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791 lines
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HTML
791 lines
30 KiB
HTML
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may distribute non-source (e.g., minimized or compacted) forms of
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</head>
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<body>
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<div id="org-div-home-and-up">
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<a accesskey="h" href=""> UP </a>
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<a accesskey="H" href="index.html"> HOME </a>
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</div><div id="content">
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<h1 class="title">Introduction</h1>
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<div id="table-of-contents">
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#orgf6e4229">1. Using QMCkl</a></li>
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<li><a href="#orge260b1e">2. Developing in QMCkl</a>
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<ul>
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<li><a href="#org50f3de5">2.1. Literate programming</a></li>
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<li><a href="#orge4c1b1a">2.2. Source code editing</a></li>
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<li><a href="#orgf9398e1">2.3. Choice of the programming language</a></li>
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<li><a href="#orgf5763e2">2.4. Coding rules</a></li>
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<li><a href="#orgd96efe5">2.5. Design of the library</a></li>
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<li><a href="#org72ee0a5">2.6. Naming conventions</a></li>
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<li><a href="#org0fce97c">2.7. Application programming interface</a></li>
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<li><a href="#org1762270">2.8. Global state</a></li>
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<li><a href="#orgc84cd62">2.9. Headers</a></li>
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<li><a href="#orgb9f7e9d">2.10. Low-level functions</a></li>
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<li><a href="#org415ff08">2.11. High-level functions</a></li>
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<li><a href="#orgf734fb0">2.12. Numerical precision</a></li>
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<li><a href="#orge455040">2.13. Algorithms</a></li>
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</ul>
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</li>
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</ul>
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</div>
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</div>
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<div id="outline-container-orgf6e4229" class="outline-2">
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<h2 id="orgf6e4229"><span class="section-number-2">1</span> Using QMCkl</h2>
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<div class="outline-text-2" id="text-1">
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<p>
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The <code>qmckl.h</code> header file installed in the <code>${prefix}/include</code> directory
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has to be included in C codes when QMCkl functions are used:
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</p>
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">"qmckl.h"</span>
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</pre>
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</div>
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<p>
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In Fortran programs, the <code>qmckl_f.f90</code> installed in
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<code>${prefix}/share/qmckl/fortran</code> interface file should be copied in the source
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code using the library, and the Fortran codes should use the <code>qmckl</code> module as
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</p>
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">use</span> <span style="color: #0000ff;">qmckl</span>
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</pre>
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</div>
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<p>
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Both files are located in the <code>include/</code> directory.
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</p>
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</div>
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</div>
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<div id="outline-container-orge260b1e" class="outline-2">
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<h2 id="orge260b1e"><span class="section-number-2">2</span> Developing in QMCkl</h2>
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<div class="outline-text-2" id="text-2">
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</div>
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<div id="outline-container-org50f3de5" class="outline-3">
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<h3 id="org50f3de5"><span class="section-number-3">2.1</span> Literate programming</h3>
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<div class="outline-text-3" id="text-2-1">
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<p>
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|
In a traditional source code, most of the lines of source files of a program
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|
are code, scripts, Makefiles, and only a few lines are comments explaining
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|
parts of the code that are non-trivial to understand. The documentation of
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the prorgam is usually written in a separate directory, and is often outdated
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compared to the code.
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</p>
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|
<p>
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|
Literate programming is a different approach to programming,
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where the program is considered as a publishable-quality document. Most of
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the lines of the source files are text, mathematical formulas, tables,
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figures, <i>etc</i>, and the lines of code are just the translation in a computer
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|
language of the ideas and algorithms expressed in the text. More importantly,
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|
the "document" is structured like a text document with sections, subsections,
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|
a bibliography, a table of contents <i>etc</i>, and the place where pieces of code
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|
appear are the places where they should belong for the reader to understand
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|
the logic of the program, not the places where the compiler expects to find
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them. Both the publishable-quality document and the binary executable are
|
|
produced from the same source files.
|
|
</p>
|
|
|
|
<p>
|
|
Literate programming is particularly well adapted in this context, as the
|
|
central part of this project is the documentation of an API. The
|
|
implementation of the algorithms is just an expression of the algorithms in a
|
|
language that can be compiled, so that the correctness of the algorithms can
|
|
be tested.
|
|
</p>
|
|
|
|
<p>
|
|
We have chosen to write the source files in <a href="https://karl-voit.at/2017/09/23/orgmode-as-markup-only/">org-mode</a> format,
|
|
as any text editor can be used to edit org-mode files. To
|
|
produce the documentation, there exists multiple possibilities to convert
|
|
org-mode files into different formats such as HTML or PDF. The source code is
|
|
easily extracted from the org-mode files invoking the Emacs text editor from
|
|
the command-line in the <code>Makefile</code>, and then the produced files are compiled.
|
|
Moreover, within the Emacs text editor the source code blocks can be executed
|
|
interactively, in the same spirit as Jupyter notebooks.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orge4c1b1a" class="outline-3">
|
|
<h3 id="orge4c1b1a"><span class="section-number-3">2.2</span> Source code editing</h3>
|
|
<div class="outline-text-3" id="text-2-2">
|
|
<p>
|
|
For a tutorial on literate programming with org-mode, follow <a href="http://www.howardism.org/Technical/Emacs/literate-programming-tutorial.html">this link</a>.
|
|
</p>
|
|
|
|
<p>
|
|
Any text editor can be used to edit org-mode files. For a better
|
|
user experience Emacs is recommended. For users hating Emacs, it
|
|
is good to know that Emacs can behave like Vim when switched into
|
|
``Evil'' mode.
|
|
</p>
|
|
|
|
<p>
|
|
In the <code>tools/init.el</code> file, we provide a minimal Emacs configuration
|
|
file for vim users. This file should be copied into <code>.emacs.d/init.el</code>.
|
|
</p>
|
|
|
|
<p>
|
|
For users with a preference for Jupyter notebooks, we also provide the
|
|
<code>tools/nb_to_org.sh</code> script can convert jupyter notebooks into org-mode
|
|
files.
|
|
</p>
|
|
|
|
<p>
|
|
Note that pandoc can be used to convert multiple markdown formats into
|
|
org-mode.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgf9398e1" class="outline-3">
|
|
<h3 id="orgf9398e1"><span class="section-number-3">2.3</span> Choice of the programming language</h3>
|
|
<div class="outline-text-3" id="text-2-3">
|
|
<p>
|
|
Most of the codes of the <a href="https://trex-coe.eu">TREX CoE</a> are written in Fortran with some scripts in
|
|
Bash and Python. Outside of the CoE, Fortran is also important (Casino, Amolqc),
|
|
and other important languages used by the community are C and C++ (QMCPack,
|
|
QWalk), and Julia is gaining in popularity. The library we design should be
|
|
compatible with all of these languages. The QMCkl API has to be compatible
|
|
with the C language since libraries with a C-compatible API can be used in
|
|
every other language.
|
|
</p>
|
|
|
|
<p>
|
|
High-performance versions of the QMCkl, with the same API, will be rewritten by
|
|
the experts in HPC. These optimized libraries will be tuned for specific
|
|
architectures, among which we can cite x86 based processors, and GPU
|
|
accelerators. Nowadays, the most efficient software tools to take advantage of
|
|
low-level features of the processor (intrinsics) and of GPUs are for C++
|
|
developers. It is highly probable that the optimized implementations will be
|
|
written in C++, and this is agreement with our choice to make the API
|
|
C-compatible.
|
|
</p>
|
|
|
|
<p>
|
|
Fortran is one of the most common languages used by the community, and is simple
|
|
enough to make the algorithms readable both by experts in QMC, and experts in
|
|
HPC. Hence we propose in this pedagogical implementation of QMCkl to use Fortran
|
|
to express the QMC algorithms. As the main languages of the library is C, this
|
|
implies that the exposed C functions call the Fortran routine. However, for
|
|
internal functions related to system programming, the C language is more natural
|
|
than Fortran.
|
|
</p>
|
|
|
|
<p>
|
|
The Fortran source files should provide a C interface using the
|
|
<code>iso_c_binding</code> module. The name of the Fortran source files should end with
|
|
<code>_f.f90</code> to be properly handled by the <code>Makefile</code>. The names of the functions
|
|
defined in Fortran should be the same as those exposed in the API suffixed by
|
|
<code>_f</code>.
|
|
</p>
|
|
|
|
<p>
|
|
For more guidelines on using Fortran to generate a C interface, see
|
|
<a href="http://fortranwiki.org/fortran/show/Generating+C+Interfaces">this link</a>.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgf5763e2" class="outline-3">
|
|
<h3 id="orgf5763e2"><span class="section-number-3">2.4</span> Coding rules</h3>
|
|
<div class="outline-text-3" id="text-2-4">
|
|
<p>
|
|
The authors should follow the recommendations of the C99
|
|
<a href="https://wiki.sei.cmu.edu/confluence/display/c/SEI+CERT+C+Coding+Standard">SEI+CERT C Coding Standard</a>.
|
|
</p>
|
|
|
|
<p>
|
|
Compliance can be checked with <code>cppcheck</code> as:
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-bash">cppcheck --addon=cert --enable=all *.c &> cppcheck.out
|
|
</pre>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgd96efe5" class="outline-3">
|
|
<h3 id="orgd96efe5"><span class="section-number-3">2.5</span> Design of the library</h3>
|
|
<div class="outline-text-3" id="text-2-5">
|
|
<p>
|
|
The proposed API should allow the library to: deal with memory transfers
|
|
between CPU and accelerators, and to use different levels of floating-point
|
|
precision. We chose a multi-layered design with low-level and high-level
|
|
functions (see below).
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org72ee0a5" class="outline-3">
|
|
<h3 id="org72ee0a5"><span class="section-number-3">2.6</span> Naming conventions</h3>
|
|
<div class="outline-text-3" id="text-2-6">
|
|
<p>
|
|
To avoid namespace collisions, we use <code>qmckl_</code> as a prefix for all exported
|
|
functions and variables. All exported header files should have a file name
|
|
prefixed with <code>qmckl_</code>.
|
|
</p>
|
|
|
|
<p>
|
|
If the name of the org-mode file is <code>xxx.org</code>, the name of the
|
|
produced C files should be <code>xxx.c</code> and <code>xxx.h</code> and the name of the
|
|
produced Fortran file should be <code>xxx.f90</code>.
|
|
</p>
|
|
|
|
<p>
|
|
Arrays are in uppercase and scalars are in lowercase.
|
|
</p>
|
|
|
|
<p>
|
|
In the names of the variables and functions, only the singular
|
|
form is allowed.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org0fce97c" class="outline-3">
|
|
<h3 id="org0fce97c"><span class="section-number-3">2.7</span> Application programming interface</h3>
|
|
<div class="outline-text-3" id="text-2-7">
|
|
<p>
|
|
In the C language, the number of bits used by the integer types can change
|
|
from one architecture to another one. To circumvent this problem, we choose to
|
|
use the integer types defined in <code><stdint.h></code> where the number of bits used for
|
|
the integers are fixed.
|
|
</p>
|
|
|
|
<p>
|
|
To ensure that the library will be easily usable in <i>any</i> other language
|
|
than C, we restrict the data types in the interfaces to the following:
|
|
</p>
|
|
<ul class="org-ul">
|
|
<li>32-bit and 64-bit integers, scalars and and arrays (<code>int32_t</code> and <code>int64_t</code>)</li>
|
|
<li>32-bit and 64-bit floats, scalars and and arrays (<code>float</code> and <code>double</code>)</li>
|
|
<li>Pointers are always casted into 64-bit integers, even on legacy 32-bit architectures</li>
|
|
<li>ASCII strings are represented as a pointers to character arrays
|
|
and terminated by a <code>'\0'</code> character (C convention).</li>
|
|
<li>Complex numbers can be represented by an array of 2 floats.</li>
|
|
<li>Boolean variables are stored as integers, <code>1</code> for <code>true</code> and <code>0</code> for <code>false</code></li>
|
|
<li>Floating point variables should be by default <code>double</code> unless explicitly mentioned</li>
|
|
<li>integers used for counting should always be <code>int64_t</code></li>
|
|
</ul>
|
|
|
|
<p>
|
|
To facilitate the use in other languages than C, we will provide some
|
|
bindings in other languages in other repositories.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org1762270" class="outline-3">
|
|
<h3 id="org1762270"><span class="section-number-3">2.8</span> Global state</h3>
|
|
<div class="outline-text-3" id="text-2-8">
|
|
<p>
|
|
Global variables should be avoided in the library, because it is
|
|
possible that one single program needs to use multiple instances
|
|
of the library. To solve this problem we propose to use a pointer
|
|
to a <a href="./qmckl_context.html"><code>context</code></a> variable, built by the library with the
|
|
<code>qmckl_context_create</code> function. The <a id="org34e995b">=context=</a> contains the global
|
|
state of the library, and is used as the first argument of many
|
|
QMCkl functions.
|
|
</p>
|
|
|
|
<p>
|
|
The internal structure of the context is not specified, to give a
|
|
maximum of freedom to the different implementations. Modifying
|
|
the state is done by setters and getters, prefixed by
|
|
<code>qmckl_set_</code> an <code>qmckl_get_</code>.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgc84cd62" class="outline-3">
|
|
<h3 id="orgc84cd62"><span class="section-number-3">2.9</span> Headers</h3>
|
|
<div class="outline-text-3" id="text-2-9">
|
|
<p>
|
|
A single <code>qmckl.h</code> header to be distributed by the library
|
|
is built by concatenating some of the produced header files.
|
|
To facilitate building the <code>qmckl.h</code> file, we separate types from
|
|
function declarations in headers. Types should be defined in header
|
|
files suffixed by <code>_type.h</code>, and functions in files suffixed by
|
|
<code>_func.h</code>.
|
|
As these files will be concatenated in a single file, they should
|
|
not be guarded by <code>#ifndef *_H</code>, and they should not include other
|
|
produced headers.
|
|
</p>
|
|
|
|
<p>
|
|
Some particular types that are not exported need to be known by the
|
|
context, and there are some functions to update instances of these
|
|
types contained inside the context. For example, a
|
|
<code>qmckl_numprec_struct</code> is present in the context, and the function
|
|
<code>qmckl_set_numprec_range</code> takes a context as a parameter, and set a
|
|
value in the <code>qmckl_numprec_struct</code> contained in the context.
|
|
Because of these intricate dependencies, a private header is
|
|
created, containing the <code>qmckl_numprec_struct</code>. This header is
|
|
included in the private header file which defines the type of the
|
|
context. Header files for private types are suffixed by <code>_private_type.h</code>
|
|
and header files for private functions are suffixed by <code>_private_func.h</code>.
|
|
Fortran interfaces should also be written in the <code>*fh_func.f90</code> file,
|
|
and the types definitions should be written in the <code>*fh_type.f90</code> file.
|
|
</p>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-left">File</th>
|
|
<th scope="col" class="org-left">Scope</th>
|
|
<th scope="col" class="org-left">Description</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left"><code>*_type.h</code></td>
|
|
<td class="org-left">Public</td>
|
|
<td class="org-left">Type definitions</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-left"><code>*_func.h</code></td>
|
|
<td class="org-left">Public</td>
|
|
<td class="org-left">Function definitions</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-left"><code>*_private_type.h</code></td>
|
|
<td class="org-left">Private</td>
|
|
<td class="org-left">Type definitions</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-left"><code>*_private_func.h</code></td>
|
|
<td class="org-left">Private</td>
|
|
<td class="org-left">Function definitions</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-left"><code>*fh_type.f90</code></td>
|
|
<td class="org-left">Public</td>
|
|
<td class="org-left">Fortran type definitions</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-left"><code>*fh_func.f90</code></td>
|
|
<td class="org-left">Public</td>
|
|
<td class="org-left">Fortran function definitions</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgb9f7e9d" class="outline-3">
|
|
<h3 id="orgb9f7e9d"><span class="section-number-3">2.10</span> Low-level functions</h3>
|
|
<div class="outline-text-3" id="text-2-10">
|
|
<p>
|
|
Low-level functions are very simple functions which are leaves of
|
|
the function call tree (they don't call any other QMCkl function).
|
|
</p>
|
|
|
|
<p>
|
|
These functions are <i>pure</i>, and unaware of the QMCkl
|
|
<a href="#org34e995b"><code>context</code></a>. They are not allowed to allocate/deallocate memory, and
|
|
if they need temporary memory it should be provided in input.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org415ff08" class="outline-3">
|
|
<h3 id="org415ff08"><span class="section-number-3">2.11</span> High-level functions</h3>
|
|
<div class="outline-text-3" id="text-2-11">
|
|
<p>
|
|
High-level functions are at the top of the function call tree.
|
|
They are able to choose which lower-level function to call
|
|
depending on the required precision, and do the corresponding type
|
|
conversions. These functions are also responsible for allocating
|
|
temporary storage, to simplify the use of accelerators.
|
|
</p>
|
|
|
|
<p>
|
|
The high-level functions should be pure, unless the introduction
|
|
of non-purity is justified. All the side effects should be made in
|
|
the <a href="#org34e995b"><code>context</code></a> variable.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgf734fb0" class="outline-3">
|
|
<h3 id="orgf734fb0"><span class="section-number-3">2.12</span> Numerical precision</h3>
|
|
<div class="outline-text-3" id="text-2-12">
|
|
<p>
|
|
The number of bits of precision required for a function should be
|
|
given as an input of low-level computational functions. This input
|
|
will be used to define the values of the different thresholds that
|
|
might be used to avoid computing unnecessary noise. High-level
|
|
functions will use the precision specified in the <a href="#org34e995b"><code>context</code></a>
|
|
variable.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orge455040" class="outline-3">
|
|
<h3 id="orge455040"><span class="section-number-3">2.13</span> Algorithms</h3>
|
|
<div class="outline-text-3" id="text-2-13">
|
|
<p>
|
|
Reducing the scaling of an algorithm usually implies also reducing
|
|
its arithmetic complexity (number of flops per byte). Therefore,
|
|
for small sizes \(\mathcal{O}(N^3)\) and \(\mathcal{O}(N^2)\)
|
|
algorithms are better adapted than linear scaling algorithms. As
|
|
QMCkl is a general purpose library, multiple algorithms should be
|
|
implemented adapted to different problem sizes.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
<div id="postamble" class="status">
|
|
<p class="author">Author: TREX CoE</p>
|
|
<p class="date">Created: 2021-07-08 Thu 06:58</p>
|
|
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
|
</div>
|
|
</body>
|
|
</html>
|