From 7dad5d27c6199fddafd557429330b849b29adb7e Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 27 May 2024 23:57:06 +0200 Subject: [PATCH 01/10] Update environment-openmpi.yml --- .ci_support/environment-openmpi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml index a1e8bcf7..3d26ba9c 100644 --- a/.ci_support/environment-openmpi.yml +++ b/.ci_support/environment-openmpi.yml @@ -3,7 +3,7 @@ channels: dependencies: - python - numpy -- openmpi +- openmpi =4.1.6 - cloudpickle =3.0.0 - mpi4py =3.1.6 - tqdm =4.66.4 From 7e4dcdd405b515f9f4ea503966c2eadfae5f86b8 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:09:30 +0200 Subject: [PATCH 02/10] Update kernel.json --- binder/kernel.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/binder/kernel.json b/binder/kernel.json index 16c69cf5..f87dbcb8 100644 --- a/binder/kernel.json +++ b/binder/kernel.json @@ -12,5 +12,10 @@ "language": "python", "metadata": { "debugger": true + }, + "env": { + "OMPI_MCA_plm": "isolated", + "OMPI_MCA_rmaps_base_oversubscribe": "yes", + "OMPI_MCA_btl_vader_single_copy_mechanism": "none" } -} \ No newline at end of file +} From 437797b6c735a9274e3bd896a3369a59b1b63d60 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:12:47 +0200 Subject: [PATCH 03/10] Update notebooks.yml --- .github/workflows/notebooks.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index c1132c72..d64f181f 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -35,4 +35,8 @@ jobs: shell: bash -l {0} run: > flux start - papermill notebooks/examples.ipynb examples-out.ipynb -k "python3" \ No newline at end of file + papermill notebooks/examples.ipynb examples-out.ipynb -k "python3" + env: + OMPI_MCA_plm: 'isolated' + OMPI_MCA_rmaps_base_oversubscribe: 'yes' + OMPI_MCA_btl_vader_single_copy_mechanism: 'none' From d7606e84ac37cdeb93ffee62ececc69c30a659c1 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:17:10 +0200 Subject: [PATCH 04/10] Update notebooks.yml --- .github/workflows/notebooks.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index d64f181f..a5889442 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -31,11 +31,13 @@ jobs: run: | pip install versioneer[toml]==0.29 pip install . --no-deps --no-build-isolation + mkdir -p ~/.local/share/jupyter/kernels/flux + cp binder/kernel.json ~/.local/share/jupyter/kernels/flux - name: Notebooks shell: bash -l {0} run: > flux start - papermill notebooks/examples.ipynb examples-out.ipynb -k "python3" + papermill notebooks/examples.ipynb examples-out.ipynb -k "flux" env: OMPI_MCA_plm: 'isolated' OMPI_MCA_rmaps_base_oversubscribe: 'yes' From 3c686551728d83897c6dae2bae046edfaa4e6d5b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:19:08 +0200 Subject: [PATCH 05/10] Update notebooks.yml --- .github/workflows/notebooks.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index a5889442..5a211e5c 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -35,10 +35,5 @@ jobs: cp binder/kernel.json ~/.local/share/jupyter/kernels/flux - name: Notebooks shell: bash -l {0} - run: > - flux start + run: | papermill notebooks/examples.ipynb examples-out.ipynb -k "flux" - env: - OMPI_MCA_plm: 'isolated' - OMPI_MCA_rmaps_base_oversubscribe: 'yes' - OMPI_MCA_btl_vader_single_copy_mechanism: 'none' From ae056919bb5d8e498101f8ea6dc68c4ee6647f98 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:52:30 +0200 Subject: [PATCH 06/10] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index c36df88c..3855433b 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -3,7 +3,7 @@ channels: dependencies: - python - numpy -- openmpi +- openmpi =4.1.6 - cloudpickle =3.0.0 - mpi4py =3.1.6 - tqdm =4.66.2 From cefbccb6ef91a66262939de236183fdaa6fa555e Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:53:23 +0200 Subject: [PATCH 07/10] Update notebooks.yml --- .github/workflows/notebooks.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index 5a211e5c..302a14bf 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -31,9 +31,8 @@ jobs: run: | pip install versioneer[toml]==0.29 pip install . --no-deps --no-build-isolation - mkdir -p ~/.local/share/jupyter/kernels/flux - cp binder/kernel.json ~/.local/share/jupyter/kernels/flux - name: Notebooks shell: bash -l {0} - run: | - papermill notebooks/examples.ipynb examples-out.ipynb -k "flux" + run: > + flux start + papermill notebooks/examples.ipynb examples-out.ipynb -k "python3" From 6fdd508ba323349a6670f1e4d131b92a60bde199 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:57:27 +0200 Subject: [PATCH 08/10] Update kernel.json --- binder/kernel.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/binder/kernel.json b/binder/kernel.json index f87dbcb8..7bdeb704 100644 --- a/binder/kernel.json +++ b/binder/kernel.json @@ -12,10 +12,5 @@ "language": "python", "metadata": { "debugger": true - }, - "env": { - "OMPI_MCA_plm": "isolated", - "OMPI_MCA_rmaps_base_oversubscribe": "yes", - "OMPI_MCA_btl_vader_single_copy_mechanism": "none" } } From 4cb4ca26132d2660afca2d4e6ec1486f13f51ec9 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 09:58:44 +0200 Subject: [PATCH 09/10] Remove openmpi specific environment variables --- .github/workflows/unittest-openmpi.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/unittest-openmpi.yml b/.github/workflows/unittest-openmpi.yml index e36b7966..df058b41 100644 --- a/.github/workflows/unittest-openmpi.yml +++ b/.github/workflows/unittest-openmpi.yml @@ -59,7 +59,3 @@ jobs: pip install . --no-deps --no-build-isolation cd tests python -m unittest discover . - env: - OMPI_MCA_plm: 'isolated' - OMPI_MCA_rmaps_base_oversubscribe: 'yes' - OMPI_MCA_btl_vader_single_copy_mechanism: 'none' From 414a21417193bd7ccb8a658d3107669bddbcb34d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 28 May 2024 10:02:00 +0200 Subject: [PATCH 10/10] Update unittest-flux.yml --- .github/workflows/unittest-flux.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/unittest-flux.yml b/.github/workflows/unittest-flux.yml index 1331f41b..3ce21135 100644 --- a/.github/workflows/unittest-flux.yml +++ b/.github/workflows/unittest-flux.yml @@ -46,10 +46,6 @@ jobs: pip install versioneer[toml]==0.29 pip install . --no-deps --no-build-isolation coverage run -a --omit="pympipool/_version.py,tests/*" -m unittest discover tests - env: - OMPI_MCA_plm: 'isolated' - OMPI_MCA_rmaps_base_oversubscribe: 'yes' - OMPI_MCA_btl_vader_single_copy_mechanism: 'none' - name: Test Flux shell: bash -l {0} timeout-minutes: 5 @@ -57,10 +53,6 @@ jobs: flux start coverage run -a --omit="pympipool/_version.py,tests/*" -m unittest tests/test_flux_executor.py tests/test_executor_backend_flux.py; coverage xml - env: - OMPI_MCA_plm: 'isolated' - OMPI_MCA_rmaps_base_oversubscribe: 'yes' - OMPI_MCA_btl_vader_single_copy_mechanism: 'none' - name: Coveralls if: matrix.label == 'linux-64-py-3-12-openmpi' uses: coverallsapp/github-action@v2