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< / head >
< body >
< div id = "org-div-home-and-up" >
< a accesskey = "h" href = "" > UP < / a >
|
< a accesskey = "H" href = "index.html" > HOME < / a >
< / div > < div id = "content" >
< h1 class = "title" > Introduction< / h1 >
< div id = "table-of-contents" >
< h2 > Table of Contents< / h2 >
< div id = "text-table-of-contents" >
< ul >
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< li > < a href = "#org50e84d7" > 1. Using QMCkl< / a > < / li >
< li > < a href = "#org398965c" > 2. Developing in QMCkl< / a >
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< ul >
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< li > < a href = "#org1a0dd97" > 2.1. Literate programming< / a > < / li >
< li > < a href = "#orgd903c2a" > 2.2. Source code editing< / a > < / li >
< li > < a href = "#orgaa1a2d5" > 2.3. Choice of the programming language< / a > < / li >
< li > < a href = "#orgc0ed43d" > 2.4. Coding rules< / a > < / li >
< li > < a href = "#orgb26147e" > 2.5. Design of the library< / a > < / li >
< li > < a href = "#org1170c7c" > 2.6. Naming conventions< / a > < / li >
< li > < a href = "#org77a8203" > 2.7. Application programming interface< / a > < / li >
< li > < a href = "#orgdc5e5ef" > 2.8. Global state< / a > < / li >
< li > < a href = "#orgebfd08f" > 2.9. Headers< / a > < / li >
< li > < a href = "#orgcc7f03f" > 2.10. Low-level functions< / a > < / li >
< li > < a href = "#org698939b" > 2.11. High-level functions< / a > < / li >
< li > < a href = "#org7e910c2" > 2.12. Numerical precision< / a > < / li >
< li > < a href = "#orgb7387fd" > 2.13. Algorithms< / a > < / li >
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< / ul >
< / li >
< / ul >
< / div >
< / div >
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< div id = "outline-container-org50e84d7" class = "outline-2" >
< h2 id = "org50e84d7" > < span class = "section-number-2" > 1< / span > Using QMCkl< / h2 >
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< div class = "outline-text-2" id = "text-1" >
< p >
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The < code > qmckl.h< / code > header file installed in the < code > ${prefix}/include< / code > directory
has to be included in C codes when QMCkl functions are used:
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< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #483d8b;" > #include< / span > < span style = "color: #8b2252;" > "qmckl.h"< / span >
< / pre >
< / div >
< p >
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In Fortran programs, the < code > qmckl_f.f90< / code > installed in
< code > ${prefix}/share/qmckl/fortran< / code > interface file should be copied in the source
code using the library, and the Fortran codes should use the < code > qmckl< / code > module as
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< / p >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > use< / span > < span style = "color: #0000ff;" > qmckl< / span >
< / pre >
< / div >
< p >
Both files are located in the < code > include/< / code > directory.
< / p >
< / div >
< / div >
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< div id = "outline-container-org398965c" class = "outline-2" >
< h2 id = "org398965c" > < span class = "section-number-2" > 2< / span > Developing in QMCkl< / h2 >
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< div class = "outline-text-2" id = "text-2" >
< / div >
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< div id = "outline-container-org1a0dd97" class = "outline-3" >
< h3 id = "org1a0dd97" > < span class = "section-number-3" > 2.1< / span > Literate programming< / h3 >
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< div class = "outline-text-3" id = "text-2-1" >
< p >
In a traditional source code, most of the lines of source files of a program
are code, scripts, Makefiles, and only a few lines are comments explaining
parts of the code that are non-trivial to understand. The documentation of
the prorgam is usually written in a separate directory, and is often outdated
compared to the code.
< / p >
< p >
Literate programming is a different approach to programming,
where the program is considered as a publishable-quality document. Most of
the lines of the source files are text, mathematical formulas, tables,
figures, < i > etc< / i > , and the lines of code are just the translation in a computer
language of the ideas and algorithms expressed in the text. More importantly,
the "document" is structured like a text document with sections, subsections,
a bibliography, a table of contents < i > etc< / i > , and the place where pieces of code
appear are the places where they should belong for the reader to understand
the logic of the program, not the places where the compiler expects to find
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 >
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< div id = "outline-container-orgd903c2a" class = "outline-3" >
< h3 id = "orgd903c2a" > < span class = "section-number-3" > 2.2< / span > Source code editing< / h3 >
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< 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 >
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< div id = "outline-container-orgaa1a2d5" class = "outline-3" >
< h3 id = "orgaa1a2d5" > < span class = "section-number-3" > 2.3< / span > Choice of the programming language< / h3 >
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< 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
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< code > _f< / code > .
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< / 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 >
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< div id = "outline-container-orgc0ed43d" class = "outline-3" >
< h3 id = "orgc0ed43d" > < span class = "section-number-3" > 2.4< / span > Coding rules< / h3 >
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< div class = "outline-text-3" id = "text-2-4" >
< p >
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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 > .
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< / p >
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< 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 >
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< / div >
< / div >
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< div id = "outline-container-orgb26147e" class = "outline-3" >
< h3 id = "orgb26147e" > < span class = "section-number-3" > 2.5< / span > Design of the library< / h3 >
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< 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).
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< h3 id = "org1170c7c" > < span class = "section-number-3" > 2.6< / span > Naming conventions< / h3 >
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< 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 >
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< h3 id = "org77a8203" > < span class = "section-number-3" > 2.7< / span > Application programming interface< / h3 >
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< 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 >
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< li > Floating point variables should be by default < code > double< / code > unless explicitly mentioned< / li >
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< 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 >
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< / div >
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< div id = "outline-container-orgdc5e5ef" class = "outline-3" >
< h3 id = "orgdc5e5ef" > < span class = "section-number-3" > 2.8< / span > Global state< / h3 >
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< 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
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< code > qmckl_context_create< / code > function. The < a id = "orga86c97b" > =context=< / a > contains the global
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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
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< code > qmckl_set_< / code > an < code > qmckl_get_< / code > .
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< / p >
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< div id = "outline-container-orgebfd08f" class = "outline-3" >
< h3 id = "orgebfd08f" > < span class = "section-number-3" > 2.9< / span > Headers< / h3 >
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< div class = "outline-text-3" id = "text-2-9" >
< p >
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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 which defines the type of the
context. Headers for private types are suffixed by < code > _private_type.h< / code >
and headers for private functions, < code > _private_func.h< / code > .
Fortran interfaces should also be written in the < code > *_f_func.f90< / code > file,
and the types definitions should be written in the < code > *_f_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 >
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< h3 id = "orgcc7f03f" > < span class = "section-number-3" > 2.10< / span > Low-level functions< / h3 >
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< div class = "outline-text-3" id = "text-2-10" >
< p >
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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
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< a href = "#orga86c97b" > < code > context< / code > < / a > . They are not allowed to allocate/deallocate memory, and
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if they need temporary memory it should be provided in input.
< / p >
< / div >
< / div >
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< h3 id = "org698939b" > < span class = "section-number-3" > 2.11< / span > High-level functions< / h3 >
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< div class = "outline-text-3" id = "text-2-11" >
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< 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
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the < a href = "#orga86c97b" > < code > context< / code > < / a > variable.
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< / p >
< / div >
< / div >
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< div id = "outline-container-org7e910c2" class = "outline-3" >
< h3 id = "org7e910c2" > < span class = "section-number-3" > 2.12< / span > Numerical precision< / h3 >
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< div class = "outline-text-3" id = "text-2-12" >
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< 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
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functions will use the precision specified in the < a href = "#orga86c97b" > < code > context< / code > < / a >
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variable.
< / p >
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< / div >
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< div id = "outline-container-orgb7387fd" class = "outline-3" >
< h3 id = "orgb7387fd" > < span class = "section-number-3" > 2.13< / span > Algorithms< / h3 >
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< div class = "outline-text-3" id = "text-2-13" >
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< 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 >
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< / div >
< div id = "postamble" class = "status" >
< p class = "author" > Author: TREX CoE< / p >
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< p class = "date" > Created: 2021-04-21 Wed 10:44< / p >
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< p class = "validation" > < a href = "http://validator.w3.org/check?uri=referer" > Validate< / a > < / p >
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< / body >
< / html >
