View source for Update Examples

There are a collection of examples showing how to run some common modules on the Magnolia cluster, the {{C|update-examples}} command is used to easily copy the collection into the [//www.wikipedia.org/wiki/Home_directory home directory].

__TOC__

=== The Examples Directory ===

When first signing on the Magnolia cluster, the home directory will consist of the following two directories:

{{Cmd|ls|output=<pre>
examples  perl5
</pre>}}

Changing to the {{Path|examples}} directory, and listing its contents reveals a {{Path|README.txt}} file.

{{Cmd|cd examples|ls|output=<pre>
README.txt
</pre>}}

The contents of {{Path|README.txt}} can be viewed using {{C|cat}}:

{{Cmd|cat README.txt|output=<pre>

Examples for submitting jobs on Magnolia Cluster
================================================

Examples will be saved, by default, in this
directory.

To get a copy of the newest version of job
submission examples, run the following command
at anytime:

          update-examples

</pre>}}

The {{Path|README.txt}} file directs up to run the {{C|update-examples}} command to get a copy of the examples.

=== Update Examples ===

Running the {{C|update-examples}} commands gives:

{{Cmd|update-examples|output=<pre>
Examples for submitting jobs on Magnolia Cluster
================================================

* CUDA        - Compiling CUDA programs
* Gaussian    - Electronic structure
* lammps      - Classical molecular dynamics
* migrate-n   - Population sizes and migration rates
* Molpro      - Electronic structure
* MPI         - Compiling MPI programs
* MrBayes     - Choosing phylogenetic and evolutionary models
* NAMD        - Molecular dynamics
* OpenMP      - Compiling OpenMP programs
* py-threads  - Using Threads in Python programs
* qe          - [Quantum ESPRESSO] Electronic-structure
* structure   - Investigate population structure
* compression - Convenience scripts to do compression on a compute node

See the README.txt file inside each directory for instructions on
how to run the examples (e.g., cat README.txt).

New examples saved to ${HOME}/examples/20210214-231213.
</pre>}}

A list of all the examples are shown, and the last line shows where the examples are stored, {{Path|${HOME}/examples/20180208-135347}}. The directory {{Path|20180208-135347}}, created inside {{Path|${HOME}/examples}}, is a date-time stamp of the format ''YYYYMMDD-HHMMSS'', indicating the date and time that {{C|update-examples}} was run. Therefore, every time {{C|update-examples}} is run, a new directory is created inside {{Path|${HOME}/examples}} with the current date and time.

Looking at the contents of the new directory shows:

{{Cmd|ls ${HOME}/examples/20210214-231213|output=<pre>
compression  Gaussian  migrate-n  MPI      NAMD    py-threads  README.txt
CUDA         lammps    Molpro     MrBayes  OpenMP  qe          structure
</pre>}}

Where each listing is a new directory corresponding to an example listed in the output of {{C|update-examples}}, plus an additional {{Path|README.txt}}. Each directory should have its own {{Path|README.txt}}, which explains in detail how to run the example on the cluster.

=== Tweaking the Examples ===

It is recommended to tweak and play with various settings of the examples to learn how they affect the runs on the cluster. Do not worry about breaking the examples; if you need to get back to a clean set of examples, simply run {{C|update-examples}} again. The new set of examples will be saved in a date-time stamped directory, and your modified examples will still be available in the original directory, so you can compared the differences if you get lost.

[[Category:Tutorials]]