vatlab / sos

SoS workflow system for daily data analysis
http://vatlab.github.io/sos-docs
BSD 3-Clause "New" or "Revised" License
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Remote checks on dependent steps not working #1502

Open pgcudahy opened 2 years ago

pgcudahy commented 2 years ago

Hello Bo, thanks again for providing this excellent tool. I have a workflow where I build a custom database for kraken and then have a subsequent step that uses kraken and the database on some samples with a dependency on the database build step. However, when I change the database build step, the subsequent steps do not re-run. Here's an example.

%sosrun depends_test -q yale_hpc_task_spooler \
-r yale_hpc_task_spooler mem="1G" cores=1 walltime="00:05:00" nodes=1

[touch_files]
output: f'/home/pgc29/scratch60/test.txt'
task: walltime='00:01:00', mem='1G', cores=1, nodes=1,
    workdir='/home/pgc29/scratch60/'

run: expand=True
    touch {_output}

[depends_test]
depends: sos_step('touch_files')
output: f'/home/pgc29/data/test2.txt'
task: walltime='00:01:00', mem='1G', cores=1, nodes=1,
    workdir='/home/pgc29/scratch60/'

run: expand=True
    touch {_output}

But if I then modify the first step to

[touch_files]
output: f'/home/pgc29/scratch60//test.txt'
task: walltime='00:01:00', mem='1G', cores=1, nodes=1,
    workdir='/home/pgc29/scratch60/'

run: expand=True
    echo "test" > {_output}

And run depends_test again, it re-runs touch_files but skips depends_test

INFO: Running touch_files: 
INFO: tce6f8d6f7553ab25 submitted to yale_hpc_task_spooler with job id 30325020
INFO: Waiting for the completion of 1 task.
INFO: tce6f8d6f7553ab25 received '/home/pgc29/scratch60/test.txt' from yale_hpc_task_spooler
INFO: touch_files output:   /home/pgc29/scratch60/test.txt
INFO: Running depends_test: 
INFO: depends_test (index=0) is ignored due to saved signature
INFO: depends_test (index=0) is ignored due to saved signature
INFO: depends_test output:   /home/pgc29/scratch60/test2.txt
INFO: Workflow depends_test (ID=w01db23b738dc700b) is executed successfully with 1 completed step, 1 ignored step and 1 completed task.
BoPeng commented 2 years ago

It is a moderately complex setup. Let me try to reproduce it and see why signature does not work.