nf-float plugin

This project contains the Nextflow plugin for MemVerge Memory Machine Cloud (aka. float).

FloatGridExecutor extends the AbstractGridExecutor and tells Nextflow how to run the workload with float command line.

Please make sure your nextflow node shares the same work directory with the worker nodes/containers. It should be a shared file system such as NFS or S3FS.

Otherwise, the worker nodes won't be able to see the task files.

License

Apache License Version 2.0

Installation

To run float with Nextflow, you must install the Nextflow and the float plugin.

Note

Nextflow and the plugin should be installed on a node that have access to the NFS which is available to all worker nodes.

Install Nextflow

Enter this command in your terminal:

curl -s https://get.nextflow.io | bash

It creates a file nextflow in the current dir.

Note:

Nextflow requires java 11 or higher. You may need to install openjdk 11 for your environment.

You could always find the latest installation guide at https://www.nextflow.io/docs/latest/getstarted.html.

Install nf-float plugin

Auto Install

The nf-float plugin is available on the Nextflow community plugins site. When Nextflow sees following configuration, it will automatically download the plugin.

Just make sure you have proper internet access.

plugins {
    id '[email protected]'
}

Manual Install

Sometimes you want to deploy a customized plugin. In this case, you can install it manually.

Go to the folder where you just install the nextflow command line. Let's call this folder the Nextflow home directory. Create the float plugin folder with:

mkdir -p .nextflow/plugins/nf-float-0.3.1

where 0.3.1 is the version of the float plugin. This version number should align with the version in of your plugin and the property in your configuration file. (check the configuration section)

Retrieve your plugin zip file and unzip it in this folder. If everything goes right, you should be able to see two sub-folders:

$ ll .nextflow/plugins/nf-float-0.3.1/
total 48
drwxr-xr-x 4 ec2-user ec2-user    51 Jan  5 07:17 classes
drwxr-xr-x 2 ec2-user ec2-user    25 Jan  5 07:17 META-INF

Configuration

Users need to update the default configuration file or supply a configuration file with the command line option -c. Here is a sample of the configuration.

plugins {
    id '[email protected]'
}

workDir = '/mnt/memverge/shared'

float {
    address = 'opcenter.compute.amazonaws.com'
    username = 'admin'
    password = 'memverge'
    nfs = 'nfs://1.2.3.4/mnt/memverge/shared'
}

process {
    executor = 'float'
}

• In the plugins section, users must specify the plugin name and version.
• workDir is where we mount the NFS and where Nextflow put the process files.
• In the float section, users must supply the address of the MMCE operation center and the proper credentials.
• In the process scope, we specify executor = 'float' to tell Nextflow to execute tasks with the Float executor.

Available float config options:

• address: address of your operation center(s). Separate multiple addresses with ,.
• username, password: the credentials for your operation center
• nfs: the location of the NFS (if using NFS for the work directory)
• migratePolicy: the migration policy used by WaveRider, specified as a map. Refer to the CLI usage for the list of available options.
• vmPolicy: the VM creation policy, specified as a map. Refer to the CLI usage for the list of available options.
• timeFactor: a float number. default to 1. An extra factor to multiply based on the time supplied by the task. Use it to resolve some task timeouts.
• commonExtra: allows the user to specify other submit CLI options. This parameter will be appended to every float submit command.

Configure with environment variables

The plugin allows the user to set credentials with environment variables. If the credentials are not available in the configuration file, it will try reading these environment variables.

• MMC_ADDRESS for operation center address. Separate multiple addresses with ,.
• MMC_USERNAME for login username
• MMC_PASSWORD for login password

Configure with Nextflow secrets

User can use Nextflow secrets to input the credentials. Here is an example:

nextflow secrets set MMC_USERNAME "..."
nextflow secrets set MMC_PASSWORD "..."

In the configuration file, you can reference the secrets like this:

float {
    username = secrets.MMC_USERNAME
    password = secrets.MMC_PASSWORD
}

If the secret is not available, Nextflow reports error like this:

Unknown config secret 'MMC_USERNAME'

Configure s3 work directory

To enable s3 as work directory, user need to set work directory to a s3 bucket.

plugins {
    id '[email protected]'
}

workDir = 's3://bucket/path'

process {
    executor = 'float'
    container = 'fedora/fedora-minimal'
}

podman.registry = 'quay.io'

float {
    address = 'op.center.address'
    username = secrets.MMC_USERNAME
    password = secrets.MMC_PASSWORD
}

aws {
  accessKey = '***'
  secretKey = '***'
  region = 'us-east-2'
}

You don't need to specify nfs in float scope. The plugin will assemble the nfs option automatically.

The plugin retrieves the s3 credentials from Nextflow. Nextflow looks for AWS credentials in the following order:

• the nextflow.config file in the pipeline execution directory
• the environment variables AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY
• the environment variables AWS_ACCESS_KEY and AWS_SECRET_KEY
• the default profile in the AWS credentials file located at ~/.aws/credentials
• the default profile in the AWS client configuration file located at ~/.aws/config
• the temporary AWS credentials provided by an IAM instance role. See IAM Roles documentation for details.

For detail, check NextFlow's document. https://www.nextflow.io/docs/latest/amazons3.html#security-credentials

Tests done for s3 work directory support:

• trivial sequence and scatter workflow.
• the test profile of nf-core/rnaseq
• the test profile of nf-core/sarek

Configure fusion FS over s3

Since release 0.3.0, we support fusion FS over s3. To enable fusion, you need to add following configurations

wave.enabled = true // 1

fusion {
  enabled = true // 2
  exportStorageCredentials = true // 3
  exportAwsAccessKeys = true // 4
}

1. fusion needs wave support.
2. enable fusion explicitly
3. export the aws credentials as environment variable.
4. same as 3. Different nextflow versions may require different option. Supply both 3 & 4 if you are not sure.

In additional, you may want to:

• point your work directory to a location in s3.
• specify your s3 credentials in the aws scope.

When fusion is enabled, you can find similar submit command line in your .nextflow.log

float -a <op-center-address> -u admin -p *** submit
    --image 'wave.seqera.io/wt/dfd4c4e2d48d/biocontainers/mulled-v2-***:***-0'
    --cpu 12
    --mem 72
    --job /tmp/nextflow5377817282489183149.command.run
    --env FUSION_WORK=/fusion/s3/cedric-memverge-test/nf-work/work/31/a4b682beb93c944fbd3a342ffc41c5
    --env AWS_ACCESS_KEY_ID=***
    --env AWS_SECRET_ACCESS_KEY=***
    --env 'FUSION_TAGS=[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)'
    --extraContainerOpts --privileged
    --customTag nf-job-id:znzjht-4

• the task image is wrapped by a layer provided by wave. note: releases prior to MMC 2.3.1 has bug that fails the image pull requests to the wave registry.
  please upgrade to the latest MMC master.
• FUSION_WORK and FUSION_TAGS is added as environment variables.
• aws credentials is added as environment variables.
• use extraContainerOpts to make sure we run the container in privileged mode. note: this option requires MMC 2.3 or later.

Tests for the fusion support.

• trivial sequence and scatter workflow.
• the test profile of nf-core/rnaseq
• the test profile of nf-core/sarek

Configure VM creation and migration policies

While the VM and migration policies can be specified like any CLI option via float.commonExtra, they can also be specified using the config options float.vmPolicy and float.migratePolicy as maps:

float {
    vmPolicy = [
        spotFirst: true,
        retryLimit: 3,
        retryInterval: '10m'
    ]

    migratePolicy = [
        cpu: [upperBoundRatio: 90, upperBoundDuration: '10s'],
        mem: [lowerBoundRatio: 20, upperBoundRatio: 90]
    ]
}

Process definition

For each process, users could supply their requirements for the CPU, memory and container image using the standard Nextflow process directives. Here is an example of a hello world workflow.

process sayHello {
  executor 'float'
  container 'cactus'
  cpus 2
  memory 4.GB
  disk 50.GB
  time '1h'

  output:
    stdout

  """
  echo "Hello from Nextflow!"
  """
}

workflow {
  sayHello | view { it.trim() }
}

The following process directives are supported for specifying task resources:

• conda (only when using Wave)
• container
• cpus
• disk (controls the size of the volume of the workload, minimal size is 40 GB)
• machineType
• memory
• resourceLabels
• time

Run the Workflow

Use the nextflow command to run the workflow. We need to include our configuration file and task file as arguments. Here is an example.

./nextflow run samples/tutorial.nf -c conf/float-rt.conf

Unit testing

Run the following command in the project root directory (ie. where the file settings.gradle is located):

./gradlew check

Testing and debugging

To run and test the plugin in a development environment, configure a local Nextflow build with the following steps:

1. Clone the Nextflow repository in your computer into a sibling directory:

   git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow

2. Configure the plugin build to use the local Nextflow code:

   echo "includeBuild('../nextflow')" >> settings.gradle

   (Make sure to not add it more than once!)

3. Compile the plugin alongside the Nextflow code:

   ./gradlew compileGroovy

4. Run Nextflow with the plugin, using ./launch.sh as a drop-in replacement for the nextflow command, and adding the option -plugins nf-hello to load the plugin:

   ./launch.sh run samples/hello.nf -c conf/float-rt.conf -plugins nf-float

Package

Run following command to create the plugin zip.

./gradlew makeZip

The output is available at ./plugins/nf-float/build/libs/