Set Limit To Maximum Concurrent Survey Jobs

common/data_refinery_common/message_queue.py

@@ -32,6 +32,7 @@ def send_job(job_type: Enum, job) -> bool:
     nomad_port = get_env_variable("NOMAD_PORT", "4646")
     nomad_client = nomad.Nomad(nomad_host, port=int(nomad_port), timeout=30)
 
+    is_processor = True
     if job_type is ProcessorPipeline.TRANSCRIPTOME_INDEX_LONG \
        or job_type is ProcessorPipeline.TRANSCRIPTOME_INDEX_SHORT:
         nomad_job = NOMAD_TRANSCRIPTOME_JOB
@@ -60,16 +61,18 @@ def send_job(job_type: Enum, job) -> bool:
     elif job_type is ProcessorPipeline.AGILENT_TWOCOLOR_TO_PCL:
         # Agilent twocolor uses the same job specification as Affy.
         nomad_job = ProcessorPipeline.AFFY_TO_PCL.value
+    elif job_type in list(Downloaders):
+        nomad_job = NOMAD_DOWNLOADER_JOB
+        is_processor = False
+    elif job_type in list(SurveyJobTypes):
+        nomad_job = job_type.value
+        is_processor = False
     elif job_type is Downloaders.NONE:
         logger.warn("Not queuing %s job.", job_type, job_id=job_id)
         raise ValueError(NONE_JOB_ERROR_TEMPLATE.format(job_type.value, "Downloader", job_id))
     elif job_type is ProcessorPipeline.NONE:
         logger.warn("Not queuing %s job.", job_type, job_id=job_id)
         raise ValueError(NONE_JOB_ERROR_TEMPLATE.format(job_type.value, "Processor", job_id))
-    elif job_type in list(Downloaders):
-        nomad_job = NOMAD_DOWNLOADER_JOB
-    elif job_type in list(SurveyJobTypes):
-        nomad_job = job_type.value
     else:
         raise ValueError("Invalid job_type: {}".format(job_type.value))
 
@@ -93,20 +96,27 @@ def send_job(job_type: Enum, job) -> bool:
     elif isinstance(job, SurveyJob):
         nomad_job = nomad_job + "_" + str(job.ram_amount)
 
-    try:
-        nomad_response = nomad_client.job.dispatch_job(nomad_job, meta={"JOB_NAME": job_type.value,
-                                                                        "JOB_ID": str(job.id)})
-        job.nomad_job_id = nomad_response["DispatchedJobID"]
+    # We only want to dispatch processor jobs directly.
+    # Everything else will be handled by the Foreman, which will increment the retry counter.
+    if is_processor:
+        try:
+            nomad_response = nomad_client.job.dispatch_job(nomad_job, meta={"JOB_NAME": job_type.value,
+                                                                            "JOB_ID": str(job.id)})
+            job.nomad_job_id = nomad_response["DispatchedJobID"]
+            job.save()
+            return True
+        except URLNotFoundNomadException:
+            logger.error("Dispatching Nomad job of type %s for job spec %s to host %s and port %s failed.",
+                         job_type, nomad_job, nomad_host, nomad_port, job=str(job.id))
+            return False
+        except Exception as e:
+            logger.exception('Unable to Dispatch Nomad Job.',
+                job_name=job_type.value,
+                job_id=str(job.id),
+                reason=str(e)
+            )
+            raise
+    else:
+        job.num_retries = job.num_retries - 1
         job.save()
-        return True
-    except URLNotFoundNomadException:
-        logger.error("Dispatching Nomad job of type %s for job spec %s to host %s and port %s failed.",
-                     job_type, nomad_job, nomad_host, nomad_port, job=str(job.id))
-        return False
-    except Exception as e:
-        logger.exception('Unable to Dispatch Nomad Job.',
-            job_name=job_type.value,
-            job_id=str(job.id),
-            reason=str(e)
-        )
-        raise
+    return True

foreman/data_refinery_foreman/foreman/main.py

@@ -32,6 +32,9 @@
 # greater than this because of the first attempt
 MAX_NUM_RETRIES = 2
 
+# This can be overritten by the env var "MAX_TOTAL_JOBS"
+DEFAULT_MAX_JOBS = 10000
+
 # The fastest each thread will repeat its checks.
 # Could be slower if the thread takes longer than this to check its jobs.
 MIN_LOOP_TIME = timedelta(minutes=2)
@@ -139,12 +142,34 @@ def requeue_downloader_job(last_job: DownloaderJob) -> None:
 
 def handle_downloader_jobs(jobs: List[DownloaderJob]) -> None:
     """For each job in jobs, either retry it or log it."""
-    for job in jobs:
+
+    nomad_host = get_env_variable("NOMAD_HOST")
+    nomad_port = get_env_variable("NOMAD_PORT", "4646")
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
+    # Maximum number of total jobs running at a time.
+    # We do this now rather than import time for testing purposes.
+    MAX_TOTAL_JOBS = int(get_env_variable_gracefully("MAX_TOTAL_JOBS", DEFAULT_MAX_JOBS))
+    len_all_jobs = len(nomad_client.jobs.get_jobs())
+    if len_all_jobs >= MAX_TOTAL_JOBS:
+        logger.info("Not requeuing job until we're running fewer jobs.")
+        return False
+
+    jobs_dispatched = 0
+    for count, job in enumerate(jobs):
         if job.num_retries < MAX_NUM_RETRIES:
             requeue_downloader_job(job)
+            jobs_dispatched = jobs_dispatched + 1
         else:
             handle_repeated_failure(job)
 
+        if (count % 100) == 0:
+            len_all_jobs = len(nomad_client.jobs.get_jobs())
+
+        if (jobs_dispatched + len_all_jobs) >= MAX_TOTAL_JOBS:
+            logger.info("We hit the maximum total jobs ceiling, so we're not handling any more downloader jobs now.")
+            return False
+
+    return True
 
 @do_forever(MIN_LOOP_TIME)
 def retry_failed_downloader_jobs() -> None:
@@ -166,7 +191,7 @@ def retry_hung_downloader_jobs() -> None:
 
     nomad_host = get_env_variable("NOMAD_HOST")
     nomad_port = get_env_variable("NOMAD_PORT", "4646")
-    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=5)
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
     hung_jobs = []
     for job in potentially_hung_jobs:
         try:
@@ -205,7 +230,7 @@ def retry_lost_downloader_jobs() -> None:
 
     nomad_host = get_env_variable("NOMAD_HOST")
     nomad_port = get_env_variable("NOMAD_PORT", "4646")
-    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=5)
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
     lost_jobs = []
     for job in potentially_lost_jobs:
         try:
@@ -306,12 +331,34 @@ def requeue_processor_job(last_job: ProcessorJob) -> None:
 
 def handle_processor_jobs(jobs: List[ProcessorJob]) -> None:
     """For each job in jobs, either retry it or log it."""
-    for job in jobs:
+
+    nomad_host = get_env_variable("NOMAD_HOST")
+    nomad_port = get_env_variable("NOMAD_PORT", "4646")
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
+    # Maximum number of total jobs running at a time.
+    # We do this now rather than import time for testing purposes.
+    MAX_TOTAL_JOBS = int(get_env_variable_gracefully("MAX_TOTAL_JOBS", DEFAULT_MAX_JOBS))
+    len_all_jobs = len(nomad_client.jobs.get_jobs())
+    if len_all_jobs >= MAX_TOTAL_JOBS:
+        logger.info("Not requeuing job until we're running fewer jobs.")
+        return False
+
+    jobs_dispatched = 0
+    for count, job in enumerate(jobs):
         if job.num_retries < MAX_NUM_RETRIES:
             requeue_processor_job(job)
+            jobs_dispatched = jobs_dispatched + 1
         else:
             handle_repeated_failure(job)
 
+        if (count % 100) == 0:
+            len_all_jobs = len(nomad_client.jobs.get_jobs())
+
+        if (jobs_dispatched + len_all_jobs) >= MAX_TOTAL_JOBS:
+            logger.info("We hit the maximum total jobs ceiling, so we're not handling any more processor jobs now.")
+            return False
+
+    return True
 
 @do_forever(MIN_LOOP_TIME)
 def retry_failed_processor_jobs() -> None:
@@ -338,7 +385,7 @@ def retry_hung_processor_jobs() -> None:
 
     nomad_host = get_env_variable("NOMAD_HOST")
     nomad_port = get_env_variable("NOMAD_PORT", "4646")
-    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=5)
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
     hung_jobs = []
     for job in potentially_hung_jobs:
         try:
@@ -425,6 +472,8 @@ def requeue_survey_job(last_job: SurveyJob) -> None:
     The new survey job will have num_retries one greater than
     last_job.num_retries.
     """
+
+    lost_jobs = []
     num_retries = last_job.num_retries + 1
 
     new_job = SurveyJob(num_retries=num_retries,
@@ -468,20 +517,44 @@ def requeue_survey_job(last_job: SurveyJob) -> None:
         # Can't communicate with nomad just now, leave the job for a later loop.
         new_job.delete()
 
+    return True
+
 
 def handle_survey_jobs(jobs: List[SurveyJob]) -> None:
     """For each job in jobs, either retry it or log it."""
-    for job in jobs:
+
+    nomad_host = get_env_variable("NOMAD_HOST")
+    nomad_port = get_env_variable("NOMAD_PORT", "4646")
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
+    # Maximum number of total jobs running at a time.
+    # We do this now rather than import time for testing purposes.
+    MAX_TOTAL_JOBS = int(get_env_variable_gracefully("MAX_TOTAL_JOBS", DEFAULT_MAX_JOBS))
+    len_all_jobs = len(nomad_client.jobs.get_jobs())
+    if len_all_jobs >= MAX_TOTAL_JOBS:
+        logger.info("Not requeuing job until we're running fewer jobs.")
+        return False
+
+    jobs_dispatched = 0
+    for count, job in enumerate(jobs):
         if job.num_retries < MAX_NUM_RETRIES:
             requeue_survey_job(job)
+            jobs_dispatched = jobs_dispatched + 1
         else:
             handle_repeated_failure(job)
 
+        if (count % 100) == 0:
+            len_all_jobs = len(nomad_client.jobs.get_jobs())
+
+        if (jobs_dispatched + len_all_jobs) >= MAX_TOTAL_JOBS:
+            logger.info("We hit the maximum total jobs ceiling, so we're not handling any more survey jobs now.")
+            return False
+
+    return True
 
 @do_forever(MIN_LOOP_TIME)
 def retry_failed_survey_jobs() -> None:
     """Handle survey jobs that were marked as a failure."""
-    failed_jobs = SurveyJob.objects.filter(success=False, retried=False)
+    failed_jobs = SurveyJob.objects.filter(success=False, retried=False).order_by('pk')
     if failed_jobs:
         logger.info(
             "Handling failed (explicitly-marked-as-failure) jobs!",
@@ -499,11 +572,11 @@ def retry_hung_survey_jobs() -> None:
         end_time=None,
         start_time__isnull=False,
         no_retry=False
-    )
+    ).order_by('pk')
 
     nomad_host = get_env_variable("NOMAD_HOST")
     nomad_port = get_env_variable("NOMAD_PORT", "4646")
-    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=5)
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
     hung_jobs = []
     for job in potentially_hung_jobs:
         try:
@@ -541,12 +614,13 @@ def retry_lost_survey_jobs() -> None:
         start_time=None,
         end_time=None,
         no_retry=False
-    )
+    ).order_by('pk')
 
     nomad_host = get_env_variable("NOMAD_HOST")
     nomad_port = get_env_variable("NOMAD_PORT", "4646")
-    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=5)
+    nomad_client = Nomad(nomad_host, port=int(nomad_port), timeout=30)
     lost_jobs = []
+
     for job in potentially_lost_jobs:
         try:
             # Surveyor jobs didn't always have nomad_job_ids. If they
@@ -583,7 +657,7 @@ def retry_lost_survey_jobs() -> None:
         handle_survey_jobs(lost_jobs)
 
 ##
-# Main loop
+# Janitor
 ##
 
 @do_forever(JANITOR_DISPATCH_TIME)
@@ -610,6 +684,9 @@ def send_janitor_jobs():
             # If we can't dispatch this job, something else has gone wrong.
             continue
 
+##
+# Main loop
+##
 
 def monitor_jobs():
     """Runs a thread for each job monitoring loop."""

foreman/data_refinery_foreman/foreman/test_main.py

@@ -14,7 +14,7 @@
     ProcessorJobOriginalFileAssociation,
     ProcessorJobDatasetAssociation,
 )
-
+from test.support import EnvironmentVarGuard # Python >=3
 
 class ForemanTestCase(TestCase):
     def create_downloader_job(self):
@@ -605,6 +605,20 @@ def test_repeated_survey_failures(self, mock_send_job):
         self.assertEqual(last_job.num_retries, main.MAX_NUM_RETRIES)
         self.assertFalse(last_job.success)
 
+        # MAX TOTAL tests
+        self.env = EnvironmentVarGuard()
+        self.env.set('MAX_TOTAL_JOBS', '0')
+        with self.env:
+            job = self.create_survey_job()
+            result = main.handle_survey_jobs([job])
+            self.assertFalse(result)
+
+        self.env.set('MAX_TOTAL_JOBS', '1000')
+        with self.env:
+            job = self.create_survey_job()
+            result = main.requeue_survey_job(job)
+            self.assertTrue(result)
+
     @patch('data_refinery_foreman.foreman.main.send_job')
     def test_retrying_failed_survey_jobs(self, mock_send_job):
         mock_send_job.return_value = True

foreman/data_refinery_foreman/surveyor/management/commands/surveyor_dispatcher.py

@@ -66,6 +66,9 @@ def queue_surveyor_for_accession(accession: str) -> None:
     """Dispatches a surveyor job for the accession code."""
     # Start at 256MB of RAM for surveyor jobs.
     survey_job = SurveyJob(ram_amount=256)
+    # Survey Jobs will actually be dispatched by the foreman retry logic as capacity allows,
+    # so we set num_retries to -1 for right now.
+    survey_job.num_retries = -1
 
     set_source_type_for_accession(survey_job, accession)
 
@@ -74,11 +77,8 @@ def queue_surveyor_for_accession(accession: str) -> None:
                                        value=accession)
     key_value_pair.save()
 
-    try:
-        send_job(SurveyJobTypes.SURVEYOR, survey_job)
-    except:
-        # If we can't dispatch this, then let the foreman retry it late.
-        pass
+    # We don't actually send the job here, we just create it.
+    # The foreman will pick it up and dispatch it when the time is appropriate.
 
 class Command(BaseCommand):
     def add_arguments(self, parser):

workers/illumina_dependencies.R

@@ -7,7 +7,7 @@ devtools::install_version('data.table', version='1.11.0')
 devtools::install_version('optparse', version='1.4.4')
 devtools::install_version('lazyeval', version='0.2.1')
 devtools::install_version('tidyverse', version='1.2.1')
-devtools::install_version('rlang', version='0.2.2')
+devtools::install_version('rlang', version='0.3.0')
 
 # devtools::install_url() requires BiocInstaller
 install.packages('https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocInstaller_1.28.0.tar.gz')

workers/install_gene_convert.R

@@ -4,7 +4,7 @@ devtools::install_version('data.table', version='1.11.0')
 devtools::install_version('optparse', version='1.4.4')
 
 devtools::install_version('tidyverse', version='1.2.1')
-devtools::install_version('rlang', version='0.2.2')
+devtools::install_version('rlang', version='0.3.0')
 
 # devtools::install_url() requires BiocInstaller
 install.packages('https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocInstaller_1.28.0.tar.gz')