@@ -98,7 +98,7 @@ to the scheduler, we use the `{{ site.sched.submit.name }}` command.
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```
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{: .bash}
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- {% include {{ site.snippets }}/13/submit_output .snip %}
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+ {% include {{ site.snippets }}/13/basic-job-script .snip %}
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And that's all we need to do to submit a job. Our work is done -- now the scheduler takes over and
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tries to run the job for us. While the job is waiting to run, it goes into a list of jobs called
@@ -110,7 +110,7 @@ the *queue*. To check on our job's status, we check the queue using the command
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```
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{: .bash}
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- {% include {{ site.snippets }}/13/statu_output .snip %}
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+ {% include {{ site.snippets }}/13/basic-job-status .snip %}
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The best way to check our job's status is with `{{ site.sched.status }}`. Of course, running
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`{{ site.sched.status }}` repeatedly to check on things can be a little tiresome. To see a real-time
@@ -179,7 +179,7 @@ and monitor it:
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```
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{: .bash}
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- {% include {{ site.snippets }}/13/statu_name_output .snip %}
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+ {% include {{ site.snippets }}/13/job-with-name-status .snip %}
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Fantastic, we've successfully changed the name of our job!
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@@ -202,7 +202,7 @@ stuck with your site's default resources, which is probably not what you want.
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The following are several key resource requests:
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- {% include {{ site.snippets }}/13/stat_options .snip %}
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+ {% include {{ site.snippets }}/13/option-flags-list .snip %}
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Note that just *requesting* these resources does not make your job run faster! We'll talk more
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about how to make sure that you're using resources effectively in a later episode of this lesson.
@@ -238,7 +238,7 @@ about how to make sure that you're using resources effectively in a later episod
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> {: .solution}
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{: .challenge}
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- {% include {{ site.snippets }}/13/env_challenge .snip %}
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+ {% include {{ site.snippets }}/13/print-sched-variables .snip %}
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Resource requests are typically binding. If you exceed them, your job will be killed. Let's use
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walltime as an example. We will request 30 seconds of walltime, and attempt to run a job for two
@@ -269,9 +269,9 @@ Submit the job and wait for it to finish. Once it is has finished, check the log
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```
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{: .bash}
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- {% include {{ site.snippets }}/13/long_job_cat .snip %}
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+ {% include {{ site.snippets }}/13/runtime-exceeded-job .snip %}
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- {% include {{ site.snippets }}/13/long_job_err .snip %}
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+ {% include {{ site.snippets }}/13/runtime-exceeded-output .snip %}
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Our job was killed for exceeding the amount of resources it requested. Although this appears harsh,
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this is actually a feature. Strict adherence to resource requests allows the scheduler to find the
@@ -294,7 +294,7 @@ to change the walltime so that it runs long enough for you to cancel it before i
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```
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{: .bash}
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- {% include {{ site.snippets }}/13/del_job_output1 .snip %}
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+ {% include {{ site.snippets }}/13/terminate-job-begin .snip %}
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Now cancel the job with its job number (printed in your terminal). A clean return of your command
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prompt indicates that the request to cancel the job was successful.
@@ -306,9 +306,9 @@ prompt indicates that the request to cancel the job was successful.
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```
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{: .bash}
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- {% include {{ site.snippets }}/13/del_job_output2 .snip %}
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+ {% include {{ site.snippets }}/13/terminate-job-cancel .snip %}
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- {% include {{ site.snippets }}/13/del_multiple_challenge .snip %}
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+ {% include {{ site.snippets }}/13/terminate-multiple-jobs .snip %}
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## Other types of jobs
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@@ -321,4 +321,4 @@ handle. A good example of this might be building a genome index for alignment wi
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[HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml). Fortunately, we can run these types of
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tasks as a one-off with `{{ site.sched.interactive }}`.
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- {% include {{ site.snippets }}/13/interactive_example .snip %}
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+ {% include {{ site.snippets }}/13/using-nodes-interactively .snip %}
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