snakemake produce Error when using "--max-jobs-per-timespan" switch #3030
Description
Snakemake version
snakemake-minimal 8.18.0 pyhdfd78af_0 bioconda
Describe the bug
snakemake produce Error when using "--max-jobs-per-timespan" switch.
Logs
$ snakemake -s snake_test --max-jobs-per-timespan 1/1s -c 1 --verbose
Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
shared_storage_local_copies: True
remote_exec: False
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
------- -------
testmax 1
tt 20
total 21
Resources before job selection: {'_cores': 1, '_nodes': 9223372036854775807, '_job_count': 9223372036854775807}
Ready jobs (20)
Select jobs to execute...
Welcome to the CBC MILP Solver
Version: 2.10.11
Build Date: Jun 6 2024
command line - cbc /tmp/b914c8533789440d987bb6466327145a-pulp.mps -max -timeMode elapsed -branch -printingOptions all -solution /tmp/b914c85337894
40d987bb6466327145a-pulp.sol (default strategy 1)
At line 2 NAME MODEL
At line 3 ROWS
At line 8 COLUMNS
At line 129 RHS
At line 133 BOUNDS
At line 154 ENDATA
Problem MODEL has 3 rows, 20 columns and 60 elements
Coin0008I MODEL read with 0 errors
Option for timeMode changed from cpu to elapsed
Continuous objective value is 2 - 0.23 seconds
Cgl0004I processed model has 0 rows, 0 columns (0 integer (0 of which binary)) and 0 elements
Cbc3007W No integer variables - nothing to do
Cuts at root node changed objective from 2 to 1.79769e+308
Probing was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Gomory was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Knapsack was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Clique was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
MixedIntegerRounding2 was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
FlowCover was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
TwoMirCuts was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
ZeroHalf was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Result - Optimal solution found
Objective value: 2.00000000
Enumerated nodes: 0
Total iterations: 0
Time (CPU seconds): 0.47
Time (Wallclock seconds): 0.01
Option for printingOptions changed from normal to all
Total time (CPU seconds): 0.93 (Wallclock seconds): 0.01
Selected jobs (1)
Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806, '_job_count': 1}
Execute 1 jobs...
[Mon Aug 19 16:12:12 2024]
localrule tt:
output: test14.test
jobid: 15
reason: Missing output files: test14.test
wildcards: idx=14
resources: tmpdir=/tmp
Completion of job ['tt'] reported to scheduler.
jobs registered as running before removal {tt}
[Mon Aug 19 16:12:13 2024]
Finished job 15.
1 of 21 steps (5%) done
Resources before job selection: {'_cores': 1, '_nodes': 9223372036854775807, '_job_count': 2}
Ready jobs (19)
Select jobs to execute...
Job rate limit reached, waiting for free slots.
unlocking
removing lock
removing lock
removed all locks
Full Traceback (most recent call last):
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/cli.py", line 2116, in args_to_api
dag_api.execute_workflow(
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/api.py", line 594, in execute_workflow
workflow.execute(
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/workflow.py", line 1261, in execute
raise e
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/workflow.py", line 1257, in execute
success = self.scheduler.schedule()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/scheduler.py", line 279, in schedule
f"Selected jobs ({len(run)})"
^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/cli.py", line 2116, in args_to_api
dag_api.execute_workflow(
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/api.py", line 594, in execute_workflow
workflow.execute(
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/workflow.py", line 1261, in execute
raise e
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/workflow.py", line 1257, in execute
success = self.scheduler.schedule()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/zhangxx/conda/snakemake_py312/lib/python3.12/site-packages/snakemake/scheduler.py", line 279, in schedule
f"Selected jobs ({len(run)})"
Minimal example
Using this test snakefile:
rule testmax:
input:
lambda wildcard:[f"test{rpt:0>2}.test" for rpt in range(0,20)]
rule tt:
output:
"test{idx}.test"
shell:
"touch test{wildcards.idx}.test"
This command produces error:
snakemake -s snake_test --max-jobs-per-timespan 1/1s -c 1
but this runs fine:
snakemake -s snake_test -c 1
Additional context
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge [38/1872]
idna 3.7 pyhd8ed1ab_0 conda-forge
immutables 0.20 py312h98912ed_1 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py312h7900ff3_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
libblas 3.9.0 23_linux64_openblas conda-forge
libcblas 3.9.0 23_linux64_openblas conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.4 h6a678d5_1
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgfortran-ng 14.1.0 h69a702a_0 conda-forge
libgfortran5 14.1.0 hc5f4f2c_0 conda-forge
libgomp 14.1.0 h77fa898_0 conda-forge
liblapack 3.9.0 23_linux64_openblas conda-forge
liblapacke 3.9.0 23_linux64_openblas conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
markupsafe 2.1.5 py312h98912ed_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
openssl 3.3.1 h4bc722e_2 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pip 24.2 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
plac 1.4.3 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
psutil 6.0.0 py312h9a8786e_0 conda-forge
pulp 2.8.0 py312h7900ff3_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.5 h2ad013b_0_cpython conda-forge
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pyyaml 6.0.2 py312h41a817b_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
reretry 0.11.8 pyhd8ed1ab_0 conda-forge
rpds-py 0.20.0 py312hf008fa9_0 conda-forge
setuptools 72.1.0 pyhd8ed1ab_0 conda-forge
smart_open 7.0.4 pyhd8ed1ab_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snakemake-executor-plugin-cluster-generic 1.0.9 pyhdfd78af_0 bioconda
snakemake-interface-common 1.17.2 pyhdfd78af_0 bioconda
snakemake-interface-executor-plugins 9.2.0 pyhdfd78af_0 bioconda
snakemake-interface-report-plugins 1.0.0 pyhdfd78af_0 bioconda
snakemake-interface-storage-plugins 3.2.3 pyhdfd78af_0 bioconda
snakemake-minimal 8.18.0 pyhdfd78af_0 bioconda
sqlite 3.46.0 h6d4b2fc_0 conda-forge
stopit 1.1.2 py_0 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toposort 1.10 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py312h98912ed_0 conda-forge
xz 5.4.6 h5eee18b_1
yaml 0.2.5 h7f98852_2 conda-forge
yte 1.5.4 pyha770c72_0 conda-forge
zipp 3.19.2 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 h4ab18f5_1 conda-forge
zstandard 0.23.0 py312h3483029_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge