From b09daa1a26d5e786fa07ced1e691ec9f8da2cf47 Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Wed, 7 Feb 2024 12:34:15 +0000 Subject: [PATCH 1/7] Set 30min timeout for GPU tests --- .github/workflows/test-gpu.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index 104396116..092a2880e 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -35,9 +35,14 @@ jobs: name: GPU Tests needs: check runs-on: "cirun-aws-gpu--${{ github.run_id }}" + # Setting a timeout of 30 minutes, as the AWS costs money + # At time of writing, a typical run takes about 5 minutes + timeout-minutes: 30 + defaults: run: shell: bash -el {0} + steps: - uses: actions/checkout@v3 with: From 43425859a266cdab93457cecd99343fcdf1beced Mon Sep 17 00:00:00 2001 From: Intron7 Date: Wed, 7 Feb 2024 14:03:00 +0100 Subject: [PATCH 2/7] added yaml for gpu_ci --- .ci/gpu_ci.yml | 12 ++++++++++++ .github/workflows/test-gpu.yml | 9 +-------- 2 files changed, 13 insertions(+), 8 deletions(-) create mode 100644 .ci/gpu_ci.yml diff --git a/.ci/gpu_ci.yml b/.ci/gpu_ci.yml new file mode 100644 index 000000000..3a33aabcc --- /dev/null +++ b/.ci/gpu_ci.yml @@ -0,0 +1,12 @@ +name: cupy_env +channels: + - nvidia + - conda-forge +dependencies: + - python=3.12 + - cuda-version=11.8 + - cupy + - numba + - pytest + - pytest-cov + - pytest-xdist diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index 104396116..5ca7643b2 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -49,14 +49,7 @@ jobs: - uses: mamba-org/setup-micromamba@v1 with: micromamba-version: "1.3.1-0" - environment-name: anndata-gpu-ci - create-args: >- - python=3.11 - cupy - numba - pytest - pytest-cov - pytest-xdist + environment-file: ci/gpu_ci.yml init-shell: >- bash generate-run-shell: false From 853dcfeb6ad5289e30dda49677cd87bf0fb23efa Mon Sep 17 00:00:00 2001 From: Intron7 Date: Wed, 7 Feb 2024 14:03:57 +0100 Subject: [PATCH 3/7] fixes typo --- .github/workflows/test-gpu.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index 5ca7643b2..8a44ac58c 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -49,7 +49,7 @@ jobs: - uses: mamba-org/setup-micromamba@v1 with: micromamba-version: "1.3.1-0" - environment-file: ci/gpu_ci.yml + environment-file: .ci/gpu_ci.yml init-shell: >- bash generate-run-shell: false From bf929437b461864d201166cae0781a34ce443902 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 7 Feb 2024 13:04:12 +0000 Subject: [PATCH 4/7] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .ci/gpu_ci.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.ci/gpu_ci.yml b/.ci/gpu_ci.yml index 3a33aabcc..9776ec3d5 100644 --- a/.ci/gpu_ci.yml +++ b/.ci/gpu_ci.yml @@ -1,12 +1,12 @@ name: cupy_env channels: - - nvidia - - conda-forge + - nvidia + - conda-forge dependencies: - - python=3.12 - - cuda-version=11.8 - - cupy - - numba - - pytest - - pytest-cov - - pytest-xdist + - python=3.12 + - cuda-version=11.8 + - cupy + - numba + - pytest + - pytest-cov + - pytest-xdist From f965aca8373885108b23a9b3ffa7b53e3d9638db Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Wed, 7 Feb 2024 13:09:01 +0000 Subject: [PATCH 5/7] List pip packages too --- .github/workflows/test-gpu.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index 092a2880e..4a34e97f0 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -69,8 +69,10 @@ jobs: - name: Install AnnData run: pip install .[dev,test,gpu] - - name: Mamba list - run: micromamba list + - name: Env list + run: | + micromamba list + pip list - name: Run test run: pytest -m gpu --cov --cov-report=xml --cov-context=test -n 4 From 3baf39d88df0325ddd32141ea06fc5fc392229b1 Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Wed, 7 Feb 2024 13:30:38 +0000 Subject: [PATCH 6/7] Bump cuda version --- .ci/gpu_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci/gpu_ci.yml b/.ci/gpu_ci.yml index 9776ec3d5..2abac0abe 100644 --- a/.ci/gpu_ci.yml +++ b/.ci/gpu_ci.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python=3.12 - - cuda-version=11.8 + - cuda-version=12.3 - cupy - numba - pytest From 1f241b174fb9b147c0a790bb1abd0fc8e3b8b2b3 Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Wed, 7 Feb 2024 13:41:47 +0000 Subject: [PATCH 7/7] downgrade to cuda 12.2 --- .ci/gpu_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci/gpu_ci.yml b/.ci/gpu_ci.yml index 2abac0abe..81906aa2d 100644 --- a/.ci/gpu_ci.yml +++ b/.ci/gpu_ci.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python=3.12 - - cuda-version=12.3 + - cuda-version=12.2 - cupy - numba - pytest