From 47fe3ae884d3b17d53919e34465ee9382b9732c0 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 6 Nov 2026 10:25:00 -0600 Subject: [PATCH 1/6] Some fixes for pressure handling --- tyff/compute/_equilibrate.py | 2 +- tyff/compute/_jacobian.py | 4 ++-- tyff/compute/_produce.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tyff/compute/_equilibrate.py b/tyff/compute/_equilibrate.py index fed9387..58f42c8 100644 --- a/tyff/compute/_equilibrate.py +++ b/tyff/compute/_equilibrate.py @@ -142,7 +142,7 @@ def _run_equilibration( output_file=files["msgpack_trajectory"].filepath, report_interval=1000, beta=1.0 / (openmm.unit.MOLAR_GAS_CONSTANT_R * compute_config["temperature"] * openmm.unit.kelvin), - pressure=pressure if pressure is None else openmm.unit.kilopascal, + pressure=pressure if pressure is None else pressure * openmm.unit.kilopascal, ) ) diff --git a/tyff/compute/_jacobian.py b/tyff/compute/_jacobian.py index 2745a06..4c74c53 100644 --- a/tyff/compute/_jacobian.py +++ b/tyff/compute/_jacobian.py @@ -78,7 +78,7 @@ def _get_ensemble_average_and_jacobian( compute_config = BulkLiquid(**json.load(f)) # type: ignore[typeddict-item] temperature = compute_config["temperature"] # kelvin, float - pressure = compute_config.get("pressure") # atmosphere, float | None + pressure = compute_config.get("pressure") # kPa, float | None interchanges = [] @@ -141,7 +141,7 @@ def _get_ensemble_average_and_jacobian( worker_force_field, frames_path, temperature * openmm.unit.kelvin, - None if pressure is None else pressure * openmm.unit.atmosphere, + None if pressure is None else pressure * openmm.unit.kilopascal, ) # originally this was sorted(means), diff --git a/tyff/compute/_produce.py b/tyff/compute/_produce.py index e5903df..a69986e 100644 --- a/tyff/compute/_produce.py +++ b/tyff/compute/_produce.py @@ -138,7 +138,7 @@ def _run_production( output_file=files["msgpack_trajectory"].filepath, report_interval=1000, beta=1.0 / (openmm.unit.MOLAR_GAS_CONSTANT_R * compute_config["temperature"] * openmm.unit.kelvin), - pressure=pressure if pressure is None else openmm.unit.kilopascal, + pressure=pressure if pressure is None else pressure * openmm.unit.kilopascal, ) ) From bf0c3cb993eca4546d8f9f23b8e136a1b08b906d Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 6 Nov 2026 15:58:01 -0600 Subject: [PATCH 2/6] Add integration test with water at different temperatures --- tyff/_tests/compute/__init__.py | 0 tyff/_tests/conftest.py | 22 +++++++ tyff/_tests/integration_tests/__init__.py | 0 .../compute/test_workflow.py | 58 +++++++++++++++++++ 4 files changed, 80 insertions(+) create mode 100644 tyff/_tests/compute/__init__.py create mode 100644 tyff/_tests/integration_tests/__init__.py create mode 100644 tyff/_tests/integration_tests/compute/test_workflow.py diff --git a/tyff/_tests/compute/__init__.py b/tyff/_tests/compute/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tyff/_tests/conftest.py b/tyff/_tests/conftest.py index d959323..a60930c 100644 --- a/tyff/_tests/conftest.py +++ b/tyff/_tests/conftest.py @@ -24,6 +24,28 @@ _E = openff.units.unit.elementary_charge +def pytest_addoption(parser): + parser.addoption( + "--run-gpu", + action="store_true", + default=False, + help="run tests marked with @pytest.mark.gpu", + ) + + +def pytest_configure(config): + config.addinivalue_line("markers", "gpu: tests that require a GPU (skipped unless --run-gpu is given)") + + +def pytest_collection_modifyitems(config, items): + if config.getoption("--run-gpu"): + return + skip_gpu = pytest.mark.skip(reason="need --run-gpu option to run") + for item in items: + if "gpu" in item.keywords: + item.add_marker(skip_gpu) + + @pytest.fixture def density_entry() -> DataEntry: return { diff --git a/tyff/_tests/integration_tests/__init__.py b/tyff/_tests/integration_tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tyff/_tests/integration_tests/compute/test_workflow.py b/tyff/_tests/integration_tests/compute/test_workflow.py new file mode 100644 index 0000000..ace58f2 --- /dev/null +++ b/tyff/_tests/integration_tests/compute/test_workflow.py @@ -0,0 +1,58 @@ +import json + +import pytest + +from tyff.compute.configs import local_config +from tyff.compute.workflow import SimulationWorkflow +from tyff.targets.thermo import create_dataset + + +@pytest.mark.gpu +def test_nonstandard_pressure(tmp_path): + + dataset = create_dataset( + *[ + { # type: ignore + "id": "high_pressure_water", + "tag": "density", + "x": [1.0], + "smiles": ["O"], + "temperature": 298.15, + "pressure": val, + "value": 1.0, + "std": 0.01, + "units": "g/mL", + "source": "test_source", + } + for val in [101.325, 101325] + ] + ) + + with SimulationWorkflow( + base_dir=tmp_path, + parsl_config=local_config(), + ) as workflow: + workflow.submit_dataset( + dataset, + force_field="openff-2.3.0.offxml", + n_molecules=480, + n_replicates=1, + ) + + workflow.wait() + + # hack - there needs to be a better way of grabbing results + job_dirs = [path for path in (tmp_path / "simulations").glob("*/") if not path.match("thermo_targets")] + + results = dict() + + for job_dir in job_dirs: + with open(job_dir / "compute_config.json") as f: + target_pressure = json.load(f)["pressure"] + + with open(job_dir / "ensemble_averages.json") as f: + density = json.load(f)["density"] + + results[target_pressure] = density + + assert results[101325.0] > results[101.325] From 027c51ea23c82ef8d2c2f6e60256d1665f31c578 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 6 Nov 2026 20:25:15 -0600 Subject: [PATCH 3/6] Add GPU-based test --- .github/workflows/gpu.yaml | 92 + pixi.lock | 3572 +++++++++-------- pixi.toml | 1 + .../compute/test_workflow.py | 6 +- 4 files changed, 1885 insertions(+), 1786 deletions(-) create mode 100644 .github/workflows/gpu.yaml diff --git a/.github/workflows/gpu.yaml b/.github/workflows/gpu.yaml new file mode 100644 index 0000000..72dd9ce --- /dev/null +++ b/.github/workflows/gpu.yaml @@ -0,0 +1,92 @@ +name: GPU-enabled CI +on: + workflow_dispatch: + pull_request: + branches: + - "main" + +concurrency: + # Specific group naming so CI is only cancelled + # within same PR or on merge to main + group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} + cancel-in-progress: true + +defaults: + run: + shell: bash -l {0} + +env: + OE_LICENSE: ${{ github.workspace }}/oe_license.txt + +jobs: + start-aws-runner: + runs-on: ubuntu-latest + permissions: + id-token: write + contents: read + outputs: + mapping: ${{ steps.aws-start.outputs.mapping }} + steps: + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@v6 + with: + role-to-assume: arn:aws:iam::649715411074:role/gh-actions-runner-role + aws-region: us-east-1 + - name: Create cloud runner + id: aws-start + uses: omsf/start-aws-gha-runner@v1.3.0 + with: + aws_image_id: ami-0d5079d9be06933e5 + aws_instance_type: g4dn.xlarge + # IAM default might be 5 GB? + aws_root_device_size: 125 + aws_region_name: us-east-1 + aws_home_dir: /home/ubuntu + env: + GH_PAT: ${{ secrets.GH_PAT }} + self-hosted-test: + name: GPU-based tests (env ${{ matrix.environment }}) + runs-on: self-hosted + strategy: + fail-fast: true + matrix: + environment: + - hpc3 # re-using an otherwise generic CUDA environment + needs: + - start-aws-runner + steps: + - uses: actions/checkout@v7 + with: + fetch-depth: 0 + + - name: Set up virtual environment + uses: prefix-dev/setup-pixi@v0.11.3 + with: + environments: ${{ matrix.environment }} + frozen: true + + - name: Run GPU-based tests + run: pixi run -e ${{ matrix.environment }} run_gpu_tests + + stop-aws-runner: + runs-on: ubuntu-latest + permissions: + id-token: write + contents: read + needs: + - start-aws-runner + - self-hosted-test + if: ${{ always() }} + steps: + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@v6 + with: + role-to-assume: arn:aws:iam::649715411074:role/gh-actions-runner-role + aws-region: us-east-1 + - name: Stop instances + uses: omsf/stop-aws-gha-runner@v1.0.0 + with: + instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }} + aws_region_name: us-east-1 + env: + GH_PAT: ${{ secrets.GH_PAT }} diff --git a/pixi.lock b/pixi.lock index 795d403..20e60cf 100644 --- a/pixi.lock +++ b/pixi.lock @@ -40,7 +40,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.13.0-ha7a2c86_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h539c000_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.8.0-py313h524ba91_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda + - 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name: markdown - version: 3.11.2 - sha256: f80390747a2a0ff2ba54da074ce4f862f72a6685f608cd2637b646a6d83993f5 - requires_dist: - - coverage ; extra == 'testing' - - pyyaml ; extra == 'testing' - - zensical==0.0.62 ; extra == 'docs' - - mdx-gh-links==0.4 ; extra == 'docs' - - mkdocstrings==1.0.6 ; extra == 'docs' - - mkdocstrings-python==1.16.8 ; extra == 'docs' - - pygments==2.21.0 ; extra == 'docs' - - pymdown-extensions==11.0.2 ; extra == 'docs' - - justhtml==3.11.2 ; extra == 'docs' - - ghp-import==2.1.0 ; extra == 'docs' - requires_python: '>=3.11' diff --git a/pixi.toml b/pixi.toml index 9946d87..61876f3 100644 --- a/pixi.toml +++ b/pixi.toml @@ -7,6 +7,7 @@ platforms = ["linux-64", "osx-arm64"] run_mvp = "python examples/mvp/run.py" run_mypy = "python -m mypy -p 'tyff'" run_tests = { cmd = "python -m pytest -n logical tyff/_tests", env = { OPENMM_DEFAULT_PLATFORM = "CPU" } } +run_gpu_tests = { cmd = "python -m pytest -n 1 --run-gpu -m gpu tyff/_tests", env = { OPENMM_DEFAULT_PLATFORM = "GPU" } } dev_tests = { cmd = "python -m pytest -s -x --pdb --lf tyff/_tests", env = { OPENMM_DEFAULT_PLATFORM = "CPU" } } [dependencies] diff --git a/tyff/_tests/integration_tests/compute/test_workflow.py b/tyff/_tests/integration_tests/compute/test_workflow.py index ace58f2..2ab939f 100644 --- a/tyff/_tests/integration_tests/compute/test_workflow.py +++ b/tyff/_tests/integration_tests/compute/test_workflow.py @@ -48,11 +48,15 @@ def test_nonstandard_pressure(tmp_path): for job_dir in job_dirs: with open(job_dir / "compute_config.json") as f: - target_pressure = json.load(f)["pressure"] + compute_config = json.load(f) + target_pressure = compute_config["pressure"] + + assert compute_config["temperature"] == 298.15 with open(job_dir / "ensemble_averages.json") as f: density = json.load(f)["density"] results[target_pressure] = density + # these should be ~1.04 and ~1.00, but certainly denser at higher pressure assert results[101325.0] > results[101.325] From 619a32dedcac06a71f75912e7d593adda6be1989 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Sun, 8 Nov 2026 10:48:28 -0600 Subject: [PATCH 4/6] More safely recurse directories --- pixi.lock | 340 +++++++++--------- pixi.toml | 2 +- .../compute/test_workflow.py | 9 +- 3 files changed, 180 insertions(+), 171 deletions(-) diff --git a/pixi.lock b/pixi.lock index 20e60cf..0684087 100644 --- a/pixi.lock +++ b/pixi.lock @@ -46,7 +46,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.1-py313h2fc2bef_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.9-hebe6cf0_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-3.3.5-hea3f660_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-3.5.0-hea3f660_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.6-h3c89d7e_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.5-py313h12b3e8d_2.conda - 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there needs to be a better way of grabbing results - job_dirs = [path for path in (tmp_path / "simulations").glob("*/") if not path.match("thermo_targets")] + job_dirs = [ + path + for path in (tmp_path).glob("*/") + if not path.match("thermo_targets") + and not path.match("reference_force_fields") + and not path.match("interchanges") + ] results = dict() @@ -58,5 +64,4 @@ def test_nonstandard_pressure(tmp_path): results[target_pressure] = density - # these should be ~1.04 and ~1.00, but certainly denser at higher pressure assert results[101325.0] > results[101.325] From 631986708b36ce54e38ccd963e51078e55bb4455 Mon Sep 17 00:00:00 2001 From: "Matthew W. 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Thompson" Date: Sun, 8 Nov 2026 15:43:49 -0600 Subject: [PATCH 6/6] Drop GPU action for now --- .github/workflows/gpu.yaml | 92 -------------------------------------- 1 file changed, 92 deletions(-) delete mode 100644 .github/workflows/gpu.yaml diff --git a/.github/workflows/gpu.yaml b/.github/workflows/gpu.yaml deleted file mode 100644 index 72dd9ce..0000000 --- a/.github/workflows/gpu.yaml +++ /dev/null @@ -1,92 +0,0 @@ -name: GPU-enabled CI -on: - workflow_dispatch: - pull_request: - branches: - - "main" - -concurrency: - # Specific group naming so CI is only cancelled - # within same PR or on merge to main - group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} - cancel-in-progress: true - -defaults: - run: - shell: bash -l {0} - -env: - OE_LICENSE: ${{ github.workspace }}/oe_license.txt - -jobs: - start-aws-runner: - runs-on: ubuntu-latest - permissions: - id-token: write - contents: read - outputs: - mapping: ${{ steps.aws-start.outputs.mapping }} - steps: - - name: Configure AWS credentials - uses: aws-actions/configure-aws-credentials@v6 - with: - role-to-assume: arn:aws:iam::649715411074:role/gh-actions-runner-role - aws-region: us-east-1 - - name: Create cloud runner - id: aws-start - uses: omsf/start-aws-gha-runner@v1.3.0 - with: - aws_image_id: ami-0d5079d9be06933e5 - aws_instance_type: g4dn.xlarge - # IAM default might be 5 GB? - aws_root_device_size: 125 - aws_region_name: us-east-1 - aws_home_dir: /home/ubuntu - env: - GH_PAT: ${{ secrets.GH_PAT }} - self-hosted-test: - name: GPU-based tests (env ${{ matrix.environment }}) - runs-on: self-hosted - strategy: - fail-fast: true - matrix: - environment: - - hpc3 # re-using an otherwise generic CUDA environment - needs: - - start-aws-runner - steps: - - uses: actions/checkout@v7 - with: - fetch-depth: 0 - - - name: Set up virtual environment - uses: prefix-dev/setup-pixi@v0.11.3 - with: - environments: ${{ matrix.environment }} - frozen: true - - - name: Run GPU-based tests - run: pixi run -e ${{ matrix.environment }} run_gpu_tests - - stop-aws-runner: - runs-on: ubuntu-latest - permissions: - id-token: write - contents: read - needs: - - start-aws-runner - - self-hosted-test - if: ${{ always() }} - steps: - - name: Configure AWS credentials - uses: aws-actions/configure-aws-credentials@v6 - with: - role-to-assume: arn:aws:iam::649715411074:role/gh-actions-runner-role - aws-region: us-east-1 - - name: Stop instances - uses: omsf/stop-aws-gha-runner@v1.0.0 - with: - instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }} - aws_region_name: us-east-1 - env: - GH_PAT: ${{ secrets.GH_PAT }}