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Initial commit to update Cromwell to v86 and Batch API
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Signed-off-by: Hatem Nawar <[email protected]>
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@hnawar
hnawar committed Oct 24, 2023
1 parent 92af677 commit 9377419
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Showing 4 changed files with 22 additions and 63 deletions.
8 changes: 4 additions & 4 deletions modules/genomics_cromwell/budget.tf
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Expand Up @@ -19,15 +19,15 @@ locals {
}

resource "google_monitoring_notification_channel" "email_notif" {
count = var.create_budget ? length(local.emails) : 0
count = var.create_budget ? length(local.emails) : 0
display_name = "Billing Budget Notification Channel - ${element(local.emails, count.index)}"
project = local.project.project_id
type = "email"
labels = {
labels = {
email_address = "${element(local.emails, count.index)}"
}
depends_on = [

depends_on = [
time_sleep.wait_120_seconds
]
}
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6 changes: 3 additions & 3 deletions modules/genomics_cromwell/main.tf
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Expand Up @@ -114,10 +114,10 @@ resource "google_storage_bucket_object" "config" {
content = templatefile("scripts/build/cromwell.conf", {
CROMWELL_PROJECT = local.project.project_id,
CROMWELL_ROOT_BUCKET = google_storage_bucket.cromwell_workflow_bucket.url,
CROMWELL_VPC = var.network_name
CROMWELL_VPC = var.network_name,
CROMWELL_REGION = var.region,
CROMWELL_SERVICE_ACCOUNT = module.cromwell_service_account.email,
CROMWELL_PAPI_LOCATION = var.cromwell_PAPI_location,
CROMWELL_PAPI_ENDPOINT = var.cromwell_PAPI_endpoint,
CROMWELL_BATCH_LOCATION = var.cromwell_batch_location,
REQUESTER_PAY_PROJECT = local.project.project_id,
CROMWELL_ZONES = "[${join(", ", var.cromwell_zones)}]"
CROMWELL_PORT = var.cromwell_port,
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58 changes: 11 additions & 47 deletions modules/genomics_cromwell/scripts/build/cromwell.conf
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Expand Up @@ -40,34 +40,23 @@ engine {
}

backend {
default = PAPIv2
default = GCPBATCH


providers {
PAPIv2 {
actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
GCPBATCH {
actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
config {
# Google project
project = "${CROMWELL_PROJECT}"

# Base bucket for workflow executions
root = "${CROMWELL_ROOT_BUCKET}"

# Make the name of the backend used for call caching purposes insensitive to the PAPI version.
name-for-call-caching-purposes: PAPI

# Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck in PAPI.
# Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck in Batch API.
slow-job-warning-time: 24 hours

# Set this to the lower of the two values "Queries per 100 seconds" and "Queries per 100 seconds per user" for
# your project.
#
# Used to help determine maximum throughput to the Google Genomics API. Setting this value too low will
# cause a drop in performance. Setting this value too high will cause QPS based locks from Google.
# 1000 is the default "Queries per 100 seconds per user", 50000 is the default "Queries per 100 seconds"
# See https://cloud.google.com/genomics/quotas for more information
genomics-api-queries-per-100-seconds = 1000

# Polling for completion backs-off gradually for slower-running jobs.
# This is the maximum polling interval (in seconds):
maximum-polling-interval = 600
Expand All @@ -84,8 +73,8 @@ backend {
# Optional configuration to use high security network (Virtual Private Cloud) for running jobs.
# See https://cromwell.readthedocs.io/en/stable/backends/Google/ for more details.
virtual-private-cloud {
network-name = "${CROMWELL_VPC}"
subnetwork-name = "${CROMWELL_VPC}"
network-name = "projects/${CROMWELL_PROJECT}/global/networks/${CROMWELL_VPC}"
subnetwork-name = "regions/${CROMWELL_REGION}/subnetworks/${CROMWELL_VPC}"
}
# Global pipeline timeout
# Defaults to 7 days; max 30 days
Expand All @@ -95,31 +84,22 @@ backend {
# A reference to an auth defined in the `google` stanza at the top. This auth is used to create
# Pipelines and manipulate auth JSONs.
auth = "application-default"


# Currently Cloud Life Sciences API is available now in more locations for the full list check
# https://cloud.google.com/life-sciences/docs/concepts/locations
location = "${CROMWELL_BATCH_LOCATION}"

// alternative service account to use on the launched compute instance
// NOTE: If combined with service account authorization, both that serivce account and this service account
// must be able to read and write to the 'root' GCS path
compute-service-account = "${CROMWELL_SERVICE_ACCOUNT}"



# Currently Cloud Life Sciences API is available now in more locations for the full list check
# https://cloud.google.com/life-sciences/docs/concepts/locations
location = "${CROMWELL_PAPI_LOCATION}"

# Endpoint for APIs. For locations other than us-central1, the endpoint needs to be updated to match the location
# For example for "europe-west4" location the endpoint-url should be "https://europe-west4-lifesciences.googleapis.com"
endpoint-url = "${CROMWELL_PAPI_ENDPOINT}"

# Restrict access to VM metadata. Useful in cases when untrusted containers are running under a service
# account not owned by the submitting user
restrict-metadata-access = false

# Pipelines v2 only: specify the number of times localization and delocalization operations should be attempted
# There is no logic to determine if the error was transient or not, everything is retried upon failure
# Defaults to 3
localization-attempts = 3

# Specifies the minimum file size for `gsutil cp` to use parallel composite uploads during delocalization.
# Parallel composite uploads can result in a significant improvement in delocalization speed for large files
# but may introduce complexities in downloading such files from GCS, please see
Expand All @@ -130,20 +110,6 @@ backend {
parallel-composite-upload-threshold="150M"
}

# Controls how batched requests to PAPI are handled:
batch-requests {
timeouts {
# Timeout when attempting to connect to PAPI to make requests:
# read = 10 seconds

# Timeout waiting for batch responses from PAPI:
#
# Note: Try raising this value if you see errors in logs like:
# WARN - PAPI request worker PAPIQueryWorker-[...] terminated. 99 run creation requests, 0 status poll requests, and 0 abort requests will be reconsidered. If any of those succeeded in the cloud before the batch request failed, they might be run twice.
# ERROR - Read timed out
# connect = 10 seconds
}
}
filesystems {
gcs {
# A reference to a potentially different auth for manipulating files via engine functions.
Expand Down Expand Up @@ -178,8 +144,6 @@ backend {
preemptible: 0
zones: ${CROMWELL_ZONES}
}

include "papi_v2_reference_image_manifest.conf"
}
}
}
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13 changes: 4 additions & 9 deletions modules/genomics_cromwell/variables.tf
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Expand Up @@ -118,14 +118,9 @@ variable "cromwell_db_tier" {

}

variable "cromwell_PAPI_endpoint" {
description = "Endpoint for Life Sciences APIs. For locations other than us-central1, the endpoint needs to be updated to match the location For example for \"europe-west4\" location the endpoint-url should be \"https://europe-west4-lifesciences.googleapi/\". {{UIMeta group=3 order=9 }}"
type = string
default = "https://lifesciences.googleapis.com"
}

variable "cromwell_PAPI_location" {
description = "Google Cloud region or multi-region where the Life Sciences API endpoint will be used. This does not affect where worker instances or data will be stored. {{UIMeta group=3 order=10 }}"
variable "cromwell_batch_location" {
description = "Google Cloud region where the Batch API endpoint will be used. This does not affect where worker instances or data will be stored. {{UIMeta group=3 order=10 }}"
type = string
default = "us-central1"
}
Expand Down Expand Up @@ -157,14 +152,14 @@ variable "cromwell_server_instance_type" {
variable "cromwell_version" {
description = "Cromwell version that will be downloaded, for the latest release version, please check https://github.com/broadinstitute/cromwell/releases for the latest releases. {{UIMeta group=3 order=6 }}"
type = string
default = "72"
default = "86"

}

variable "cromwell_zones" {
description = "GCP Zones that will be set as the default runtime in Cromwell config file. {{UIMeta group=3 order=7 }}"
type = list(any)
default = ["us-central1-a", "us-central1-b"]
default = ["us-central1-a"]
}

variable "db_service_network_cidr_range" {
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