Deploy docs to develop by GitHub Actions triggered by fd5e9a5

manual/develop/en/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 09cbd1640c31fca0989e41f0ebfe898d
+config: d0577335a099bbf09bab264ed0265eb4
 tags: 645f666f9bcd5a90fca523b33c5a78b7

manual/develop/en/html/_sources/moller/about/index.rst.txt

@@ -23,6 +23,8 @@ Contributors
 
 This software was developed by the following contributors.
 
+-  ver.1.0.0 (Released on 2024/03/06)
+
 -  ver.1.0-beta (Released on 2023/12/28)
 
    -  Developers

manual/develop/en/html/_sources/moller/command/index.rst.txt

@@ -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``
 
@@ -91,5 +91,5 @@ DESCRIPTION:
 
 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.
 

manual/develop/en/html/_sources/moller/tutorial/basic.rst.txt

@@ -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.
 
@@ -128,3 +128,34 @@ An example of the output is shown below:
 
 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.
+

manual/develop/en/html/_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '1.0-dev',
+    VERSION: '1.1-dev',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

manual/develop/en/html/genindex.html

@@ -4,11 +4,11 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>Index &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
-    <script src="_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="_static/documentation_options.js?v=5f12b55d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="#" />
@@ -93,7 +93,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

manual/develop/en/html/index.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Moller Users Guide &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>Moller Users Guide &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
-    <script src="_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="_static/documentation_options.js?v=5f12b55d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -107,7 +107,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="_sources/index.rst.txt"

manual/develop/en/html/moller/about/index.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>1. Introduction &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>1. Introduction &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
-    <script src="../../_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="../../_static/documentation_options.js?v=5f12b55d"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -53,6 +53,7 @@ <h2><span class="section-number">1.2. </span>License<a class="headerlink" href="
 <h2><span class="section-number">1.3. </span>Contributors<a class="headerlink" href="#contributors" title="Link to this heading">¶</a></h2>
 <p>This software was developed by the following contributors.</p>
 <ul class="simple">
+<li><p>ver.1.0.0 (Released on 2024/03/06)</p></li>
 <li><p>ver.1.0-beta (Released on 2023/12/28)</p>
 <ul>
 <li><p>Developers</p>
@@ -158,7 +159,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="../../_sources/moller/about/index.rst.txt"

manual/develop/en/html/moller/appendix/index.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>6. Extension guide &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>6. Extension guide &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
-    <script src="../../_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="../../_static/documentation_options.js?v=5f12b55d"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -307,7 +307,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="../../_sources/moller/appendix/index.rst.txt"

manual/develop/en/html/moller/basic-usage.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>2. Installation and basic usage &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>2. Installation and basic usage &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
-    <script src="../_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="../_static/documentation_options.js?v=5f12b55d"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -245,7 +245,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="../_sources/moller/basic-usage.rst.txt"

manual/develop/en/html/moller/command/index.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>4. Command reference &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>4. Command reference &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
-    <script src="../../_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="../../_static/documentation_options.js?v=5f12b55d"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -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>
@@ -119,7 +119,7 @@ <h2><span class="section-number">4.2. </span>moller_status<a class="headerlink"
 </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>
@@ -192,7 +192,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="../../_sources/moller/command/index.rst.txt"

manual/develop/en/html/moller/filespec/index.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>5. File format &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>5. File format &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=94bc0932" />
     <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
-    <script src="../../_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="../../_static/documentation_options.js?v=5f12b55d"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -239,7 +239,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="../../_sources/moller/filespec/index.rst.txt"

manual/develop/en/html/moller/index.html

@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Comprehensive Calculation Utility (moller) &#8212; Moller Users Guide 1.0-dev documentation</title>
+    <title>Comprehensive Calculation Utility (moller) &#8212; Moller Users Guide 1.1-dev documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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     <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
-    <script src="../_static/documentation_options.js?v=a2628a1b"></script>
+    <script src="../_static/documentation_options.js?v=5f12b55d"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -138,7 +138,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.15</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
       |
       <a href="../_sources/moller/index.rst.txt"