fractal-server 2.3.4__py3-none-any.whl → 2.3.6__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.3.4"
+__VERSION__ = "2.3.6"

fractal_server/app/models/v2/task.py

@@ -1,5 +1,3 @@
-import json
-import logging
 from typing import Any
 from typing import Optional
 
@@ -41,53 +39,3 @@ class TaskV2(SQLModel, table=True):
 
     input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
     output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
-
-    @property
-    def default_args_non_parallel_from_args_schema(self) -> dict[str, Any]:
-        """
-        Extract default arguments from args_schema
-        """
-        # Return {} if there is no args_schema
-        if self.args_schema_non_parallel is None:
-            return {}
-        # Try to construct default_args
-        try:
-            default_args = {}
-            properties = self.args_schema_non_parallel["properties"]
-            for prop_name, prop_schema in properties.items():
-                default_value = prop_schema.get("default", None)
-                if default_value is not None:
-                    default_args[prop_name] = default_value
-            return default_args
-        except KeyError as e:
-            logging.warning(
-                "Cannot set default_args from args_schema_non_parallel="
-                f"{json.dumps(self.args_schema_non_parallel)}\n"
-                f"Original KeyError: {str(e)}"
-            )
-            return {}
-
-    @property
-    def default_args_parallel_from_args_schema(self) -> dict[str, Any]:
-        """
-        Extract default arguments from args_schema
-        """
-        # Return {} if there is no args_schema
-        if self.args_schema_parallel is None:
-            return {}
-        # Try to construct default_args
-        try:
-            default_args = {}
-            properties = self.args_schema_parallel["properties"]
-            for prop_name, prop_schema in properties.items():
-                default_value = prop_schema.get("default", None)
-                if default_value is not None:
-                    default_args[prop_name] = default_value
-            return default_args
-        except KeyError as e:
-            logging.warning(
-                "Cannot set default_args from args_schema_parallel="
-                f"{json.dumps(self.args_schema_parallel)}\n"
-                f"Original KeyError: {str(e)}"
-            )
-            return {}

fractal_server/app/routes/api/v2/_aux_functions.py

@@ -422,6 +422,8 @@ async def _workflow_insert_task(
 
     # Get task from db, and extract default arguments via a Task property
     # method
+    # NOTE: this logic remains there for V1 tasks only. When we deprecate V1
+    # tasks, we can simplify this block
     if is_legacy_task is True:
         db_task = await db.get(Task, task_id)
         if db_task is None:
@@ -439,12 +441,8 @@ async def _workflow_insert_task(
             raise ValueError(f"TaskV2 {task_id} not found.")
         task_type = db_task.type
 
-        final_args_non_parallel = (
-            db_task.default_args_non_parallel_from_args_schema.copy()
-        )
-        final_args_parallel = (
-            db_task.default_args_parallel_from_args_schema.copy()
-        )
+        final_args_non_parallel = {}
+        final_args_parallel = {}
         final_meta_parallel = (db_task.meta_parallel or {}).copy()
         final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
 

fractal_server/app/routes/api/v2/workflowtask.py

@@ -186,34 +186,17 @@ async def update_workflowtask(
                 default_args = (
                     db_wf_task.task_legacy.default_args_from_args_schema
                 )
+                actual_args = deepcopy(default_args)
+                if value is not None:
+                    for k, v in value.items():
+                        actual_args[k] = v
             else:
-                default_args = (
-                    db_wf_task.task.default_args_parallel_from_args_schema
-                )
-            # Override default_args with args value items
-            actual_args = deepcopy(default_args)
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
+                actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)
         elif key == "args_non_parallel":
-            # Get default arguments via a Task property method
-            if db_wf_task.is_legacy_task:
-                # This is only needed so that we don't have to modify the rest
-                # of this block, but legacy task cannot take any non-parallel
-                # args (see checks above).
-                default_args = {}
-            else:
-                default_args = deepcopy(
-                    db_wf_task.task.default_args_non_parallel_from_args_schema
-                )
-            # Override default_args with args value items
-            actual_args = default_args.copy()
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
+            actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)

fractal_server/app/runner/executors/slurm/_slurm_config.py

@@ -62,6 +62,8 @@ class _SlurmConfigSet(BaseModel, extra=Extra.forbid):
     time: Optional[str]
     account: Optional[str]
     extra_lines: Optional[list[str]]
+    pre_submission_commands: Optional[list[str]]
+    gpus: Optional[str]
 
 
 class _BatchingConfigSet(BaseModel, extra=Extra.forbid):
@@ -219,6 +221,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
         constraint: Corresponds to SLURM option.
         gres: Corresponds to SLURM option.
         account: Corresponds to SLURM option.
+        gpus: Corresponds to SLURM option.
         time: Corresponds to SLURM option (WARNING: not fully supported).
         prefix: Prefix of configuration lines in SLURM submission scripts.
         shebang_line: Shebang line for SLURM submission scripts.
@@ -240,6 +243,8 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
             Key-value pairs to be included as `export`-ed variables in SLURM
             submission script, after prepending values with the user's cache
             directory.
+        pre_submission_commands: List of commands to be prepended to the sbatch
+            command.
     """
 
     # Required SLURM parameters (note that the integer attributes are those
@@ -254,6 +259,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
     job_name: Optional[str] = None
     constraint: Optional[str] = None
     gres: Optional[str] = None
+    gpus: Optional[str] = None
     time: Optional[str] = None
     account: Optional[str] = None
 
@@ -274,6 +280,8 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
     target_num_jobs: int
     max_num_jobs: int
 
+    pre_submission_commands: list[str] = Field(default_factory=list)
+
     def _sorted_extra_lines(self) -> list[str]:
         """
         Return a copy of `self.extra_lines`, where lines starting with
@@ -340,7 +348,14 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
             f"{self.prefix} --cpus-per-task={self.cpus_per_task}",
             f"{self.prefix} --mem={mem_per_job_MB}M",
         ]
-        for key in ["job_name", "constraint", "gres", "time", "account"]:
+        for key in [
+            "job_name",
+            "constraint",
+            "gres",
+            "gpus",
+            "time",
+            "account",
+        ]:
             value = getattr(self, key)
             if value is not None:
                 # Handle the `time` parameter

fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -869,9 +869,22 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         # Submit job to SLURM, and get jobid
         sbatch_command = f"sbatch --parsable {job.slurm_script_remote}"
-        sbatch_stdout = self.fractal_ssh.run_command(
-            cmd=sbatch_command,
-        )
+        pre_submission_cmds = job.slurm_config.pre_submission_commands
+        if len(pre_submission_cmds) == 0:
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=sbatch_command)
+        else:
+            logger.debug(f"Now using {pre_submission_cmds=}")
+            script_lines = pre_submission_cmds + [sbatch_command]
+            script_content = "\n".join(script_lines)
+            script_content = f"{script_content}\n"
+            script_path_remote = (
+                f"{job.slurm_script_remote.as_posix()}_wrapper.sh"
+            )
+            self.fractal_ssh.write_remote_file(
+                path=script_path_remote, content=script_content
+            )
+            cmd = f"bash {script_path_remote}"
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=cmd)
 
         # Extract SLURM job ID from stdout
         try:
@@ -881,7 +894,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             error_msg = (
                 f"Submit command `{sbatch_command}` returned "
                 f"`{stdout=}` which cannot be cast to an integer "
-                f"SLURM-job ID. Original error:\n{str(e)}"
+                f"SLURM-job ID.\n"
+                f"Note that {pre_submission_cmds=}.\n"
+                f"Original error:\n{str(e)}"
             )
             logger.error(error_msg)
             raise JobExecutionError(info=error_msg)

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -1121,6 +1121,12 @@ class FractalSlurmExecutor(SlurmExecutor):
             slurm_err_path=str(job.slurm_stderr),
         )
 
+        # Print warning for ignored parameter
+        if len(job.slurm_config.pre_submission_commands) > 0:
+            logger.warning(
+                f"Ignoring {job.slurm_config.pre_submission_commands=}."
+            )
+
         # Submit job via sbatch, and retrieve jobid
 
         # Write script content to a job.slurm_script

fractal_server/app/runner/v2/__init__.py

@@ -36,8 +36,8 @@ from ._local import process_workflow as local_process_workflow
 from ._local_experimental import (
     process_workflow as local_experimental_process_workflow,
 )
-from ._slurm import process_workflow as slurm_sudo_process_workflow
 from ._slurm_ssh import process_workflow as slurm_ssh_process_workflow
+from ._slurm_sudo import process_workflow as slurm_sudo_process_workflow
 from .handle_failed_job import assemble_filters_failed_job
 from .handle_failed_job import assemble_history_failed_job
 from .handle_failed_job import assemble_images_failed_job

fractal_server/app/runner/v2/{_slurm_ssh → _slurm_common}/get_slurm_config.py

@@ -18,8 +18,6 @@ from fractal_server.app.runner.executors.slurm._slurm_config import (
 
 def get_slurm_config(
     wftask: WorkflowTaskV2,
-    workflow_dir_local: Path,
-    workflow_dir_remote: Path,
     which_type: Literal["non_parallel", "parallel"],
     config_path: Optional[Path] = None,
 ) -> SlurmConfig:
@@ -43,13 +41,6 @@ def get_slurm_config(
         wftask:
             WorkflowTask for which the SLURM configuration is is to be
             prepared.
-        workflow_dir_local:
-            Server-owned directory to store all task-execution-related relevant
-            files (inputs, outputs, errors, and all meta files related to the
-            job execution). Note: users cannot write directly to this folder.
-        workflow_dir_remote:
-            User-side directory with the same scope as `workflow_dir_local`,
-            and where a user can write.
         config_path:
             Path of a Fractal SLURM configuration file; if `None`, use
             `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
@@ -99,13 +90,13 @@ def get_slurm_config(
     # 1. This block of definitions takes priority over other definitions from
     #    slurm_env which are not under the `needs_gpu` subgroup
     # 2. This block of definitions has lower priority than whatever comes next
-    #    (i.e. from WorkflowTask.meta).
+    #    (i.e. from WorkflowTask.meta_parallel).
     if wftask_meta is not None:
         needs_gpu = wftask_meta.get("needs_gpu", False)
     else:
         needs_gpu = False
     logger.debug(f"[get_slurm_config] {needs_gpu=}")
-    if needs_gpu and slurm_env.gpu_slurm_config is not None:  # FIXME
+    if needs_gpu:
         for key, value in slurm_env.gpu_slurm_config.dict(
             exclude_unset=True, exclude={"mem"}
         ).items():
@@ -143,9 +134,9 @@ def get_slurm_config(
             )
             logger.error(error_msg)
             raise SlurmConfigError(error_msg)
-        for key in ["time", "gres", "constraint"]:
+        for key in ["time", "gres", "gpus", "constraint"]:
             value = wftask_meta.get(key, None)
-            if value:
+            if value is not None:
                 slurm_dict[key] = value
     if wftask_meta is not None:
         extra_lines = wftask_meta.get("extra_lines", [])

fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py

@@ -17,8 +17,10 @@ from pathlib import Path
 from typing import Literal
 
 from ...task_files import get_task_file_paths
-from .get_slurm_config import get_slurm_config
 from fractal_server.app.models.v2 import WorkflowTaskV2
+from fractal_server.app.runner.v2._slurm_common.get_slurm_config import (
+    get_slurm_config,
+)
 
 
 def _slurm_submit_setup(
@@ -62,8 +64,6 @@ def _slurm_submit_setup(
     # Get SlurmConfig object
     slurm_config = get_slurm_config(
         wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
         which_type=which_type,
     )
 

fractal_server/app/runner/v2/{_slurm → _slurm_sudo}/_submit_setup.py

@@ -17,8 +17,10 @@ from pathlib import Path
 from typing import Literal
 
 from ...task_files import get_task_file_paths
-from .get_slurm_config import get_slurm_config
 from fractal_server.app.models.v2 import WorkflowTaskV2
+from fractal_server.app.runner.v2._slurm_common.get_slurm_config import (
+    get_slurm_config,
+)
 
 
 def _slurm_submit_setup(
@@ -62,8 +64,6 @@ def _slurm_submit_setup(
     # Get SlurmConfig object
     slurm_config = get_slurm_config(
         wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
         which_type=which_type,
     )
 

fractal_server/ssh/_fabric.py

@@ -306,6 +306,28 @@ class FractalSSH(object):
             cmd = f"rm -r {folder}"
             self.run_command(cmd=cmd)
 
+    def write_remote_file(
+        self,
+        *,
+        path: str,
+        content: str,
+        lock_timeout: Optional[float] = None,
+    ) -> None:
+        """
+        Open a remote file via SFTP and write it.
+
+        Args:
+            path: Absolute path
+            contents: File contents
+            lock_timeout:
+        """
+        actual_lock_timeout = self.default_lock_timeout
+        if lock_timeout is not None:
+            actual_lock_timeout = lock_timeout
+        with self.acquire_timeout(timeout=actual_lock_timeout):
+            with self.sftp().open(filename=path, mode="w") as f:
+                f.write(content)
+
 
 def get_ssh_connection(
     *,

{fractal_server-2.3.4.dist-info → fractal_server-2.3.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.4
+Version: 2.3.6
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -33,7 +33,7 @@ Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0) ; extra == "postgres-psycopg-bin
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
-Requires-Dist: sqlmodel (>=0.0.19,<0.0.20)
+Requires-Dist: sqlmodel (>=0.0.21,<0.0.22)
 Requires-Dist: uvicorn (>=0.29.0,<0.30.0)
 Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server

{fractal_server-2.3.4.dist-info → fractal_server-2.3.6.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=eG9nilkh3fQGESwdGxiBx9bAq-mIR2ueRWgDXGopc1M,22
+fractal_server/__init__.py,sha256=lCtPuZps1Hbf7xTBL9gN0BnZZFuDzV5N5mezQVbB9lA,22
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -18,7 +18,7 @@ fractal_server/app/models/v2/collection_state.py,sha256=nxb042i8tt8rCpmgbFJoBCYW
 fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0SRvqS2iOQU,1455
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
 fractal_server/app/models/v2/project.py,sha256=CRBnZ8QITNp6u1f5bMxvi1_mcvEfXpWyitsWB5f7gn8,759
-fractal_server/app/models/v2/task.py,sha256=9ZPhug3VWyeqgT8wQ9_8ZXQ2crSiiicRipxrxTslOso,3257
+fractal_server/app/models/v2/task.py,sha256=Esf2j9c-0pGYjdbb__Ptpdx7NCAKVxqbQMoza524miU,1286
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=3jEkObsSnlI05Pur_dSsXYdJxRqPL60Z7tK5-EJLOks,1532
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,7 +36,7 @@ fractal_server/app/routes/api/v1/task_collection.py,sha256=82XBsJHlPiDPCbpLa-16o
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
 fractal_server/app/routes/api/v1/workflowtask.py,sha256=qcHQlzlSFf_k8gtId-mA3tnyzgSR7i1m7pvR4R86blE,5582
 fractal_server/app/routes/api/v2/__init__.py,sha256=JrPWfKIJy9btRCP-zw2nZwLpSdBxEKY5emuCuJbqG0s,1813
-fractal_server/app/routes/api/v2/_aux_functions.py,sha256=tYJr5EPaA0CVGp-Y4jottFJUVToWvjcSY6PJqN_d--s,14938
+fractal_server/app/routes/api/v2/_aux_functions.py,sha256=yeA0650pBk43M5ZQGpVQ17nH5D97NIGY-3tNNLQIW1M,14901
 fractal_server/app/routes/api/v2/dataset.py,sha256=_HjKNP9XsMGoqyubGdF2ZyeW7vXC3VdK_0_TaUxgIF0,8248
 fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZU0gWdKneZcNG4,7894
 fractal_server/app/routes/api/v2/job.py,sha256=RkIj7ANK-nkxUvcG9K2r4dFdPnvGomx7jdB6U9bqOVQ,5202
@@ -48,7 +48,7 @@ fractal_server/app/routes/api/v2/task_collection.py,sha256=BiZ5s6DwdQbM79s_dPivg
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=cvZorN_Xt57Rj-2JATRrdtSw6I_5befB0ua3FWh6hW4,5988
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
 fractal_server/app/routes/api/v2/workflow.py,sha256=2GlcYNjpvCdjwC_Kn7y0UP16B3pOLSNXBvIVsVDtDKM,11863
-fractal_server/app/routes/api/v2/workflowtask.py,sha256=l4eTD5IIun5cOdYzsxh3ajmnOISaSccYA_mVf15Cjtw,8802
+fractal_server/app/routes/api/v2/workflowtask.py,sha256=l_eQPniK1zR0u249bJj4c2hFlyDwsSJgsFR6hxJaOjs,8007
 fractal_server/app/routes/auth.py,sha256=Xv80iqdyfY3lyicYs2Y8B6zEDEnyUu_H6_6psYtv3R4,4885
 fractal_server/app/routes/aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/aux/_job.py,sha256=HUItNm0SZFAYsyL1rXSjBre1-rXSe6x51qH9KAQWS1w,1361
@@ -62,17 +62,17 @@ fractal_server/app/runner/exceptions.py,sha256=_qZ_t8O4umAdJ1ikockiF5rDJuxnEskrG
 fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm/_batching.py,sha256=3mfeFuYm3UA4EXh4VWuqZTF-dcINECZgTHoPOaOszDo,8840
-fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=KtLQ5l_wmWcrSPVrG9nugzgjRKmycmSOkVrkTR0I7Rs,15660
+fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=iyhtDi1qveqq7I4S1tycVKsp3VfyocvBgGugYDpOzAs,16069
 fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77JRK82g_2hx0iBKTiMghuIo,5852
 fractal_server/app/runner/executors/slurm/ssh/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py,sha256=jM4G-wiHynZhNERusVGLtDTepJDiYjCDloWZyflaMV0,3482
 fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb4nSlFjsQJdaCgfM1J6YGcjb8yYxlqc,4506
-fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=O3BV7Qo7W8qEJmIeaajxtCCbkbYQDEXZbfS7GKCO5LQ,55338
+fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=rfLEO6mN3sZvZYHqs3lmYvPYFGLmXyMPWl1Bg0mq-6k,56109
 fractal_server/app/runner/executors/slurm/sudo/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py,sha256=wAgwpVcr6JIslKHOuS0FhRa_6T1KCManyRJqA-fifzw,1909
 fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=z5LlhaiqAb8pHsF1WwdzXN39C5anQmwjo1rSQgtRAYE,4422
 fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py,sha256=uZgmxP0ZneGpzTVt-GT-6EgNKUh1sW2-QH7LFYc1tNI,5132
-fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=nu1mcg3veOEaDwqPLyrf9_pMUc34-uXhd8er3IsMQZw,48236
+fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=74jfNauDgQOdcILHcCLJM4Awm_SThsZYgc0Vwx0hnB8,48460
 fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
 fractal_server/app/runner/run_subprocess.py,sha256=KTkJnWLrLQdR2WRJ3jGu0RBu4330L3mtCAE_B0wDx3M,818
@@ -90,7 +90,7 @@ fractal_server/app/runner/v1/_slurm/_submit_setup.py,sha256=KO9c694d318adoPQh9UG
 fractal_server/app/runner/v1/_slurm/get_slurm_config.py,sha256=6pQNNx997bLIfLp0guF09t_O0ZYRXnbEGLktSAcKnic,5999
 fractal_server/app/runner/v1/common.py,sha256=_L-vjLnWato80VdlB_BFN4G8P4jSM07u-5cnl1T3S34,3294
 fractal_server/app/runner/v1/handle_failed_job.py,sha256=bHzScC_aIlU3q-bQxGW6rfWV4xbZ2tho_sktjsAs1no,4684
-fractal_server/app/runner/v2/__init__.py,sha256=AFX2TiHfu8vAugvILz484ps4ehZpVHmc3kXGtbhi2zE,16912
+fractal_server/app/runner/v2/__init__.py,sha256=nD4uFi-RGsN6JAmJNpV2dS603u8KqFuGwXZS8jIrf50,16917
 fractal_server/app/runner/v2/_local/__init__.py,sha256=KTj14K6jH8fXGUi5P7u5_RqEE1zF4aXtgPxCKzw46iw,5971
 fractal_server/app/runner/v2/_local/_local_config.py,sha256=9oi209Dlp35ANfxb_DISqmMKKc6DPaMsmYVWbZLseME,3630
 fractal_server/app/runner/v2/_local/_submit_setup.py,sha256=MucNOo8Er0F5ZIwH7CnTeXgnFMc6d3pKPkv563QNVi0,1630
@@ -99,12 +99,12 @@ fractal_server/app/runner/v2/_local_experimental/__init__.py,sha256=53yS8a-l0dMT
 fractal_server/app/runner/v2/_local_experimental/_local_config.py,sha256=QiS5ODe-iGmUQdIT8QgpbyMc7-ZpIRv1V_f2q3qfPQ8,3211
 fractal_server/app/runner/v2/_local_experimental/_submit_setup.py,sha256=we7r-sQf0CJ9gxbfbgHcYdC6pKjx8eXweljIjthxkv8,1212
 fractal_server/app/runner/v2/_local_experimental/executor.py,sha256=vcBKjireIIyF5WgIQLatD6ojlWEydbTwyIG0bcpIjys,5438
-fractal_server/app/runner/v2/_slurm/__init__.py,sha256=q2fwiKqtNpXtfs5wUFQjwJxdYqKPPTbCy1ieBhhi-Bw,4316
-fractal_server/app/runner/v2/_slurm/_submit_setup.py,sha256=rvhMOK1QkqsxVWUvekT62KbDDlqpw49nq9mzQXSY3H0,2883
-fractal_server/app/runner/v2/_slurm/get_slurm_config.py,sha256=btGmbZB0fO6bg2WujFxbGEV2iWzaMKbHgV1r2hm_4a0,6748
+fractal_server/app/runner/v2/_slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py,sha256=V47uckqA4Vp-7m5esDnTitekc-yabLhaZSlPj4jN_D8,6307
 fractal_server/app/runner/v2/_slurm_ssh/__init__.py,sha256=1p6d_ppXBqRNPXPGxM8cmIOffEsfkEPEfvDeT-_90dE,3990
-fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py,sha256=rvhMOK1QkqsxVWUvekT62KbDDlqpw49nq9mzQXSY3H0,2883
-fractal_server/app/runner/v2/_slurm_ssh/get_slurm_config.py,sha256=ZK_yvZhe-nzMAvg54JB6TcaCBplKD9vje92m5-cTxsI,6801
+fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py,sha256=a5_FDPH_yxYmrjAjMRLgh_Y4DSG3mRslCLQodGM3-t4,2838
+fractal_server/app/runner/v2/_slurm_sudo/__init__.py,sha256=q2fwiKqtNpXtfs5wUFQjwJxdYqKPPTbCy1ieBhhi-Bw,4316
+fractal_server/app/runner/v2/_slurm_sudo/_submit_setup.py,sha256=a5_FDPH_yxYmrjAjMRLgh_Y4DSG3mRslCLQodGM3-t4,2838
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=-imwO7OB7ATADEnqVbTElUwoY0YIJCTf_SbWJNN9OZg,639
 fractal_server/app/runner/v2/handle_failed_job.py,sha256=M1r3dnrbUMo_AI2qjaVuGhieMAyLh5gcvB10YOBpjvI,5415
 fractal_server/app/runner/v2/merge_outputs.py,sha256=IHuHqbKmk97K35BFvTrKVBs60z3e_--OzXTnsvmA02c,1281
@@ -168,7 +168,7 @@ fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=4B6D0F2bWWho1V_xdDDBWYAHno9h_6Smp7_FP2n8jYo,10739
+fractal_server/ssh/_fabric.py,sha256=9xcsOEwbCgbJtupkIeG8OOtT8ct8c7_ruIehhNmD4wc,11379
 fractal_server/string_tools.py,sha256=KThgTLn_FHNSuEUGLabryJAP6DaFd7bpi-hF5FgkBjw,1268
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
@@ -193,8 +193,8 @@ fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=GrJ19uHYQxANEy9JaeNJZVTq
 fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kqXRM,1657
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.3.4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.3.4.dist-info/METADATA,sha256=mfO_uoRAUY2bfiBN0AU1exGu0orny30foijJx6SR1Xc,4425
-fractal_server-2.3.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.3.4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.3.4.dist-info/RECORD,,
+fractal_server-2.3.6.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.3.6.dist-info/METADATA,sha256=WrV14I1NR6DeXCeuHJTZqsnJfCf4EqdY-IZSeeGPAPM,4425
+fractal_server-2.3.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.3.6.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.3.6.dist-info/RECORD,,

fractal_server/app/runner/v2/_slurm/get_slurm_config.py

@@ -1,182 +0,0 @@
-from pathlib import Path
-from typing import Literal
-from typing import Optional
-
-from fractal_server.app.models.v2 import WorkflowTaskV2
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    _parse_mem_value,
-)
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    load_slurm_config_file,
-)
-from fractal_server.app.runner.executors.slurm._slurm_config import logger
-from fractal_server.app.runner.executors.slurm._slurm_config import SlurmConfig
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    SlurmConfigError,
-)
-
-
-def get_slurm_config(
-    wftask: WorkflowTaskV2,
-    workflow_dir_local: Path,
-    workflow_dir_remote: Path,
-    which_type: Literal["non_parallel", "parallel"],
-    config_path: Optional[Path] = None,
-) -> SlurmConfig:
-    """
-    Prepare a `SlurmConfig` configuration object
-
-    The argument `which_type` determines whether we use `wftask.meta_parallel`
-    or `wftask.meta_non_parallel`. In the following descritpion, let us assume
-    that `which_type="parallel"`.
-
-    The sources for `SlurmConfig` attributes, in increasing priority order, are
-
-    1. The general content of the Fractal SLURM configuration file.
-    2. The GPU-specific content of the Fractal SLURM configuration file, if
-        appropriate.
-    3. Properties in `wftask.meta_parallel` (which typically include those in
-       `wftask.task.meta_parallel`). Note that `wftask.meta_parallel` may be
-       `None`.
-
-    Arguments:
-        wftask:
-            WorkflowTask for which the SLURM configuration is is to be
-            prepared.
-        workflow_dir_local:
-            Server-owned directory to store all task-execution-related relevant
-            files (inputs, outputs, errors, and all meta files related to the
-            job execution). Note: users cannot write directly to this folder.
-        workflow_dir_remote:
-            User-side directory with the same scope as `workflow_dir_local`,
-            and where a user can write.
-        config_path:
-            Path of a Fractal SLURM configuration file; if `None`, use
-            `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
-        which_type:
-            Determines whether to use `meta_parallel` or `meta_non_parallel`.
-
-    Returns:
-        slurm_config:
-            The SlurmConfig object
-    """
-
-    if which_type == "non_parallel":
-        wftask_meta = wftask.meta_non_parallel
-    elif which_type == "parallel":
-        wftask_meta = wftask.meta_parallel
-    else:
-        raise ValueError(
-            f"get_slurm_config received invalid argument {which_type=}."
-        )
-
-    logger.debug(
-        "[get_slurm_config] WorkflowTask meta attribute: {wftask_meta=}"
-    )
-
-    # Incorporate slurm_env.default_slurm_config
-    slurm_env = load_slurm_config_file(config_path=config_path)
-    slurm_dict = slurm_env.default_slurm_config.dict(
-        exclude_unset=True, exclude={"mem"}
-    )
-    if slurm_env.default_slurm_config.mem:
-        slurm_dict["mem_per_task_MB"] = slurm_env.default_slurm_config.mem
-
-    # Incorporate slurm_env.batching_config
-    for key, value in slurm_env.batching_config.dict().items():
-        slurm_dict[key] = value
-
-    # Incorporate slurm_env.user_local_exports
-    slurm_dict["user_local_exports"] = slurm_env.user_local_exports
-
-    logger.debug(
-        "[get_slurm_config] Fractal SLURM configuration file: "
-        f"{slurm_env.dict()=}"
-    )
-
-    # GPU-related options
-    # Notes about priority:
-    # 1. This block of definitions takes priority over other definitions from
-    #    slurm_env which are not under the `needs_gpu` subgroup
-    # 2. This block of definitions has lower priority than whatever comes next
-    #    (i.e. from WorkflowTask.meta).
-    if wftask_meta is not None:
-        needs_gpu = wftask_meta.get("needs_gpu", False)
-    else:
-        needs_gpu = False
-    logger.debug(f"[get_slurm_config] {needs_gpu=}")
-    if needs_gpu:
-        for key, value in slurm_env.gpu_slurm_config.dict(
-            exclude_unset=True, exclude={"mem"}
-        ).items():
-            slurm_dict[key] = value
-        if slurm_env.gpu_slurm_config.mem:
-            slurm_dict["mem_per_task_MB"] = slurm_env.gpu_slurm_config.mem
-
-    # Number of CPUs per task, for multithreading
-    if wftask_meta is not None and "cpus_per_task" in wftask_meta:
-        cpus_per_task = int(wftask_meta["cpus_per_task"])
-        slurm_dict["cpus_per_task"] = cpus_per_task
-
-    # Required memory per task, in MB
-    if wftask_meta is not None and "mem" in wftask_meta:
-        raw_mem = wftask_meta["mem"]
-        mem_per_task_MB = _parse_mem_value(raw_mem)
-        slurm_dict["mem_per_task_MB"] = mem_per_task_MB
-
-    # Job name
-    if wftask.is_legacy_task:
-        job_name = wftask.task_legacy.name.replace(" ", "_")
-    else:
-        job_name = wftask.task.name.replace(" ", "_")
-    slurm_dict["job_name"] = job_name
-
-    # Optional SLURM arguments and extra lines
-    if wftask_meta is not None:
-        account = wftask_meta.get("account", None)
-        if account is not None:
-            error_msg = (
-                f"Invalid {account=} property in WorkflowTask `meta` "
-                "attribute.\n"
-                "SLURM account must be set in the request body of the "
-                "apply-workflow endpoint, or by modifying the user properties."
-            )
-            logger.error(error_msg)
-            raise SlurmConfigError(error_msg)
-        for key in ["time", "gres", "constraint"]:
-            value = wftask_meta.get(key, None)
-            if value:
-                slurm_dict[key] = value
-    if wftask_meta is not None:
-        extra_lines = wftask_meta.get("extra_lines", [])
-    else:
-        extra_lines = []
-    extra_lines = slurm_dict.get("extra_lines", []) + extra_lines
-    if len(set(extra_lines)) != len(extra_lines):
-        logger.debug(
-            "[get_slurm_config] Removing repeated elements "
-            f"from {extra_lines=}."
-        )
-        extra_lines = list(set(extra_lines))
-    slurm_dict["extra_lines"] = extra_lines
-
-    # Job-batching parameters (if None, they will be determined heuristically)
-    if wftask_meta is not None:
-        tasks_per_job = wftask_meta.get("tasks_per_job", None)
-        parallel_tasks_per_job = wftask_meta.get(
-            "parallel_tasks_per_job", None
-        )
-    else:
-        tasks_per_job = None
-        parallel_tasks_per_job = None
-    slurm_dict["tasks_per_job"] = tasks_per_job
-    slurm_dict["parallel_tasks_per_job"] = parallel_tasks_per_job
-
-    # Put everything together
-    logger.debug(
-        "[get_slurm_config] Now create a SlurmConfig object based "
-        f"on {slurm_dict=}"
-    )
-    slurm_config = SlurmConfig(**slurm_dict)
-
-    return slurm_config