diff --git a/.github/dco.yml b/.github/dco.yml new file mode 100644 index 0000000..de6cd3b --- /dev/null +++ b/.github/dco.yml @@ -0,0 +1,4 @@ +# This enables DCO bot for you, please take a look https://github.com/probot/dco +# for more details. +require: + members: false diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..f34a22e --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,69 @@ +## Contributing In General +Our project welcomes external contributions. If you have an itch, please feel +free to scratch it. + +To contribute code or documentation, please submit a [pull request](https://github.com/st4sd/st4sd-datastore/pulls). + +A good way to familiarize yourself with the codebase and contribution process is +to look for and tackle low-hanging fruit in the [issue tracker](https://github.com/st4sd/st4sd-datastore/issues). +Before embarking on a more ambitious contribution, please quickly [get in touch](MAINTAINERS.md) with us. + +**Note: We appreciate your effort, and want to avoid a situation where a contribution +requires extensive rework (by you or by us), sits in backlog for a long time, or +cannot be accepted at all!** + +### Proposing new features + +If you would like to implement a new feature, please [raise an issue](https://github.com/st4sd/st4sd-datastore/issues) +before sending a pull request so the feature can be discussed. This is to avoid +you wasting your valuable time working on a feature that the project developers +are not interested in accepting into the code base. + +### Fixing bugs + +If you would like to fix a bug, please [raise an issue](https://github.com/st4sd/st4sd-datastore/issues) before sending a +pull request so it can be tracked. + +### Merge approval + +The project maintainers use LGTM (Looks Good To Me) in comments on the code +review to indicate acceptance. A change requires LGTMs from two of the +maintainers of each component affected. + +For a list of the maintainers, see the [MAINTAINERS.md](MAINTAINERS.md) page. + +## Legal + +Each source file must include a license header for the Apache +Software License 2.0. Using the SPDX format is the simplest approach. +e.g. + +``` +/* +Copyright IBM Inc. All Rights Reserved. + +SPDX-License-Identifier: Apache-2.0 +*/ +``` + +We have tried to make it as easy as possible to make contributions. 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All rights reserved + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/MAINTAINERS.md b/MAINTAINERS.md new file mode 100644 index 0000000..546cc16 --- /dev/null +++ b/MAINTAINERS.md @@ -0,0 +1,10 @@ +# MAINTAINERS + +Following is the current list of maintainers on this project + +The maintainers are listed in alphabetical order. + +- Michael Johnston ([michael-johnston](https://github.com/michael-johnston)) +- Alessandro Pomponio ([AlessandroPomponio](https://github.com/AlessandroPomponio)) +- Edward Pyzer-Knapp ([epyzerk3](https://github.com/epyzerk3)) +- Vassilis Vassiliadis ([VassilisVassiliadis](https://github.com/VassilisVassiliadis)) diff --git a/README.md b/README.md new file mode 100644 index 0000000..f90a179 --- /dev/null +++ b/README.md @@ -0,0 +1,58 @@ +# ST4SD Example: Sum numbers + +Toy example demonstrating the most common features of our virtual experiment Domain Specific Language (DSL) `FlowIR`. +We recommend using this source code to follow along with our [sum numbers tutorial](https://st4sd.github.io/overview/tutorial/). + +For more information on FlowIR visit our [FlowIR documentation website](https://st4sd.github.io/overview/workflow-specification/). + +## Quick links + +- [Getting started](#getting-started) +- [Development](#development) +- [Help and Support](#help-and-support) +- [Contributing](#contributing) +- [License](#license) + +## Getting started + +#### Python + +Running and developing this project requires a recent Python version, it is suggested to use Python 3.7 or above. You +can find instructions on how to install Python on the [official website](https://www.python.org/downloads/). + +#### Python module st4sd-runtime-core + +Create a python 3.7+ and install the python module `st4sd-runtime-core` in it. +For more information, see the installation instructions of [st4sd-runtime-core](https://github.com/st4sd/st4sd-runtime-core). + +#### Executing the example + +Instructions below assume that your python 3.7 virtual environment is under `${HOME}/venvs/st4sd` + +```bash +git clone http://github.com/st4sd/sum-numbers.git +source ${HOME}/venvs/st4sd/bin/activate + +# Delete the previous runs if it exists +rm -rf sum-numbers.instance +elaunch.py sum-numbers --nostamp +``` + +After the virtual experiment terminates, you should have a look inside the `sum-numbers.instance` directory. +For more information see our [sum-numbers tutorial](https://st4sd.github.io/overview/tutorial/). + +## Development + +Coming soon. + +## Help and Support + +Please feel free to reach out to one of the maintainers listed in the [MAINTAINERS.md](MAINTAINERS.md) page. + +## Contributing + +We always welcome external contributions. Please see our [guidance](CONTRIBUTING.md) for details on how to do so. + +## License + +This project is licensed under the Apache 2.0 license. Please [see details here](LICENSE.md). diff --git a/bin/extract_row.py b/bin/extract_row.py new file mode 100755 index 0000000..3d57c28 --- /dev/null +++ b/bin/extract_row.py @@ -0,0 +1,23 @@ +#! /usr/bin/env python + +# Copyright IBM Inc. All Rights Reserved. +# SPDX-License-Identifier: Apache-2.0 +# Authors: +# Vassilis Vassiliadis + + +from __future__ import print_function +import sys + +file_path = sys.argv[1] +row_idx = int(sys.argv[2]) + +with open(file_path, 'r') as f: + for row in range(row_idx): + f.readline() + line = f.readline().strip() + +if len(line) == 0: + raise ValueError("Could not fetch row %d from file %s" % (row_idx, file_path)) + +print(line) \ No newline at end of file diff --git a/bin/generate_input_file.py b/bin/generate_input_file.py new file mode 100755 index 0000000..88736c5 --- /dev/null +++ b/bin/generate_input_file.py @@ -0,0 +1,23 @@ +#! /usr/bin/env python + +# Copyright IBM Inc. All Rights Reserved. +# SPDX-License-Identifier: Apache-2.0 +# Authors: +# Vassilis Vassiliadis + +from __future__ import print_function +import sys +import random + +num_rows = int(sys.argv[1]) + +if len(sys.argv) == 3: + print("Seeding with %s" % sys.argv[2]) + random.seed(int(sys.argv[2])) + +with open('output.csv', 'w') as f: + for row in range(num_rows): + line = ' '.join(map(str, [random.randint(0, 10), random.randint(0, 10)])) + f.write(line + '\n') + +print("Generated %d rows" % num_rows) diff --git a/bin/sum.py b/bin/sum.py new file mode 100755 index 0000000..c7d21ea --- /dev/null +++ b/bin/sum.py @@ -0,0 +1,16 @@ +#! /usr/bin/env python + +# Copyright IBM Inc. All Rights Reserved. +# SPDX-License-Identifier: Apache-2.0 +# Authors: +# Vassilis Vassiliadis + +from __future__ import print_function +import sys + +total = 0 + +for num in sys.argv[1:]: + total += int(num) + +print("%d" % total) diff --git a/conf/flowir_package.yaml b/conf/flowir_package.yaml new file mode 100644 index 0000000..9710ae0 --- /dev/null +++ b/conf/flowir_package.yaml @@ -0,0 +1,112 @@ +# Copyright IBM Inc. All Rights Reserved. +# SPDX-License-Identifier: Apache-2.0 +# Authors: +# Vassilis Vassiliadis + +# For more information see our sum-numbers tutorial at https://st4sd.github.io/overview/tutorial/ + +# `variables` contain the platform/stage scopes of variables which +# components can override +variables: + default: + global: + numberOfPoints: 3 + stages: + 0: + my_random_seed: "" + 2: + addToSum: 10 + + openshift: + stages: + 2: + addToSum: -5 + +blueprint: + default: + global: + command: + environment: environment + + openshift: + global: + resourceRequest: + memory: 100Mi + resourceManager: + config: + backend: kubernetes + kubernetes: + image: quay.io/st4sd/official-base/st4sd-runtime-core + + scafellpike: + global: + resourceManager: + config: + backend: lsf + + stages: + 1: + resourceRequest: + memory: 150Mi + +environments: + default: + # Defining 'default.environment' here sets the default env a job uses. If this wasn't defined, the job would use the + # same env as the Flow process (ie: the same as elaunch.py) + environment: + DEFAULTS: PATH:LD_LIBRARY_PATH + PATH: $PATH + LD_LIBRARY_PATH: $LD_LIBRARY_PATH + + openshift: + environment: + PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + + +components: +- stage: 0 + name: GenerateInput + command: + executable: "bin/generate_input_file.py" + arguments: "%(numberOfPoints)s %(my_random_seed)s" + + +- stage: 1 + name: ExtractRow + command: + executable: "bin/extract_row.py" + arguments: "stage0.GenerateInput/output.csv:ref %(replica)s" + references: + - "stage0.GenerateInput/output.csv:ref" + workflowAttributes: + replicate: "%(numberOfPoints)s" + +- stage: 1 + name: PartialSum + command: + executable: "bin/sum.py" + arguments: "ExtractRow:output" + references: + - "ExtractRow:output" + +- stage: 2 + name: Sum + command: + executable: "bin/sum.py" + arguments: "stage1.PartialSum:output %(addToSum)s" + references: + - "stage1.PartialSum:output" + workflowAttributes: + aggregate: True + +- stage: 3 + name: Cat + command: + executable: "cat" + arguments: "cat_me.txt" + references: + - "data/cat_me.txt:copy" + +output: + TotalSum: + data-in: "stage2.Sum/out.stdout:copy" diff --git a/data/cat_me.txt b/data/cat_me.txt new file mode 100644 index 0000000..deb0ed6 --- /dev/null +++ b/data/cat_me.txt @@ -0,0 +1 @@ +default message in data/cat_me.txt \ No newline at end of file diff --git a/hello_world.md b/hello_world.md new file mode 100644 index 0000000..dbe6def --- /dev/null +++ b/hello_world.md @@ -0,0 +1,83 @@ +# Hello world example + +This is the most basic workflow definition. + +## Hello world workflow definition using the FlowIR format in YAML + +```yaml +components: # Contains a list of component definitions +- name: hi # A component definition is just a multi-level dictionary + command: + executable: echo + arguments: hello world +``` + +Here, we define a workflow which contains just 1 component that has 2 top-level keys a `name` and a `command` definition. The `command` is just an `executable` and its `arguments`. ST4SD supports grouping components in stages by specifying the component top-level key `stage` (integer). Components with no `stage` key are automatically inserted to stage 0. Here's the same workflow but using an explicit stage index: + +```yaml +components: +- name: hi + stage: 0 + command: + executable: echo + arguments: hello world +``` + +In both examples, the full name of the component is `stage0.hi`. We refer to the full name of a component as the `reference` of the component. You can find more information about workflow definitions and the FlowIR schema in the [README.MD](README.md) file. + +>**Note**: _You may also skip the `command.arguments` field of a component altogether. The component will just invoke its executable with no arguments._ + +>**Note**: _For more information on FlowIR visit our [FlowIR documentation website](https://st4sd.github.io/overview/workflow-specification)._ + +## Executing the hello world example + +This section assumes that you've already installed [st4sd-runtime-core](https://github.com/st4ssd/st4sd-runtime-core). If you've installed `st4sd-runtime-core` in a virtual environment take a moment to load it before continuing. + +First, let's create a package for our workflow definition. Workflow packages, in their most basic form, simply contain the workflow definition. But they can also contain binary and data files. For this hello-world example, we'll just create a workflow package with just the workflow definition file. + +```bash +cd /tmp +mkdir /tmp/hello-world /tmp/hello-world/conf +cat >/tmp/hello-world/conf/flowir_package.yaml <**Note**: _If the `mkdir` commands fail, that means that the `/tmp/hello-world` folder already exists. Try deleting that folder and then rerunning the commands above._ + +Invoke the `elaunch.py` script of ST4SD to execute the workflow. + +```bash +elaunch.py --nostamp hello-world +# Wait for it to terminate and then view the list of files associated with `hi` +ls -lth hello-world.instance/stages/stage0/hi +# Now look at its stdout +cat hello-world.instance/stages/stage0/hi/out.stdout +``` + +>**Note**: _If the `elaunch.py` script fails it will also print an error message in its stderr. Given the simplicity of this hello-world workflow, an error likely means that you've already run hello-world before with the `--nostamp` argument. If that's the case, simply delete `/tmp/hello-world.instance` and re-run `elaunch.py`._ + +>**Note 2**: _The `--nostamp` argument instructs the workflow scheduler to not prefix the name of the workflow instance directory that it generates with a timestamp. This just makes it easier for this guide to tell you where files are. In practice you'd want to include timestamps in your workflow instance directory names._ + +The `elaunch.py` script will print out a summary of the execution right before it terminates. Expect to see a text similar to the one below in your terminal: + +``` +INFO MainThread root : 2021-02-12 11:42:13,074: Clean-up - Final status was +cost=0 +current-stage=stage0 +exit-status=Success +experiment-state=finished +stage-progress=1.0 +stage-state=finished +stages=['stage0'] +total-progress=1.0 +updated=2021-02-12 11:42:13.073179 +``` + +The `elaunch.py` script will create the `/tmp/hello-world.instance` folder. If you like, you can take a moment to poke around the folder structure that `elaunch.py` generated. The files associated with your very first `hi` component are stored under `/tmp/hello-world.instance/stages/stage0/hi`. + +See the [sum numbers readme file](README.md) for a more advanced, but still toy, workflow description.