[BUG] ImportError: libdbCore.so.7.0.10.99.0: cannot open shared object file: No such file or directory

[konosubakonoakua]

(venv) xilinx@Pynq-IMPCAS-ZU9:/opt/epics$ python -V
Python 3.11.14
(venv) xilinx@Pynq-IMPCAS-ZU9:/opt/epics$ uname -a
Linux Pynq-IMPCAS-ZU9 6.6.10-xilinx-v2024.1-g1594cb1cd9ce #1 SMP Sat Apr 27 05:22:24 UTC 2024 aarch64 aarch64 aarch64 GNU/Linux
(venv) xilinx@Pynq-IMPCAS-ZU9:/opt/epics$ uv pip install caproto pyepics pcaspy softioc
Using Python 3.11.14 environment at: venv
Resolved 12 packages in 51ms
      Built pcaspy==0.8.1
      Built epicscorelibs==7.0.7.99.1.2
      Built pvxslibs==1.4.1
      Built softioc==4.6.1
Prepared 4 packages in 34m 19s
Installed 12 packages in 154ms
 + caproto==1.3.0
 + epicscorelibs==7.0.7.99.1.2
 + epicsdbbuilder==1.5
 + numpy==2.4.0
 + pcaspy==0.8.1
 + pvxslibs==1.4.1
 + pyepics==3.5.9
 + pyparsing==3.3.1
 + pyyaml==6.0.3
 + setuptools==80.9.0
 + setuptools-dso==2.12.2
 + softioc==4.6.1
(venv) xilinx@Pynq-IMPCAS-ZU9:/opt/epics$ python -c "import softioc"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/epics/venv/lib/python3.11/site-packages/softioc/__init__.py", line 14, in <module>
    from .imports import dbLoadDatabase, registerRecordDeviceDriver
  File "/opt/epics/venv/lib/python3.11/site-packages/softioc/imports.py", line 10, in <module>
    from . import _extension
ImportError: libdbCore.so.7.0.10.99.0: cannot open shared object file: No such file or directory

[konosubakonoakua]

Workaround:

uv pip install epicscorelibs==7.0.10.99.0.0
uv pip install softioc==4.6.1 --no-deps
uv pip install pyyaml cothread pvxslibs epicsdbbuilder

[OCopping]

I noticed this too in my techui-builder repo, when attempting to run py3.13 CI, and also fixed by installing epicscorelibs>=7.0.10 manually

[AlexanderWells-diamond]

Thank you for the report @konosubakonoakua . This issue is due to a recent release of epicscorelibs, and a discrepancy between softioc's build-time and run-time dependencies on epicscorelibs. This is happening for you as we don't have any aarch64 wheels in PyPi. It is happening for @OCopping because we don't have any wheels for Python >= 3.13. So both of you are building the wheels yourself locally and exposing this issue.

[AlexanderWells-diamond]

I'm still struggling to work out why epicscorelibs downgrades itself between build-time and run-time. Here's a verbose logfile that shows softioc wanting a version of epicscorelibs>=7.0.7.99.1.2a1, <7.0.7.99.2:

$ uv venv --clear --python 3.13 && uv pip install --verbose softioc
Using CPython 3.13.9
Creating virtual environment at: .venv
Activate with: source .venv/bin/activate
DEBUG uv 0.9.9
DEBUG Acquired shared lock for `/root/.cache/uv`
DEBUG Searching for default Python interpreter in virtual environments
DEBUG Found `cpython-3.13.9-linux-x86_64-gnu` at `/.venv/bin/python3` (virtual environment)
DEBUG Using Python 3.13.9 environment at: /.venv
DEBUG Acquired lock for `/.venv`
DEBUG At least one requirement is not satisfied: softioc
DEBUG Using request timeout of 30s
DEBUG Solving with installed Python version: 3.13.9
DEBUG Solving with target Python version: >=3.13.9
DEBUG Adding direct dependency: softioc*
DEBUG Found fresh response for: https://pypi.org/simple/softioc/
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/8f/46/689554640712513ddffdedd452b5ba6627f4fcd78844dd4a489c32bdd22d/softioc-4.6.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata
DEBUG Searching for a compatible version of softioc (*)
DEBUG Selecting: softioc==4.6.1 [compatible] (softioc-4.6.1.tar.gz)
DEBUG Adding transitive dependency for softioc==4.6.1: epicscorelibs>=7.0.7.99.1.2a1, <7.0.7.99.2
DEBUG Adding transitive dependency for softioc==4.6.1: pvxslibs>=1.3.2a2
DEBUG Adding transitive dependency for softioc==4.6.1: numpy*
DEBUG Adding transitive dependency for softioc==4.6.1: epicsdbbuilder>=1.4
DEBUG Adding transitive dependency for softioc==4.6.1: pyyaml>=6.0
DEBUG Found fresh response for: https://pypi.org/simple/epicscorelibs/
DEBUG Found fresh response for: https://pypi.org/simple/numpy/
DEBUG Searching for a compatible version of epicscorelibs (>=7.0.7.99.1.2a1, <7.0.7.99.2)
DEBUG Selecting: epicscorelibs==7.0.7.99.1.2 [compatible] (epicscorelibs-7.0.7.99.1.2-cp313-cp313-manylinux2014_x86_64.whl)
DEBUG Found fresh response for: https://pypi.org/simple/pvxslibs/
DEBUG Found fresh response for: https://pypi.org/simple/epicsdbbuilder/
DEBUG Found fresh response for: https://pypi.org/simple/pyyaml/
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/99/98/9d4ad53b0e9ef901c2ef1d550d2136f5ac42d3fd2988390a6def32e23e48/numpy-2.4.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/92/50/841821efaa33dbde9adf8c8b803eb7f48ea53f8f69928fefba4b8aadb040/pvxslibs-1.5.0-cp313-cp313-manylinux2014_x86_64.whl.metadata
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/a2/af/6bb0e1de4fb7218fa4ba95fe91ba1fd4a5661dd28a461eff6a0f609c996c/epicscorelibs-7.0.7.99.1.2-cp313-cp313-manylinux2014_x86_64.whl.metadata
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/10/f8/858c81f516cb9d1c1f73e8bf379be2cbec4388c93f48a4eb118c47f32d4d/epicsdbbuilder-1.5-py3-none-any.whl.metadata
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/74/27/e5b8f34d02d9995b80abcef563ea1f8b56d20134d8f4e5e81733b1feceb2/pyyaml-6.0.3-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
DEBUG Adding transitive dependency for epicscorelibs==7.0.7.99.1.2: setuptools*
DEBUG Adding transitive dependency for epicscorelibs==7.0.7.99.1.2: setuptools-dso>=2.11a2
DEBUG Adding transitive dependency for epicscorelibs==7.0.7.99.1.2: numpy*
DEBUG Searching for a compatible version of pvxslibs (>=1.3.2a2)
DEBUG Selecting: pvxslibs==1.5.0 [compatible] (pvxslibs-1.5.0-cp313-cp313-manylinux2014_x86_64.whl)
DEBUG Adding transitive dependency for pvxslibs==1.5.0: setuptools-dso>=2.7a1
DEBUG Adding transitive dependency for pvxslibs==1.5.0: epicscorelibs>=7.0.10.99.0.0, <7.0.10.99.1
DEBUG Recording unit propagation conflict of pvxslibs from incompatibility of (pvxslibs, epicscorelibs)
DEBUG Searching for a compatible version of epicscorelibs (>=7.0.7.99.1.2a1, <7.0.7.99.2)
DEBUG Selecting: epicscorelibs==7.0.7.99.1.2 [compatible] (epicscorelibs-7.0.7.99.1.2-cp313-cp313-manylinux2014_x86_64.whl)
DEBUG Searching for a compatible version of pvxslibs (>=1.3.2a2, <1.5.0 | >1.5.0)
DEBUG Selecting: pvxslibs==1.4.1 [compatible] (pvxslibs-1.4.1-cp313-cp313-manylinux2014_x86_64.whl)
DEBUG Found fresh response for: https://pypi.org/simple/setuptools-dso/
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/6a/d7/d69204cdc4f8cca9fbbee262d044dbfc4891dc3cd96a6df64871db970026/pvxslibs-1.4.1-cp313-cp313-manylinux2014_x86_64.whl.metadata
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/b9/36/c101788fad13e8ea65c5b3d3dee8ff996500800cd554ae6ff72143690247/setuptools_dso-2.12.2-py2.py3-none-any.whl.metadata
DEBUG Adding transitive dependency for pvxslibs==1.4.1: setuptools-dso>=2.7a1
DEBUG Adding transitive dependency for pvxslibs==1.4.1: epicscorelibs>=7.0.7.99.1.2, <7.0.7.99.2
DEBUG Searching for a compatible version of numpy (*)
DEBUG Selecting: numpy==2.4.0 [compatible] (numpy-2.4.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl)
DEBUG Searching for a compatible version of epicsdbbuilder (>=1.4)
DEBUG Selecting: epicsdbbuilder==1.5 [compatible] (epicsdbbuilder-1.5-py3-none-any.whl)
DEBUG Searching for a compatible version of pyyaml (>=6.0)
DEBUG Selecting: pyyaml==6.0.3 [compatible] (pyyaml-6.0.3-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl)
DEBUG Found fresh response for: https://pypi.org/simple/setuptools/
DEBUG Searching for a compatible version of setuptools (*)
DEBUG Selecting: setuptools==80.9.0 [compatible] (setuptools-80.9.0-py3-none-any.whl)
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl.metadata
DEBUG Searching for a compatible version of setuptools-dso (>=2.11a2)
DEBUG Selecting: setuptools-dso==2.12.2 [compatible] (setuptools_dso-2.12.2-py2.py3-none-any.whl)
DEBUG Adding transitive dependency for setuptools-dso==2.12.2: setuptools*
DEBUG Tried 9 versions: pvxslibs 2, epicscorelibs 1, epicsdbbuilder 1, numpy 1, pyyaml 1, setuptools 1, setuptools-dso 1, softioc 1
DEBUG marker environment resolution took 0.005s
Resolved 8 packages in 9ms
DEBUG Registry requirement already cached: pvxslibs==1.4.1
DEBUG Registry requirement already cached: epicscorelibs==7.0.7.99.1.2
DEBUG Registry requirement already cached: pyyaml==6.0.3
DEBUG Registry requirement already cached: epicsdbbuilder==1.5
DEBUG Registry requirement already cached: softioc==4.6.1
DEBUG Registry requirement already cached: setuptools-dso==2.12.2
DEBUG Registry requirement already cached: numpy==2.4.0
DEBUG Registry requirement already cached: setuptools==80.9.0
Installed 8 packages in 121ms
 + epicscorelibs==7.0.7.99.1.2
 + epicsdbbuilder==1.5
 + numpy==2.4.0
 + pvxslibs==1.4.1
 + pyyaml==6.0.3
 + setuptools==80.9.0
 + setuptools-dso==2.12.2
 + softioc==4.6.1
DEBUG Released lock at `/.venv/.lock`
DEBUG Released lock at `/root/.cache/uv/.lock`
root ➜ / 
$ 

This log shows why we also get an old version of pvxslibs - it tries to find a version of it that is compatible with the lower version of epicscorelibs.

@mdavidsaver notes here that it may be a bug in epicscorelibs.version.abi_requires (although I suspect by the time we invoke it it's too late - surely we've already got a version of epicscorelibs installed in order to run that function?) or that uv may somehow be affecting it - but I think the above log file counteracts that, as uv pip ... should just be a wrapper around pip itself. Tomorrow I should try and recreate it using just pip.

[mdavidsaver]

This log shows why we also get an old version of pvxslibs ...

I am not convinced of this, and a little confused about what I read. At what point is the softioc package built?

DEBUG Selecting: softioc==4.6.1 [compatible] (softioc-4.6.1.tar.gz)
DEBUG Adding transitive dependency for softioc==4.6.1: epicscorelibs>=7.0.7.99.1.2a1, <7.0.7.99.2
DEBUG Adding transitive dependency for softioc==4.6.1: pvxslibs>=1.3.2a2

Selecting: softioc==4.6.1 suggests to me that a build from source would be done, using the build dependency from pyproject.toml, which is not epicscorelibs>=7.0.7.99.1.2a1, <7.0.7.99.2.

[mdavidsaver]

In a manylinux2014_amd64 container, if I run:

/opt/python/cp313-cp313/bin/pip install --user -v --only-binary numpy softioc

The resulting build downloads epicscorelibs-7.0.10.99.0.0-cp313-cp313-manylinux2014_x86_64.whl. The resulting softioc-4.6.1.dist-info/METADATA contains:

Requires-Dist: epicscorelibs<7.0.10.99.1,>=7.0.10.99.0.0
Requires-Dist: pvxslibs>=1.3.2a2

And readelf -d softioc/_extension.cpython-313-x86_64-linux-gnu.so shows:

 0x0000000000000001 (NEEDED)             Shared library: [libdbRecStd.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libdbCore.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libca.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libCom.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x000000000000000f (RPATH)              Library rpath: [\$ORIGIN/../epicscorelibs/lib:$ORIGIN/../epicscorelibs/lib]

Which is all as I expect.

Full pip output

[mdavidsaver]

Selecting: softioc==4.6.1 suggests to me that a build from source would be done, using the build dependency from pyproject.toml, which is not epicscorelibs>=7.0.7.99.1.2a1, <7.0.7.99.2.

For reasons I can not fathom, despite running in py3.13, and needing to build from .tar.gz, uv seems to be looking at the meta-data for the py3.10 wheel for softioc!

DEBUG Found fresh response for: https://pypi.org/simple/softioc/
DEBUG Found fresh response for: https://files.pythonhosted.org/packages/8f/46/689554640712513ddffdedd452b5ba6627f4fcd78844dd4a489c32bdd22d/softioc-4.6.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata

Looking at the resulting situation, softioc is correctly built against 7.0.10.

$ cat .venv/lib/python3.13/site-packages/softioc-4.6.1.dist-info/METADATA
...
Requires-Dist: epicscorelibs<7.0.10.99.1,>=7.0.10.99.0.0
Requires-Dist: pvxslibs>=1.3.2a2
...

$ readelf -d /.venv/lib/python3.13/site-packages/softioc/_extension.cpython-313-x86_64-linux-gnu.so
...
 0x0000000000000001 (NEEDED)             Shared library: [libdbRecStd.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libdbCore.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libca.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libCom.so.7.0.10.99.0]
 0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 ...

... however, 7.0.7 is left installed.

$  /opt/python/cp313-cp313/bin/uv pip freeze
Using Python 3.13.11 environment at: /.venv
epicscorelibs==7.0.7.99.1.2
epicsdbbuilder==1.5
numpy==2.2.6
pvxslibs==1.4.1
pyyaml==6.0.3
setuptools==80.9.0
setuptools-dso==2.12.2
softioc==4.6.1

To my mind, this looks like a bug in the dependency resolver of uv.