merge changes from main

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3-slim
+FROM python:3.10-slim
 
 WORKDIR /balsam
 

balsam/__init__.py

@@ -1,4 +1,4 @@
 from balsam.util import config_root_logger
 
-__version__ = "0.7.0.a21"
+__version__ = "0.7.0.a22"
 config_root_logger()

balsam/_api/bases.py

@@ -370,6 +370,7 @@ def acquire_jobs(
         max_nodes_per_job: Optional[int] = None,
         max_aggregate_nodes: Optional[float] = None,
         serial_only: bool = False,
+        sort_by: Optional[str] = None,
         filter_tags: Optional[Dict[str, str]] = None,
         states: Set[JobState] = RUNNABLE_STATES,
         app_ids: Optional[Set[int]] = None,
@@ -385,6 +386,7 @@ def acquire_jobs(
             max_nodes_per_job=max_nodes_per_job,
             max_aggregate_nodes=max_aggregate_nodes,
             serial_only=serial_only,
+            sort_by=sort_by,
             filter_tags=filter_tags,
             states=states,
             app_ids=app_ids,

balsam/_api/manager.py

@@ -10,7 +10,7 @@
 if TYPE_CHECKING:
     from balsam.client import RESTClient
 
-FILTER_CHUNK_SIZE = 512
+FILTER_CHUNK_SIZE = 500
 
 logger = logging.getLogger(__name__)
 T = TypeVar("T", bound=BalsamModel)

balsam/_api/model.py

@@ -186,7 +186,7 @@ def __repr__(self) -> str:
 
     def __str__(self) -> str:
         d = self.display_dict()
-        return yaml.dump(d, sort_keys=False, indent=4)  # type: ignore
+        return yaml.dump(d, sort_keys=False, indent=4)
 
     def __eq__(self, other: Any) -> bool:
         if not isinstance(other, BalsamModel):

balsam/_api/models.py

@@ -1,5 +1,5 @@
-# This file was auto-generated via /Users/turam/opt/miniconda3/bin/python balsam/schemas/api_generator.py
-# [git rev ce4bdce]
+# This file was auto-generated via /home/turam/miniconda3/bin/python balsam/schemas/api_generator.py
+# [git rev 7634992]
 # Do *not* make changes to the API by changing this file!
 
 import datetime
@@ -765,7 +765,7 @@ class BatchJob(balsam._api.bases.BatchJobBase):
     job_mode = Field[balsam.schemas.batchjob.JobMode]()
     optional_params = Field[typing.Dict[str, str]]()
     filter_tags = Field[typing.Dict[str, str]]()
-    partitions = Field[typing.Optional[typing.List[balsam.schemas.batchjob.BatchJobPartition]]]()
+    partitions = Field[Optional[typing.Union[typing.List[balsam.schemas.batchjob.BatchJobPartition], None]]]()
     site_id = Field[int]()
     project = Field[str]()
     queue = Field[str]()
@@ -786,7 +786,7 @@ def __init__(
         queue: str,
         optional_params: Optional[typing.Dict[str, str]] = None,
         filter_tags: Optional[typing.Dict[str, str]] = None,
-        partitions: Optional[typing.Optional[typing.List[balsam.schemas.batchjob.BatchJobPartition]]] = None,
+        partitions: Optional[typing.Union[typing.List[balsam.schemas.batchjob.BatchJobPartition], None]] = None,
         **kwargs: Any,
     ) -> None:
         """
@@ -918,7 +918,7 @@ def create(
         queue: str,
         optional_params: Optional[typing.Dict[str, str]] = None,
         filter_tags: Optional[typing.Dict[str, str]] = None,
-        partitions: Optional[typing.Optional[typing.List[balsam.schemas.batchjob.BatchJobPartition]]] = None,
+        partitions: Optional[typing.Union[typing.List[balsam.schemas.batchjob.BatchJobPartition], None]] = None,
     ) -> BatchJob:
         """
         Create a new BatchJob object and save it to the API in one step.

balsam/cmdline/app.py

@@ -45,20 +45,72 @@ def ls(site_selector: str, verbose: bool) -> None:
 
 
 @app.command()
-@click.option("-n", "--name", required=True)
+@click.option("-n", "--name", "name_selector", default=None)
 @click.option("-s", "--site", "site_selector", default="")
-def rm(site_selector: str, name: str) -> None:
+@click.option("-a", "--all", is_flag=True, default=False)
+def rm(site_selector: str, name_selector: str, all: bool) -> None:
+    """
+    Remove Apps
+
+    1) Remove named app
+
+        balsam app rm -n hello_world
+
+    1) Remove all apps across a site
+
+        balsam app rm --all --site=123,my_site_folder
+
+    2) Filter apps by specific site IDs or Path fragments
+
+        balsam app rm -n hello_world --site=123,my_site_folder
+
+    """
     client = ClientSettings.load_from_file().build_client()
     qs = client.App.objects.all()
     qs = filter_by_sites(qs, site_selector)
 
-    resolved_app = qs.get(name=name)
-    resolved_id = resolved_app.id
-    appstr = f"App(id={resolved_id}, name={resolved_app.name})"
-    job_count = client.Job.objects.filter(app_id=resolved_id).count()
-    if job_count == 0:
-        resolved_app.delete()
-        click.echo(f"Deleted {appstr}: there were no associated jobs.")
-    elif click.confirm(f"Really Delete {appstr}?? There are {job_count} Jobs that will be ERASED!"):
-        resolved_app.delete()
-        click.echo(f"Deleted App {resolved_id} ({name})")
+    if all and name_selector is not None:
+        raise click.BadParameter("Specify app name or --all, but not both")
+    elif not all and name_selector is None:
+        raise click.BadParameter("Specify app name with -n or specify --all")
+    else:
+        app_list = []
+
+        if all and site_selector == "":
+            raise click.BadParameter("balsam app rm --all requires that you specify --site to remove jobs")
+        elif all and site_selector != "":
+            click.echo("THIS WILL DELETE ALL APPS IN SITE! CAUTION!")
+            app_list = [a.name for a in list(qs)]
+            num_apps = 0
+            num_jobs = 0
+        elif name_selector is not None:
+            app_list = [name_selector]
+
+        if len(app_list) > 0:
+            for name in app_list:
+                resolved_app = qs.get(name=name)
+                resolved_id = resolved_app.id
+                job_count = client.Job.objects.filter(app_id=resolved_id).count()
+
+                if name_selector is not None:
+                    appstr = f"App(id={resolved_id}, name={resolved_app.name}, site={resolved_app.site_id})"
+                    if job_count == 0:
+                        resolved_app.delete()
+                        click.echo(f"Deleted {appstr}: there were no associated jobs.")
+                    elif click.confirm(f"Really Delete {appstr}?? There are {job_count} Jobs that will be ERASED!"):
+                        resolved_app.delete()
+                        click.echo(f"Deleted App {resolved_id} ({name})")
+                else:
+                    num_apps += 1
+                    num_jobs += job_count
+
+            if all:
+                if click.confirm(
+                    f"Really DELETE {num_apps} apps and {num_jobs} jobs from site {site_selector}?? They will be ERASED!"
+                ):
+                    for name in app_list:
+                        resolved_app = qs.get(name=name)
+                        resolved_app.delete()
+                    click.echo(f"Deleted {num_apps} apps and {num_jobs} jobs from site {site_selector}")
+        else:
+            click.echo("Found no apps to Delete")

balsam/cmdline/job.py

@@ -315,8 +315,9 @@ def ls(
 
 @job.command()
 @click.option("-i", "--id", "job_ids", multiple=True, type=int)
+@click.option("-t", "--tag", "tags", multiple=True, type=str, callback=validate_tags)
 @click.option("-s", "--state", "state", type=str)
-def modify(job_ids: List[int], state: JobState) -> None:
+def modify(job_ids: List[int], tags: List[str], state: JobState) -> None:
     """
     Modify Jobs
 
@@ -328,6 +329,8 @@ def modify(job_ids: List[int], state: JobState) -> None:
     jobs = client.Job.objects.all()
     if job_ids:
         jobs = jobs.filter(id=job_ids)
+    elif tags:
+        jobs = jobs.filter(tags=tags)
     else:
         raise click.BadParameter("Provide either list of Job ids or tags to delete")
     count = jobs.count()

balsam/cmdline/scheduler.py

@@ -84,9 +84,12 @@ def submit(
 
 
 @queue.command()
+@click.option("-n", "--num", default=0, type=int)
 @click.option("-h", "--history", is_flag=True, default=False)
+@click.option("-v", "--verbose", is_flag=True, default=False)
 @click.option("--site", "site_selector", default="")
-def ls(history: bool, site_selector: str) -> None:
+@click.option("--scheduler_id", "scheduler_id", type=int, default=None)
+def ls(history: bool, verbose: bool, num: int, site_selector: str, scheduler_id: int) -> None:
     """
     List BatchJobs
 
@@ -97,49 +100,72 @@ def ls(history: bool, site_selector: str) -> None:
     2) View historical BatchJobs at all sites
 
         balsam queue ls --history --site all
+
+    3) View verbose record for BatchJob with scheduler id
+
+        balsam queue ls --scheduler_id 12345 -v
+
+    4) View the last n BatchJobs
+
+        balsam queue ls --num n
+
     """
     client = load_client()
     BatchJob = client.BatchJob
     qs = filter_by_sites(BatchJob.objects.all(), site_selector)
-    if not history:
+
+    if not history and scheduler_id is None and num == 0:
         qs = qs.filter(state=["pending_submission", "queued", "running", "pending_deletion"])
+        if len(qs) == 0:
+            click.echo("No active batch jobs.  Use --history option to list completed batch jobs.")
+
+    if scheduler_id is not None:
+        qs = qs.filter(scheduler_id=scheduler_id)
 
     jobs = [j.display_dict() for j in qs]
-    sites = {site.id: site for site in client.Site.objects.all()}
-    for job in jobs:
-        site = sites[job["site_id"]]
-        path_str = site.path.as_posix()
-        if len(path_str) > 27:
-            path_str = "..." + path_str[-27:]
-        job["site"] = f"{site.name}"
-
-    fields = [
-        "id",
-        "site",
-        "scheduler_id",
-        "state",
-        "filter_tags",
-        "project",
-        "queue",
-        "num_nodes",
-        "wall_time_min",
-        "job_mode",
-    ]
-    rows = [[str(j[field]) for field in fields] for j in jobs]
-
-    col_widths = [len(f) for f in fields]
-    for row in rows:
-        for col_idx, width in enumerate(col_widths):
-            col_widths[col_idx] = max(width, len(row[col_idx]))
-
-    for i, field in enumerate(fields):
-        fields[i] = field.rjust(col_widths[i] + 1)
-
-    print(*fields)
-    for row in rows:
-        for i, col in enumerate(row):
-            row[i] = col.rjust(col_widths[i] + 1)
-        print(*row)
+    if not history and num > 0 and scheduler_id is None:
+        click.echo(f"Displaying records for last {num} Batch Jobs")
+        jobs = jobs[-num:]
+
+    if verbose:
+        for j in jobs:
+            click.echo(j)
+    else:
+        sites = {site.id: site for site in client.Site.objects.all()}
+        for job in jobs:
+            site = sites[job["site_id"]]
+            path_str = site.path.as_posix()
+            if len(path_str) > 27:
+                path_str = "..." + path_str[-27:]
+            job["site"] = f"{site.name}"
+
+        fields = [
+            "id",
+            "site",
+            "scheduler_id",
+            "state",
+            "filter_tags",
+            "project",
+            "queue",
+            "num_nodes",
+            "wall_time_min",
+            "job_mode",
+        ]
+        rows = [[str(j[field]) for field in fields] for j in jobs]
+
+        col_widths = [len(f) for f in fields]
+        for row in rows:
+            for col_idx, width in enumerate(col_widths):
+                col_widths[col_idx] = max(width, len(row[col_idx]))
+
+        for i, field in enumerate(fields):
+            fields[i] = field.rjust(col_widths[i] + 1)
+
+        print(*fields)
+        for row in rows:
+            for i, col in enumerate(row):
+                row[i] = col.rjust(col_widths[i] + 1)
+            print(*row)
 
 
 @queue.command()

balsam/cmdline/site.py

@@ -1,3 +1,4 @@
+import os
 import shutil
 import socket
 import sys
@@ -128,23 +129,40 @@ def mv(src: Union[Path, str], dest: Union[Path, str]) -> None:
 
 
 @site.command()
-@click.argument("path", type=click.Path(exists=True, file_okay=False))
-def rm(path: Union[str, Path]) -> None:
+# @click.argument("path", type=click.Path(exists=True, file_okay=False))
+@click.argument("path", type=click.Path())
+@click.option("-f", "--force", is_flag=True, default=False)
+def rm(path: str, force: bool) -> None:
     """
     Remove a balsam site
 
     balsam site rm /path/to/site
     """
-    cf = SiteConfig(path)
-    client = cf.client
-    site = client.Site.objects.get(id=cf.site_id)
-    jobcount = client.Job.objects.filter(site_id=site.id).count()
-    warning = f"This will wipe out {jobcount} jobs inside!" if jobcount else ""
-
-    if click.confirm(f"Do you really want to destroy {Path(path).name}? {warning}"):
-        site.delete()
-        shutil.rmtree(path)
-        click.echo(f"Deleted site {path}")
+    if not force:
+        if os.path.exists(path):
+            cf = SiteConfig(path)
+            client = cf.client
+            site = client.Site.objects.get(id=cf.site_id)
+            jobcount = client.Job.objects.filter(site_id=site.id).count()
+            warning = f"This will wipe out {jobcount} jobs inside!" if jobcount else ""
+
+            if click.confirm(f"Do you really want to destroy {Path(path).name}? {warning}"):
+                site.delete()
+                shutil.rmtree(path)
+                click.echo(f"Deleted site {path}")
+        else:
+            raise click.BadParameter("Path doesn't exist")
+    else:
+        client = ClientSettings.load_from_file().build_client()
+        qs = client.Site.objects.all()
+        qs = qs.filter(path=path)
+        if len(qs) > 1:
+            raise click.BadParameter(f"Path found in {len(qs)} sites")
+        else:
+            site_id = qs[0].id
+            site = client.Site.objects.get(id=site_id)
+            site.delete()
+            click.echo("Forced site deletion; check for path to clean up")
 
 
 @site.command()

balsam/config/config.py

@@ -193,6 +193,7 @@ class LauncherSettings(BaseSettings):
     local_app_launcher: Type[AppRun] = Field("balsam.platform.app_run.LocalAppRun")
     mpirun_allows_node_packing: bool = False
     serial_mode_prefetch_per_rank: int = 64
+    sort_by: Optional[str] = None
     serial_mode_startup_params: Dict[str, str] = {"cpu_affinity": "none"}
 
     @validator("compute_node", pre=True, always=True)
@@ -235,13 +236,10 @@ def save(self, path: Union[str, Path]) -> None:
             fp.write(self.dump_yaml())
 
     def dump_yaml(self) -> str:
-        return cast(
-            str,
-            yaml.dump(
-                json.loads(self.json()),
-                sort_keys=False,
-                indent=4,
-            ),
+        return yaml.dump(
+            json.loads(self.json()),
+            sort_keys=False,
+            indent=4,
         )
 
     @classmethod