Merge pull request #197 from populationgenomics/pool-name

Allow to select a pool for a job through a label

batch/batch/driver/instance_collection/pool.py

@@ -109,6 +109,7 @@ def __init__(
         self.data_disk_size_gb = config.data_disk_size_gb
         self.data_disk_size_standing_gb = config.data_disk_size_standing_gb
         self.preemptible = config.preemptible
+        self.label = config.label
 
     @property
     def local_ssd_data_disk(self) -> bool:
@@ -130,6 +131,7 @@ def config(self):
             'max_instances': self.max_instances,
             'max_live_instances': self.max_live_instances,
             'preemptible': self.preemptible,
+            'label': self.label,
         }
 
     def configure(self, pool_config: PoolConfig):
@@ -148,6 +150,7 @@ def configure(self, pool_config: PoolConfig):
         self.max_instances = pool_config.max_instances
         self.max_live_instances = pool_config.max_live_instances
         self.preemptible = pool_config.preemptible
+        self.label = pool_config.label
 
     def adjust_for_remove_instance(self, instance):
         super().adjust_for_remove_instance(instance)

batch/batch/driver/main.py

@@ -485,6 +485,8 @@ async def pool_config_update(request, userdata):  # pylint: disable=unused-argum
             session, 'Max live instances', post['max_live_instances'], lambda v: v > 0, 'a positive integer'
         )
 
+        label = post['label']
+
         enable_standing_worker = 'enable_standing_worker' in post
 
         possible_worker_cores = []
@@ -537,6 +539,7 @@ async def pool_config_update(request, userdata):  # pylint: disable=unused-argum
             max_instances,
             max_live_instances,
             pool.preemptible,
+            label,
         )
         await pool_config.update_database(db)
         pool.configure(pool_config)

batch/batch/driver/templates/pool.html

@@ -31,6 +31,7 @@ <h2>Configuration</h2>
     <div>Standing worker cores: <input name="standing_worker_cores" value="{{ pool.standing_worker_cores }}" /></div>
     <div>Max instances: <input name="max_instances" value="{{ pool.max_instances }}" /></div>
     <div>Max live instances: <input name="max_live_instances" value="{{ pool.max_live_instances }}" /></div>
+    <div>Label: <input name="label" value="{{ pool.label }}" /></div>
     <input type="hidden" name="_csrf" value="{{ csrf_token }}"/>
     <button>
       Update

batch/batch/front_end/front_end.py

@@ -886,6 +886,7 @@ async def _create_jobs(userdata: dict, job_specs: dict, batch_id: int, app: aioh
 
                 worker_type = None
                 machine_type = resources.get('machine_type')
+                pool_label = resources.get('pool_label') or ''
                 preemptible = resources.get('preemptible', BATCH_JOB_DEFAULT_PREEMPTIBLE)
 
                 if machine_type and machine_type not in valid_machine_types(cloud):
@@ -894,6 +895,9 @@ async def _create_jobs(userdata: dict, job_specs: dict, batch_id: int, app: aioh
                 if machine_type and ('cpu' in resources or 'memory' in resources):
                     raise web.HTTPBadRequest(reason='cannot specify cpu and memory with machine_type')
 
+                if machine_type and pool_label:
+                    raise web.HTTPBadRequest(reason='cannot specify pool label with machine_type')
+
                 if spec['process']['type'] == 'jvm':
                     jvm_requested_cpu = parse_cpu_in_mcpu(resources.get('cpu', BATCH_JOB_DEFAULT_CPU))
                     if 'cpu' in resources and jvm_requested_cpu not in (1000, 8000):
@@ -961,7 +965,7 @@ async def _create_jobs(userdata: dict, job_specs: dict, batch_id: int, app: aioh
                 inst_coll_configs: InstanceCollectionConfigs = app['inst_coll_configs']
 
                 result, exc = inst_coll_configs.select_inst_coll(
-                    cloud, machine_type, preemptible, worker_type, req_cores_mcpu, req_memory_bytes, req_storage_bytes
+                    cloud, machine_type, pool_label, preemptible, worker_type, req_cores_mcpu, req_memory_bytes, req_storage_bytes
                 )
 
                 if exc:

batch/batch/front_end/validate.py

@@ -86,6 +86,7 @@
                 'cpu': regex(CPU_REGEXPAT, CPU_REGEX),
                 'storage': regex(STORAGE_REGEXPAT, STORAGE_REGEX),
                 'machine_type': str_type,
+                'pool_label': str_type,
                 'preemptible': bool_type,
             }
         ),

batch/batch/inst_coll_config.py

@@ -78,6 +78,7 @@ def from_record(record):
             max_instances=record['max_instances'],
             max_live_instances=record['max_live_instances'],
             preemptible=bool(record['preemptible']),
+            label=record['label'],
         )
 
     async def update_database(self, db: Database):
@@ -93,7 +94,8 @@ async def update_database(self, db: Database):
     boot_disk_size_gb = %s,
     max_instances = %s,
     max_live_instances = %s,
-    preemptible = %s
+    preemptible = %s,
+    label = %s
 WHERE pools.name = %s;
 ''',
             (
@@ -106,6 +108,7 @@ async def update_database(self, db: Database):
                 self.max_instances,
                 self.max_live_instances,
                 self.preemptible,
+                self.label,
                 self.name,
             ),
         )
@@ -124,6 +127,7 @@ def __init__(
         max_instances: int,
         max_live_instances: int,
         preemptible: bool,
+        label: str,
     ):
         self.name = name
         self.cloud = cloud
@@ -137,6 +141,7 @@ def __init__(
         self.max_instances = max_instances
         self.max_live_instances = max_live_instances
         self.preemptible = preemptible
+        self.label = label
 
     def instance_config(self, product_versions: ProductVersions, location: str) -> InstanceConfig:
         return instance_config_from_pool_config(self, product_versions, location)
@@ -273,13 +278,13 @@ async def refresh(self, db: Database):
         self.resource_rates = resource_rates
         self.product_versions.update(product_versions_data)
 
-    def select_pool_from_cost(self, cloud, cores_mcpu, memory_bytes, storage_bytes, preemptible):
+    def select_pool_from_cost(self, cloud, pool_label, cores_mcpu, memory_bytes, storage_bytes, preemptible):
         assert self.resource_rates is not None
 
         optimal_result = None
         optimal_cost = None
         for pool in self.name_pool_config.values():
-            if pool.cloud != cloud or pool.preemptible != preemptible:
+            if pool.cloud != cloud or pool.preemptible != preemptible or pool.label != pool_label:
                 continue
 
             result = pool.convert_requests_to_resources(cores_mcpu, memory_bytes, storage_bytes)
@@ -304,9 +309,9 @@ def select_pool_from_cost(self, cloud, cores_mcpu, memory_bytes, storage_bytes,
                     optimal_result = (pool.name, maybe_cores_mcpu, maybe_memory_bytes, maybe_storage_gib)
         return optimal_result
 
-    def select_pool_from_worker_type(self, cloud, worker_type, cores_mcpu, memory_bytes, storage_bytes, preemptible):
+    def select_pool_from_worker_type(self, cloud, pool_label, worker_type, cores_mcpu, memory_bytes, storage_bytes, preemptible):
         for pool in self.name_pool_config.values():
-            if pool.cloud == cloud and pool.worker_type == worker_type and pool.preemptible == preemptible:
+            if pool.cloud == cloud and pool.worker_type == worker_type and pool.preemptible == preemptible and pool.label == pool_label:
                 result = pool.convert_requests_to_resources(cores_mcpu, memory_bytes, storage_bytes)
                 if result:
                     actual_cores_mcpu, actual_memory_bytes, acutal_storage_gib = result
@@ -319,11 +324,12 @@ def select_job_private(self, cloud, machine_type, storage_bytes):
         return self.jpim_config.convert_requests_to_resources(machine_type, storage_bytes)
 
     def select_inst_coll(
-        self, cloud, machine_type, preemptible, worker_type, req_cores_mcpu, req_memory_bytes, req_storage_bytes
+        self, cloud, machine_type, pool_label, preemptible, worker_type, req_cores_mcpu, req_memory_bytes, req_storage_bytes
     ):
         if worker_type is not None and machine_type is None:
             result = self.select_pool_from_worker_type(
                 cloud=cloud,
+                pool_label=pool_label,
                 worker_type=worker_type,
                 cores_mcpu=req_cores_mcpu,
                 memory_bytes=req_memory_bytes,
@@ -333,6 +339,7 @@ def select_inst_coll(
         elif worker_type is None and machine_type is None:
             result = self.select_pool_from_cost(
                 cloud=cloud,
+                pool_label=pool_label,
                 cores_mcpu=req_cores_mcpu,
                 memory_bytes=req_memory_bytes,
                 storage_bytes=req_storage_bytes,

batch/sql/add-pool-label.sql

@@ -0,0 +1 @@
+ALTER TABLE `pools` ADD `label` VARCHAR(100) NOT NULL;

batch/sql/add-seqr-pools.sql

@@ -0,0 +1,43 @@
+-- Adds dedicated pools for the seqr loading pipeline, with the 'seqr' pool label.
+
+INSERT INTO inst_colls (`name`, `is_pool`, `boot_disk_size_gb`, `max_instances`, `max_live_instances`, `cloud`)
+SELECT 'seqr-standard', 1, boot_disk_size_gb, max_instances, max_live_instances, cloud
+FROM inst_colls
+WHERE name = 'standard';
+
+INSERT INTO inst_colls (`name`, `is_pool`, `boot_disk_size_gb`, `max_instances`, `max_live_instances`, `cloud`)
+SELECT 'seqr-highmem', 1, boot_disk_size_gb, max_instances, max_live_instances, cloud
+FROM inst_colls
+WHERE name = 'highmem';
+
+INSERT INTO inst_colls (`name`, `is_pool`, `boot_disk_size_gb`, `max_instances`, `max_live_instances`, `cloud`)
+SELECT 'seqr-highcpu', 1, boot_disk_size_gb, max_instances, max_live_instances, cloud
+FROM inst_colls
+WHERE name = 'highcpu';
+
+INSERT INTO pools (`name`, `worker_type`, `worker_cores`, `worker_local_ssd_data_disk`,
+  `worker_external_ssd_data_disk_size_gb`, `enable_standing_worker`, `standing_worker_cores`,
+  `preemptible`, `label`)
+SELECT 'seqr-standard', worker_type, worker_cores, worker_local_ssd_data_disk,
+  worker_external_ssd_data_disk_size_gb, FALSE, standing_worker_cores,
+  TRUE, 'seqr'
+FROM pools
+WHERE name = 'standard';
+
+INSERT INTO pools (`name`, `worker_type`, `worker_cores`, `worker_local_ssd_data_disk`,
+  `worker_external_ssd_data_disk_size_gb`, `enable_standing_worker`, `standing_worker_cores`,
+  `preemptible`, `label`)
+SELECT 'seqr-highmem', worker_type, worker_cores, worker_local_ssd_data_disk,
+  worker_external_ssd_data_disk_size_gb, FALSE, standing_worker_cores,
+  TRUE, 'seqr'
+FROM pools
+WHERE name = 'highmem';
+
+INSERT INTO pools (`name`, `worker_type`, `worker_cores`, `worker_local_ssd_data_disk`,
+  `worker_external_ssd_data_disk_size_gb`, `enable_standing_worker`, `standing_worker_cores`,
+  `preemptible`, `label`)
+SELECT 'seqr-highcpu', worker_type, worker_cores, worker_local_ssd_data_disk,
+  worker_external_ssd_data_disk_size_gb, FALSE, standing_worker_cores,
+  TRUE, 'seqr'
+FROM pools
+WHERE name = 'highcpu';

build.yaml

@@ -2003,6 +2003,8 @@ steps:
         script: /io/sql/kill-mjc-deadlocks.sql
       - name: add-nonpreemptible-pools
         script: /io/sql/add-nonpreemptible-pools.sql
+      - name: add-pool-label
+        script: /io/sql/add-pool-label.sql
     inputs:
       - from: /repo/batch/sql
         to: /io/sql

hail/python/hailtop/batch/backend.py

@@ -657,6 +657,8 @@ async def compile_job(job):
                 resources['storage'] = job._storage
             if job._machine_type:
                 resources['machine_type'] = job._machine_type
+            if job._pool_label:
+                resources['pool_label'] = job._pool_label
             if job._preemptible is not None:
                 resources['preemptible'] = job._preemptible
 

hail/python/hailtop/batch/job.py

@@ -79,6 +79,7 @@ def __init__(self,
         self._always_run: bool = False
         self._preemptible: Optional[bool] = None
         self._machine_type: Optional[str] = None
+        self._pool_label: Optional[str] = None
         self._timeout: Optional[Union[int, float]] = None
         self._cloudfuse: List[Tuple[str, str, bool]] = []
         self._env: Dict[str, str] = {}