Dflow is a Python framework for constructing scientific computing workflows employing Argo Workflows as the workflow engine.
Project description
DFLOW
Dflow is a Python framework for constructing scientific computing workflows (e.g. concurrent learning workflows) employing Argo Workflows as the workflow engine.
For dflow's users (e.g. ML application developers), dflow offers user-friendly functional programming interfaces for building their own workflows. Users need not be concerned with process control, task scheduling, observability and disaster tolerance. Users can track workflow status and handle exceptions by APIs as well as from frontend UI. Thereby users are enabled to concentrate on implementing operations (OPs) and orchestrating workflows.
For dflow's developers, dflow wraps on argo SDK, keeps details of computing and storage resources from users, and provides extension abilities. While argo is a cloud-native workflow engine, dflow uses containers to decouple computing logic and scheduling logic, and uses Kubernetes to make workflows observable, reproducible and robust. Dflow is designed to be based on a distributed, heterogeneous infrastructure. The most common computing resources in scientific computing may be HPC clusters. User can either use executor to manage HPC jobs within dflow (dflow-extender) or using DPDispatcher plugin, or use virtual node technique to uniformly manage HPC resources in the framework of Kubernetes (wlm-operator).
Dflow's OPs can be reused among workflows and shared among users. Dflow provides a cookie cutter recipe dflow-op-cutter for template a new OP package. Start developing an OP package at once from
pip install cookiecutter
cookiecutter https://github.com/deepmodeling/dflow-op-cutter.git
-
- 1.1. Architecture
- 1.2. Common layer
- 1.2.1. Parameters and artifacts
- 1.2.2. OP template
- 1.2.3. Step
- 1.2.4. Workflow
- 1.3. Interface layer
- 1.3.1. Python OP
-
- 2.1. Prepare Kubernetes cluster
- 2.2. Setup Argo Workflows
- 2.3. Install dflow
- 2.4. Run an example
-
- 3.1. Common layer
- 3.1.1. Workflow management
- 3.1.2. Upload/download artifact
- 3.1.3. Steps
- 3.1.4. DAG
- 3.1.5. Output parameters and artifacts of Steps
- 3.1.6. Conditional step, parameters and artifacts
- 3.1.7. Produce parallel steps using loop
- 3.1.8. Timeout
- 3.1.9. Continue on failed
- 3.1.10. Continue on success number/ratio of parallel steps
- 3.1.11. Optional input artifacts
- 3.1.12. Default value for output parameters
- 3.1.13. Key of a step
- 3.1.14. Resubmit a workflow
- 3.1.15. Executor
- 3.1.16. Submit Slurm job via slurm executor
- 3.1.17. Submit HPC job via dispatcher plugin
- 3.1.18. Submit Slurm job via virtual node
- 3.1.19. Use resources in Kubernetes
- 3.2. Interface layer
- 3.2.1. Slices
- 3.2.2. Retry and error handling
- 3.2.3. Progress
- 3.2.4. Upload python packages for development
- 3.1. Common layer
1. Overview
1.1. Architecture
The dflow consists of a common layer and an interface layer. Interface layer takes various OP templates from users, usually in the form of python classes, and transforms them into base OP templates that common layer can handle.
1.2. Common layer
Common layer is an extension over argo client which provides functionalities such as file processing, computing resources management, workflow submission and management, etc.
1.2.1. Parameters and artifacts
Parameters and artifacts are data stored by the workflow and passed within the workflow. Parameters are saved as strings which can be displayed in the UI, while artifacts are saved as files.
1.2.2. OP template
OP template (shown as base OP in the figure above) is the fundamental building block of a workflow. It defines an operation to be executed given the input and output. Both the input and output can be parameters and/or artifacts. The most common OP template is the container OP template. Necessary arguments to be defined for the operation are the container image and scripts to be executed. Currently, two types of container OP templates are supported: ShellOPTemplate
, PythonScriptOPTemplate
. Shell OP template (ShellOPTemplate
) defines an operation by a shell script and Python script OP template (PythonScriptOPTemplate
) defines an operation by a Python script.
To use the ShellOPTemplate
:
from dflow import ShellOPTemplate
simple_example_templ = ShellOPTemplate(
name="Hello",
image="alpine:latest",
script="cp /tmp/foo.txt /tmp/bar.txt && echo {{inputs.parameters.msg}} > /tmp/msg.txt",
)
The above example defines a ShellOPTemplate
with name = "Hello"
and container image alpine:latest
. The operation is to copy /tmp/foo.txt
(input artifacts) to /tmp/bar.txt
(output artifacts) and printout the properties of the parameters with name msg
(input parameters) and redirect it to /tmp/msg.txt
(value in the file is the properties of the output parameters).
To define the parameters and artifacts of this OPTemplate:
from dflow import InputParameter, InputArtifact, OutputParameter, OutputArtifact
# define input
simple_example_templ.inputs.parameters = {"msg": InputParameter()}
simple_example_templ.inputs.artifacts = {"inp_art": InputArtifact(path="/tmp/foo.txt")}
# define output
simple_example_templ.outputs.parameters = {
"msg": OutputParameter(value_from_path="/tmp/msg.txt")
}
simple_example_templ.outputs.artifacts = {
"out_art": OutputArtifact(path="/tmp/bar.txt")
}
In the above example, there are three things to clarify.
- The value of the input parameter is optional for the OP template, if provided, it will be regarded as the default value which can be overridden at run time.
- For the output parameter, the source where its value comes from should be specified. For the container OP template, the value may come from a certain file generated in the container (
value_from_path
). - The paths to the input and output artifact in the container are required to be specified.
On the same level, one can also define a PythonScriptOPTemplate
to achieve the same operation.
1.2.3. Step
Step
is the central block for building a workflow. A step
is created by instantiating an OP template. When a step
is initialized, values of all input parameters and sources of all input artifacts declared in the OP template must be specified.
from dflow import Step
simple_example_step = Step(
name="step0",
template=simple_example_templ,
parameters={"msg": "HelloWorld!"},
artifacts={"inp_art": foo},
)
This step will instantiate the OP template created in 1.2.2. Note that foo is an artifact either uploaded from local or output of another step.
1.2.4. Workflow
Workflow
is the connecting block for building a workflow. A workflow
is created by adding step
s together.
from dflow import Workflow
wf = Workflow(name="hello-world")
wf.add(simple_example_step)
Submit a workflow by
wf.submit()
One can also add a list of step
s to a workflow to make them run in parallel
wf.add([hello2, hello3])
An example using all the elements discussed in 1.2 is shown here:
1.3. Interface layer
Interface layer handles more Python-native OPs defined in the form of class.
1.3.1. Python OP
PythonOPTemplate
is another kind of OP template. It inherits from PythonScriptOPTemplate
but allows users to define operation (OP) in the form of a Python class. As Python is a weak typed language, we impose strict type checking to PythonOP
to alleviate ambiguity and unexpected behaviors.
The structures of the inputs and outputs of a PythonOP
are defined in the static methods get_input_sign
and get_output_sign
. Each of them returns a OPIOSign
object, which is a dictionary mapping from the name of a parameter/artifact to its sign.
The execution of the PythonOP
is defined in the execute
method. The execute
method receives a OPIO
object as input and outputs a OPIO
object. OPIO
is a dictionary mapping from the name of a parameter/artifact to its value/path. The type of the parameter value or the artifact path should be in accord with that declared in the sign. Type checking is implemented before and after the execute
method.
from dflow.python import OP, OPIO, OPIOSign, Artifact
from pathlib import Path
import shutil
class SimpleExample(OP):
def __init__(self):
pass
@classmethod
def get_input_sign(cls):
return OPIOSign(
{
"msg": str,
"inp_art": Artifact(Path),
}
)
@classmethod
def get_output_sign(cls):
return OPIOSign(
{
"msg": str,
"out_art": Artifact(Path),
}
)
@OP.exec_sign_check
def execute(
self,
op_in: OPIO,
) -> OPIO:
shutil.copy(op_in["inp_art"], "bar.txt")
out_msg = op_in["msg"]
op_out = OPIO(
{
"msg": out_msg,
"out_art": Path("bar.txt"),
}
)
return op_out
The above example defines an OP SimpleExample
. The operation is to copy foo.txt
to bar.txt
and write the properties of the parameters with name msg to msg.txt
.
To use the above class as a PythonOPTemplate, we need to pass the above class to PythonOPTemplate
and specify the container image. Note that pydflow
must be installed in this image
from dflow.python import PythonOPTemplate
simple_example_templ = PythonOPTemplate(SimpleExample, image="python:3.8")
An example using all the elements discussed in 1.3 is shown here:
2. Quick Start
2.1. Prepare Kubernetes cluster
Firstly, you will need a Kubernetes cluster. To setup a Kubernetes cluster on your laptop, you can download the Minikube on your PC and make sure you have Docker up and running on you PC.
After downloading, you can initiate the Kubernetes cluster using:
minikube start
2.2. Setup Argo Workflows
To get started quickly, you can use the quick start manifest. It will install Argo Workflow as well as some commonly used components:
kubectl create ns argo
kubectl apply -n argo -f https://raw.githubusercontent.com/deepmodeling/dflow/master/manifests/quick-start-postgres.yaml
If you are running Argo Workflows locally (e.g. using Minikube or Docker for Desktop), open a port-forward so you can access the namespace:
kubectl -n argo port-forward deployment/argo-server 2746:2746
This will serve the user interface on https://localhost:2746
For access to the minio object storage, open a port-forward for minio
kubectl -n argo port-forward deployment/minio 9000:9000
2.3. Install dflow
Make sure your Python version is not less than 3.6 and install dflow
pip install pydflow
2.4. Run an example
Submit a simple workflow
python examples/test_steps.py
Then you can check the submitted workflow through argo's UI.
3. User Guide (dflow-doc)
3.1. Common layer
3.1.1. Workflow management
After submitting a workflow by wf.submit()
, or getting a history workflow by wf = Workflow(id="xxx")
, one can track its real-time status with APIs
wf.id
: workflow ID in argowf.query_status()
: query workflow status, return"Pending"
,"Running"
,"Suceeded"
, etc.wf.query_step(name=None)
: query step by name (support for regex), return a list of argo step objectsstep.phase
: phase of a step,"Pending"
,"Running"
,Succeeded
, etc.step.outputs.parameters
: a dictionary of output parametersstep.outputs.artifacts
: a dictionary of output artifacts
3.1.2. Upload/download artifact
Dflow offers tools for uploading files to Minio and downloading files from Minio (default object storage in the quick start). User can upload a list of files or directories and get an artifact object, which can be used as argument of a step
artifact = upload_artifact([path1, path2])
step = Step(
...
artifacts={"foo": artifact}
)
User can also download the output artifact of a step queried from a workflow (to current directory for default)
step = wf.query_step(name="hello")
download_artifact(step.outputs.artifacts["bar"])
Modify dflow.s3_config
to configure S3 globally.
Note: dflow retains the relative path of the uploaded file/directory with respect to the current directory during uploading. If file/directory outside current directory is uploaded, its absolute path is used as the relative path in the artifact. If you want a different directory structure in the artifact with the local one, you can make soft links and then upload.
3.1.3. Steps
Steps
is another kind of OP template which is defined by its constituent step
s instead of a container. It can be seen as a sub-workflow or a super OP template consisting of some smaller OPs. Steps
is a sequential array of concurrent Step
. A simple example goes like [[s00,s01],[s10,s11,s12]]
, where inner array represent concurrent tasks while outer array is sequential. Add a step
to a steps
just like for a workflow
steps.add(step)
Steps
can be used as the template to define a bigger step
. Thus one can construct complex workflows of nested structure. One is also allowed to recursively use a Steps
as the template of a building bloack inside it self to achieve dynamic loop.
3.1.4. DAG
DAG
is another kind of OP template which is defined by its constituent task
s and their dependencies. The usage of DAG
is similar to that of steps
. To add a task
to a DAG
, use
dag.add(task)
The usage of task
is also similar to that of step
. Dflow will automatically detect dependencies among task
s of a DAG
(from input/output relations). Additional dependencies can be declared by
task_3 = Task(..., dependencies=[task_1, task_2])
3.1.5. Output parameters and artifacts of Steps
The output parameter of a Steps
can be set to come from a step of it by steps.outputs.parameters["msg"].value_from_parameter = step.outputs.parameters["msg"]
. Here, step
must be contained in steps
. For assigning output artifact for a Steps
, use steps.outputs.artifacts["foo"]._from = step.outputs.parameters["foo"]
.
3.1.6. Conditional step, parameters and artifacts
Set a step to be conditional by Step(..., when=expr)
where expr
is an boolean expression in string format. Such as "%s < %s" % (par1, par2)
. The when
argument is often used as the breaking condition of recursive steps. The output parameter of a Steps
can be assigned as optional by
steps.outputs.parameters["msg"].value_from_expression = if_expression(
_if=par1 < par2,
_then=par3,
_else=par4
)
Similarly, the output artifact of a Steps
can be assigned as optional by
steps.outputs.artifacts["foo"].from_expression = if_expression(
_if=par1 < par2,
_then=art1,
_else=art2
)
3.1.7. Produce parallel steps using loop
with_param
and with_sequence
are 2 arguments of Step
for automatically generating a list of parallel steps. These steps share a common OP template, and only differ in the input parameters.
A step using with_param
option generates parallel steps on a list (either a constant list or referring to another parameter, e.g. an output parameter of another step or an input parameter of the steps
or DAG
context), the parallelism equals to the length of the list. Each parallel step picks an item from the list by "{{item}}"
, such as
step = Step(
...
parameters={"msg": "{{item}}"},
with_param=steps.inputs.parameters["msg_list"]
)
A step using with_sequence
option generates parallel steps on a numeric sequence. with_sequence
is usually used in coordination with argo_sequence
which returns an Argo's sequence. For argo_sequence
, the number at which to start the sequence is specified by start
(default: 0). One can either specify the number of elements in the sequence by count
or the number at which to end the sequence by end
. The printf format string can be specified by format
to format the value in the sequence. Each argument can be passed with a parameter, argo_len
which returns the length of a list may be useful. Each parallel step picks an element from the sequence by "{{item}}"
, such as
step = Step(
...
parameters={"i": "{{item}}"},
with_sequence=argo_sequence(argo_len(steps.inputs.parameters["msg_list"]))
)
3.1.8. Timeout
Set the timeout of a step by Step(..., timeout=t)
. The unit is second.
3.1.9. Continue on failed
Set the workflow to continue when a step fails by Step(..., continue_on_failed=True)
.
3.1.10. Continue on success number/ratio of parallel steps
Set the workflow to continue when certain number/ratio of parallel steps succeed by Step(..., continue_on_num_success=n)
or Step(..., continue_on_success_ratio=r)
.
3.1.11. Optional input artifacts
Set an input artifact to be optional by op_template.inputs.artifacts["foo"].optional = True
.
3.1.12. Default value for output parameters
Set default value for an output parameter by op_template.outputs.parameters["msg"].default = default_value
. The default value will be used when the expression in value_from_expression
fails or the step is skipped.
3.1.13. Key of a step
You can set a key for a step by Step(..., key="some-key")
for the convenience of locating the step. The key can be regarded as an input parameter which may contain reference of other parameters. For instance, the key of a step can change with iterations of a dynamic loop. Once key is assigned to a step, the step can be query by wf.query_step(key="some-key")
. If the key is unique within the workflow, the query_step
method returns a list consist of only one element.
3.1.14. Resubmit a workflow
Workflows often have some steps that are expensive to compute. The outputs of previously run steps can be reused for submitting a new workflow. E.g. a failed workflow can be restarted from a certain point after some modification of the workflow template or even outputs of completed steps. For example, submit a workflow with reused steps by wf.submit(reuse_step=[step0, step1])
. Here, step0
and step1
are previously run steps returned by query_step
method. Before the new workflow runs a step, it will detect if there exists a reused step whose key matches that of the step about to run. If hit, the workflow will skip the step and set its outputs as those of the reused step. To modify outputs of a step before reusing, use step0.modify_output_parameter(par_name, value)
for parameters and step0.modify_output_artifact(art_name, artifact)
for artifacts.
3.1.15. Executor
By default, for a "script step" (a step whose template is a script OP template), the Shell script or Python script runs in the container directly. Alternatively, one can modify the executor to run the script. Dflow offers an extension point for "script step" Step(..., executor=my_executor)
. Here, my_executor
should be an instance of class derived from Executor
. A Executor
-derived class should implement a method render
which converts original template to a new template.
class Executor(object):
def render(self, template):
pass
A context is similar to an executor, but assigned to a workflow Workflow(context=...)
and affect every step.
3.1.16. Submit Slurm job via slurm executor
SlurmRemoteExecutor
is provided as an example of executor. The executor submits a slurm job to a remote host and synchronize its status and logs to the dflow step. The central logic of the executor is implemented in the Golang project Dflow-extender. If you want to run a step on a slurm cluster remotely, do something like
Step(
...,
executor=SlurmRemoteExecutor(host="1.2.3.4",
username="myuser",
header="""#!/bin/bash
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -p cpu""")
)
There are 3 options for SSH authentication, using password, specify path of private key file locally, or upload authorized private key to each node (or equivalently add each node to the authorized host list).
3.1.17. Submit HPC job via dispatcher plugin
DPDispatcher is a python package used to generate HPC scheduler systems (Slurm/PBS/LSF) jobs input scripts and submit these scripts to HPC systems and poke until they finish. Dflow provides simple interface to invoke dispatcher as executor to complete script steps. E.g.
from dflow.plugins.dispatcher import DispatcherExecutor
Step(
...,
executor=DispatcherExecutor(host="1.2.3.4",
username="myuser",
queue_name="V100")
)
For SSH authentication, one can either specify path of private key file locally, or upload authorized private key to each node (or equivalently add each node to the authorized host list). For configuring extra machine, resources or task parameters for dispatcher, use DispatcherExecutor(..., machine_dict=m, resources_dict=r, task_dict=t)
.
3.1.18. Submit Slurm job via virtual node
Following the installation steps in the wlm-operator project to add Slurm partitions as virtual nodes to Kubernetes (use manifests configurator.yaml, operator-rbac.yaml, operator.yaml in this project which modified some RBAC configurations)
$ kubectl get nodes
NAME STATUS ROLES AGE VERSION
minikube Ready control-plane,master 49d v1.22.3
slurm-minikube-cpu Ready agent 131m v1.13.1-vk-N/A
slurm-minikube-dplc-ai-v100x8 Ready agent 131m v1.13.1-vk-N/A
slurm-minikube-v100 Ready agent 131m v1.13.1-vk-N/A
Then you can assign a step to be executed on a virtual node (i.e. submit a Slurm job to the corresponding partition to complete the step)
step = Step(
...
executor=SlurmJobTemplate(
header="#!/bin/sh\n#SBATCH --nodes=1",
node_selector={"kubernetes.io/hostname": "slurm-minikube-v100"}
)
)
3.1.19. Use resources in Kubernetes
A step can also be completed by a Kubernetes resource (e.g. Job or custom resources). At the beginning, a manifest is applied to Kubernetes. Then the status of the resource is monitered until the success condition or the failure condition is satisfied.
class Resource(object):
action = None
success_condition = None
failure_condition = None
def get_manifest(self, template):
pass
3.2. Interface layer
3.2.1. Slices
Slices
helps user to slice input parameters/artifacts (which must be lists) to feed parallel steps and stack their output parameters/artifacts to lists in the same pattern. For example,
step = Step(name="parallel-tasks",
template=PythonOPTemplate(
...,
slices=Slices("{{item}}",
input_parameter=["msg"],
input_artifact=["data"],
output_artifact=["log"])
),
parameters = {
"msg": msg_list
},
artifacts={
"data": data_list
},
with_param=argo_range(5)
)
In this example, each item in msg_list
is passed to a parallel step as the input parameter msg
, each part in data_list
is passed to a parallel step as the input artifact data
. Finally, the output artifacts log
of all parallel steps are collected to one artifact step.outputs.artifacts["log"]
.
It should be noticed that this feature by default passes full input artifacts to each parallel step which may only use some slices of these artifacts. In comparison, the subpath mode of slices only passes one single slice of the input artifacts to each parallel step. To use the subpath mode of slices,
step = Step(name="parallel-tasks",
template=PythonOPTemplate(
...,
slices=Slices(sub_path=True,
input_parameter=["msg"],
input_artifact=["data"],
output_artifact=["log"])
),
parameters = {
"msg": msg_list
},
artifacts={
"data": data_list
})
Here, the slice pattern ({{item}}
) of PythonOPTemplate
and the with_param
argument of the Step
need not to be set, because they are fixed in this mode. Each input parameter and artifact to be sliced must be of the same length, and the parallelism equals to this length. Another noticeable point is that in order to use the subpath of the artifacts, these artifacts must be saved without compression when they are generated. E.g. declare Artifact(..., archive=None)
in the output signs of Python OP, or specify upload_artifact(..., archive=None)
while uploading artifacts. Besides, one can use dflow.config["archive_mode"] = None
to set default archive mode to no compression globally.
3.2.2. Retry and error handling
Dflow catches TransientError
and FatalError
thrown from OP
. User can set maximum number of retries on TransientError
by PythonOPTemplate(..., retry_on_transient_error=n)
. Timeout error is regarded as fatal error for default. To treat timeout error as transient error, set PythonOPTemplate(..., timeout_as_transient_error=True)
.
3.2.3. Progress
A OP
can update progress in the runtime so that user can track its real-time progress
class Progress(OP):
progress_total = 100
...
def execute(op_in):
for i in range(10):
self.progress_current = 10 * (i + 1)
...
3.2.4. Upload python packages for development
To avoid frequently making image during development, dflow offers an interface to upload local packages into container and add them to $PYTHONPATH
, such as PythonOPTemplate(..., python_packages=["/opt/anaconda3/lib/python3.9/site-packages/numpy"])
. One can also globally specify packages to be uploaded, which will affect all OP
s
from dflow.python import upload_packages
upload_packages.append("/opt/anaconda3/lib/python3.9/site-packages/numpy")
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