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fix: bug when requesting extended benchmark with slurm #2855

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merged 2 commits into from
May 2, 2024
Merged

fix: bug when requesting extended benchmark with slurm #2855

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0d520c7
Fix bug when requesting extended benchmark with slurm
fgvieira Apr 30, 2024
07a235f
Remove debug logs
fgvieira May 2, 2024
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4 changes: 2 additions & 2 deletions docs/snakefiles/rules.rst
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Expand Up @@ -1942,7 +1942,7 @@ benchmarks the
* `mean_load`: CPU load = CPU time (`cpu_usage`) divided by wall clock time (`s`),
* `cpu_time`: CPU time user+system (seconds),

Since version X.X, it is possible to have extra benchmark metrics with the command ``--benchmark-extended``:
Since version 8.11.0, it is possible to have extra benchmark metrics with the command ``--benchmark-extended``:
* `jobid`: Internal job ID,
* `rule_name`: Name of rule,
* `wildcards`: Wildcards of this job,
Expand Down Expand Up @@ -1972,7 +1972,7 @@ However, the benchmark file can be annotated with the desired number of repeats,
will instruct Snakemake to run each job of this rule three times and store all measurements in the benchmark file.
The resulting `tsv` file can be used as input for other rules, just like any other output file.

Since version X.X, it is also possible to have the benchmark metrics in different formats (depending on the extension); currently only the `.jsonl` extension (JSONL format; i.e. one JSON record per line) is supported and all other extensions will be treated as TSV.
Since version 8.11.0, it is also possible to have the benchmark metrics in different formats (depending on the extension); currently only the `.jsonl` extension (JSONL format; i.e. one JSON record per line) is supported and all other extensions will be treated as TSV.

.. sidebar:: Note

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2 changes: 0 additions & 2 deletions snakemake/path_modifier.py
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Expand Up @@ -40,10 +40,8 @@ def modify(self, path, property=None):
return path

modified_path = self.apply_default_storage(self.replace_prefix(path, property))
logger.debug(f"Path {path}, converted to {modified_path}")
if modified_path == path:
# nothing has changed
logger.debug("Path did not change after prefix replace")
return path

# Important, update with previous flags in case of AnnotatedString #596
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1 change: 1 addition & 0 deletions snakemake/spawn_jobs.py
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Expand Up @@ -287,6 +287,7 @@ def general_args(
w2a("overwrite_configfiles", flag="--configfiles"),
w2a("config_settings.config_args", flag="--config"),
w2a("output_settings.printshellcmds"),
w2a("output_settings.benchmark_extended"),
w2a("execution_settings.latency_wait"),
w2a("scheduling_settings.scheduler", flag="--scheduler"),
local_storage_prefix,
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