PyObject*)':
  >> 312      /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyfxmxdpzjy7t/lib/python3.10/site-packages/p
            yarrow/src/arrow/python/datetime.h:62:11: error: 'PyDateTime_TIME_GET_HOUR' was not declared in this scope                                                         
     313         62 |   return (PyDateTime_TIME_GET_HOUR(pytime) * 3600000000LL +
     314            |           ^~~~~~~~~~~~~~~~~~~~~~~~
  >> 315      /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyfxmxdpzjy7t/lib/python3.10/site-packages/p
            yarrow/src/arrow/python/datetime.h:63:11: error: 'PyDateTime_TIME_GET_MINUTE' was not declared in this scope                                                       
     316         63 |           PyDateTime_TIME_GET_MINUTE(pytime) * 60000000LL +
     317            |           ^~~~~~~~~~~~~~~~~~~~~~~~~~
  >> 318      /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyfxmxdpzjy7t/lib/python3.10/site-packages/p
            yarrow/src/arrow/python/datetime.h:64:11: error: 'PyDateTime_TIME_GET_SECOND' was not declared in this scope                                                       
     319         64 |           PyDateTime_TIME_GET_SECOND(pytime) * 1000000LL +
     320            |           ^~~~~~~~~~~~~~~~~~~~~~~~~~

...

Can you guess what the problem is? (my cython version in use is 0.29.33)
Thank you,
Etienne

[sjperkins]

Hi @orliac

My best guess is that the Python headers aren't being passed to the compilation commands:

/work/backup/ska/orliac/spack_0200/lib/spack/env/gcc/g++
-Darrow_tables_EXPORTS
-I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/arcae/PkgConfig::casacore
-I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-qa5dzazodts7cvjtmy2cyfxmxdpzjy7t/lib/python3.10/site-packages/pyarrow/include
-I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-numpy-1.24.3-a24j2n7xqpnc4qlygxwkatwvmpbbbwxm/lib/python3.10/site-packages/numpy/core/include
-I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/cpp
-I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.10.4-tl3vrz4pgbao3vfzuyldkj5bn7qpic4g/include/python3.10
-I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/cpp/PkgConfig::casacore
-isystem
/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/vcpkg/installed/x64-linux-dynamic-cxx17-abi0-rel/lib/pkgconfig/../../include
-O3 -DNDEBUG -std=c++17 -fPIC -D_GLIBCXX_USE_CXX11_ABI=0 -MD
-MT arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o
-MF arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o.d
-o arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o
-c /tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/_skbuild/linux-x86_64-3.10/cmake-build/arcae/arrow_tables.cxx

Also, the following looks a bit strange to me. arcae is using sckit-build to build the cython extension and I wonder if something is going wrong here in the construction of includes. But I'm not sure.

-isystem
/tmp/orliac/spack-stage/spack-stage-py-arcae-main-bgre6mp2qhikmyafc2yzgfv5nab3cnja/spack-src/vcpkg/installed/x64-linux-dynamic-cxx17-abi0-rel/lib/pkgconfig/../../include

P.S. Aiming to have wheels out on pypi soon. Would this be helpful?

[orliac]

Hi Simon,
Thanks for the feedback.
In the cython generated arrow_tables.cxx file, in this block:

/* Early includes */
#include "ios"
#include "new"
#include "stdexcept"
#include "typeinfo"
#include <utility>

    #if __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600)
    // move should be defined for these versions of MSVC, but __cplusplus isn't set usefully
    #include <type_traits>

    namespace cython_std {
    template <typename T> typename std::remove_reference<T>::type&& move(T& t) noexcept { return std::move(t); }
    template <typename T> typename std::remove_reference<T>::type&& move(T&& t) noexcept { return std::move(t); }
    }

    #endif
    
#include <map>
#include <memory>
#include <string.h>
#include <string>
#include <vector>
#include <stdint.h>
#include <functional>
#include <unordered_map>
#include <unordered_set>
#include <stdio.h>
#include "pythread.h"
#include "datetime.h"
#include <optional>

it includes (in my env)

/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-yydvt3qe4zsv6afseskclwv5s7p7jpqp/lib/python3.10/site-packages/p
            yarrow/src/arrow/python/datetime.h

but shouldn't it be including this one instead?
/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.10.4-tl3vrz4pgbao3vfzuyldkj5bn7qpic4g/include/python3.10/datetime.h ?

[sjperkins]

The inclusion of the lib/python3.10/site-packages/pyarrow/src/arrow/python/datetime.h seens correct to me. It's this file in the source code.

This SO answer implies that Python might need to be compiled in a particular way? https://stackoverflow.com/a/70911512

Also, python/cpython#96822 (comment) says the following:

Note: currently, datetime.h is not included by Python.h and is excluded from the limited C API.

It looks like PEP 0670 made it into 3.11. Perhaps this has something todo with how SPACK packages Python 3.11?

Unfortunately these are just leads in the investigation, I don't have a comprehensive answer.

[orliac]

Thanks @sjperkins.

For information, I've opened an issue on pyarrow's side earlier on: apache/arrow#36438.
What is not clear to me is where should the definition of PyDateTime_CAPI come from when PYPY_VERSION is not defined and therefore datetime.h is not included. See https://github.com/apache/arrow/blob/0b7bd74daef8fe120fed997975431e7a88f67e5a/python/pyarrow/src/arrow/python/datetime.h#L32C1-L54C7.

I'm currently rebuilding my stack based on Python 3.11.2 (was on 3.10.4 before) but it will take a bit of time, so I'll post the outcome later on.

[orliac]

Using Python 3.11.2 did not improve the situation:

    303      [9/11] Building CXX object arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o
  >> 304    FAILED: arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o
     305      /work/backup/ska/orliac/spack_0200/lib/spack/env/gcc/g++ -Darrow_tables_EXPORTS -I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-z6eptsmwuwneacgiqa6swg
            pi6crewk7x/spack-src/arcae/PkgConfig::casacore -I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-numpy-1.24.3-wnq3x2p5wwxh
            x7qklhneb2emeaowfsva/lib/python3.11/site-packages/numpy/core/include -I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-z6eptsmwuwneacgiqa6swgpi6crewk7x/sp
            ack-src/cpp -I/work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/python-3.11.2-3tbonxwosnvt7mok7m6mhaojvjvw2f2f/include/python3.
            11 -I/tmp/orliac/spack-stage/spack-stage-py-arcae-main-z6eptsmwuwneacgiqa6swgpi6crewk7x/spack-src/cpp/PkgConfig::casacore -isystem /tmp/orliac/spack-stage/s
            pack-stage-py-arcae-main-z6eptsmwuwneacgiqa6swgpi6crewk7x/spack-src/vcpkg/installed/x64-linux-dynamic-cxx17-abi0-rel/lib/pkgconfig/../../include -O3 -DNDEBU
            G -std=c++17 -fPIC -D_GLIBCXX_USE_CXX11_ABI=0 -MD -MT arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o -MF arcae/CMakeFiles/arrow_tables.dir/arrow_table
            s.cxx.o.d -o arcae/CMakeFiles/arrow_tables.dir/arrow_tables.cxx.o -c /tmp/orliac/spack-stage/spack-stage-py-arcae-main-z6eptsmwuwneacgiqa6swgpi6crewk7x/spac
            k-src/_skbuild/linux-x86_64-3.11/cmake-build/arcae/arrow_tables.cxx
     306      In file included from /tmp/orliac/spack-stage/spack-stage-py-arcae-main-z6eptsmwuwneacgiqa6swgpi6crewk7x/spack-src/_skbuild/linux-x86_64-3.11/cmake-build/
            arcae/arrow_tables.cxx:786:
  >> 307      /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-pyarrow-12.0.0-wcxrxbguxaabwgtmmu6zkti5rbdsht4k/lib/python3.11/site-pack
            ages/pyarrow/src/arrow/python/datetime.h:50:8: error: 'PyDateTime_CAPI' does not name a type; did you mean 'PyDateTimeAPI'?                                  
     308         50 | extern PyDateTime_CAPI* datetime_api;
     309            |        ^~~~~~~~~~~~~~~
     310            |        PyDateTimeAPI

[sjperkins]

I think Python 3.10 would be required to work around PEP 0670 (if it is the problem).

[orliac]

Hello @sjperkins
I tried to install using the pypi 0.1.0 distribution. In that case it installs but it fails at runtime.

==> Installing py-arcae-0.1.0-n2yj7al5xxvwa25lrw46cyzixea2d6sg
==> No binary for py-arcae-0.1.0-n2yj7al5xxvwa25lrw46cyzixea2d6sg found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/arcae/arcae-0.1.0.tar.gz
==> No patches needed for py-arcae
==> py-arcae: Executing phase: 'install'
==> py-arcae: Successfully installed py-arcae-0.1.0-n2yj7al5xxvwa25lrw46cyzixea2d6sg
  Stage: 1.90s.  Install: 18.81s.  Post-install: 0.21s.  Total: 25.33s
[+] /work/ska/soft/spack/blackhole/v2/opt/spack/linux-rhel8-cascadelake/gcc-11.3.0/py-arcae-0.1.0-n2yj7al5xxvwa25lrw46cyzixea2d6sg

[bipp-izar-gcc] [orliac@i45 ~]$ python test_arcae.py 
Traceback (most recent call last):
  File "/home/orliac/test_arcae.py", line 10, in <module>
    casa_table = arcae.table("~/SKA/epfl-radio-astro/bipp-bench/gauss4_t201806301100_SBL180.MS")
  File "/work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/lib/python3.10/site-packages/arcae/__init__.py", line 13, in table
    from arcae.lib.arrow_tables import Table
ModuleNotFoundError: No module named 'arcae.lib.arrow_tables'

Will try the wheels and will let you know.

[orliac]

Using the wheel I face an ABI incompatibility:

[bipp-izar-gcc] [orliac@i44 ~]$ python test_arcae.py 
Traceback (most recent call last):
  File "/home/orliac/test_arcae.py", line 10, in <module>
    casa_table = arcae.table("~/SKA/epfl-radio-astro/bipp-bench/gauss4_t201806301100_SBL180.MS")
  File "/work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/lib/python3.10/site-packages/arcae/__init__.py", line 13, in table
    from arcae.lib.arrow_tables import Table
ImportError: /work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/lib/python3.10/site-packages/arcae/lib/libarcae.so: undefined symbol: _ZNK5arrow8DataType18ComputeFingerprintEv

Looking at the symbols in libarcae and libarrow:

[bipp-izar-gcc] [orliac@i44 ~]$ strings /work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/lib/python3.10/site-packages/arcae/lib/libarcae.so | grep _ZNK5arrow8DataType18ComputeFingerprintEv
_ZNK5arrow8DataType18ComputeFingerprintEv
_ZNK5arrow8DataType18ComputeFingerprintEv

[bipp-izar-gcc] [orliac@i44 ~]$ strings /work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/lib64/libarrow.so.1200 | grep _ZNK5arrow8DataType18ComputeFingerprintEv 

(nothing found) whereas:

[bipp-izar-gcc] [orliac@i44 ~]$ strings /work/ska/soft/spack/blackhole/v2/opt/view__bipp-izar-gcc/lib64/libarrow.so.1200 | grep _ZNK5arrow8DataType18ComputeFingerprint
_ZNK5arrow8DataType18ComputeFingerprintB5cxx11Ev
_ZNK5arrow8DataType18ComputeFingerprintB5cxx11Ev.localalias
_ZNK5arrow8DataType18ComputeFingerprintB5cxx11Ev

So I guess it means that the wheel was built with -D_GLIBCXX_USE_CXX11_ABI=0.
If that was the intention, I can try to build arrow accordingly.

[sjperkins]

Using the wheel I face an ABI incompatibility:

Yes, currently arcae is built with manylinux2014 wheels (which use the older ABI), mostly because manylinux_2_28 (using the new ABI) is currently not that prevalent. Having said that, it may start becoming available in arrow 13.0.0: apache/arrow#34818, although this further increases the number of continuous integration build actions. manylinux2014 (based on CENTOS 7 will be deprecated in July 2024).

[sjperkins]

Hello @sjperkins I tried to install using the pypi 0.1.0 distribution. In that case it installs but it fails at runtime.

It looks like it's trying to build from source. I don't think it's possible to build a working source build from scratch (because of the dependency on shared libraries built by vcpkg). At least this seems possible for me locally

$ git clone git@github.com:ratt-ru/arcae.git
$ virtualenv -p python3.9 ~/venv/arcaesrc
$ . ~/venv/arcaesrc/bin/activate
(arcaesrc) $ cd /
(arcaesrc) $ pip install --no-binary=arcae ~/code/arcae[dev,test]
Processing ./code/arcae
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting appdirs (from arcae==0.1.0)
....
Building wheels for collected packages: arcae
  Building wheel for arcae (pyproject.toml) ... done
  Created wheel for arcae: filename=arcae-0.1.0-cp39-cp39-linux_x86_64.whl size=268963 sha256=65bbc6fe77142a92906d5a962753274ff2e9f12ffa790cc69bff15a02bbb1c98
  Stored in directory: /tmp/pip-ephem-wheel-cache-35s3x43f/wheels/57/ca/66/ab589a3e8a6ecef38d467333fd4a0c91fd222b5fc2cbc98785
Successfully built arcae
Installing collected packages: mccabe, duckdb, docopt, appdirs, urllib3, unidecode, typing-extensions, tomlkit, tomli, tabulate, six, pygments, pyflakes, pycodestyle, pluggy, platformdirs, pathspec, packaging, numpy, mypy-extensions, mdurl, iniconfig, idna, exceptiongroup, contextlib2, colorama, click, charset-normalizer, certifi, schema, requests, python-casacore, pytest, pyarrow, markdown-it-py, flake8, cli-ui, black, tbump, rich, arcae
Successfully installed appdirs-1.4.4 arcae-0.1.0 black-22.1.0 certifi-2023.5.7 charset-normalizer-3.1.0 cli-ui-0.17.2 click-8.1.3 colorama-0.4.6 contextlib2-21.6.0 docopt-0.6.2 duckdb-0.8.1 exceptiongroup-1.1.2 flake8-4.0.1 idna-3.4 iniconfig-2.0.0 markdown-it-py-3.0.0 mccabe-0.6.1 mdurl-0.1.2 mypy-extensions-1.0.0 numpy-1.25.0 packaging-23.1 pathspec-0.11.1 platformdirs-3.8.0 pluggy-1.2.0 pyarrow-12.0.0 pycodestyle-2.8.0 pyflakes-2.4.0 pygments-2.15.1 pytest-7.4.0 python-casacore-3.5.2 requests-2.31.0 rich-13.4.2 schema-0.7.5 six-1.16.0 tabulate-0.8.10 tbump-6.10.0 tomli-2.0.1 tomlkit-0.11.8 typing-extensions-4.7.1 unidecode-1.3.6 urllib3-2.0.3

This seems to correctly install the arrow_tables*.so cython extension, as well as libarcae.so in site-packages

$ tree ~/venv/arcaesrc/lib/python3.9/site-packages/arcae -I __pycache__
/home/simon/venv/arcaesrc/lib/python3.9/site-packages/arcae
├── __init__.py
├── applications
│   ├── __init__.py
│   ├── entrypoint.py
│   └── ms_export.py
├── config.py
├── lib
│   ├── __init__.py
│   ├── arrow_tables.cpython-39-x86_64-linux-gnu.so
│   └── libarcae.so
└── tests
    ├── __init__.py
    ├── conftest.py
    └── test_pytable.py

3 directories, 11 files

However, LD_LIBRARY_PATH must be set to discover the casacore and other shared objects built by vcpkg in order for things to work properly:

(arcaesrc) $ export LD_LIBRARY_PATH=~/code/arcae/vcpkg/installed/x64-linux-dynamic-cxx17-abi0-rel/lib
(arcaesrc) $ py.test -s -vvv --pyargs arcae

The wheels correctly package the built casacore shared objects and dependencies via auditwheel, which is why I don't think source builds will ever be viable.

[sjperkins]

Did you have any luck here @orliac ?

[orliac]

Hello @sjperkins
Sorry for the silence and thank you for your last input.
In the end I managed to install arcae from the wheel but I had to adapt the Spack recipes of arrow, py-pyarrow and re2 in order to switch GLIBCXX_USE_CXX11_ABI to 0. At least I could run the example you provide under https://github.com/ratt-ru/arcae#usage (where AT should be replaced by arrow_table btw). Not sure if there will be side effects though.
When I have a bit more time I'll come back on the compilation from source but at least now I should be able to start experimenting with arcae.