_docs/examples/example_01_jupyterhub.html

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<h2 id="HPC-Runner-Submission">HPC Runner Submission<a class="anchor-link" href="#HPC-Runner-Submission">&#182;</a></h2>
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<div class=" highlight hl-ipython3"><pre><span></span>%%bash

cat example_001/preprocess.sh
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<pre>#HPC jobname=preprocess
#HPC commands_per_node=1
#HPC walltime=00:00:30
#HPC module=gencore/1 gencore_dev
echo &quot;preprocess sample1&quot; &amp;&amp; sleep 30 
echo &quot;preprocess sample2&quot; &amp;&amp; sleep 30 
echo &quot;preprocess sample3&quot; &amp;&amp; sleep 30
echo &quot;preprocess sample4&quot; &amp;&amp; sleep 30
echo &quot;preprocess sample5&quot; &amp;&amp; sleep 30
echo &quot;preprocess sample6&quot; &amp;&amp; sleep 30
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<pre><code>hpcrunner.pl submit_jobs --infile preprocess.sh</code></pre>

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<pre><code>[2016/11/03 08:50:03] Beginning to submit jobs to the scheduler 
[2016/11/03 08:50:03] Schedule is preprocess 
[2016/11/03 08:50:03] Submitting all preprocess job types 
[2016/11/03 08:50:04] Submitted batch job 23162

[2016/11/03 08:50:04] Submited job /scratch/gencore/nov_dalma_training/example_001/hpc-runner/scratch/001_preprocess.sh
        With Slurm jobid 23162 
[2016/11/03 08:50:04] There are 6 batches for job type preprocess</code></pre>

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<h2 id="Directory-Structure">Directory Structure<a class="anchor-link" href="#Directory-Structure">&#182;</a></h2>
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<div class=" highlight hl-ipython3"><pre><span></span>%%bash

tree example_001
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<pre>example_001
├── hpc-runner
│   ├── logs
│   │   ├── 2016-11-03-001_preprocess
│   │   │   ├── 2016-11-03-CMD_001-PID_13774.md
│   │   │   ├── 2016-11-03-CMD_002-PID_13778.md
│   │   │   ├── 2016-11-03-CMD_003-PID_13776.md
│   │   │   ├── 2016-11-03-CMD_004-PID_16555.md
│   │   │   ├── 2016-11-03-CMD_005-PID_16553.md
│   │   │   ├── 2016-11-03-CMD_006-PID_16551.md
│   │   │   └── MAIN_2016-11-03.log
│   │   └── 2016-11-03-hpcrunner_logs
│   │       ├── 001_preprocess.log
│   │       └── 001-process_table.md
│   └── scratch
│       ├── 001_preprocess_001.in
│       ├── 001_preprocess_002.in
│       ├── 001_preprocess_003.in
│       ├── 001_preprocess_004.in
│       ├── 001_preprocess_005.in
│       ├── 001_preprocess_006.in
│       └── 001_preprocess.sh
└── preprocess.sh

5 directories, 17 files
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<p>Each individual task gets its own output file. The structure is date of submission, jobtype, date of executition, task count, and processID.</p>

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<div class=" highlight hl-ipython3"><pre><span></span>%%bash

cat example_001/hpc-runner/logs/2016-11-03-001_preprocess/2016-11-03-CMD_001-PID_13774.md
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<pre>2016/11/03 08:50:11: INFO Starting Job: 1 
Cmd is echo &quot;preprocess sample1&quot; &amp;&amp; sleep 30 
 2016/11/03 08:50:11: INFO preprocess sample1
 2016/11/03 08:50:41: INFO Finishing job 1 with ExitCode 0
 2016/11/03 08:50:41: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds
 </pre>
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<h2 id="Slurm-Log-Output">Slurm Log Output<a class="anchor-link" href="#Slurm-Log-Output">&#182;</a></h2>
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<p>Additionally, all output from the scheduler is logged. This is useful when debugging submissions. If, for instance, we had mistyped a module name, submitted to the wrong queue, or requested impossible resources, this would be recorded here.</p>

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<div class=" highlight hl-ipython3"><pre><span></span>%%bash

cat example_001/hpc-runner/logs/2016-11-03-hpcrunner_logs/001_preprocess.log
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<pre>Module &apos;gencore/1&apos; is already loaded
Module &apos;gencore/1&apos; is already loaded
Module &apos;gencore/1&apos; is already loaded
Module &apos;gencore/1&apos; is already loadedModule &apos;gencore/1&apos; is already loadedModule &apos;gencore/1&apos; is already loaded


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<h2 id="Process-Table-Output">Process Table Output<a class="anchor-link" href="#Process-Table-Output">&#182;</a></h2>
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<p>The process table is a table for the whole job. It records version ( more on this later), the Slurm scheduler ID, the Slurm jobname, any task tags, and process pid, the exit code and the duration.</p>
<p>It is highly recommended to record this table in a project management tool.</p>

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<div class=" highlight hl-ipython3"><pre><span></span>%%bash

ls example_001/hpc-runner/logs/2016-11-03-hpcrunner_logs/001-process_table.md
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<pre>example_001/hpc-runner/logs/2016-11-03-hpcrunner_logs/001-process_table.md
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<table>
<thead><tr>
<th>Version</th>
<th>Scheduler Id</th>
<th>Jobname</th>
<th>Task Tags</th>
<th>ProcessID</th>
<th>ExitCode</th>
<th>Duration</th>
</tr>
</thead>
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<tr>
<td>0.0</td>
<td>23162</td>
<td>001_preprocess</td>
<td></td>
<td>16551</td>
<td>0</td>
<td>0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds</td>
</tr>
<tr>
<td>0.0</td>
<td>23167</td>
<td>001_preprocess</td>
<td></td>
<td>16553</td>
<td>0</td>
<td>0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds</td>
</tr>
<tr>
<td>0.0</td>
<td>23163</td>
<td>001_preprocess</td>
<td></td>
<td>13774</td>
<td>0</td>
<td>0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds</td>
</tr>
<tr>
<td>0.0</td>
<td>23166</td>
<td>001_preprocess</td>
<td></td>
<td>16555</td>
<td>0</td>
<td>0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds</td>
</tr>
<tr>
<td>0.0</td>
<td>23165</td>
<td>001_preprocess</td>
<td></td>
<td>13776</td>
<td>0</td>
<td>0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds</td>
</tr>
<tr>
<td>0.0</td>
<td>23164</td>
<td>001_preprocess</td>
<td></td>
<td>13778</td>
<td>0</td>
<td>0 years, 00 months, 0 days, 00 hours, 00 minutes, 30 seconds</td>
</tr>
</tbody>
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