Merge pull request #128 from kbase/dev-service

Download files to NERSC on job submission

cdmtaskservice/app_state.py

@@ -14,6 +14,7 @@
 from fastapi import FastAPI, Request
 from cdmtaskservice import models
 from cdmtaskservice.config import CDMTaskServiceConfig
+from cdmtaskservice.coroutine_manager import CoroutineWrangler
 from cdmtaskservice.image_remote_lookup import DockerImageInfo
 from cdmtaskservice.images import Images
 from cdmtaskservice.jobflows.nersc_jaws import NERSCJAWSRunner
@@ -57,6 +58,7 @@ async def build_app(
     # This method is getting pretty long but it's stupid simple so...
     # May want to parallelize some of this for faster startups. would need to rework prints
     logr = logging.getLogger(__name__)
+    coman = await CoroutineWrangler.create()
     logr.info("Connecting to KBase auth service... ")
     auth = await KBaseAuth.create(
         cfg.auth_url,
@@ -102,7 +104,7 @@ async def build_app(
         runners = {models.Cluster.PERLMUTTER_JAWS: nerscjawsflow}
         imginfo = await DockerImageInfo.create(Path(cfg.crane_path).expanduser().absolute())
         images = Images(mongodao, imginfo)
-        job_submit = JobSubmit(mongodao, s3)
+        job_submit = JobSubmit(mongodao, s3, coman, runners)
         app.state._mongo = mongocli
         app.state._cdmstate = AppState(
             auth, sfapi_client, s3, job_submit, job_state, images, runners

cdmtaskservice/callback_url_paths.py

@@ -0,0 +1,20 @@
+"""
+A module for determining paths for callback URLs for the service.
+"""
+
+
+_CALLBACK = "callback"
+_DOWNLOAD_COMPLETE = "download"
+
+
+def get_download_complete_callback(root_url: str = None, job_id: str = None):
+    """
+    Get a url or path for a service callback to communicate that a download is complete.
+    
+    root_url - prepend the path with the given root url.
+    job_id - suffix the path with a job ID.
+    """
+    cb = [root_url] if root_url else []
+    cb += [_CALLBACK, _DOWNLOAD_COMPLETE]
+    cb += [job_id] if job_id else []
+    return "/".join(cb)

cdmtaskservice/job_submit.py

@@ -3,10 +3,12 @@
 """
 
 import uuid
+from typing import Any
 
 from cdmtaskservice import kb_auth
 from cdmtaskservice import models
 from cdmtaskservice.arg_checkers import not_falsy as _not_falsy
+from cdmtaskservice.coroutine_manager import CoroutineWrangler
 from cdmtaskservice.image_remote_lookup import parse_image_name
 from cdmtaskservice.mongo import MongoDAO
 from cdmtaskservice.s3.client import S3Client
@@ -18,13 +20,23 @@ class JobSubmit:
     A manager for submitting CDM jobs.
     """
 
-    def __init__(self, mongo: MongoDAO, s3client: S3Client):
+    def __init__(
+        self,
+        mongo: MongoDAO,
+        s3client: S3Client,
+        coro_manager: CoroutineWrangler,
+        job_runners: dict[models.Cluster, Any],  # Make abstract class if necessary
+    ):
         """
         mongo - a MongoDB DAO object.
         s3Client - an S3Client pointed at the S3 storage system to use.
+        coro_manager - a coroutine manager.
+        job_runners - a mapping of remote compute cluster to the job runner for that cluster.
         """
         self._s3 = _not_falsy(s3client, "s3client")
         self._mongo = _not_falsy(mongo, "mongo")
+        self._coman = _not_falsy(coro_manager, "coro_manager")
+        self._runners = _not_falsy(job_runners, "job_runners")
 
     async def submit(self, job_input: models.JobInput, user: kb_auth.KBaseUser) -> str:
         """
@@ -76,6 +88,7 @@ async def submit(self, job_input: models.JobInput, user: kb_auth.KBaseUser) -> s
         )
         # TDDO JOBSUBMIT if reference data is required, is it staged?
         await self._mongo.save_job(job)
+        await self._coman.run_coroutine(self._runners[job.job_input.cluster].start_job(job))
         return job_id
 
 

cdmtaskservice/jobflows/nersc_jaws.py

@@ -2,10 +2,15 @@
 Manages running jobs at NERSC using the JAWS system.
 """
 
+import logging
+
+from cdmtaskservice import models
 from cdmtaskservice.arg_checkers import not_falsy as _not_falsy, require_string as _require_string
 from cdmtaskservice.job_state import JobState
 from cdmtaskservice.nersc.manager import NERSCManager
 from cdmtaskservice.s3.client import S3Client
+from cdmtaskservice.s3.paths import S3Paths
+from cdmtaskservice.callback_url_paths import get_download_complete_callback
 
 # Not sure how other flows would work and how much code they might share. For now just make
 # this work and pull it apart / refactor later.
@@ -50,3 +55,45 @@ def __init__(
         self._jtoken = _require_string(jaws_token, "jaws_token")
         self._jgroup = _require_string(jaws_group, "jaws_group")
         self._callback_root = _require_string(service_root_url, "service_root_url")
+
+    async def start_job(self, job: models.Job):
+        """
+        Start running a job. It is expected that the Job has been persisted to the data
+        storage system and is in the created state. It is further assumed that the input files
+        are of the S3File type, not bare strings.
+        """
+        if _not_falsy(job, "job").state != models.JobState.CREATED:
+            raise ValueError("job must be in the created state")
+        logr = logging.getLogger(__name__)
+        # TODO PERF this validates the file paths yet again. Maybe the way to go is just have
+        #           a validate method on S3Paths which can be called or not as needed, with
+        #           a validated state boolean
+        paths = S3Paths([p.file for p in job.job_input.input_files])
+        try:
+            # This is making an S3 call again after the call in job_submit. If that's too expensive
+            # pass in the S3meta as well
+            # TODO PERF config / set concurrency
+            # TODO NOW pass this in to avoid race conditions w/ etags
+            meta = await self._s3.get_object_meta(paths)
+            # TODO RELIABILITY config / set expiration time
+            presigned = await self._s3ext.presign_get_urls(paths)
+            callback_url = get_download_complete_callback(self._callback_root, job.id)
+            # TODO PERF config / set concurrency
+            # TODO PERF CACHING if the same files are used for a different job they're d/ld again
+            #                   Instead d/l to a shared file location by etag or something
+            #                   Need to ensure atomic writes otherwise 2 processes trying to
+            #                   d/l the same file could corrupt it
+            #                   Either make cache in JAWS staging area, in which case files
+            #                   will be deleted automatically by JAWS, or need own file deletion
+            # TODO DISKSPACE will need to clean up job downloads @ NERSC
+            # TODO LOGGING make the remote code log summary of results and upload and store
+            # TODO NOW how get remote paths at next step? 
+            # TODO NOW store task IDs
+            task_id = await self._nman.download_s3_files(
+                job.id, meta, presigned, callback_url, insecure_ssl=self._s3insecure
+            )
+        except Exception as e:
+            # TODO LOGGING figure out how logging it going to work etc.
+            logr.exception(f"Error starting download for job {job.id}")
+            # TODO IMPORTANT ERRORHANDLING update job state to ERROR w/ message and don't raise
+            raise e

cdmtaskservice/nersc/manager.py

@@ -28,6 +28,11 @@
 
 # TODO CLEANUP clean up old code versions @NERSC somehow. Not particularly important
 
+_DT_TARGET = Machine.dtns
+# TDOO NERSCUIPDATE delete the following line when DTN downloads work.
+#       See https://nersc.servicenowservices.com/sp?sys_id=ad33e85f1b5a5610ac81a820f54bcba0&view=sp&id=ticket&table=incident
+_DT_TARGET = Machine.perlmutter
+
 _COMMAND_PATH = "utilities/command"
 
 _MIN_TIMEOUT_SEC = 300
@@ -125,7 +130,7 @@ async def _setup_remote_code(self):
         # TODO RELIABILITY atomically write files. For these small ones probably doesn't matter?
         cli = self._client_provider()
         perlmutter = await cli.compute(Machine.perlmutter)
-        dtns = await cli.compute(Machine.dtns)
+        dt = await cli.compute(_DT_TARGET)
         async with asyncio.TaskGroup() as tg:
             for mod in _CTS_DEPENDENCIES:
                 target = self._nersc_code_path
@@ -142,7 +147,7 @@ async def _setup_remote_code(self):
                 bio=io.BytesIO(_PROCESS_DATA_XFER_MANIFEST.encode()),
                 make_exe=True,
             ))
-            res = tg.create_task(dtns.run('bash -c "echo $SCRATCH"'))
+            res = tg.create_task(dt.run('bash -c "echo $SCRATCH"'))
             if _PIP_DEPENDENCIES:
                 deps = " ".join(
                     # may need to do something else if module doesn't have __version__
@@ -252,9 +257,9 @@ async def _process_manifest(
     ):
         path = self._dtn_scratch / _CTS_SCRATCH_ROOT_DIR / job_id / filename
         cli = self._client_provider()
-        dtn = await cli.compute(Machine.dtns)
+        dt = await cli.compute(_DT_TARGET)
         # TODO CLEANUP manifests after some period of time
-        await self._upload_file_to_nersc(dtn, path, bio=manifest)
+        await self._upload_file_to_nersc(dt, path, bio=manifest)
         command = (
             "bash -c '"
                 + f"export CTS_CODE_LOCATION={self._nersc_code_path}; "
@@ -264,7 +269,7 @@ async def _process_manifest(
                 + f'"$CTS_CODE_LOCATION"/{_PROCESS_DATA_XFER_MANIFEST_FILENAME}'
             + "'"
         )
-        task_id  = (await self._run_command(cli, Machine.dtns, command))["task_id"]
+        task_id  = (await self._run_command(cli, _DT_TARGET, command))["task_id"]
         # TODO LOGGING figure out how to handle logging, see other logging todos
         logging.getLogger(__name__).info(
             f"Created {task_type} task with id {task_id} for job {job_id}")

cdmtaskservice/nersc/remote.py

@@ -30,13 +30,16 @@ def process_data_transfer_manifest(manifest_file_path: str, callback_url: str):
     # TODO TEST add tests for this and its dependency functions, including logging
     # Potential performance improvement could include a shared cross job cache for files
     #    only useful if jobs are reusing the same files, whcih seems def possible
+    # TODO LOGGINNG logging doesn't work
+    # TODO IMPORTANT ERRORHANDLING write an output file that can be read by the CTS
+    #                sfapi tasks only last for 10 minutes after completions
     log = logging.getLogger(__name__)
     try:
         with open(manifest_file_path) as f:
             manifest = json.load(f)
         asyncio.run(s3_pdtm(manifest["file-transfers"]))
     finally:
-        log.info(f"pinging callback url {callback_url}")
+        log.info(f"Pinging callback url {callback_url}")
         ret = requests.get(callback_url)
         if ret.status_code < 200 or ret.status_code > 299:
             log.error(ret.text)

docker-compose.yaml

@@ -11,6 +11,11 @@ services:
       dockerfile: Dockerfile
     ports:
       - 5000:5000
+    #extra_hosts:
+      # TODO DOCKERUPGRADE after upgrading docker switch from host mode
+      # See https://stackoverflow.com/a/43541732/643675
+      #- "host.docker.internal:host-gateway"
+    network_mode: host
     depends_on:
       - mongodb
       - minio
@@ -25,12 +30,19 @@ services:
       # Don't commit your token to github please
       - KBCTS_JAWS_TOKEN=tokengoeshere
       - KBCTS_JAWS_GROUP=kbase
-      - KBCTS_S3_URL=http://minio:9000
+      # TODO DOCKERUPGRADE after upgrading docker switch to host.docker.internal
+      - KBCTS_S3_URL=http://localhost:9002
+      #- KBCTS_S3_URL=http://host.docker.internal:9002
+      # local Minio, only useful if not running jobs on NERSC
+      #- KBCTS_S3_URL=http://minio:9000
       - KBCTS_S3_EXTERNAL_URL=https://ci.berkeley.kbase.us:9000
       - KBCTS_VERIFY_S3_EXTERNAL_URL=false
       - KBCTS_S3_ACCESS_KEY=miniouser
       - KBCTS_S3_ACCESS_SECRET=miniopassword
-      - KBCTS_MONGO_HOST=mongodb://mongodb:27017
+      - KBCTS_S3_ALLOW_INSECURE=true
+      # TODO DOCKERUPGRADE switch back when host mode no longer needed
+      - KBCTS_MONGO_HOST=mongodb://localhost:27017
+      #- KBCTS_MONGO_HOST=mongodb://mongodb:27017
       - KBCTS_MONGO_DB=cdmtaskservice
       # TODO MONGOAUTH need to add a user to the cmdtaskservice db before this works out
       #                of the box.

test/callback_url_paths_test.py

@@ -0,0 +1,7 @@
+# TODO TEST add tests
+
+from cdmtaskservice import callback_url_paths  # @UnusedImport
+
+
+def test_noop():
+    pass