Comments (10)
Simplifying the test case to
[global]
parameter: mem = "16G"
[A]
output: 'test_file'
task: mem = mem
bash: expand=True
touch {_output}
[B]
input: output_from("A")
bash:
touch {_input}.processed
with command error being
> sos run test_task_params.sos B -s force -q localhost
INFO: Running A:
ERROR: [A (A)]: [A]: Failed to execute process
"'bash(fr"""touch {_output}\n\n""")\n'"
name 'mem' is not defined
[B]: Exits with 1 pending step (B)
Note that the pipeline works without -q localhost
.
from sos.
Could you test if branch issue1457 works?
from sos.
Could you test if branch issue1457 works?
I am not sure how to install this branch into my cluster. I have been installing sos via pip.
from sos.
@hsun3163 you clone that branch to your computer, cd
to it and install via pip install .
from sos.
I can successfully run the new testing example you created. But when I try to run my original example, or any other notebook with task statement. I recieved the following error:
ERROR: Failed to parse statement: trunk_workers = 1, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}'
in exec mode
from sos.
Just pushed another commit. Please try again.
from sos.
I works now, thank you!
from sos.
Great. I will create a new release of sos after more testing.
from sos.
@BoPeng shall we make a new release so others will benefit from the fix? Currently this works well on our end.
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ok. I have just released sos 0.22.7. I have tried to make all sos tests run in the past few days. The problem was that the tests were using subprocess-based sos runs so all file handles will be reclaimed even if sos run
failed. I have changed most of the tests to execute_workflow
so many tests fail due to an insufficient number of file handlers, apparently caused by (intentionally) failed tests. The entire execution step is complicated so I have not figured out a good way to clean up properly.
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Related Issues (20)
- Inconsistent behavior of R_library() between released version 0.22.7 and current github 0.22.8 HOT 2
- Tasks with completed signature but missing output files are still ignored. HOT 8
- Error message of subtasks are not aggregated to tasks
- Remote signature does not appear to work
- MD5Sum for output, as an action option HOT 30
- Removing (corrupted) output files before the execution of steps.
- Additional flags for containers HOT 4
- Remote checks on dependent steps not working HOT 1
- kernel dead after launching jupyter or jupyterlab on macbook pro M1 HOT 3
- doesn't work with python 3.9 on macbook pro m1 with conda install. HOT 4
- Tab completion crashing IRkernel HOT 2
- sos syntax conflict with Python dataclass
- A summary of files generated by a step HOT 3
- remote computer wall time format HH:MM HOT 3
- Unable to use remote with dual factor auth HOT 3
- Missing tmp files HOT 11
- sos status show the uname of the machine HOT 7
- Combined use of -r and -q
- Singularity exec vs run HOT 6
- bug found in entrypoint version HOT 1
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