--- /dev/null
- .. _continuous integration server used by GROMACS: http://jenkins.gromacs.org
- .. _Jenkins: http://jenkins-ci.org
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
+# Copyright (c) 2020, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# -*- coding: utf-8 -*-
+#
+# GROMACS documentation build configuration file, created by
+# sphinx-quickstart on Tue Jan 13 14:28:44 2015.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import datetime
+import os
+import sys
+
+# The following definitions are completed via CMake machinery.
+gmx_containers_path = '@GMX_ADMIN_DIR@/containers'
+gmx_sphinx_extension_path = '@SPHINX_EXTENSION_PATH@'
+gmxapi_staging_path = '@GMXAPI_PYTHON_STAGING_DIR@'
+releng_path = '@RELENG_PATH@'
+gmx_version_string = '@GMX_VERSION_STRING@'
+gmx_version_string_full = '@GMX_VERSION_STRING_FULL@'
+regressiontest_version = '@REGRESSIONTEST_VERSION@'
+gmx_min_sphinx = '@EXPECTED_SPHINX_VERSION@'
+gmx_image_convert = '@IMAGE_CONVERT_STRING@'
+variables = [
+ ('EXPECTED_DOXYGEN_VERSION', '@EXPECTED_DOXYGEN_VERSION@'),
+ ('EXPECTED_SPHINX_VERSION', '@EXPECTED_SPHINX_VERSION@'),
+ ('CMAKE_MINIMUM_REQUIRED_VERSION', '@CMAKE_MINIMUM_REQUIRED_VERSION@'),
+ ('REQUIRED_CUDA_VERSION', '@REQUIRED_CUDA_VERSION@'),
+ ('REQUIRED_CUDA_COMPUTE_CAPABILITY', '@REQUIRED_CUDA_COMPUTE_CAPABILITY@'),
+ ('REQUIRED_OPENCL_MIN_VERSION', '@REQUIRED_OPENCL_MIN_VERSION@'),
+ ('SOURCE_MD5SUM', '@SOURCE_MD5SUM@'),
+ ('REGRESSIONTEST_MD5SUM', '@REGRESSIONTEST_MD5SUM_STRING@'),
+ ('GMX_TNG_MINIMUM_REQUIRED_VERSION', '@GMX_TNG_MINIMUM_REQUIRED_VERSION@'),
+ ('GMX_LMFIT_REQUIRED_VERSION', '@GMX_LMFIT_REQUIRED_VERSION@'),
+ ('GMX_MANUAL_DOI_STRING', '@GMX_MANUAL_DOI_STRING@'),
+ ('GMX_SOURCE_DOI_STRING', '@GMX_SOURCE_DOI_STRING@')
+]
+# End of build-time substitutions.
+
+sys.path.append(gmx_containers_path)
+sys.path.append(gmx_sphinx_extension_path)
+if releng_path and os.path.isdir(releng_path):
+ sys.path.append(releng_path)
+if gmxapi_staging_path and os.path.isdir(gmxapi_staging_path):
+ sys.path.append(gmxapi_staging_path)
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+# gmx_min_sphinx is set from the expected minimum version of Sphinx
+# in CMakeLists.txt
+needs_sphinx = gmx_min_sphinx
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.graphviz',
+ 'sphinx.ext.extlinks',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.ifconfig',
+ 'sphinx.ext.intersphinx',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.todo',
+ # The viewcode extension requires extra configuration or consideration to
+ # avoid collecting sources for external packages (through intersphninx) or
+ # generating broken links for compiled extension modules that do not have
+ # inspectable 'code' member data.
+ # Ref: https://www.sphinx-doc.org/en/master/usage/extensions/viewcode.html
+ # Please run linkchecker and inspect the generated
+ # docs/html/_modules/index.html page before committing a change that enables
+ # 'sphinx.ext.viewcode',
+ 'gmxsphinx'
+]
+extlinks = {'issue': ('https://gitlab.com/gromacs/gromacs/-/issues/%s',
+ 'Issue ')}
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'GROMACS'
+copyright = str(datetime.datetime.now().year) + u', GROMACS development team'
+thisyear_string = str(datetime.datetime.now().year)
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = gmx_version_string
+# The full version, including alpha/beta/rc tags.
+release = gmx_version_string_full
+# default file extension for plots
+plotext = u'.eps'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['fragments']
+if not tags.has('do_man'):
+ exclude_patterns += ['man']
+
+# Set variable if documentation build can convert images or not
+# to selectively include files in reference manual
+def setup(app):
+ app.add_config_value('gmx_image_convert', 'impossible', 'env')
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+default_role = 'any'
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+# Configure the values for all the variables that might later configure any of the .rst files.
+substitutions = ['.. |{0}| replace:: {1}'.format(*x) for x in variables if x[1]]
+substitutions.extend(['.. |{0}| replace:: unknown'.format(x[0]) for x in variables if x[1] == ''])
+rst_epilog = "\n".join(substitutions)
+rst_epilog += """
+.. |Gromacs| replace:: GROMACS
+.. _gmx-manual: manual-{gmx_version_string}.pdf
+.. _gmx-manual-parent-dir: ../manual-{gmx_version_string}.pdf
+.. |gmx-source-package-ftp| replace:: As ftp ftp://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
+.. |gmx-source-package-http| replace:: As http http://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
+.. |gmx-regressiontests-package| replace:: http://ftp.gromacs.org/pub/regressiontests/regressiontests-{regressiontest_version}.tar.gz
+.. _up-to-date installation instructions: http://manual.gromacs.org/documentation/current/install-guide/index.html
+.. _CUDA: http://www.nvidia.com/object/cuda_home_new.html
+.. _OpenCL: https://www.khronos.org/opencl/
+.. _OpenMPI: http://www.open-mpi.org
+.. _MPICH: http://www.mpich.org
+.. _LAM-MPI: http://www.lam-mpi.org
+.. _OpenMP: http://en.wikipedia.org/wiki/OpenMP
+.. _CMake installation page: http://www.cmake.org/install/
+.. _Ubuntu toolchain ppa page: https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test
+.. _EPEL page: https://fedoraproject.org/wiki/EPEL
+.. _running CMake: http://www.cmake.org/runningcmake/
+.. _CMake environment variables: http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables
+.. _FFTW: http://www.fftw.org
+.. _FFTW installation guide: http://www.fftw.org/doc/Installation-and-Customization.html#Installation-and-Customization
+.. _MKL: https://software.intel.com/en-us/intel-mkl
+.. _VMD: http://www.ks.uiuc.edu/Research/vmd/
+.. _PyMOL: http://www.pymol.org
- .. _issues: https://gitlab.com/gromacs/gromacs/-/issues/
+.. _webpage: http://www.gromacs.org
+.. _ftp site: ftp://ftp.gromacs.org/pub/gromacs/
+.. _tutorials: http://www.gromacs.org/Documentation/Tutorials
+.. _issue tracker: https://gitlab.com/gromacs/gromacs/-/issues/
- .. _redmine: http://redmine.gromacs.org
- .. _gerrit: http://gerrit.gromacs.org
+.. _gitlab: https://gitlab.com/gromacs/gromacs/
+.. _download: ../download.html
+.. |thisyear| replace:: {thisyear_string}
+""".format(gmx_version_string=gmx_version_string, regressiontest_version=regressiontest_version, thisyear_string=thisyear_string)
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'classic'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+html_theme_path = ['']
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+html_title = u'GROMACS ' + release + ' documentation'
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+html_short_title = u'GROMACS ' + version
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Gromacsdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+'papersize': 'a4paper',
+
+
+# The font size ('10pt', '11pt' or '12pt').
+'pointsize': '11',
+
+# Additional stuff for the LaTeX preamble.
+# The tocdepth setting is needed to overwrite the default value set by Sphinx
+# to get a more detailed toctree in the pdf version of the manual.
+ 'preamble': r'''
+ \usepackage{here}
+ \usepackage{picins}
+ \usepackage{underscore}
+ \usepackage{tabularx}
+ \usepackage{multicol}
+ \usepackage{dcolumn}
+ \usepackage{makeidx}
+ \usepackage{times}
+ \usepackage{ifthen}
+ \usepackage{enumitem}
+ \usepackage{longtable}
+ \usepackage{pdflscape}
+ \pagenumbering{roman}
+ \usepackage{array}
+ \setcounter{tocdepth}{2}
+ ''',
+# Format output to avoid empty pages
+ 'classoptions': ',openany,oneside'
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ ('index', 'gromacs.tex', u'GROMACS Documentation',
+ u'GROMACS development team', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = 'reference-manual/plots/peregrine.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+latex_use_parts = True
+
+# If true, show page references after internal links.
+latex_show_pagerefs = True
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+if tags.has('do_man'):
+ exec(open('conf-man.py').read())
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'GROMACS', u'GROMACS Documentation',
+ u'GROMACS development team', 'GROMACS', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
+
+# Make it possible to use numbered labels for figures and tables
+numfig = True
+
+# -- Options for autodoc extension ----------------------------------------
+
+# http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autodoc-mock-imports
+autodoc_mock_imports = ['hpccm', 'hpccm.config']
+
+# -- Options for intersphinx extension ------------------------------------
+
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
+intersphinx_cache_limit = -1
+intersphinx_timeout = 10
--- /dev/null
- * is not clear whether the problem is the compiler or the standard
- * library. Fortunately, this function is not performance sensitive,
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Defines routine for activating potentially deactivated cores
+ * so they can be detected.
+ *
+ * The use of std::thread makes for brittle interaction with std
+ * library headers. Its caller also handles GPU detection and
+ * allocation of device-specific data structures. This is more
+ * manageable when separated into two distinct translation units.
+ *
+ * \author Erik Lindahl <erik.lindahl@scilifelab.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_hardware
+ */
+#include "gmxpre.h"
+
+#include "prepare_detection.h"
+
+#include "config.h"
+
+#include <cstdio>
+
+#include <chrono>
+#include <thread>
+#include <vector>
+
+#include "architecture.h"
+
+#ifdef HAVE_UNISTD_H
+# include <unistd.h> // sysconf()
+#endif
+
+namespace gmx
+{
+
+/*! \brief Utility that does dummy computing for max 2 seconds to spin up cores
+ *
+ * This routine will check the number of cores configured and online
+ * (using sysconf), and the spins doing dummy compute operations for up to
+ * 2 seconds, or until all cores have come online. This can be used prior to
+ * hardware detection for platforms that take unused processors offline.
+ *
+ * This routine will not throw exceptions. In principle it should be
+ * declared noexcept, but at least icc 19.1 and 21-beta08 with the
+ * libstdc++-7.5 has difficulty implementing a std::vector of
+ * std::thread started with this function when declared noexcept. It
++ * is a known compiler bug that should be fixed after 19.1.
++ * Fortunately, this function is not performance sensitive,
+ * and only runs on platforms other than x86 and POWER (ie ARM),
+ * so the possible overhead introduced by omitting noexcept is not
+ * important.
+ */
+static void spinUpCore()
+{
+#if defined(HAVE_SYSCONF) && defined(_SC_NPROCESSORS_CONF) && defined(_SC_NPROCESSORS_ONLN)
+ float dummy = 0.1;
+ int countConfigured = sysconf(_SC_NPROCESSORS_CONF); // noexcept
+ auto start = std::chrono::steady_clock::now(); // noexcept
+
+ while (sysconf(_SC_NPROCESSORS_ONLN) < countConfigured
+ && std::chrono::steady_clock::now() - start < std::chrono::seconds(2))
+ {
+ for (int i = 1; i < 10000; i++)
+ {
+ dummy /= i;
+ }
+ }
+
+ if (dummy < 0)
+ {
+ printf("This cannot happen, but prevents loop from being optimized away.");
+ }
+#endif
+}
+
+void hardwareTopologyPrepareDetection()
+{
+#if defined(HAVE_SYSCONF) && defined(_SC_NPROCESSORS_CONF) \
+ && (defined(THREAD_PTHREADS) || defined(THREAD_WINDOWS))
+
+ // Modify this conditional when/if x86 or PowerPC starts to sleep some cores
+ if (c_architecture != Architecture::X86 && c_architecture != Architecture::PowerPC)
+ {
+ int countConfigured = sysconf(_SC_NPROCESSORS_CONF);
+ std::vector<std::thread> workThreads(countConfigured);
+
+ for (auto& t : workThreads)
+ {
+ t = std::thread(spinUpCore);
+ }
+
+ for (auto& t : workThreads)
+ {
+ t.join();
+ }
+ }
+#endif
+}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff