Merge pull request galaxyproject#20862 from jmchilton/pulsar_15_10

Various Container Execution Enhancements (including GCP Batch support)

Author: jmchilton

lib/galaxy/config/sample/job_conf.sample.yml

@@ -338,6 +338,27 @@ runners:
     #app: {}
     #pulsar_config: path/to/pulsar/app.yml
 
+  # Using Pulsar and co-execution to run jobs against a TES service.
+  # - https://www.ga4gh.org/product/task-execution-service-tes/
+  # - https://pulsar.readthedocs.io/en/latest/containers.html#ga4gh-tes
+  pulsar_tes:
+    load: galaxy.jobs.runners.pulsar:PulsarTesJobRunner
+    # RabbitMQ URL from Galaxy server (include credentials).
+    amqp_url: <amqp_url>
+    # If Pulsar needs to talk to Galaxy at a particular host and port, set that here.
+    #galaxy_url: <galaxy_url>  
+
+  # Using Pulsar and co-execution to run jobs against Google Cloud Platform's Batch service.
+  # - https://cloud.google.com/batch/docs/get-started
+  # - https://pulsar.readthedocs.io/en/latest/containers.html#google-cloud-platform-batch
+  pulsar_gcp:
+    load: galaxy.jobs.runners.pulsar:PulsarGcpBatchJobRunner
+    # RabbitMQ URL from Galaxy server (include credentials).
+    amqp_url: <amqp_url>
+    # If Pulsar needs to talk to Galaxy at a particular host and port, set that here.
+    #galaxy_url: <galaxy_url>
+
+
 # Job handler configuration - for a full discussion of job handlers, see the documentation at:
 #     https://docs.galaxyproject.org/en/latest/admin/scaling.html
 handling:
@@ -916,6 +937,55 @@ execution:
       # Path to Kubernetes configuration fil (see Kubernetes runner description.)
       #k8s_config_path: /path/to/kubeconfig
 
+    pulsar_tes_environment:
+      runner: pulsar_tes
+      # A tes_url is required
+      tes_url: "<tes_url>"
+      #basic_auth:
+      #  username: <username>
+      #  password: <password>
+      #cpu_cores: 1
+      # Define if the task is allowed to run on preemptible compute instances,\nfor example, AWS Spot. This option may have no effect when utilized\non some backends that don't have the concept of preemptible jobs.
+      #preemptible: false
+      #ram_gb: 8
+      #disk_gb: 40
+      # Request that the task be run in these compute zones. How this string is utilized will be dependent on the backend system. For example, a\nsystem based on a cluster queueing system may use this string to define\npriorty queue to which the job is assigned.
+      #zones: us-west-1
+      #backend_parameters: {}
+      #backend_parameters_strict: false
+      # Configure the embedded Pulsar app, only message_queue_url is required but
+      # other options may be useful (unsure).
+      pulsar_app_config:
+          # This needs to be the RabbitMQ server, but this should be the host
+          # and port that your TES nodes would connect to the server via.
+          message_queue_url: "<amqp_url>"
+
+    pulsar_gcp_environment:
+      runner: pulsar_gcp
+      # required
+      project_id: <gcp_project_id>
+      # Path to GCP service account credentials file. (not sure if ~ would be implicitly respected in this example)
+      #credentials_file: ~/.config/gcloud/application_default_credentials.json
+      # GCP region or zone to use (optional)
+      #region: us-central1
+      # Max walltime to use in seconds (defaults to 60 * 60 * 24)
+      #walltime_limit: 216000
+      # Maximum number of retries for the job. Maps to TaskSpec.max_retry_count.
+      #retry_count: 2
+      # Name of the SSD volume to be mounted in the task. Shared among all containers in job.
+      #ssd_name: pulsar_staging
+      # Size of the shared local SSD disk in GB (must be a multiple of 375).
+      #disk_size: 375
+      # Machine type for the job's VM.
+      #machine_type: n1-standard-1
+      #labels: {}
+      # Configure the embedded Pulsar app, only message_queue_url is required but
+      # other options may be useful (unsure).
+      pulsar_app_config:
+          # This needs to be the RabbitMQ server, but this should be the host
+          # and port that your GCP compute would connect to the server via.
+          message_queue_url: "<amqp_url>"
+
     # Example CLI runners.
     ssh_torque:
       runner: cli

lib/galaxy/jobs/runners/__init__.py

@@ -818,6 +818,13 @@ def register_cleanup_file_attribute(self, attribute):
         if attribute not in self.cleanup_file_attributes:
             self.cleanup_file_attributes.append(attribute)
 
+    def init_job_stream_files(self):
+        """For runners that don't create explicit job scripts - create job stream files."""
+        with open(self.output_file, "w"):
+            pass
+        with open(self.error_file, "w"):
+            pass
+
 
 class AsynchronousJobRunner(BaseJobRunner, Monitors):
     """Parent class for any job runner that runs jobs asynchronously (e.g. via
@@ -907,17 +914,7 @@ def check_watched_items(self):
     def check_watched_item(self, job_state: AsynchronousJobState) -> Union[AsynchronousJobState, None]:
         raise NotImplementedError()
 
-    def finish_job(self, job_state: AsynchronousJobState):
-        """
-        Get the output/error for a finished job, pass to `job_wrapper.finish`
-        and cleanup all the job's temporary files.
-        """
-        galaxy_id_tag = job_state.job_wrapper.get_id_tag()
-        external_job_id = job_state.job_id
-
-        # To ensure that files below are readable, ownership must be reclaimed first
-        job_state.job_wrapper.reclaim_ownership()
-
+    def _collect_job_output(self, job_id: int, external_job_id: Optional[str], job_state: JobState):
         # wait for the files to appear
         which_try = 0
         collect_output_success = True
@@ -931,11 +928,25 @@ def finish_job(self, job_state: AsynchronousJobState):
                 if which_try == self.app.config.retry_job_output_collection:
                     stdout = ""
                     stderr = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
-                    log.error("(%s/%s) %s: %s", galaxy_id_tag, external_job_id, stderr, unicodify(e))
+                    log.error("(%s/%s) %s: %s", job_id, external_job_id, stderr, unicodify(e))
                     collect_output_success = False
                 else:
                     time.sleep(1)
                 which_try += 1
+        return collect_output_success, stdout, stderr
+
+    def finish_job(self, job_state: AsynchronousJobState):
+        """
+        Get the output/error for a finished job, pass to `job_wrapper.finish`
+        and cleanup all the job's temporary files.
+        """
+        galaxy_id_tag = job_state.job_wrapper.get_id_tag()
+        external_job_id = job_state.job_id
+
+        # To ensure that files below are readable, ownership must be reclaimed first
+        job_state.job_wrapper.reclaim_ownership()
+
+        collect_output_success, stdout, stderr = self._collect_job_output(galaxy_id_tag, external_job_id, job_state)
 
         if not collect_output_success:
             job_state.fail_message = stderr

lib/galaxy/jobs/runners/kubernetes.py

@@ -7,7 +7,6 @@
 import math
 import os
 import re
-import time
 from dataclasses import dataclass
 from datetime import datetime
 from typing import Union
@@ -50,7 +49,6 @@
     Service,
     service_object_dict,
 )
-from galaxy.util import unicodify
 from galaxy.util.bytesize import ByteSize
 
 log = logging.getLogger(__name__)
@@ -175,12 +173,8 @@ def queue_job(self, job_wrapper):
             job_wrapper=job_wrapper,
             job_destination=job_wrapper.job_destination,
         )
-        # Kubernetes doesn't really produce meaningful "job stdout", but file needs to be present
-        with open(ajs.output_file, "w"):
-            pass
-        with open(ajs.error_file, "w"):
-            pass
-
+        # Kubernetes doesn't really produce a "job script", but job stream files needs to be present
+        ajs.init_job_stream_files()
         if not self.prepare_job(
             job_wrapper,
             include_metadata=False,
@@ -680,26 +674,6 @@ def __transform_memory_value(self, mem_value):
         """
         return ByteSize(mem_value).value
 
-    def __assemble_k8s_container_image_name(self, job_wrapper):
-        """Assembles the container image name as repo/owner/image:tag, where repo, owner and tag are optional"""
-        job_destination = job_wrapper.job_destination
-
-        # Determine the job's Kubernetes destination (context, namespace) and options from the job destination
-        # definition
-        repo = ""
-        owner = ""
-        if "repo" in job_destination.params:
-            repo = f"{job_destination.params['repo']}/"
-        if "owner" in job_destination.params:
-            owner = f"{job_destination.params['owner']}/"
-
-        k8s_cont_image = repo + owner + job_destination.params["image"]
-
-        if "tag" in job_destination.params:
-            k8s_cont_image += f":{job_destination.params['tag']}"
-
-        return k8s_cont_image
-
     def __get_k8s_container_name(self, job_wrapper):
         # These must follow a specific regex for Kubernetes.
         raw_id = job_wrapper.job_destination.id
@@ -1115,22 +1089,7 @@ def fail_job(self, job_state: "JobState", exception=False, message="Job failed",
         # To ensure that files below are readable, ownership must be reclaimed first
         job_state.job_wrapper.reclaim_ownership()
 
-        # wait for the files to appear
-        which_try = 0
-        while which_try < self.app.config.retry_job_output_collection + 1:
-            try:
-                with open(job_state.output_file, "rb") as stdout_file, open(job_state.error_file, "rb") as stderr_file:
-                    job_stdout = self._job_io_for_db(stdout_file)
-                    job_stderr = self._job_io_for_db(stderr_file)
-                break
-            except Exception as e:
-                if which_try == self.app.config.retry_job_output_collection:
-                    job_stdout = ""
-                    job_stderr = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
-                    log.error(f"{gxy_job.id}/{gxy_job.job_runner_external_id} {job_stderr}: {unicodify(e)}")
-                else:
-                    time.sleep(1)
-                which_try += 1
+        _, job_stdout, job_stderr = self._collect_job_output(gxy_job.id, gxy_job.job_runner_external_id, job_state)
 
         # get stderr and stdout to database
         outputs_directory = os.path.join(job_state.job_wrapper.working_directory, "outputs")

lib/galaxy/jobs/runners/pulsar.py

@@ -210,6 +210,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
     default_build_pulsar_app = False
     use_mq = False
     poll = True
+    client_manager_kwargs: dict[str, Any] = {}
 
     def __init__(self, app, nworkers, **kwds):
         """Start the job runner."""
@@ -240,19 +241,27 @@ def _init_client_manager(self):
             pulsar_conf_file = self.runner_params.get("pulsar_config", None)
         self.__init_pulsar_app(pulsar_conf, pulsar_conf_file)
 
-        client_manager_kwargs = {}
-        for kwd in "manager", "cache", "transport", "persistence_directory":
-            client_manager_kwargs[kwd] = self.runner_params[kwd]
+        client_manager_kwargs = self._pulsar_client_manager_args()
         if self.pulsar_app is not None:
             client_manager_kwargs["pulsar_app"] = self.pulsar_app
-            # TODO: Hack remove this following line pulsar lib update
-            # that includes https://github.com/galaxyproject/pulsar/commit/ce0636a5b64fae52d165bcad77b2caa3f0e9c232
-            client_manager_kwargs["file_cache"] = None
+        self.client_manager = build_client_manager(**client_manager_kwargs)
+
+    def _pulsar_client_manager_args(self):
+        """Most connection parameters can be specified as environment parameters, but...
+
+        ... global parameters about message queues, what Pulsar client to use, etc... must
+        be specified as runner parameters. This method returns a configuration based
+        on the runner parameters that is ready for Pulsar's build_client_manager.
+        """
+        client_manager_kwargs = self.client_manager_kwargs.copy()
+        for kwd in "manager", "cache", "transport", "persistence_directory":
+            client_manager_kwargs[kwd] = self.runner_params[kwd]
 
         for kwd in self.runner_params.keys():
             if kwd.startswith("amqp_") or kwd.startswith("transport_"):
                 client_manager_kwargs[kwd] = self.runner_params[kwd]
-        self.client_manager = build_client_manager(**client_manager_kwargs)
+
+        return client_manager_kwargs
 
     def __init_pulsar_app(self, conf, pulsar_conf_path):
         if conf is None and pulsar_conf_path is None and not self.default_build_pulsar_app:
@@ -1050,45 +1059,57 @@ class PulsarMQJobRunner(PulsarJobRunner):
 COEXECUTION_DESTINATION_DEFAULTS = {
     "default_file_action": "remote_transfer",
     "rewrite_parameters": "true",
-    "jobs_directory": "/pulsar_staging",
     "pulsar_container_image": DEFAULT_PULSAR_CONTAINER,
     "remote_container_handling": True,
     "url": PARAMETER_SPECIFICATION_IGNORED,
     "private_token": PARAMETER_SPECIFICATION_IGNORED,
 }
 
 
-class PulsarCoexecutionJobRunner(PulsarMQJobRunner):
+class PulsarCoexecutionJobRunner(PulsarJobRunner):
     destination_defaults = COEXECUTION_DESTINATION_DEFAULTS
 
-    def _populate_parameter_defaults(self, job_destination):
-        super()._populate_parameter_defaults(job_destination)
-        params = job_destination.params
-        # Set some sensible defaults for Pulsar application that runs in staging container.
-        if "pulsar_app_config" not in params:
-            params["pulsar_app_config"] = {}
-        pulsar_app_config = params["pulsar_app_config"]
-        if "staging_directory" not in pulsar_app_config:
-            # coexecution always uses a fixed path for staging directory
-            pulsar_app_config["staging_directory"] = params.get("jobs_directory")
-
 
 KUBERNETES_DESTINATION_DEFAULTS: dict[str, Any] = {"k8s_enabled": True, **COEXECUTION_DESTINATION_DEFAULTS}
 
+KUBERNETES_CLIENT_MANAGER_KWARGS = {"k8s_enabled": True}
+
 
 class PulsarKubernetesJobRunner(PulsarCoexecutionJobRunner):
     destination_defaults = KUBERNETES_DESTINATION_DEFAULTS
+    use_mq = True
     poll = True  # Poll so we can check API for pod IP for ITs.
+    client_manager_kwargs = KUBERNETES_CLIENT_MANAGER_KWARGS
 
 
 TES_DESTINATION_DEFAULTS: dict[str, Any] = {
     "tes_url": PARAMETER_SPECIFICATION_REQUIRED,
     **COEXECUTION_DESTINATION_DEFAULTS,
 }
 
+TES_CLIENT_MANAGER_KWARGS = {"tes_enabled": True}
+
 
 class PulsarTesJobRunner(PulsarCoexecutionJobRunner):
     destination_defaults = TES_DESTINATION_DEFAULTS
+    client_manager_kwargs = TES_CLIENT_MANAGER_KWARGS
+    use_mq = True
+    poll = False
+
+
+GCP_DESTINATION_DEFAULTS: dict[str, Any] = {
+    "project_id": PARAMETER_SPECIFICATION_REQUIRED,
+    **COEXECUTION_DESTINATION_DEFAULTS,
+}
+GCP_BATCH_CLIENT_MANAGER_KWARGS = {"gcp_batch_enabled": True}
+
+
+class PulsarGcpBatchJobRunner(PulsarCoexecutionJobRunner):
+    use_mq = True
+    poll = False
+
+    client_manager_kwargs = GCP_BATCH_CLIENT_MANAGER_KWARGS
+    destination_defaults = GCP_DESTINATION_DEFAULTS
 
 
 class PulsarRESTJobRunner(PulsarJobRunner):

pyproject.toml

@@ -70,7 +70,7 @@ dependencies = [
     "pebble",
     "pillow",
     "psutil",
-    "pulsar-galaxy-lib>=0.15.0.dev0",
+    "pulsar-galaxy-lib>=0.15.10",
     "pycryptodome",
     "pydantic[email]>=2.7.4",  # https://github.com/pydantic/pydantic/pull/9639
     "PyJWT",