diff --git a/docs/source/_static/babs_cli.png b/docs/source/_static/babs_cli.png index a4a460ba..db5108c3 100644 Binary files a/docs/source/_static/babs_cli.png and b/docs/source/_static/babs_cli.png differ diff --git a/docs/source/jobs.rst b/docs/source/jobs.rst index b902103f..8df48cb6 100644 --- a/docs/source/jobs.rst +++ b/docs/source/jobs.rst @@ -180,16 +180,15 @@ As you can see, in the summary ``Job status``, there are multiple sections: #. Line #9-16: Overall summary of number of jobs to complete, as well as their breakdowns: number of jobs submitted/finished/pending/running/failed; -#. Line 18-22: Summary of failed jobs, based on the provided section **alert_log_messages** in +#. Line #18-22: Summary of failed jobs, based on the provided section **alert_log_messages** in ``--container-config-yaml-file``, BABS tried to find user-defined alert messages in failed jobs' log files; -#. Line 24-25: If there are jobs that failed but don't have defined alert message, +#. Line #24-25: If there are jobs that failed but don't have defined alert message, and ``--job-account`` is requested, BABS will then run job account and try to extract more information and summarize. For each of these jobs, BABS runs job account command and extracts messages from it. - * In the above case, as ``hard_runtime_limit: "48:00:00"`` was set, - those 56 failed jobs without alert messages failed probably due to exceeding this runtime limit - (``h_rt limit`` in the line #25). + * In the above case, line #25 tells us that these jobs were killed by the cluster + because they exceeded resource limits. * For SGE clusters: BABS uses command ``qacct`` for job account, and pulls out the code and message from ``failed`` section in ``qacct``. * For Slurm clusters: BABS uses command ``sacct`` for job account, diff --git a/docs/source/walkthrough.rst b/docs/source/walkthrough.rst index 292407c5..4f616977 100644 --- a/docs/source/walkthrough.rst +++ b/docs/source/walkthrough.rst @@ -646,9 +646,9 @@ We'll iteratively use ``babs-submit`` and ``babs-status`` to submit jobs and che We first use ``babs-status`` to check the number of jobs we initially expect to finish successfully. In this example walkthrough, as no initial list was provided, -BABS determines this number based on the number of subject/session pairs in the input BIDS dataset. +BABS determines this number based on the number of sessions in the input BIDS dataset. We did not request extra filtering (based on required files) in our YAML file either, -so BABS will submit one job per subject/session pair. +so BABS will submit one job for each session. .. code-block:: console