build MPI by njzjz · Pull Request #133 · conda-forge/ambertools-feedstock

njzjz · 2023-12-12T02:26:21Z

Checklist

Used a personal fork of the feedstock to propose changes
Bumped the build number (if the version is unchanged)
Reset the build number to 0 (if the version changed)
Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
Ensured the license file is being packaged.

Fix #132.

njzjz · 2023-12-12T02:26:27Z

@conda-forge-admin, please rerender

conda-forge-webservices · 2023-12-12T02:26:36Z

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 (recipe) and found some lint.

Here's what I've got...

For recipe:

The source section contained an unexpected subsection name. string is not a valid subsection name.

njzjz · 2023-12-12T02:27:25Z

@conda-forge-admin, please rerender

conda-forge-webservices · 2023-12-12T02:27:48Z

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

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

…nda-forge-pinning 2023.12.11.22.38.11

Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>

njzjz

Now it passes on my computer after multiple retries. I am going to see if it passes here

njzjz · 2024-01-03T08:40:27Z

Got this error for osx-arm64:

2024-01-03T08:16:13.8739220Z + conda install --yes --no-deps --force-reinstall -p /Users/runner/miniforge3/conda-bld/ambertools_1704269182095/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol xorg-xproto xorg-libx11
2024-01-03T08:16:13.8769280Z + local cmd=install
2024-01-03T08:16:13.8842690Z + case "$cmd" in
2024-01-03T08:16:13.8871280Z + __conda_exe install --yes --no-deps --force-reinstall -p /Users/runner/miniforge3/conda-bld/ambertools_1704269182095/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol xorg-xproto xorg-libx11
2024-01-03T08:16:13.8873080Z + /Users/runner/miniforge3/bin/conda install --yes --no-deps --force-reinstall -p /Users/runner/miniforge3/conda-bld/ambertools_1704269182095/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol xorg-xproto xorg-libx11
2024-01-03T08:16:16.5440100Z Channels:
2024-01-03T08:16:16.5440880Z  - conda-forge
2024-01-03T08:16:16.5441260Z Platform: osx-64
2024-01-03T08:16:50.9159540Z Collecting package metadata (repodata.json): ...working... done
2024-01-03T08:16:51.2541850Z Solving environment: ...working... failed
2024-01-03T08:16:51.2545380Z 
2024-01-03T08:16:51.2546940Z InvalidSpec: The package "conda-forge/osx-arm64::python_abi==3.9=4_cp39" is not available for the specified platform

It's not related to this PR but should be resolved.

@jaimergp, could you please clarify why they need to be reinstalled? Should they be installed for the host or target platform? Thanks!

njzjz · 2024-01-05T00:55:48Z

Oh, I see these comments:

ambertools-feedstock/recipe/build.sh

Lines 39 to 45 in f14f875

    
           # Workarounds for issue #20 
        
           #  In MacOS, `tk` ships some X11 headers that interfere with the X11 libraries 
        
           #  1) delete clobbered X11 headers (mix of tk and xorg) 
        
           rm -rf ${PREFIX}/include/X11/{DECkeysym,HPkeysym,Sunkeysym,X,XF86keysym,Xatom,Xfuncproto}.h 
        
           rm -rf ${PREFIX}/include/X11/{ap_keysym,keysym,keysymdef,Xlib,Xutil,cursorfont}.h 
        
           #  2) Reinstall Xorg dependencies 
        
           #     We temporarily disable the (de)activation scripts because they fail otherwise

I think it should be reinstalled for the host platform.

njzjz · 2024-01-05T06:02:12Z

All builds pass. Now I'll build for other Python versions.

njzjz · 2024-01-05T06:02:29Z

@conda-forge-admin, please rerender

…nda-forge-pinning 2024.01.04.16.29.16

mattwthompson · 2024-01-05T17:30:54Z

    mv ${BUILD_PREFIX}/etc/conda/{activate.d,activate.d.bak}
    mv ${BUILD_PREFIX}/etc/conda/{deactivate.d,deactivate.d.bak}
-    conda install --yes --no-deps --force-reinstall -p ${PREFIX} xorg-xproto xorg-libx11
+    CONDA_SUBDIR="$target_platform" conda install --yes --no-deps --force-reinstall -p ${PREFIX} xorg-xproto xorg-libx11


I don't understand why this change is needed - could you help me out?

Got this error: #133 (comment)

njzjz · 2024-01-14T00:57:52Z

Hi @conda-forge/ambertools, could someone take a review and merge the PR? Everything should be fine.

…nda-forge-pinning 2023.12.11.22.38.11

Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>

…nda-forge-pinning 2024.01.04.16.29.16

…nda-forge-pinning 2024.04.08.06.19.54

…nda-forge-pinning 2024.05.01.20.49.02

…nda-forge-pinning 2024.05.02.11.25.06

njzjz · 2024-05-02T21:16:18Z

openmpi tests encounter the same error as conda-forge/openmpi-feedstock#152

mattwthompson · 2024-05-02T21:21:45Z

That's weird. Any ideas besides bringing down openssh ... ?

njzjz · 2024-05-02T22:01:49Z

I set export OMPI_MCA_plm_ssh_agent=false as suggested by conda-forge/openmpi-feedstock#152 (comment).

njzjz · 2024-05-03T00:40:02Z

I set export OMPI_MCA_plm_ssh_agent=false as suggested by conda-forge/openmpi-feedstock#152 (comment).

Oh, it doesn't work :(

github-actions · 2024-05-03T13:11:22Z

Hi! This is the friendly conda-forge automerge bot!

I considered the following status checks when analyzing this PR:

linter: passed
azure: passed

Thus the PR was passing and merged! Have a great day!

mattwthompson · 2024-05-03T13:14:06Z

Works well enough for us 🙃

Thanks for your work and patience @njzjz - I think people will like this addition

build MPI

4c08a24

njzjz requested review from dacase, j-wags, jaimergp, mattwthompson, mikemhenry, simonbray and swails as code owners December 12, 2023 02:26

string is under build

759ace0

conda-forge-webservices[bot] and others added 3 commits December 12, 2023 02:29

MNT: Re-rendered with conda-build 3.28.1, conda-smithy 3.30.1, and co…

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…nda-forge-pinning 2023.12.11.22.38.11

fix nompi

f1bf6b5

use external mpi4py

199f23f

mikemhenry reviewed Dec 12, 2023

View reviewed changes

Comment thread recipe/meta.yaml Outdated

jaimergp reviewed Dec 18, 2023

View reviewed changes

Comment thread recipe/meta.yaml Outdated

njzjz and others added 2 commits December 21, 2023 13:42

Apply suggestions from code review

2e28c2c

Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>

add a patch to avoid cleaning compiler flags set by conda-forge

b9dc271

njzjz commented Jan 3, 2024

View reviewed changes

Comment thread recipe/meta.yaml Outdated

set CONDA_SUBDIR

b65b403

build for other Python versions

f49e6f0

MNT: Re-rendered with conda-build 3.28.2, conda-smithy 3.30.2, and co…

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mattwthompson reviewed Jan 5, 2024

View reviewed changes

mattwthompson and others added 17 commits May 2, 2024 13:35

build MPI

a92cdd7

string is under build

be01dbb

MNT: Re-rendered with conda-build 3.28.1, conda-smithy 3.30.1, and co…

711428f

…nda-forge-pinning 2023.12.11.22.38.11

fix nompi

86d45f6

use external mpi4py

72bb630

Apply suggestions from code review

df439f7

Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>

add a patch to avoid cleaning compiler flags set by conda-forge

298d29a

build for other Python versions

8bdf6ca

MNT: Re-rendered with conda-build 3.28.2, conda-smithy 3.30.2, and co…

4f7d2fe

…nda-forge-pinning 2024.01.04.16.29.16

MNT: Re-rendered with conda-build 24.3.0, conda-smithy 3.34.1, and co…

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…nda-forge-pinning 2024.04.08.06.19.54

Dummy check sander and sander.MPI

bbfb1e2

MNT: Re-rendered with conda-build 24.3.0, conda-smithy 3.35.0, and co…

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…nda-forge-pinning 2024.05.01.20.49.02

Skip sander.MPI check when nompi

b246efc

Skip older Python versions

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MNT: Re-rendered with conda-build 24.3.0, conda-smithy 3.35.0, and co…

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…nda-forge-pinning 2024.05.02.11.25.06

MNT: Re-rendered with conda-build 24.3.0, conda-smithy 3.35.0, and co…

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…nda-forge-pinning 2024.05.02.11.25.06

MNT: Re-rendered with conda-build 24.3.0, conda-smithy 3.35.0, and co…

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…nda-forge-pinning 2024.05.02.11.25.06

mattwthompson approved these changes May 2, 2024

View reviewed changes

njzjz mentioned this pull request May 2, 2024

Failure on systems without SSH conda-forge/openmpi-feedstock#152

Closed

export OMPI_MCA_plm_ssh_agent=false

b8dfe33

skip openmpi tests

018d9d0

mattwthompson added the automerge Merge the PR when CI passes label May 3, 2024

github-actions Bot merged commit d87173b into conda-forge:main May 3, 2024

mattwthompson mentioned this pull request May 29, 2024

Release 24 #141

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