v0.6

.gitignore

@@ -12,4 +12,7 @@ wheels/
 
 # Codecov
 htmlcov/
-.coverage
+.coverage
+
+# Documentations
+docs/

.readthedocs.yaml

@@ -0,0 +1,15 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py

CHANGELOG.md

@@ -1,3 +1,28 @@
+## Version 0.6.0
+
+### Support for per-node resources
+- Number of CPU cores, number of GPUs, the amount of memory and the amount of storage can be now requested per-node using the submission options `ncpus-per-node`, `ngpus-per-node`, `mem-per-node`, and `work-size-per-node`. Per-node properties override per-cpu properties (`mem-per-cpu`, `work-size-per-cpu`) but are overriden by "total" properties (`ncpus`, `ngpus`, `mem`, `work-size`).
+
+### Changes in Gromacs run scripts
+- The scripts now by default try to allocate the maximum possible number of MPI ranks.
+- Numbers of MPI ranks are now specified per node (in `*_md` scripts) or per client (in `*_re` scripts).
+
+### Bug fixes and minor improvements
+- The available types of working directories for the current environment are now shown in the output of `qq submit -h`.
+- Fixed a regression from v0.5: missing size property in `qq nodes` is now correctly intepreted as zero size.
+- When a job is killed, runtime files are copied to the input directory only after the executed process finishes.
+- Changed the way working directories on Karolina and LUMI are created allowing their complete removal.
+- Collection of Slurm jobs (which is complicated by Slurm's architecture) is now performed in parallel and is consequently much faster.
+
+### Internal changes
+- `Wiper.delete` method has been renamed to `Wiper.wipe`.
+- `Killer.terminate` method has been renamed to `Killer.kill`.
+- `SubmitterFactory` no longer requires a list of supported parameters and instead loads it itself.
+- Added getter methods to `Submitter`.
+- `Submitter` no longer requires to provide the "command line". Command line is no longer written into qq info files.
+
+***
+
 ## Version 0.5.1
 
 - If no info file is detected when running `qq go`, `qq info`, `qq kill`, `qq sync`, and `qq wipe`, an error message is printed. (This fixes a regression in v0.5.0.)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "qq"
-version = "0.5.1"
+version = "0.6.0-dev.2"
 description = "A friendly interface to batch processing"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -40,6 +40,7 @@ Documentation = "https://ladme.github.io/qq-manual"
 [dependency-groups]
 dev = [
     "codecov>=2.1.13",
+    "pdoc>=16.0.0",
     "pre-commit>=4.3.0",
     "pyinstaller>=6.16.0",
     "pytest>=8.4.2",
@@ -49,6 +50,9 @@ dev = [
     "ty>=0.0.1a24",
 ]
 
+[tool.ruff]
+extend-include = ["scripts/qq_scripts/*"]
+
 [tool.ruff.lint]
 extend-select = [
     "F",   # Pyflakes rules
@@ -68,4 +72,4 @@ extend-select = [
     "NPY", # Some numpy-specific things
     "ARG", # Catch incorrect use of arguments
 ]
-ignore = ["E501"]
+ignore = ["E501"]

scripts/qq_scripts/gmx-eta

@@ -0,0 +1,103 @@
+#!/usr/bin/env -S uv run --script
+
+# Released under MIT License.
+# Copyright (c) 2025 Ladislav Bartos and Robert Vacha Lab
+
+"""
+Get the estimated time of a Gromacs simulation finishing.
+Version 0.2.
+Requires `uv`: https://docs.astral.sh/uv
+"""
+
+# /// script
+# requires-python = ">=3.12"
+# dependencies = [
+#     "qq",
+# ]
+#
+# [tool.uv.sources]
+# qq = { git = "https://github.com/Ladme/qq.git", tag = "v0.6.0" }
+# ///
+
+import argparse
+from datetime import datetime
+from pathlib import Path
+
+from rich import print
+
+from qq_lib.batch.interface import BatchMeta
+from qq_lib.core.common import format_duration_wdhhmmss, get_info_files
+from qq_lib.core.navigator import Navigator
+from qq_lib.info import Informer
+
+
+def get_informer(id: str | None) -> Informer:
+    """Get informer for the given job id or for the newest job in the current directory."""
+    if id:
+        return Informer.fromJobId(id)
+    return Informer.fromFile(get_info_files(Path())[-1])
+
+
+def get_eta_from_content(content: str) -> datetime | None:
+    """Get the time at which the Gromacs simulation is expected to finish."""
+
+    # find the last line containing the ETA
+    eta_line = next((s for s in content if "will finish" in s), None)
+    if not eta_line:
+        return None
+
+    # assuming the time information is stored in the last 5 words
+    eta = " ".join(eta_line.split()[-5:])
+
+    try:
+        return datetime.strptime(eta, "%a %b %d %H:%M:%S %Y")
+    except Exception:
+        return None
+
+
+def main():
+    # parse command line options
+    parser = argparse.ArgumentParser(
+        "gmx-eta",
+        description="Get the estimated time of a Gromacs simulation finishing.",
+    )
+    parser.add_argument("job_id", nargs="?", help="Job ID. Optional.", default=None)
+    args = parser.parse_args()
+
+    informer = get_informer(args.job_id)
+    navigator = Navigator.fromInformer(informer)
+
+    if (main_node := navigator.getMainNode()) and (work_dir := navigator.getWorkDir()):
+        BatchSystem = BatchMeta.fromEnvVarOrGuess()
+        # use the batch system to read the remote file with Gromacs output
+        # split the lines and reverse the content to read from the end
+        try:
+            content = reversed(
+                BatchSystem.readRemoteFile(
+                    main_node, work_dir / informer.info.stderr_file
+                ).splitlines()
+            )
+        except Exception as e:
+            print(f"No information is available: {e}")
+            return
+
+        # get eta
+        eta = get_eta_from_content(content)
+        if eta and datetime.now() <= eta:
+            print(
+                f"Simulation will finish in [bright_blue bold]{format_duration_wdhhmmss(eta - datetime.now())}[/bright_blue bold]."
+            )
+        elif eta and datetime.now() > eta:
+            print(
+                f"Simulation has finished at [bright_green bold]{str(eta)}[/bright_green bold]."
+            )
+        else:
+            print("No information is available.")
+
+    else:
+        print("No information is available: job does not have a working directory.")
+        return
+
+
+if __name__ == "__main__":
+    main()