Add pybammsolvers #28748

prady0t · 2025-01-03T22:07:23Z

Checklist

Signed-off-by: Pradyot Ranjan <[email protected]>

github-actions · 2025-01-03T22:08:42Z

Hi! This is the staged-recipes linter and your PR looks excellent! 🚀

conda-forge-admin · 2025-01-03T22:09:06Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/pybammsolvers/meta.yaml) and found some lint.

Here's what I've got...

For recipes/pybammsolvers/meta.yaml:

❌ The home item is expected in the about section.
❌ Non noarch packages should have python requirement without any version constraints.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/13464369326. Examine the logs at this URL for more detail.}

prady0t · 2025-01-03T22:13:57Z

@agriyakhetarpal @Saransh-cpp @arjxn-py @kratman
Locally I have problems with gfortran

kratman · 2025-01-03T22:21:26Z

Ok I will take a look on Sunday

agriyakhetarpal

Thanks @prady0t, looks like a good start! #28748 (comment) would need to be addressed as far as the recipe's static analysis goes, and then I've left other comments below about how the packaging of the recipe should go:

agriyakhetarpal · 2025-01-04T19:29:19Z

recipes/pybammsolvers/build.sh

+### Compile and install SUITESPARSE ###
+# SuiteSparse is required to compile SUNDIALS's
+# KLU solver.


Suggested change

### Compile and install SUITESPARSE ###

# SuiteSparse is required to compile SUNDIALS's

# KLU solver.

### Compile and install SUITESPARSE ###

# SuiteSparse is required to compile SUNDIALS's

# KLU solver.

Nitpicking: if you do wish to keep comments for future reference in this recipe, maybe consolidating them in one place is one way to go. That said, I don't think the comments themselves will add much, could you add links to the docs here?

Completely forgot about this. Let me resolve this in the next commits.

recipes/pybammsolvers/build.sh

agriyakhetarpal · 2025-01-04T19:32:39Z

recipes/pybammsolvers/meta.yaml

+requirements:
+  build:
+    - {{ compiler('c') }}
+  host:
+    - python >=3.9,<3.13
+    - setuptools >=64
+    - wheel
+    - casadi >=3.6.7  # [not win]
+    - cmake  # [not win]
+    - pip
+  run:
+    - python >=3.9,<3.13
+    - casadi
+    - numpy <2.0
+


We can use conda-forge's {{ python_min }} syntax here, at least for the minimum version of Python:

See https://github.com/conda-forge/cfep/blob/main/cfep-25.md

For some reason this fails for conda-build locally, so can't test this part locally.

That's strange. Let's keep this conversation unresolved for now, so that we can add it back in just before this is merged.

agriyakhetarpal · 2025-01-04T19:35:27Z

recipes/pybammsolvers/meta.yaml

+
+requirements:
+  build:
+    - {{ compiler('c') }}


You'll also need stdlib('c') (libc), compiler('c++'), and compiler('fortran') here – does that help with your issue? Or, are you currently testing your changes using build_locally.py and Docker?

Yes, I can compile Sundials now. I don't think it's necessary to have stdlib('c') here, a c compiler should automatically get standard c libraries. Also {{ stdlib("c") }} causes :

Could not solve for environment specs The following package could not be installed └─ c_osx-arm64 =* * does not exist (perhaps a typo or a missing channel).

But I may be doing something wrong. I'm commenting out this step until further discussion, as I can still compile without it.

I'm currently only using conda-build. Should I choose docker instead?

I'm sorry I didn't see the lint bot comments. We do need {{ stdlib("c") }}

Yes. I think it wouldn't hurt to try using Docker, since getting it to work on Linux before macOS would be nice, and it being isolated doesn't modify your local development environment.

recipes/pybammsolvers/build.sh

recipes/pybammsolvers/meta.yaml

agriyakhetarpal · 2025-01-04T19:39:34Z

recipes/pybammsolvers/meta.yaml

+    - casadi >=3.6.7  # [not win]
+    - cmake  # [not win]


Suggested change

- casadi >=3.6.7 # [not win]

- cmake # [not win]

- casadi >=3.6.7

- cmake

Our packaging is going to differ here because we won't use Vcpkg and MSVC – we'll use Clang that conda-forge provides, so we'll need CasADi and CMake too.

Though, it would be better to compile CasADi (just the C++ interface, that is – which means, with WITH_PYTHON3 set to OFF ) on our own as well so that we guarantee ABI compatibility with CasADi's conda-forge package.

We could then patch these lines: https://github.com/pybamm-team/PyBaMM/blob/a5616c960ac4769db7ff98a04628a04789e8bf7e/CMakeLists.txt#L119-L139 to turn off our lookup for the CasADi Python interface. The reason for this is that we wouldn't want to link against PyPI dependencies with conda-forge ones; both follow different methodologies for ABI compatibility. Let's revisit this once we have some progress and when we have SuiteSparse and SUNDIALS being compiled correctly...

agriyakhetarpal · 2025-01-04T19:40:16Z

recipes/pybammsolvers/build.sh

Not to be addressed right away, but we'll also need a build.bat equivalent of this script for Windows.

Yes I'm aware. Once the sh script works, I'll try replication the steps for bat file.

Co-authored-by: Agriya Khetarpal <[email protected]>

Signed-off-by: Pradyot Ranjan <[email protected]>

prady0t · 2025-01-05T22:14:21Z

recipes/pybammsolvers/build.sh

+for dir in SuiteSparse_config AMD COLAMD BTF KLU
+do
+    make -C $SUITESPARSE_DIR/$dir library
+    make -C $SUITESPARSE_DIR/$dir install INSTALL=$PREFIX


I've used $PREFIX here and for the Sundials installation as well because there were permission problems with usr. Let me know if this is not preferable.

I can still see the CI fails due to the same problem.

Yes, $PREFIX is the ideal location to store them, usr/ is not user-writeable on most CI runners.

prady0t · 2025-01-05T22:21:50Z

We have some progress, I can now compile both Suitesparse and Sundials. The failure now is conda-build cannot import pybammsolvers which suggests the build was not completed.

kratman

Just starting to take a look at this repo. I will share anything I find

kratman · 2025-01-06T17:07:34Z

recipes/pybammsolvers/meta.yaml

+
+extra:
+  recipe-maintainers:
+    - prady0t


This should be the IDAKLU maintainers group from pybamm team

It's common for conda-forge feedstocks for packages to be maintained by folks other than the upstream package maintainers, so I will suggest keeping both – unless you did mean that, of course.

I always find it easier to add maintainers once the feedstock is up, otherwise -

GitHub users listed in the maintainer section have posted a comment confirming they are willing to be listed there

which is cumbersome (and will make the CI fail).

recipes/pybammsolvers/meta.yaml

Co-authored-by: Agriya Khetarpal <[email protected]>

agriyakhetarpal

It proceeds to compile now but fails to find a BLAS distribution:

recipes/pybammsolvers/meta.yaml

agriyakhetarpal · 2025-01-08T19:30:40Z

How about we don't attempt to compile SuiteSparse and directly add SUNDIALS as a host dependency – it's linked with KLU like we need it to be, and version 6.5.0 is available as well. That would be much easier :) Chaste and Octave use SUNDIALS in this manner. It would also circumvent our BLAS requirement that we're not able to fix here.

agriyakhetarpal · 2025-01-16T01:24:12Z

Yes, we'll need the libs and the CMake directory for CasADi. We rely on the CasADi Python wheels we get from PyPI, but we don't have that option in this case. So, as I mentioned somewhere earlier/before, we can't use this command

import os; import sysconfig; print(os.path.join(sysconfig.get_path('purelib'), 'casadi', 'cmake'))

anymore, and need to find CasADi's CMake file in other ways. We can do this with two options:

A) Use casadi as a host dependency and see where it stores these files. Then, we can point CMake, the compiler, the linker, etc., to them.
B) Compile CasADi (without the Python interface) ourselves at the cost of ~4 minutes of extra CI time

I would recommend going with A) first, as it is the less intrusive and better approach. You'll need to patch that line for it to happen (in this case, we didn't have CMakeLists.txt in the sdist, so we can just replace those lines for the patch)

I do remember that these .cmake files are stored in the archive indeed; you would most likely find them in casadi_3.6.7_py3X_<...>/lib/cmake/casadi, but if you could confirm that with https://github.com/conda/conda-package-handling or similar, it would be great.

Signed-off-by: Pradyot Ranjan <[email protected]>

prady0t · 2025-01-18T19:10:22Z

I was able to find casadi but some packages nvector/nvector_openmp.h cannot be found.

  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/Solution.cpp:1:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/Solution.hpp:4:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector            */
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP_solvers.cpp:1:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP_solvers.hpp:4:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP.hpp:4:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolver.hpp:4:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector            */
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolverGroup.cpp:1:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolverGroup.hpp:4:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolver.hpp:4:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector            */
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolver.cpp:1:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IDAKLUSolver.hpp:4:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector            */
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/SolutionData.cpp:1:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/SolutionData.hpp:5:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector            */
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IdakluJax.cpp:1:
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/IdakluJax.hpp:4:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector            */
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.cpp:1:
  /opt/miniconda3/envs/pybammsolvers-build/conda-bld/pybammsolvers_1737224830610/work/src/pybammsolvers/idaklu_source/common.hpp:10:10: fatal error: 'nvector/nvector_openmp.h' file not found
     10 | #include <nvector/nvector_openmp.h>  /* access to openmp N_Vector

agriyakhetarpal · 2025-01-21T20:58:55Z

Thanks! It might be good to see what the CI jobs need in comparison to your local build, as it is difficult for us to look at your build the full logs.

As for finding nvector_openmp.h file, that should be present in the solvers source code. As the logs are truncated, I'm not sure why it fails – in the full logs, is there a longer stack trace? If it fails to find OpenMP, I'm not sure why that would be the case. This is because SUNDIALS does build with it, at least on Linux: https://github.com/conda-forge/sundials-feedstock/blob/bd8b70c3d07d845eae73222010e3cef7a4120d80/recipe/build-sundials.sh#L7-L11

Signed-off-by: Pradyot Ranjan <[email protected]>

prady0t · 2025-01-22T05:14:30Z

Mostly, the CI logs represent my local build failures. For osx, I think OpenMP was not found. Even inside $PREFIX/include/nvector, I cannot find OpenMP related files and these are its only contents:

nvector_manyvector.h
nvector_serial.h

Same for Windows builds. For linux now we cannot find klu. Might it be possible KLU linked Sundials is not available across all platforms?

agriyakhetarpal · 2025-01-28T20:02:48Z

From https://github.com/conda-forge/sundials-feedstock/blob/bd8b70c3d07d845eae73222010e3cef7a4120d80/recipe/build-sundials.sh#L7-L11, SUNDIALS builds without OpenMP for Darwin, but builds with it for Linux. And, checking build.bat, it uses OpenMP for Windows. So we would indeed need to switch to a custom build of SUNDIALS for all platforms, where we properly link against both KLU and OpenMP (llvm-openmp on macOS and libgomp on Linux).

Signed-off-by: Pradyot Ranjan <[email protected]>

prady0t · 2025-02-06T12:29:17Z

Sundials is build successfully. I've used pre-build Suitesparse from conda-forge and linked KLU against it. I don't know about the error in CI

    raise OverLinkingError(overlinking_errors)
conda_build.exceptions.OverLinkingError: <exception str() failed>

Locally it fails as it's not able to run tests, even though all steps pass without failure.

agriyakhetarpal · 2025-02-06T15:16:55Z

The overlinking means that some dependencies are included as a part of the runtime, which aren't needed – for example, SUNDIALS and SuiteSparse are required only at build time, and not at runtime.

Also, is the IDAKLU solver being compiled? I ask because the CMakeLists.txt file was removed, so I'm not sure if it is. Could you add a test for the IDAKLU solver import?

prady0t · 2025-02-06T19:20:36Z

I missed that. Thanks! But tests for importing pybamsolvers are still failing?

agriyakhetarpal · 2025-02-06T23:11:05Z

I'm not sure if I see an import failure in the logs, though. Could you copy that, if you have some logs from a local build?

Also, @Saransh-cpp, @kratman, and I discussed this PR briefly in-person today. Would it be fine with you if we were to take over this PR in case you feel it will take some time over the next few weeks or so? Eric is planning for a v25.2 release at the end of February, and we will be two releases behind by then. I think contributing to the same PR should be fine for preserving authorship. I also have access to your fork already, so I can help push a few changes next week. If it's a yes from you, please grant Eric access in a few weeks as well.

I think the plan of action at the moment will be as follows:

get the CMakeLists.txt file back
patch CMakeLists.txt to look for the CasADi libs + headers under the prefix dirs, wherever they are (with CasADi set as a host dependency so that the libs and headers are available)
remove whichever overlinked dependencies are left
test that the import pybammsolvers statement works across all platforms.

prady0t · 2025-02-08T10:09:16Z

Yes, it's totally fine! I've already sent the access to all of you.

Signed-off-by: Pradyot Ranjan <[email protected]>

recipes/pybammsolvers/meta.yaml

agriyakhetarpal · 2025-02-13T04:34:14Z

There are errors like:

  ERROR (pybammsolvers,lib/libsundials_sunlinsollapackband.so.4.5.0): Needed DSO lib/libopenblas.so.0 found in ['conda-forge/linux-64::libopenblas==0.3.28=pthreads_h94d23a6_1']
  ERROR (pybammsolvers,lib/libsundials_sunlinsollapackband.so.4.5.0): .. but ['conda-forge/linux-64::libopenblas==0.3.28=pthreads_h94d23a6_1'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely)

in the logs, which we'll need to fix. I noticed SuiteSparse offers libklu as a separate package as its recipe contains multiple outputs. Please bear with me while I try to make more changes.

agriyakhetarpal · 2025-02-13T04:40:36Z

Okay, I fixed the overlinking issue with SuiteSparse and OpenBLAS – we now need to compile pybammsolvers.

agriyakhetarpal · 2025-02-13T05:21:10Z

I think this should be unblocked enough for you to proceed with the following steps, @prady0t. The next thing on the list would be to point to the KLU headers correctly – they will be in $PREFIX/include, so we can patch these lines: https://github.com/pybamm-team/pybammsolvers/blob/791677d64aff3b62025a62e85e97bb73736a0391/setup.py#L14-L16 so that we look for them in the right location.

Signed-off-by: Pradyot Ranjan <[email protected]>

prady0t · 2025-02-21T19:52:26Z

Cannot find sundials_legacy_wrapper.hpp but it was removed. We might have to wait for a new release (the latest release still has it).

Signed-off-by: Pradyot Ranjan <[email protected]>

Add pybammsolvers

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Download IDAKLU from pybammsolvers pybamm-team/PyBaMM#4487

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Conda-forge recipe pybamm-team/pybammsolvers#20

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Try to find BLAS again

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Using ${PREFIX} instead of /usr/local

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pybamm v25.1.0 conda-forge/pybamm-feedstock#72

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finding casadi

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Add SuiteSparse to run: (can't hurt to try)

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Add pybammsolvers #28748

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prady0t commented Jan 5, 2025

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agriyakhetarpal commented Jan 8, 2025 • edited Loading

agriyakhetarpal commented Jan 16, 2025 • edited Loading

prady0t commented Jan 18, 2025

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prady0t commented Feb 8, 2025

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prady0t commented Feb 21, 2025

conda-forge-admin commented Jan 3, 2025 •

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agriyakhetarpal commented Jan 8, 2025 •

edited

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agriyakhetarpal commented Jan 16, 2025 •

edited

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