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Build HEAD of v2.10 branch, enabling metatensor #5

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Build HEAD of v2.10 branch, enabling metatensor #5

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49bcc45
Rename label to tutorials-2024
Luthaf Oct 11, 2024
1b8e6fc
Build HEAD of v2.10 branch, and enable metatensor package
Luthaf Oct 14, 2024
e4e9758
Add py-plumed to the build
Luthaf Oct 14, 2024
4eb7dd1
Only define CONDA_BUILD_SYSROOT on CI
Luthaf Oct 14, 2024
c70c69e
Update version/build string handling
Luthaf Oct 15, 2024
b11220c
macos-11 builders are not provided anymore
Luthaf Oct 16, 2024
0878ef1
Do not pull binutils/hwloc on macos-arm64
Luthaf Oct 16, 2024
76f1c33
Do not try to deploy to anaconda when building PR
Luthaf Dec 10, 2024
8e0b0b2
Upgrade to the latest 2.10 commit
Luthaf Dec 10, 2024
5ffd14c
Increase Lammps build number
Luthaf Dec 10, 2024
168ebbf
Use macos sdk version 11.0 everywhere
Luthaf Dec 10, 2024
7ceadd0
Split build of different packages
Luthaf Dec 10, 2024
9b0e6b7
Upgrade to gromacs 2023.5
Luthaf Dec 10, 2024
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3 changes: 3 additions & 0 deletions .github/conda_build_config.yaml
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@@ -0,0 +1,3 @@
CONDA_BUILD_SYSROOT:
- /opt/MacOSX10.13.sdk # [osx and x86_64]
- /opt/MacOSX11.0.sdk # [osx and arm64]
24 changes: 13 additions & 11 deletions .github/workflows/ci.yml
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Expand Up @@ -9,7 +9,7 @@ jobs:
strategy:
fail-fast: false
matrix:
os: [ubuntu-22.04 , macos-11]
os: [ubuntu-22.04, macos-11, macos-14]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v2
Expand All @@ -23,29 +23,31 @@ jobs:
export MAKEFLAGS=-j3
conda create --name build
source activate build
conda-build -c conda-forge plumed
conda-build -c conda-forge gromacs
conda-build -c conda-forge lammps
conda-build -m .github/conda_build_config.yaml -c conda-forge plumed
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conda-build -m .github/conda_build_config.yaml -c conda-forge py-plumed
conda-build -m .github/conda_build_config.yaml -c conda-forge gromacs
conda-build -m .github/conda_build_config.yaml -c conda-forge lammps
- name: Deploy
env:
CONDA_UPLOAD_TOKEN: ${{ secrets.CONDA_UPLOAD_TOKEN }}
run: |
source activate base # needed to have correct CONDA_PREFIX
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l cecam-2023 $CONDA_PREFIX/conda-bld/*/lammps*.tar.bz2 --force
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l cecam-2023 $CONDA_PREFIX/conda-bld/*/plumed*.tar.bz2 --force
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l cecam-2023 $CONDA_PREFIX/conda-bld/*/gromacs*.tar.bz2 --force
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l tutorials-2024 $CONDA_PREFIX/conda-bld/*/lammps*.tar.bz2 --force
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l tutorials-2024 $CONDA_PREFIX/conda-bld/*/plumed*.tar.bz2 --force
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l tutorials-2024 $CONDA_PREFIX/conda-bld/*/py-plumed*.tar.bz2 --force
anaconda -t $CONDA_UPLOAD_TOKEN upload -u plumed -l tutorials-2024 $CONDA_PREFIX/conda-bld/*/gromacs*.tar.bz2 --force
- name: Test
run: |
conda create --name plumed-masterclass
conda create --name plumed-masterclass
source activate plumed-masterclass
conda install -y -c conda-forge plumed py-plumed numpy pandas matplotlib notebook mdtraj mdanalysis git
# check if python module is working
python -c "import plumed; p=plumed.Plumed(); print(p)"
# first install serial gromacs
conda install -y --strict-channel-priority -c plumed/label/masterclass -c conda-forge gromacs
# then replace with parallel gromacs and plumed
conda install -y --strict-channel-priority -c plumed/label/cecam-2023 -c conda-forge plumed
conda install -y --strict-channel-priority -c plumed/label/cecam-2023 -c conda-forge gromacs
conda install -y --strict-channel-priority -c plumed/label/tutorials-2024 -c conda-forge plumed
conda install -y --strict-channel-priority -c plumed/label/tutorials-2024 -c conda-forge gromacs
# check if python module is working
python -c "import plumed; p=plumed.Plumed(); print(p)"
cd test
Expand All @@ -55,7 +57,7 @@ jobs:
cat dir*/colvar*.dat
# install lammps
cd -
conda install -y --strict-channel-priority -c plumed/label/cecam-2023 -c conda-forge plumed lammps
conda install -y --strict-channel-priority -c plumed/label/tutorial-2024 -c conda-forge plumed lammps
cd test-lammps
mpiexec lmp -in start.lmp
cat COLVAR
2 changes: 0 additions & 2 deletions gromacs/conda_build_config.yaml
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This file was deleted.

2 changes: 0 additions & 2 deletions lammps/conda_build_config.yaml
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This file was deleted.

15 changes: 13 additions & 2 deletions plumed/build.sh
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Expand Up @@ -18,6 +18,10 @@ export CXXFLAGS="${CXXFLAGS//-O2/-O3}"

# libraries are explicitly listed here due to --disable-libsearch
export LIBS="-lboost_serialization -lfftw3 -lgsl -lgslcblas -llapack -lblas -lz $LIBS"
export LIBS="-lmetatensor_torch -lmetatensor -ltorch -lc10 -ltorch_cpu $LIBS"
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# libtorch puts some headers in a non-standard place
export CPPFLAGS="-I$PREFIX/include/torch/csrc/api/include $CPPFLAGS"

# enable MPI
export CXX=mpic++
Expand All @@ -26,8 +30,15 @@ export CXX=mpic++
# --disable-libsearch forces to link only explicitely requested libraries
# --disable-static-patch avoid tests that are only required for static patches
# --disable-static-archive makes package smaller
./configure --prefix=$PREFIX --disable-python --disable-libsearch --disable-static-patch --disable-static-archive --enable-modules=all --enable-boost_serialization
./configure --prefix=$PREFIX \
--disable-python \
--disable-libsearch \
--disable-static-patch \
--disable-static-archive \
--enable-modules=all \
--enable-boost_serialization \
--enable-metatensor \
--enable-libtorch

make -j3
make install

2 changes: 0 additions & 2 deletions plumed/conda_build_config.yaml
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@@ -1,5 +1,3 @@
CONDA_BUILD_SYSROOT:
- /opt/MacOSX10.9.sdk # [osx]
mpi:
- mpich
- openmpi
17 changes: 11 additions & 6 deletions plumed/meta.yaml
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@@ -1,15 +1,16 @@
{% set name = "plumed" %}
{% set version = "2.9.0" %}
{% set version = "2.10" %}
{% set git_rev = "b0ffcb55ad8cc3c71ec5c30a1bd46f68dd33bceb" %}

package:
name: {{ name|lower }}
version: {{ version }}
version: {{ version }}.git.{{ git_rev }}

source:
url: https://github.com/plumed/plumed2/archive/v{{ version }}.tar.gz
sha256: 612d2387416b5f82dd8545709921440370e144fd46cef633654cf0ee43bac5f8
#git_url: https://github.com/plumed/plumed2.git
#git_rev: ddb59d16b21d6afb054fd9f6352f5d290e8575bf
# url: https://github.com/plumed/plumed2/archive/v{{ version }}.tar.gz
# sha256: 612d2387416b5f82dd8545709921440370e144fd46cef633654cf0ee43bac5f8
git_url: https://github.com/plumed/plumed2.git
git_rev: {{ git_rev }}

build:
number: 0
Expand All @@ -34,12 +35,16 @@ requirements:
- liblapack
- llvm-openmp # [osx]
- zlib
- libtorch
- libmetatensor-torch >=0.5.0,<0.6.0
run:
# for some not clear reason boost-cpp is needed here as well
- boost-cpp
- openmpi
- gawk
- llvm-openmp # [osx]
- libtorch
- libmetatensor-torch >=0.5.0,<0.6.0

test:
commands:
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9 changes: 9 additions & 0 deletions py-plumed/build.sh
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#! /usr/bin/env bash

cd python
make pip
export plumed_default_kernel=$PREFIX/lib/libplumedKernel$SHLIB_EXT
#export plumed_disable_rtld_deepbind=yes

$PYTHON -m pip install . --no-deps -vv

6 changes: 6 additions & 0 deletions py-plumed/conda_build_config.yaml
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python:
- 3.8
- 3.9
- 3.10
- 3.11
- 3.12
52 changes: 52 additions & 0 deletions py-plumed/meta.yaml
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{% set name = "py-plumed" %}
{% set version = "2.10" %}
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Is there a standard way to make sure the date is baked in the version in some way? What I am thinking about is if a few weeks we release 2.10 it should override this one. Or shall we just increase the build: number below?

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If you look below, the actual version ends up being 2.10.git.<hash>. I'm not sure if this will be treated as an alpha version by conda, but I can check that. If that's the case, the future 2.10 release should have priority over the alpha release!

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Ok, I changed this to have the version be 2.10.dev1 and store the git sha in the build string instead. The whole package is then plumed-2.10.dev1-git.b0ffcb55ad8cc3c71ec5c30a1bd46f68dd33bceb.

This means that when 2.10 is released, it will be used instead of this one, since conda is following PEP440: https://peps.python.org/pep-0440/

{% set git_rev = "b0ffcb55ad8cc3c71ec5c30a1bd46f68dd33bceb" %}

package:
name: {{ name|lower }}
version: {{ version }}.git.{{ git_rev }}

source:
# url: https://github.com/plumed/plumed2/archive/v{{ version }}.tar.gz
# sha256: 612d2387416b5f82dd8545709921440370e144fd46cef633654cf0ee43bac5f8
git_url: https://github.com/plumed/plumed2.git
git_rev: {{ git_rev }}

build:
number: 0
skip: True # [win or py2k]

requirements:
build:
- {{ compiler('c') }}
- make
host:
- python
- pip
- cython
run:
- plumed
- python

test:
imports:
- plumed
commands:
- python -c "import plumed; p=plumed.Plumed(); print(p)"

about:
home: http://www.plumed.org/
license: LGPL-3.0
license_family: GPL
license_file: COPYING.LESSER
summary: 'Python wrappers for plumed library'
description: |
PLUMED is an open source library for free energy calculations in
molecular systems which works together with some of the most
popular molecular dynamics engines.
doc_url: https://www.plumed.org/doc
dev_url: https://github.com/plumed/plumed2

extra:
recipe-maintainers:
- GiovanniBussi