snakemake-executor-plugin-slurm 1.7.0__py3-none-any.whl → 1.9.0__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -18,6 +18,7 @@ import uuid
 
 from snakemake_interface_executor_plugins.executors.base import SubmittedJobInfo
 from snakemake_interface_executor_plugins.executors.remote import RemoteExecutor
+
 from snakemake_interface_executor_plugins.settings import (
     ExecutorSettingsBase,
     CommonSettings,
@@ -34,6 +35,7 @@ from .utils import (
 )
 from .efficiency_report import create_efficiency_report
 from .submit_string import get_submit_command
+from .validation import validate_slurm_extra
 
 
 @dataclass
@@ -307,7 +309,7 @@ class Executor(RemoteExecutor):
             "run_uuid": self.run_uuid,
             "slurm_logfile": slurm_logfile,
             "comment_str": comment_str,
-            "account": self.get_account_arg(job),
+            "account": next(self.get_account_arg(job)),
             "partition": self.get_partition_arg(job),
             "workdir": self.workflow.workdir_init,
         }
@@ -339,17 +341,6 @@ class Executor(RemoteExecutor):
                 "- submitting without. This might or might not work on your cluster."
             )
 
-        # MPI job
-        if job.resources.get("mpi", False):
-            if not job.resources.get("tasks_per_node") and not job.resources.get(
-                "nodes"
-            ):
-                self.logger.warning(
-                    "MPI job detected, but no 'tasks_per_node' or 'nodes' "
-                    "specified. Assuming 'tasks_per_node=1'."
-                    "Probably not what you want."
-                )
-
         exec_job = self.format_job_exec(job)
 
         # and finally the job to execute with all the snakemake parameters
@@ -668,10 +659,22 @@ We leave it to SLURM to resume your job(s)"""
         else raises an error - implicetly.
         """
         if job.resources.get("slurm_account"):
-            # here, we check whether the given or guessed account is valid
-            # if not, a WorkflowError is raised
-            self.test_account(job.resources.slurm_account)
-            return f" -A '{job.resources.slurm_account}'"
+            # split the account upon ',' and whitespace, to allow
+            # multiple accounts being given
+            accounts = [
+                a for a in re.split(r"[,\s]+", job.resources.slurm_account) if a
+            ]
+            for account in accounts:
+                # here, we check whether the given or guessed account is valid
+                # if not, a WorkflowError is raised
+                self.test_account(account)
+            # sbatch only allows one account per submission
+            # yield one after the other, if multiple were given
+            # we have to quote the account, because it might
+            # contain build-in shell commands - see issue #354
+            for account in accounts:
+                self.test_account(account)
+                yield f" -A {shlex.quote(account)}"
         else:
             if self._fallback_account_arg is None:
                 self.logger.warning("No SLURM account given, trying to guess.")
@@ -679,7 +682,7 @@ We leave it to SLURM to resume your job(s)"""
                 if account:
                     self.logger.warning(f"Guessed SLURM account: {account}")
                     self.test_account(f"{account}")
-                    self._fallback_account_arg = f" -A {account}"
+                    self._fallback_account_arg = f" -A {shlex.quote(account)}"
                 else:
                     self.logger.warning(
                         "Unable to guess SLURM account. Trying to proceed without."
@@ -687,7 +690,7 @@ We leave it to SLURM to resume your job(s)"""
                     self._fallback_account_arg = (
                         ""  # no account specific args for sbatch
                     )
-            return self._fallback_account_arg
+            yield self._fallback_account_arg
 
     def get_partition_arg(self, job: JobExecutorInterface):
         """
@@ -702,7 +705,9 @@ We leave it to SLURM to resume your job(s)"""
                 self._fallback_partition = self.get_default_partition(job)
             partition = self._fallback_partition
         if partition:
-            return f" -p {partition}"
+            # we have to quote the partition, because it might
+            # contain build-in shell commands
+            return f" -p {shlex.quote(partition)}"
         else:
             return ""
 
@@ -730,32 +735,35 @@ We leave it to SLURM to resume your job(s)"""
         """
         tests whether the given account is registered, raises an error, if not
         """
-        cmd = "sshare -U --format Account%256 --noheader"
+        # first we need to test with sacctmgr because sshare might not
+        # work in a multicluster environment
+        cmd = f'sacctmgr -n -s list user "{os.environ["USER"]}" format=account%256'
+        sacctmgr_report = sshare_report = ""
         try:
             accounts = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE
             )
         except subprocess.CalledProcessError as e:
-            sshare_report = (
+            sacctmgr_report = (
                 "Unable to test the validity of the given or guessed"
-                f" SLURM account '{account}' with sshare: {e.stderr}."
+                f" SLURM account '{account}' with sacctmgr: {e.stderr}."
             )
             accounts = ""
 
         if not accounts.strip():
-            cmd = f'sacctmgr -n -s list user "{os.environ["USER"]}" format=account%256'
+            cmd = "sshare -U --format Account%256 --noheader"
             try:
                 accounts = subprocess.check_output(
                     cmd, shell=True, text=True, stderr=subprocess.PIPE
                 )
             except subprocess.CalledProcessError as e:
-                sacctmgr_report = (
+                sshare_report = (
                     "Unable to test the validity of the given or guessed "
-                    f"SLURM account '{account}' with sacctmgr: {e.stderr}."
+                    f"SLURM account '{account}' with sshare: {e.stderr}."
                 )
                 raise WorkflowError(
-                    f"The 'sshare' reported: '{sshare_report}' "
-                    f"and likewise 'sacctmgr' reported: '{sacctmgr_report}'."
+                    f"The 'sacctmgr' reported: '{sacctmgr_report}' "
+                    f"and likewise 'sshare' reported: '{sshare_report}'."
                 )
 
         # The set() has been introduced during review to eliminate
@@ -764,7 +772,7 @@ We leave it to SLURM to resume your job(s)"""
 
         if not accounts:
             self.logger.warning(
-                f"Both 'sshare' and 'sacctmgr' returned empty results for account "
+                f"Both 'sacctmgr' and 'sshare' returned empty results for account "
                 f"'{account}'. Proceeding without account validation."
             )
             return ""
@@ -804,13 +812,5 @@ We leave it to SLURM to resume your job(s)"""
         return ""
 
     def check_slurm_extra(self, job):
-        jobname = re.compile(r"--job-name[=?|\s+]|-J\s?")
-        if re.search(jobname, job.resources.slurm_extra):
-            raise WorkflowError(
-                "The --job-name option is not allowed in the 'slurm_extra' parameter. "
-                "The job name is set by snakemake and must not be overwritten. "
-                "It is internally used to check the stati of the all submitted jobs "
-                "by this workflow."
-                "Please consult the documentation if you are unsure how to "
-                "query the status of your jobs."
-            )
+        """Validate that slurm_extra doesn't contain executor-managed options."""
+        validate_slurm_extra(job)

snakemake_executor_plugin_slurm/efficiency_report.py

@@ -3,24 +3,67 @@ import pandas as pd
 from pathlib import Path
 import subprocess
 import shlex
-
-import os  # only temporarily needed for printf debugging
+from datetime import datetime
 import numpy as np
+import os
 
 
 def time_to_seconds(time_str):
-    """Convert SLURM time format to seconds."""
-    if pd.isna(time_str) or time_str.strip() == "":
+    """
+    Convert SLURM sacct time format to seconds.
+
+    Handles sacct output formats:
+    - Elapsed: [D-]HH:MM:SS or [DD-]HH:MM:SS (no fractional seconds)
+    - TotalCPU: [D-][HH:]MM:SS or [DD-][HH:]MM:SS (with fractional seconds)
+
+    Examples:
+    - "1-12:30:45" -> 131445 seconds (1 day + 12h 30m 45s)
+    - "23:59:59" -> 86399 seconds
+    - "45:30" -> 2730 seconds (45 minutes 30 seconds)
+    - "30.5" -> 30.5 seconds (fractional seconds for TotalCPU)
+    """
+    if (
+        pd.isna(time_str)
+        or str(time_str).strip() == ""
+        or str(time_str).strip() == "invalid"
+    ):
         return 0
-    parts = time_str.split(":")
-
-    if len(parts) == 3:  # H:M:S
-        return int(parts[0]) * 3600 + int(parts[1]) * 60 + float(parts[2])
-    elif len(parts) == 2:  # M:S
-        return int(parts[0]) * 60 + float(parts[1])
-    elif len(parts) == 1:  # S
-        return float(parts[0])
-    return 0
+
+    time_str = str(time_str).strip()
+
+    # Try different SLURM time formats with datetime parsing
+    time_formats = [
+        "%d-%H:%M:%S.%f",  # D-HH:MM:SS.ffffff (with fractional seconds)
+        "%d-%H:%M:%S",  # D-HH:MM:SS
+        "%d-%M:%S",  # D-MM:SS
+        "%d-%M:%S.%f",  # D-MM:SS.ffffff (with fractional seconds)
+        "%H:%M:%S.%f",  # HH:MM:SS.ffffff (with fractional seconds)
+        "%H:%M:%S",  # HH:MM:SS
+        "%M:%S.%f",  # MM:SS.ffffff (with fractional seconds)
+        "%M:%S",  # MM:SS
+        "%S.%f",  # SS.ffffff (with fractional seconds)
+        "%S",  # SS
+    ]
+
+    for fmt in time_formats:
+        try:
+            time_obj = datetime.strptime(time_str, fmt)
+
+            total_seconds = (
+                time_obj.hour * 3600
+                + time_obj.minute * 60
+                + time_obj.second
+                + time_obj.microsecond / 1000000
+            )
+
+            # Add days if present (datetime treats day 1 as the first day)
+            if fmt.startswith("%d-"):
+                total_seconds += time_obj.day * 86400
+
+            return total_seconds
+        except ValueError:
+            continue
+    return 0  # If all parsing attempts fail, return 0
 
 
 def parse_maxrss(maxrss):

snakemake_executor_plugin_slurm/submit_string.py

@@ -1,5 +1,19 @@
+from snakemake_interface_common.exceptions import WorkflowError
 from snakemake_executor_plugin_slurm_jobstep import get_cpu_setting
 from types import SimpleNamespace
+import shlex
+
+
+def safe_quote(value):
+    """
+    Safely quote a parameter value using shlex.quote.
+    Handles None values and converts to string if needed.
+    Returns empty quotes for empty strings.
+    """
+    str_value = str(value)
+    if str_value == "":
+        return "''"
+    return shlex.quote(str_value)
 
 
 def get_submit_command(job, params):
@@ -10,37 +24,41 @@ def get_submit_command(job, params):
     params = SimpleNamespace(**params)
 
     call = (
-        f"sbatch "
-        f"--parsable "
-        f"--job-name {params.run_uuid} "
-        f'--output "{params.slurm_logfile}" '
-        f"--export=ALL "
-        f'--comment "{params.comment_str}"'
+        "sbatch "
+        "--parsable "
+        f"--job-name {safe_quote(params.run_uuid)} "
+        f"--output {safe_quote(params.slurm_logfile)} "
+        "--export=ALL "
+        f"--comment {safe_quote(params.comment_str)}"
     )
 
     # No accout or partition checking is required, here.
     # Checking is done in the submit function.
 
     # here, only the string is used, as it already contains
-    # '-A {account_name}'
+    # "-A '{account_name}'"
     call += f" {params.account}"
     # here, only the string is used, as it already contains
-    # '- p {partition_name}'
+    # "- p '{partition_name}'"
     call += f" {params.partition}"
 
     if job.resources.get("clusters"):
-        call += f" --clusters {job.resources.clusters}"
+        call += f" --clusters {safe_quote(job.resources.clusters)}"
 
     if job.resources.get("runtime"):
-        call += f" -t {job.resources.runtime}"
+        call += f" -t {safe_quote(job.resources.runtime)}"
 
-    if job.resources.get("constraint") or isinstance(
-        job.resources.get("constraint"), str
-    ):
-        call += f" -C '{job.resources.get('constraint')}'"
+    # Both, constraint and qos are optional.
+    # If not set, they will not be added to the sbatch call.
+    # If explicitly set to an empty string,
+    # `--constraint ''` or `--qos ''` will be added.
+    constraint = job.resources.get("constraint")
+    if constraint is not None:
+        call += f" -C {safe_quote(constraint)}"
 
-    if job.resources.get("qos") or isinstance(job.resources.get("qos"), str):
-        call += f" --qos='{job.resources.qos}'"
+    qos = job.resources.get("qos")
+    if qos is not None:
+        call += f" --qos={safe_quote(qos)}"
 
     if job.resources.get("mem_mb_per_cpu"):
         call += f" --mem-per-cpu {job.resources.mem_mb_per_cpu}"
@@ -66,7 +84,36 @@ def get_submit_command(job, params):
     else:
         # fixes #40 - set ntasks regardless of mpi, because
         # SLURM v22.05 will require it for all jobs
-        call += f" --ntasks={job.resources.get('tasks') or 1}"
+        # if the job is a MPI job, ntasks will be set later
+        if not job.resources.get("mpi", False):
+            call += f" --ntasks={job.resources.get('tasks') or 1}"
+
+    # if the job is an MPI job, we need to have some task setting:
+    if job.resources.get("mpi", False):
+        if not job.resources.get("tasks_per_node") and not job.resources.get("tasks"):
+            raise WorkflowError(
+                "For MPI jobs, please specify either "
+                "'tasks_per_node' or 'tasks' (at least one is required)."
+            )
+        # raise an error if both task settings are used
+        if job.resources.get("tasks_per_node") and job.resources.get("tasks"):
+            raise WorkflowError(
+                "For MPI jobs, please specify either 'tasks_per_node' or 'tasks', "
+                "but not both."
+            )
+        if job.resources.get("tasks_per_node"):
+            if job.resources.get("tasks_per_node") <= 1:
+                raise WorkflowError(
+                    "For MPI jobs, 'tasks_per_node' must be greater than 1."
+                )
+            call += f" --ntasks-per-node={job.resources.tasks_per_node}"
+        elif job.resources.get("tasks"):
+            if job.resources.get("tasks") == 1:
+                raise WorkflowError("For MPI jobs, 'tasks' must be greater than 1.")
+            call += f" --ntasks={job.resources.tasks}"
+        # nodes CAN be set independently of tasks or tasks_per_node
+        # this is at a user's discretion. The nodes flag might already
+        # be set above, if the user specified it.
 
     # we need to set cpus-per-task OR cpus-per-gpu, the function
     # will return a string with the corresponding value
@@ -77,6 +124,7 @@ def get_submit_command(job, params):
     # ensure that workdir is set correctly
     # use short argument as this is the same in all slurm versions
     # (see https://github.com/snakemake/snakemake/issues/2014)
-    call += f" -D '{params.workdir}'"
+    if params.workdir:
+        call += f" -D {safe_quote(params.workdir)}"
 
     return call

snakemake_executor_plugin_slurm/validation.py

@@ -0,0 +1,75 @@
+"""
+SLURM parameter validation functions for the Snakemake executor plugin.
+"""
+
+import re
+from snakemake_interface_common.exceptions import WorkflowError
+
+
+def get_forbidden_slurm_options():
+    """
+    Return a dictionary of forbidden SLURM options that the executor manages.
+
+    Returns:
+        dict: Mapping of regex patterns to human-readable option names
+    """
+    return {
+        # Job identification and output
+        r"--job-name[=\s]|-J\s?": "job name",
+        r"--output[=\s]|-o\s": "output file",
+        r"--error[=\s]|-e\s": "error file",
+        r"--parsable": "parsable output",
+        r"--export[=\s]": "environment export",
+        r"--comment[=\s]": "job comment",
+        r"--workdir[=\s]|-D\s": "working directory",
+        # Account and partition
+        r"--account[=\s]|-A\s": "account",
+        r"--partition[=\s]|-p\s": "partition",
+        # Memory options
+        r"--mem[=\s]": "memory",
+        r"--mem-per-cpu[=\s]": "memory per CPU",
+        # CPU and task options
+        r"--ntasks[=\s]|-n\s": "number of tasks",
+        r"--ntasks-per-gpu[=\s]": "tasks per GPU",
+        r"--cpus-per-task[=\s]|-c\s": "CPUs per task",
+        r"--cpus-per-gpu[=\s]": "CPUs per GPU",
+        # Time and resource constraints
+        r"--time[=\s]|-t\s": "runtime/time limit",
+        r"--constraint[=\s]|-C\s": "node constraints",
+        r"--qos[=\s]": "quality of service",
+        r"--nodes[=\s]|-N\s": "number of nodes",
+        r"--clusters[=\s]": "cluster specification",
+        # GPU options
+        r"--gres[=\s]": "generic resources (GRES)",
+        r"--gpus[=\s]": "GPU allocation",
+    }
+
+
+def validate_slurm_extra(job):
+    """
+    Validate that slurm_extra doesn't contain executor-managed options.
+
+    Args:
+        job: Snakemake job object with resources attribute
+
+    Raises:
+        WorkflowError: If forbidden SLURM options are found in slurm_extra
+    """
+    # skip testing if no slurm_extra is set
+    slurm_extra = getattr(job.resources, "slurm_extra", None)
+    if not slurm_extra:
+        return
+
+    forbidden_options = get_forbidden_slurm_options()
+
+    for pattern, option_name in forbidden_options.items():
+        if re.search(pattern, slurm_extra):
+            raise WorkflowError(
+                f"The --{option_name.replace(' ', '-')} option is not "
+                f"allowed in the 'slurm_extra' parameter. "
+                f"The {option_name} is set by the snakemake executor plugin "
+                f"and must not be overwritten. "
+                f"Please use the appropriate snakemake resource "
+                f"specification instead. "
+                f"Consult the documentation for proper resource configuration."
+            )

{snakemake_executor_plugin_slurm-1.7.0.dist-info → snakemake_executor_plugin_slurm-1.9.0.dist-info}/METADATA

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: snakemake-executor-plugin-slurm
-Version: 1.7.0
+Version: 1.9.0
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 License: MIT
+License-File: LICENSE
 Keywords: snakemake,plugin,executor,cluster,slurm
 Author: Christian Meesters
 Author-email: meesters@uni-mainz.de
@@ -12,6 +13,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: numpy (>=1.26.4,<3)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.3.0,<0.4.0)

snakemake_executor_plugin_slurm-1.9.0.dist-info/RECORD

@@ -0,0 +1,9 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=YUFJMWKlrbId4VgRreaea3B0JXJ_xTB1zNBJgAZ59Vw,33953
+snakemake_executor_plugin_slurm/efficiency_report.py,sha256=3F6AqkKOZBn9MxI7T27u3FF3-OAxY_ee_toHXnTGirs,8812
+snakemake_executor_plugin_slurm/submit_string.py,sha256=HL2QyT7-_HRu4yg_7tJSs1VtxGebNODOV8OQd2hYirg,5021
+snakemake_executor_plugin_slurm/utils.py,sha256=7XVXtzu7bg_89wWZisW-Zk7TNQyEgK4v_y4Y3F9uOwc,4491
+snakemake_executor_plugin_slurm/validation.py,sha256=hyWQWDjqHDLhO7caksYILTKjA2Ak91CMJeFwEcltYFo,2702
+snakemake_executor_plugin_slurm-1.9.0.dist-info/METADATA,sha256=UxDm36Px5LDOM8PtDP3LMv8mHyWUzuuNqVD2CW1CA_Y,1507
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+snakemake_executor_plugin_slurm-1.9.0.dist-info/licenses/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-1.9.0.dist-info/RECORD,,

{snakemake_executor_plugin_slurm-1.7.0.dist-info → snakemake_executor_plugin_slurm-1.9.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any

snakemake_executor_plugin_slurm-1.7.0.dist-info/RECORD

@@ -1,8 +0,0 @@
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-snakemake_executor_plugin_slurm/efficiency_report.py,sha256=crPfJDK4NojfRbu_wEw3ZmC3suMRABr5r-1rO5q3WEo,7429
-snakemake_executor_plugin_slurm/submit_string.py,sha256=Cn9qopyQwBqs1MvZFxSyRR_7mZzCVj8_vO_JNzbiqew,2896
-snakemake_executor_plugin_slurm/utils.py,sha256=7XVXtzu7bg_89wWZisW-Zk7TNQyEgK4v_y4Y3F9uOwc,4491
-snakemake_executor_plugin_slurm-1.7.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-1.7.0.dist-info/METADATA,sha256=XiUbU8KRQKmnK55EVkfrEKRYny3I4IF2WpbrfP43Acc,1434
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-snakemake_executor_plugin_slurm-1.7.0.dist-info/RECORD,,