Update Examples: Difference between revisions

Revision as of 16:44, 8 February 2018

There are a collection of examples showing how to running some common modules on the Magnolia cluster, the update-examples command is used to easily copy the collection into the home directory, ${HOME}.

The Examples Directory

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

user $ls

examples  perl5

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

user $cd examples

user $ls

README.txt

The contents of README.txt can be viewed using cat:

user $cat README.txt


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

The README.txt file directs up to run the update-examples command to get a copy of the examples.

Update Examples

Running the update-examples commands gives:

user $update-examples

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

* CUDA      - Compiling CUDA programs
* lammps    - Classical molecular dynamics
* migrate-n - Population sizes and migration rates
* Molpro    - Electronic structure
* MPI       - Compiling MPI programs
* MrBayes   - Choosing phylogenetic and evolutionary models
* qe        - [Quantum ESPRESSO] Electronic-structure
* structure - Investigate population structure

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/20180208-135347.

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

Looking at the contents of the new directory shows:

user $ls ${HOME}/examples/20180208-135347

CUDA  lammps  migrate-n  Molpro  MPI  MrBayes  qe  README.txt  structure

Where each listing is a new directory corresponding to an example listed in the output of update-examples, plus an additional README.txt. Each directory should have its own 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 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.

@@ Line 1: / Line 1: @@
-There are a collection of examples for running 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], {{Path|${HOME}}}.
+There are a collection of examples showing how to running some common modules on the Magnolia cluster, the {{C|update-examples}} command is used to easily copy the collection into the [//www.wikipedia.org/wiki/Home_directory home directory], {{Path|${HOME}}}.
-=== Initial ===
+__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>
@@ Line 26: / Line 34: @@
 </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>
@@ Line 45: / Line 59: @@
 New examples saved to ${HOME}/examples/20180208-135347.
 </pre>}}
+A list of all the examples are shown, and the last line shows where the examples are stored, {{Path|${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/20180208-135347|output=<pre>
 CUDA  lammps  migrate-n  Molpro  MPI  MrBayes  qe  README.txt  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]]