Merge pull request #149 from kbase/dev-service

Remove scratch sharing and JAWS --quiet flag

Author: MrCreosote

cdmtaskservice/app_state.py

@@ -74,7 +74,6 @@ async def build_app(
     nerscman = await NERSCManager.create(
         sfapi_client.get_client,
         Path(cfg.nersc_remote_code_dir) / VERSION,
-        cfg.nersc_file_group,
         cfg.jaws_token,
         cfg.jaws_group,
     )

cdmtaskservice/config.py

@@ -32,7 +32,6 @@ class CDMTaskServiceConfig:
         as the remaining lines.
     sfapi_user: str - the user name of the user accociated with the credentials.
     nersc_remote_code_dir: str - the location at NERSC to upload remote code.
-    nersc_file_group: str - the NERSC group with which downloaded files must be shared. 
     jaws_token: str - the JAWS token used to run jobs.
     jaws_group: str - the JAWS group used to run jobs.
     s3_url: str - the URL of the S3 instance to use for data storage.
@@ -79,7 +78,6 @@ def __init__(self, config_file: BinaryIO):
         self.sfapi_cred_path = _get_string_required(config, _SEC_NERSC, "sfapi_cred_path")
         self.sfapi_user = _get_string_required(config, _SEC_NERSC, "sfapi_user")
         self.nersc_remote_code_dir = _get_string_required(config, _SEC_NERSC, "remote_code_dir")
-        self.nersc_file_group = _get_string_required(config, _SEC_NERSC, "file_group")
         self.jaws_token = _get_string_required(config, _SEC_JAWS, "token")
         self.jaws_group = _get_string_required(config, _SEC_JAWS, "group")
         self.s3_url = _get_string_required(config, _SEC_S3, "url")
@@ -118,7 +116,6 @@ def print_config(self, output: TextIO):
             f"NERSC client credential path: {self.sfapi_cred_path}",
             f"NERSC client user: {self.sfapi_user}",
             f"NERSC remote code dir: {self.nersc_remote_code_dir}",
-            f"NERSC file group: {self.nersc_file_group}",
             "JAWS token: REDACTED FOR THE NATIONAL SECURITY OF GONDWANALAND",
             f"JAWS group: {self.jaws_group}",
             f"S3 URL: {self.s3_url}",

cdmtaskservice/nersc/manager.py

@@ -62,7 +62,7 @@
 module use /global/cfs/projectdirs/kbase/jaws/modulefiles
 module load jaws
 export JAWS_USER_CONFIG=~/{_JAWS_CONF_FILENAME}
-jaws submit --quiet --tag {{job_id}} {{wdlpath}} {{inputjsonpath}} {{site}}
+jaws submit --tag {{job_id}} {{wdlpath}} {{inputjsonpath}} {{site}}
 """
 _JAWS_SITE_PERLMUTTER = "kbase"  # add lawrencium later, maybe
 _JAWS_INPUT_WDL = "input.wdl"
@@ -127,7 +127,6 @@ async def create(
         cls,
         client_provider: Callable[[], AsyncClient],
         nersc_code_path: Path,
-        file_group: str,
         jaws_token: str,
         jaws_group: str,
     ) -> Self:
@@ -138,13 +137,11 @@ async def create(
             the user associated with the client does not change.
         nersc_code_path - the path in which to store remote code at NERSC. It is advised to
             include version information in the path to avoid code conflicts.
-        file_group - the group with which to share downloaded files at NERSC.
         jaws_token - a token for the JGI JAWS system.
         jaws_group - the group to use for running JAWS jobs.
         """
         nm = NERSCManager(client_provider, nersc_code_path)
         await nm._setup_remote_code(
-            _require_string(file_group, "file_group"),
             _require_string(jaws_token, "jaws_token"),
             _require_string(jaws_group, "jaws_group"),
         )
@@ -165,7 +162,7 @@ def _check_path(self, path: Path, name: str):
             raise ValueError(f"{name} must be absolute to the NERSC root dir")
         return path
 
-    async def _setup_remote_code(self, file_group: str, jaws_token: str, jaws_group: str):
+    async def _setup_remote_code(self, jaws_token: str, jaws_group: str):
         # TODO RELIABILITY atomically write files. For these small ones probably doesn't matter?
         cli = self._client_provider()
         perlmutter = await cli.compute(Machine.perlmutter)
@@ -195,7 +192,7 @@ async def _setup_remote_code(self, file_group: str, jaws_token: str, jaws_group:
                 chmod = "600"
             ))
             pm_scratch = tg.create_task(perlmutter.run("echo $SCRATCH"))
-            dtn_scratch = tg.create_task(self._set_up_dtn_scratch(cli, file_group))
+            dtn_scratch = tg.create_task(self._set_up_dtn_scratch(cli))
             if _PIP_DEPENDENCIES:
                 deps = " ".join(
                     # may need to do something else if module doesn't have __version__
@@ -215,16 +212,13 @@ async def _setup_remote_code(self, file_group: str, jaws_token: str, jaws_group:
             f"NERSC perlmutter scratch path: {self._perlmutter_scratch}"
         )
 
-    async def _set_up_dtn_scratch(self, client: AsyncClient, file_group: str) -> Path:
+    async def _set_up_dtn_scratch(self, client: AsyncClient) -> Path:
         dt = await client.compute(_DT_TARGET)
         scratch = await dt.run(f"{_DT_WORKAROUND}; echo $SCRATCH")
         scratch = scratch.strip()
         if not scratch:
             raise ValueError("Unable to determine $SCRATCH variable for NERSC dtns")
         logging.getLogger(__name__).info(f"NERSC DTN scratch path: {scratch}")
-        await dt.run(
-            f"{_DT_WORKAROUND}; set -e; chgrp {file_group} {scratch}; chmod g+rsx {scratch}"
-        )
         return Path(scratch)
 
     async def _run_command(self, client: AsyncClient, machine: Machine, exe: str):

cdmtaskservice_config.toml.jinja

@@ -30,18 +30,13 @@ sfapi_cred_path = "{{ KBCTS_SFAPI_CRED_PATH or "" }}"
 # The user associated with the client credentials. The user's default shell must be bash.
 # If the client credentials are updated but the user doesn't match they will not be accepted.
 # It is advised to create a collaboration user for the service.
-# The user's scratch directory will be shared with the file_group below.
 # The jaws.conf file will be created in the user's home directory on service startup, overwriting
 # any extant file.
 sfapi_user = "{{ KBCTS_SFAPI_USER or "" }}"
 
 # Where to store remote code at NERSC. This must be writeable by the service account.
 remote_code_dir = "{{ KBCTS_NERSC_REMOTE_CODE_DIR or "/global/cfs/cdirs/kbase/cdm_task_service" }}"
 
-# The group with which to share downloaded data files. The JAWS user that will run jobs must
-# be in the same group so it can read the input files.
-file_group = "{{ KBCTS_NERSC_FILE_GROUP or "kbase" }}"
-
 [JAWS]
 
 # The JGI JAWS token to use to run jobs. This can be obtained from a JAWS representative.

docker-compose.yaml

@@ -27,7 +27,6 @@ services:
       - KBCTS_SFAPI_CRED_PATH=/creds/sfapi_creds
       - KBCTS_SFAPI_USER=cdm_ts
       - KBCTS_NERSC_REMOTE_CODE_DIR=/global/cfs/cdirs/kbase/cdm_task_service
-      - KBCTS_NERSC_FILE_GROUP=kbase
       # Don't commit your token to github please
       - KBCTS_JAWS_TOKEN=tokengoeshere
       - KBCTS_JAWS_GROUP=kbase