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HTP-tools Developers committed Mar 1, 2024
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4 changes: 2 additions & 2 deletions manual/main/en/html/_sources/moller/command/index.rst.txt
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Expand Up @@ -57,7 +57,7 @@ DESCRIPTION:

- ``list_file``

specifies the file that contains list of job directories. If this file is not specified, the list will be obtained from the logfile of the batch job ``log_{task}.dat``.
specifies the file that contains list of job directories. If this file is not specified, the list will be obtained from the logfile of the batch job ``stat_{task}.dat``.

- ``-o``, ``--output`` ``output_file``

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FILES:

When the programs are executed concurrently using the job script generated by ``moller``, the status of the tasks are written in log files ``log_{task}.dat``. ``moller_status`` reads these log files and makes a summary.
When the programs are executed concurrently using the job script generated by ``moller``, the status of the tasks are written in log files ``stat_{task}.dat``. ``moller_status`` reads these log files and makes a summary.

33 changes: 32 additions & 1 deletion manual/main/en/html/_sources/moller/tutorial/basic.rst.txt
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Expand Up @@ -78,7 +78,7 @@ A list of jobs is to be created. ``moller`` is designed so that each job is exec

.. code-block:: bash
$ /usr/bin/ls -1d > list.dat
$ /usr/bin/ls -1d * > list.dat
In this tutorial, an utility script ``make_inputs.sh`` is enclosed which generates datasets and a list file.

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where "o" corresponds to a task that has been completed successfully, "x" corresponds to a failed task, "-" corresponds to a skipped task because the previous task has been terminated with errors, and "." corresponds to a task yet unexecuted.
In the above example, the all tasks have been completed successfully.


Rerun failed tasks
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If a task fails, the subsequent tasks within the job will not be executed.
The following is an example of job status in which each task fails by 10% change.

.. literalinclude:: ../../../../tutorial/moller/reference/status_failed.txt

There, the jobs of dataset_0003 and dataset_0004 failed at task1, and the subsequent task2 and task3 were not executed. The other jobs were successful at task1, and proceeded to task2.
In this way, each job is executed independently of other jobs.

Users can rerun the failed tasks by submitting the batch job with the retry option.
For SLURM job scheduler (e.g. used in ISSP system B), resubmit the job as follows:

.. code-block:: bash
$ sbatch job.sh --retry list.dat
For PBS job scheduler (e.g. used in ISSP system C), edit the job script so that the line ``retry=0`` is replaced by ``retry=1``, and resubmit the job.

.. literalinclude:: ../../../../tutorial/moller/reference/status_retry.txt

The tasks that have failed will be executed in the second run.
In the above example, the task1 for dataset_0003 was successful, but the task2 failed.
For dataset_0004, task1, task2, and task3 were successfully executed.
For the jobs of datasets whose tasks have already finished successfully, the second run will not do anything.

N.B. the list file must not be modified on the rerun. The jobs are managed according to the order of entries in the list file, and therefore, if the order is changed, the jobs will not be executed properly.

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2 changes: 1 addition & 1 deletion manual/main/en/html/genindex.html
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Expand Up @@ -93,7 +93,7 @@ <h3 id="searchlabel">Quick search</h3>

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2 changes: 1 addition & 1 deletion manual/main/en/html/moller/about/index.html
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6 changes: 3 additions & 3 deletions manual/main/en/html/moller/command/index.html
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Expand Up @@ -90,7 +90,7 @@ <h2><span class="section-number">4.2. </span>moller_status<a class="headerlink"
<p>specifies the job description file for <code class="docutils literal notranslate"><span class="pre">moller</span></code>.</p>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">list_file</span></code></p>
<p>specifies the file that contains list of job directories. If this file is not specified, the list will be obtained from the logfile of the batch job <code class="docutils literal notranslate"><span class="pre">log_{task}.dat</span></code>.</p>
<p>specifies the file that contains list of job directories. If this file is not specified, the list will be obtained from the logfile of the batch job <code class="docutils literal notranslate"><span class="pre">stat_{task}.dat</span></code>.</p>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">-o</span></code>, <code class="docutils literal notranslate"><span class="pre">--output</span></code> <code class="docutils literal notranslate"><span class="pre">output_file</span></code></p>
<p>specifies the output file name. If it is omitted, the result is written to the standard output.</p>
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</div></blockquote>
<p>FILES:</p>
<blockquote>
<div><p>When the programs are executed concurrently using the job script generated by <code class="docutils literal notranslate"><span class="pre">moller</span></code>, the status of the tasks are written in log files <code class="docutils literal notranslate"><span class="pre">log_{task}.dat</span></code>. <code class="docutils literal notranslate"><span class="pre">moller_status</span></code> reads these log files and makes a summary.</p>
<div><p>When the programs are executed concurrently using the job script generated by <code class="docutils literal notranslate"><span class="pre">moller</span></code>, the status of the tasks are written in log files <code class="docutils literal notranslate"><span class="pre">stat_{task}.dat</span></code>. <code class="docutils literal notranslate"><span class="pre">moller_status</span></code> reads these log files and makes a summary.</p>
</div></blockquote>
</section>
</section>
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