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Chenying Zhao
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Merge pull request #135 from PennLINC/docs/minor_fix
[DOCS] minor fix in docs
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docs/source/_static/babs_cli.png

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docs/source/jobs.rst

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@@ -180,16 +180,15 @@ As you can see, in the summary ``Job status``, there are multiple sections:
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#. Line #9-16: Overall summary of number of jobs to complete,
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as well as their breakdowns: number of jobs submitted/finished/pending/running/failed;
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#. Line 18-22: Summary of failed jobs, based on the provided section **alert_log_messages** in
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#. Line #18-22: Summary of failed jobs, based on the provided section **alert_log_messages** in
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``--container-config-yaml-file``, BABS tried to find user-defined alert messages in failed jobs' log files;
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#. Line 24-25: If there are jobs that failed but don't have defined alert message,
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#. Line #24-25: If there are jobs that failed but don't have defined alert message,
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and ``--job-account`` is requested, BABS will then run job account
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and try to extract more information and summarize.
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For each of these jobs, BABS runs job account command and extracts messages from it.
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* In the above case, as ``hard_runtime_limit: "48:00:00"`` was set,
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those 56 failed jobs without alert messages failed probably due to exceeding this runtime limit
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(``h_rt limit`` in the line #25).
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* In the above case, line #25 tells us that these jobs were killed by the cluster
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because they exceeded resource limits.
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* For SGE clusters: BABS uses command ``qacct`` for job account,
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and pulls out the code and message from ``failed`` section in ``qacct``.
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* For Slurm clusters: BABS uses command ``sacct`` for job account,

docs/source/walkthrough.rst

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@@ -646,9 +646,9 @@ We'll iteratively use ``babs-submit`` and ``babs-status`` to submit jobs and che
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We first use ``babs-status`` to check the number of jobs we initially expect to finish successfully.
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In this example walkthrough, as no initial list was provided,
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BABS determines this number based on the number of subject/session pairs in the input BIDS dataset.
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BABS determines this number based on the number of sessions in the input BIDS dataset.
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We did not request extra filtering (based on required files) in our YAML file either,
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so BABS will submit one job per subject/session pair.
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so BABS will submit one job for each session.
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.. code-block:: console
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