From cc41ec92a9250d2e26f9db4d5007e5b75f87a027 Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Fri, 25 Mar 2022 11:12:40 +0000 Subject: [PATCH 1/9] invoke hellocontain --- docs/setting_up_aml.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/setting_up_aml.md b/docs/setting_up_aml.md index 90a13f442..46e2356fe 100644 --- a/docs/setting_up_aml.md +++ b/docs/setting_up_aml.md @@ -218,5 +218,14 @@ variables: You should be all set now. +You can verify that your AzureML setup works by running in a shell: + +```shell +python InnerEye/ML/runner.py --model=HelloContainer --azureml +``` + +This will start a simple model training job in AzureML. At the end of the submission process, it will print out "Run URL: ...". Paste that +URL into a browser, and it will take you to the AzureML portal where you can monitor that job. + You can now go to the next step, [creating a dataset](creating_dataset.md), to learn how segmentation datasets should be structured, and how to get your data ready for use in training. From c0f1b740002118ff485d0faa3267d801be6b51ea Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Fri, 25 Mar 2022 11:20:26 +0000 Subject: [PATCH 2/9] update order --- README.md | 2 +- docs/hello_world_model.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a571b5ebc..3746c32f8 100644 --- a/README.md +++ b/README.md @@ -97,8 +97,8 @@ If it fails, please check the Further detailed instructions, including setup in Azure, are here: 1. [Setting up your environment](docs/environment.md) -1. [Training a Hello World segmentation model](docs/hello_world_model.md) 1. [Setting up Azure Machine Learning](docs/setting_up_aml.md) +1. [Training a simple segmentation model in Azure ML](docs/hello_world_model.md) 1. [Creating a dataset](docs/creating_dataset.md) 1. [Building models in Azure ML](docs/building_models.md) 1. [Sample Segmentation and Classification tasks](docs/sample_tasks.md) diff --git a/docs/hello_world_model.md b/docs/hello_world_model.md index d2e812345..046b1a98f 100644 --- a/docs/hello_world_model.md +++ b/docs/hello_world_model.md @@ -77,5 +77,5 @@ Then execute: ```shell conda activate InnerEye -python InnerEye/ML/runner.py --model=HelloWorld +python InnerEye/ML/runner.py --model=HelloWorld --azureml ``` From ce7ee7e23eab6891ab92de9838cd28ea833696b8 Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Fri, 25 Mar 2022 11:20:46 +0000 Subject: [PATCH 3/9] account for relative paths when starting --- InnerEye/ML/runner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/InnerEye/ML/runner.py b/InnerEye/ML/runner.py index 26c6d495f..b7cccdf98 100755 --- a/InnerEye/ML/runner.py +++ b/InnerEye/ML/runner.py @@ -12,7 +12,7 @@ # Workaround for an issue with how AzureML and Pytorch Lightning interact: When spawning additional processes for DDP, # the working directory is not correctly picked up in sys.path print(f"Starting InnerEye runner at {sys.argv[0]}") -innereye_root = Path(__file__).absolute().parent.parent.parent +innereye_root = Path(__file__).resolve().parent.parent.parent if (innereye_root / "InnerEye").is_dir(): innereye_root_str = str(innereye_root) if innereye_root_str not in sys.path: From ba5b58bfd8a28f5124862b06f9f2c77931f65b08 Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Fri, 25 Mar 2022 13:48:04 +0000 Subject: [PATCH 4/9] submodule --- hi-ml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hi-ml b/hi-ml index 0250715c5..781f65958 160000 --- a/hi-ml +++ b/hi-ml @@ -1 +1 @@ -Subproject commit 0250715c5ac1ef09227b51388df44b568a496f65 +Subproject commit 781f659588ed29c8f8c6777e8abb1097768af589 From f5657704a0fbfc6ef0c67e9d4768c1b7dad4e54b Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Tue, 29 Mar 2022 16:08:44 +0100 Subject: [PATCH 5/9] add vscode folder --- .gitignore | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.gitignore b/.gitignore index 166728cf2..4c3846007 100644 --- a/.gitignore +++ b/.gitignore @@ -129,10 +129,6 @@ venv.bak/ .dmypy.json dmypy.json -# other -.vscode/ -.devcontainer/ - /InnerEye/ML/src/aml_config *.exe *.suo From 32bda1157738761dd98002a516490cac71cb1c85 Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Tue, 29 Mar 2022 16:09:03 +0100 Subject: [PATCH 6/9] submodule --- hi-ml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hi-ml b/hi-ml index 781f65958..6cfc73ed8 160000 --- a/hi-ml +++ b/hi-ml @@ -1 +1 @@ -Subproject commit 781f659588ed29c8f8c6777e8abb1097768af589 +Subproject commit 6cfc73ed8825100e88543697fab0b69cc0b09183 From 28d1d09d0025c8b1a46a68e3d3da58af1228493f Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Tue, 29 Mar 2022 16:09:23 +0100 Subject: [PATCH 7/9] color --- .vscode/settings.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 2b005ff5d..040cb9c89 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,5 +4,10 @@ "Tests" ], "python.testing.unittestEnabled": false, - "python.testing.pytestEnabled": true + "python.testing.pytestEnabled": true, + "workbench.colorCustomizations": { + "activityBar.background": "#8b0707", + "titleBar.activeBackground": "#8b0707", + "titleBar.activeForeground": "#F8FCE5" + } } \ No newline at end of file From d9bcb75c00f65a2842eed91ca716e2371587a82c Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Tue, 29 Mar 2022 16:11:36 +0100 Subject: [PATCH 8/9] undo color --- .vscode/settings.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 040cb9c89..16ea71b4b 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -5,9 +5,4 @@ ], "python.testing.unittestEnabled": false, "python.testing.pytestEnabled": true, - "workbench.colorCustomizations": { - "activityBar.background": "#8b0707", - "titleBar.activeBackground": "#8b0707", - "titleBar.activeForeground": "#F8FCE5" - } } \ No newline at end of file From a70da688b53be1807df5491b91329caa5daa2c2f Mon Sep 17 00:00:00 2001 From: Anton Schwaighofer Date: Tue, 29 Mar 2022 16:11:56 +0100 Subject: [PATCH 9/9] color --- .vscode/settings.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 16ea71b4b..2b005ff5d 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,5 +4,5 @@ "Tests" ], "python.testing.unittestEnabled": false, - "python.testing.pytestEnabled": true, + "python.testing.pytestEnabled": true } \ No newline at end of file