Commit a387d103 authored by Alan O'Cais's avatar Alan O'Cais

Add a template for the pilot projects

Add directories for Silvia and Hideki
parent 8de28346
......@@ -32,11 +32,27 @@ This definition is deliberately broader than the traditional concept of a module
Perhaps more important than exactly what a module is, is how it is written and used. A final E-CAM module adheres to current best-practice programming style conventions, is well documented and comes with either regression or unit tests (and any necessary associated data). E-CAM modules should be written in such a way that they can potentially take advantage of anticipated hardware developments in the near future (and this is one of the training objectives of E-CAM).
Pilot Projects
==============
One of primary activity of E-CAM is to engage with pilot projects with industrial partners. These projects are conceived
together with the partner and typically are to facilitate or improve the scope of computational simulation within the
partner. The related code development for the pilot projects are open source (where the licence of the underlying
software allows this) and are described in the modules associated with the pilot projects.
Below is a list of the current pilot projects within E-CAM:
.. toctree::
:glob:
:maxdepth: 1
./modules/example_pilot/readme
Extended Software Development Workshops
=======================================
DL_MESO_DPD
-------------------
-----------
The following modules connected to the DL_MESO_DPD code have been produce so far:
.. toctree::
......
......@@ -80,10 +80,10 @@ If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2002]_. Note that citations may get rearranged, e.g., to the bottom of the
If you want to add a citation, such as [CIT2009]_. Note that citations may get rearranged, e.g., to the bottom of the
"page".
.. [CIT2002] A citation (as often used in journals).
.. [CIT2009] A citation (as often used in journals).
Background Information
______________________
......
.. _patch_extreme:
#####################
Patch file for module
#####################
To include a patch file do something like the following:
.. literalinclude:: ./simple.patch
:language: c
:emphasize-lines: 2,9-11
:linenos:
:download:`Downloadable version of patch file <simple.patch>`
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded
and followed by white space (if you see warnings when this file is built they this is a common origin for problems).
.. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in
progress, please help us improve it. We use *definition lists* of ReST_ to make this readable.
.. sidebar:: Software Technical Information
Language
Please indicate the primary language(s) used by the module. Please also state if interfaces for other languages are
available.
Licence
Specify the licence under which the software is released. Provide a link to the full online description of the
licence. You'll find descriptions of the most common licences at https://opensource.org/licenses .
An example here would be: `GPL <https://opensource.org/licenses/gpl-license>`_
Documentation Tool
All source code created for this module should be documented so please indicate what tool has been used for
documentation. Doxygen covers most languages but for Fortran you might want to use
`Ford <http://fortranwiki.org/fortran/show/FORD>`_, for Python ReST_, etc.
Application Documentation
Provide a link to any documentation for the application.
Relevant Training Material
Add a link to any relevant training material. If there currently is none then say 'Not currently available.'
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _extreme_example:
############################
E-CAM example extreme module
############################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
This is an example of what a *module* for E-CAM looks like. The original source of this page (:download:`readme.rst`)
contains lots of additional comments to help you create your module (and understand ReST_ syntax) so please use this as
a starting point. You are free add any level of complexity you wish (within the bounds of what ReST_ can do). More
general instructions for making your contribution can be found in ":ref:`contributing`".
Remember that for a module to be accepted into the E-CAM repository, your source code changes in the target application
must pass a number of acceptance criteria:
* Style *(use meaningful variable names, no global variables,...)*
* Source code documentation *(each function should be documented with each argument explained)*
* Tests *(everything you add should have either unit or regression tests)*
* Performance *(If what you introduce has a significant computational load you should make some performance optimisation
effort using an appropriate tool. You should be able to verify that your changes have not introduced unexpected
performance penalties, are threadsafe if needed,...)*
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
it fits into the larger picture of what you want to achieve.
If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2004]_. Note that citations may get rearranged, e.g., to the bottom of the
"page".
.. [CIT2004] A citation (as often used in journals).
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
If the modifications are to an existing code base (which is typical) then this would be the place to name that
application. List any relevant urls and explain how to get access to that code. There needs to be enough information
here so that the person reading knows where to get the source code for the application, what version this information is
relevant for, whether this requires any additional patches/plugins, etc.
Overall, this module is supposed to be self-contained, but linking to specific URLs with more detailed information is
encouraged. In other words, the reader should not need to do a websearch to understand the context of this module, all
the links they need should be already in this module.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Provide the build information for the module here and explain how tests are run. This needs to be adequately detailed,
explaining if necessary any deviations from the normal build procedure of the application (and links to information
about the normal build process needs to be provided).
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_
Here link the source code *that was created for the module*. If you are using Github or GitLab and the `Gitflow Workflow
<https://www.atlassian.com/git/tutorials/comparing-workflows#gitflow-workflow>`_ you can point to your feature branch.
Linking to your pull/merge requests is even better. Otherwise you can link to the explicit commits. In this example I'm
using a patch file to highlight my source code changes, for that reason I need to explain what code (including exact
version information), the source code is for.
You can create a similar patch file by (for example if you are using git for your version control) making your changes
for the module in a feature branch and then doing something like the following:
.. Don't forget the white space around the "literal block" (a literal block keeps all spacing and is a good way to
include terminal output, file contents, etc.)
::
[adam@mbp2600 example (master)]$ git checkout -b tmpsquash
Switched to a new branch "tmpsquash"
[adam@mbp2600 example (tmpsquash)]$ git merge --squash newlines
Updating 4d2de39..b6768b2
Fast forward
Squash commit -- not updating HEAD
test.txt | 2 ++
1 files changed, 2 insertions(+), 0 deletions(-)
[adam@mbp2600 example (tmpsquash)]$ git commit -a -m "My squashed commits"
[tmpsquash]: created 75b0a89: "My squashed commits"
1 files changed, 2 insertions(+), 0 deletions(-)
[adam@mbp2600 example (tmpsquash)]$ git format-patch master
0001-My-squashed-commits.patch
To include a patch file do something like the following (take a look at the source code of this document to see the
syntax required to get this):
.. Below I am telling Sphinx that the included file is C code, if possible it will then do syntax highlighting. I can
even emphasise partiuclar lines (here 2 and 9-11)
.. literalinclude:: ./simple.patch
:language: c
:emphasize-lines: 2,9-11
:linenos:
If the patch is very long you will probably want to add it as a subpage which can be done as follows
.. toctree::
:glob:
:maxdepth: 1
patch
.. Remember to change the reference "patch" for something unique in your patch file subpage or you will have
cross-referencing problems
you can reference it with :ref:`patch`
.. Here are the URL references used (which is alternative method to the one described above)
.. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
Always remember that a good patch file should have a comment inside about what the patch is for....just like this
--- hello.c 2014-10-07 18:17:49.000000000 +0530
+++ hello_new.c 2014-10-07 18:17:54.000000000 +0530
@@ -1,5 +1,6 @@
#include <stdio.h>
-int main() {
+int main(int argc, char *argv[]) {
printf("Hello World\n");
+ return 0;
}
\ No newline at end of file
.. _patch_pilot:
#####################
Patch file for module
#####################
To include a patch file do something like the following:
.. literalinclude:: ./simple.patch
:language: c
:emphasize-lines: 2,9-11
:linenos:
:download:`Downloadable version of patch file <simple.patch>`
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded
and followed by white space (if you see warnings when this file is built they this is a common origin for problems).
.. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in
progress, please help us improve it. We use *definition lists* of ReST_ to make this readable.
.. sidebar:: Software Technical Information
Language
Please indicate the primary language(s) used by the module. Please also state if interfaces for other languages are
available.
Licence
Specify the licence under which the software is released. Provide a link to the full online description of the
licence. You'll find descriptions of the most common licences at https://opensource.org/licenses .
An example here would be: `GPL <https://opensource.org/licenses/gpl-license>`_
Documentation Tool
All source code created for this module should be documented so please indicate what tool has been used for
documentation. Doxygen covers most languages but for Fortran you might want to use
`Ford <http://fortranwiki.org/fortran/show/FORD>`_, for Python ReST_, etc.
Application Documentation
Provide a link to any documentation for the application.
Relevant Training Material
Add a link to any relevant training material. If there currently is none then say 'Not currently available.'
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _pilot_example:
##########################
E-CAM example pilot module
##########################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
This is an example of what a *module* for E-CAM looks like. The original source of this page (:download:`readme.rst`)
contains lots of additional comments to help you create your module (and understand ReST_ syntax) so please use this as
a starting point. You are free add any level of complexity you wish (within the bounds of what ReST_ can do). More
general instructions for making your contribution can be found in ":ref:`contributing`".
Remember that for a module to be accepted into the E-CAM repository, your source code changes in the target application
must pass a number of acceptance criteria:
* Style *(use meaningful variable names, no global variables,...)*
* Source code documentation *(each function should be documented with each argument explained)*
* Tests *(everything you add should have either unit or regression tests)*
* Performance *(If what you introduce has a significant computational load you should make some performance optimisation
effort using an appropriate tool. You should be able to verify that your changes have not introduced unexpected
performance penalties, are threadsafe if needed,...)*
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
it fits into the larger picture of what you want to achieve.
If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2003]_. Note that citations may get rearranged, e.g., to the bottom of the
"page".
.. [CIT2003] A citation (as often used in journals).
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
If the modifications are to an existing code base (which is typical) then this would be the place to name that
application. List any relevant urls and explain how to get access to that code. There needs to be enough information
here so that the person reading knows where to get the source code for the application, what version this information is
relevant for, whether this requires any additional patches/plugins, etc.
Overall, this module is supposed to be self-contained, but linking to specific URLs with more detailed information is
encouraged. In other words, the reader should not need to do a websearch to understand the context of this module, all
the links they need should be already in this module.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Provide the build information for the module here and explain how tests are run. This needs to be adequately detailed,
explaining if necessary any deviations from the normal build procedure of the application (and links to information
about the normal build process needs to be provided).
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_
Here link the source code *that was created for the module*. If you are using Github or GitLab and the `Gitflow Workflow
<https://www.atlassian.com/git/tutorials/comparing-workflows#gitflow-workflow>`_ you can point to your feature branch.
Linking to your pull/merge requests is even better. Otherwise you can link to the explicit commits. In this example I'm
using a patch file to highlight my source code changes, for that reason I need to explain what code (including exact
version information), the source code is for.
You can create a similar patch file by (for example if you are using git for your version control) making your changes
for the module in a feature branch and then doing something like the following:
.. Don't forget the white space around the "literal block" (a literal block keeps all spacing and is a good way to
include terminal output, file contents, etc.)
::
[adam@mbp2600 example (master)]$ git checkout -b tmpsquash
Switched to a new branch "tmpsquash"
[adam@mbp2600 example (tmpsquash)]$ git merge --squash newlines
Updating 4d2de39..b6768b2
Fast forward
Squash commit -- not updating HEAD
test.txt | 2 ++
1 files changed, 2 insertions(+), 0 deletions(-)
[adam@mbp2600 example (tmpsquash)]$ git commit -a -m "My squashed commits"
[tmpsquash]: created 75b0a89: "My squashed commits"
1 files changed, 2 insertions(+), 0 deletions(-)
[adam@mbp2600 example (tmpsquash)]$ git format-patch master
0001-My-squashed-commits.patch
To include a patch file do something like the following (take a look at the source code of this document to see the
syntax required to get this):
.. Below I am telling Sphinx that the included file is C code, if possible it will then do syntax highlighting. I can
even emphasise partiuclar lines (here 2 and 9-11)
.. literalinclude:: ./simple.patch
:language: c
:emphasize-lines: 2,9-11
:linenos:
If the patch is very long you will probably want to add it as a subpage which can be done as follows
.. toctree::
:glob:
:maxdepth: 1
patch
.. Remember to change the reference "patch" for something unique in your patch file subpage or you will have
cross-referencing problems
you can reference it with :ref:`patch`
.. Here are the URL references used (which is alternative method to the one described above)
.. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
Always remember that a good patch file should have a comment inside about what the patch is for....just like this
--- hello.c 2014-10-07 18:17:49.000000000 +0530
+++ hello_new.c 2014-10-07 18:17:54.000000000 +0530
@@ -1,5 +1,6 @@
#include <stdio.h>
-int main() {
+int main(int argc, char *argv[]) {
printf("Hello World\n");
+ return 0;
}
\ No newline at end of file
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded
and followed by white space (if you see warnings when this file is built they this is a common origin for problems).
.. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in
progress, please help us improve it. We use *definition lists* of ReST_ to make this readable. The "Software" here
is the main software application used by your pilot project
.. sidebar:: Software Technical Information
Language
Please indicate the primary language(s) used by the module. Please also state if interfaces for other languages are
available.
Licence
Specify the licence under which the software is released. Provide a link to the full online description of the
licence. You'll find descriptions of the most common licences at https://opensource.org/licenses .
An example here would be: `GPL <https://opensource.org/licenses/gpl-license>`_
Documentation Tool
All source code created for this module should be documented so please indicate what tool has been used for
documentation. Doxygen covers most languages but for Fortran you might want to use
`Ford <http://fortranwiki.org/fortran/show/FORD>`_, for Python ReST_, etc.
Application Documentation
Provide a link to any documentation for the application.
Relevant Training Material
Add a link to any relevant training material. If there currently is none then say 'Not currently available.'
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`pilot`"). You *MUST* change the reference below from "pilot" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _pilot:
##################
Pilot Project Name
##################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of what the
objective of the pilot project is. You should confirm this text with your industrial partner (and ensure that they
are willing to have their name and other details published).
This is an example of what a *pilot project* for E-CAM looks like. The original source of this page (:download:`readme.rst`)
contains lots of additional comments to help you create your pilot project (and understand ReST_ syntax) so please use
this as a starting point. You are free add any level of complexity you wish (within the bounds of what ReST_ can do).
More general instructions for making your contribution can be found in ":ref:`contributing`".
Remember that for any associated modules to be accepted into the E-CAM repository, your source code changes in the
target application must pass a number of acceptance criteria:
* Style *(use meaningful variable names, no global variables,...)*
* Source code documentation *(each function should be documented with each argument explained)*
* Tests *(everything you add should have either unit or regression tests)*
* Performance *(If what you introduce has a significant computational load you should make some performance optimisation
effort using an appropriate tool. You should be able to verify that your changes have not introduced unexpected
performance penalties, are threadsafe if needed,...)*
Development Plan
________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Decompose your plan of how you will implement the project into an ordered list of *modules* that you will develop. The
idea is that once you have achieved all modules then the project will be considered complete.
The number of modules you should list here is related to the length of the pilot project, but as a rule of thumb there
should at least 1 module for every 2 months that you will spend on the project.
For each module you list, give a few lines of description of what it is about and the expected delivery date. You could
also give a brief overview how it fits into the larger picture of what you want to achieve.
If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2001]_. Note that citations may get rearranged, e.g., to the bottom of the
"page".
.. Copy the lines from toctree to after :ref: to repeat this subsection for your other modules. We include the docs but
hide the contents, instead using the reference :ref:`pilot_example` to link to what is inside
.. toctree::
:hidden:
./pilot_modules/example_module/readme
:ref:`pilot_example`
~~~~~~~~~~~~~~~~~~~~
Do your explaining of the module here and add an expected date for delivery. Say that full details can be found in
:ref:`pilot_example`.
.. [CIT2001] A citation (as often used in journals).
Related extreme-scale modules
_____________________________
Each pilot project is expected to have components related to HPC. WP7 will assist you in this respect, but the modules
you develop above will also need to have aspects that connect with an effort to do simulation on large scale resources.
The modules related to EasyBuild, Singularity and JUBE for the application will also appear here (these will be created
by WP7).
.. Copy the lines from toctree to after :ref: to repeat this subsection for your other modules. We include the docs but
hide the contents, instead using the reference :ref:`extreme_example` to link to what is inside
.. toctree::
:hidden:
./extreme_modules/example_module/readme
:ref:`extreme_example`
~~~~~~~~~~~~~~~~~~~~~~
Do your explaining of the module here and add an expected date for delivery. Say that full details can be found in
:ref:`extreme_example`.
.. Here are the URL references used (which is alternative method to the one described above)
.. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
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