Commit 316912c4 authored by Andreas Tille's avatar Andreas Tille

New upstream version 2016.4

parent e994b304

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

language: cpp
before_install:
- echo "yes" | sudo add-apt-repository ppa:kalakris/cmake #https://github.com/travis-ci/travis-ci/issues/2212
- sudo apt-get update
- sudo apt-get install libfftw3-dev libopenmpi-dev libx11-dev zlib1g-dev libgsl0-dev libxml2-dev libblas-dev liblapack-dev libboost-dev cmake
env:
matrix:
- GMX_DOUBLE=OFF GMX_MPI=OFF
- GMX_DOUBLE=OFF GMX_MPI=ON
- GMX_DOUBLE=ON GMX_MPI=OFF
- GMX_DOUBLE=ON GMX_MPI=ON
script:
- mkdir build && pushd build && cmake -DGMX_DOUBLE=$GMX_DOUBLE -DGMX_MPI=$GMX_MPI .. && make -j4
compiler:
- clang
- gcc
Current lead developers:
Mark Abraham <mark.j.abraham@gmail.com>
David van der Spoel <spoel@gromacs.org>
Berk Hess <hess@gromacs.org>
Erik Lindahl <lindahl@gromacs.org>
A full list of GROMACS contributors is available at http://www.gromacs.org/About_Gromacs/People
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#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015, 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.
set(BUILDING_SOURCE_PACKAGE OFF)
# The essential difference in building a source package is that install() rules
# from the CMake project are not considered when deciding what to package.
# Instead, only the listed directories are packaged (and the listed directories
# contain the source tree).
if (NOT CPACK_INSTALL_CMAKE_PROJECTS)
set(BUILDING_SOURCE_PACKAGE ON)
endif()
if (BUILDING_SOURCE_PACKAGE)
# TODO: add check that source doesn't contain any untracked files
get_filename_component(CMAKE_BINARY_DIR ${CPACK_OUTPUT_CONFIG_FILE} PATH)
# TODO: The list could be generated at the same time as the list of
# directories to include to keep the probe file names at the same place.
# And this does not detect if things have been built in the past, but are
# outdated.
if (NOT EXISTS "${CMAKE_BINARY_DIR}/docs/man/gmx-view.1" OR
NOT EXISTS "${CMAKE_BINARY_DIR}/docs/install-guide/text/INSTALL" OR
NOT EXISTS "${CMAKE_BINARY_DIR}/src/programs/completion/gmx-completion.bash")
message(FATAL_ERROR
"To create a complete source package, bash completions, "
"man pages, and INSTALL need to be generated. "
"Run 'make completion man install-guide' to build "
"these parts (you will need Sphinx). You can also configure with "
"GMX_BUILD_HELP=ON to automatically build the completions.")
endif()
else()
# TODO: If GMX_BUILD_HELP is AUTO, it may happen that the generation
# fails, and things are silently left out.
# Also, it is currently impossible to get these files into the binary
# package for cross-compilation. However, binary packages are not
# currently used much, either...
if (NOT CPACK_GMX_BUILD_HELP)
message(WARNING
"To create a complete binary package, bash completions and "
"man pages need to be generated. "
"You need to configure with GMX_BUILD_HELP=ON to include all "
"in the binary package.")
# Building the man etc. targets is not sufficient because then the
# install is still not done.
endif()
endif()
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2011,2014, 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.
SET(CTEST_PROJECT_NAME "Gromacs")
SET(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
IF(NOT DEFINED CTEST_DROP_METHOD)
SET(CTEST_DROP_METHOD "http")
ENDIF()
IF(CTEST_DROP_METHOD STREQUAL "http")
SET(CTEST_DROP_SITE "cdash.gromacs.org")
SET(CTEST_DROP_LOCATION "/submit.php?project=Gromacs")
SET(CTEST_DROP_SITE_CDASH TRUE)
ENDIF()
This diff is collapsed.
Welcome to the official version of GROMACS!
If you are familiar with Unix, it should be fairly trivial to compile and
install GROMACS. GROMACS uses only the CMake build sytem, and our
installation guide can be found at
http://www.gromacs.org/Documentation/Installation_Instructions.
Of course we will do our utmost to help you with any problems, but PLEASE
READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US!
There are also several other online resources available from the homepage,
and special information for developers.
If you are a developer, or change the source for any other reason, check
out http://www.gromacs.org/Developer_Zone.
* * * * *
GROMACS is free software, distributed under the GNU Lesser General
Public License, version 2.1 However, scientific software is a little
special compared to most other programs. Both you, we, and all other
GROMACS users depend on the quality of the code, and when we find bugs
(every piece of software has them) it is crucial that we can correct
it and say that it was fixed in version X of the file or package
release. For the same reason, it is important that you can reproduce
other people's result from a certain GROMACS version.
The easiest way to avoid this kind of problems is to get your modifications
included in the main distribution. We'll be happy to consider any decent
code. If it's a separate program it can probably be included in the contrib
directory straight away (not supported by us), but for major changes in the
main code we appreciate if you first test that it works with (and without)
MPI, threads, double precision, etc.
If you still want to distribute a modified version or use part of GROMACS
in your own program, remember that the entire project must be licensed
according to the requirements of the LGPL v2.1 license under which you
received this copy of GROMACS. We request that it must clearly be labeled as
derived work. It should not use the name "official GROMACS", and make
sure support questions are directed to you instead of the GROMACS developers.
Sorry for the hard wording, but it is meant to protect YOUR reseach results!
* * * * *
The development of GROMACS is mainly funded by academic research grants.
To help us fund development, we humbly ask that you cite the GROMACS papers:
* GROMACS: A message-passing parallel molecular dynamics implementation
H.J.C. Berendsen, D. van der Spoel and R. van Drunen
Comp. Phys. Comm. 91, 43-56 (1995)
DOI: 10.1016/0010-4655(95)00042-E
* GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
J. Chem. Theory Comput. 4 (2008) pp. 435-447
DOI: 10.1021/ct700301q
* GROMACS 4.5: a high-throughput and highly parallel open source
molecular simulation toolkit
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar,
Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson,
David van der Spoel, Berk Hess, Erik Lindahl.
Bioinformatics 29 (2013) pp. 845-54
DOI: 10.1093/bioinformatics/btt055
* Tackling Exascale Software Challenges in Molecular Dynamics Simulations
with GROMACS
Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale,
8759 (2015) pp. 3–27
DOI: 10.1007/978-3-319-15976-8_1
There are a lot of cool features we'd like to include in future versions,
but our resources are limited. All kinds of donations are welcome, both in
form of code, hardware and funding! Industrial users who choose to pay
for a license pro bono (it is still LGPL and can be redistributed freely) or
contribute in other ways are listed as GROMACS supporters on our webpages.
Don't hesitate to contact us if you are interested.
Good luck with your simulations!
The GROMACS Crew
GROMACS is a versatile and high-performance toolkit for molecular simulations, and extensively used both in biomolecular and materials sciences.
The precompiled binary distributions come with threads support for efficient parallelization on multi-core workstations, but if you want to use large-scale MPI parallelization you will need to build from source on the target system due to MPI library compatibility issues.
If you have problems, you can find lots of documentation at http://www.gromacs.org. You can also post to the mailing lists, but considering these are very high volume it might be a good idea to use the archive search functionality on the website first.
This installer will place the Gromacs command line tools in the default location, which is typically /usr/local/gromacs for Unix, Mac, and Linux, and a location like C:\Program Files\gromacs on Windows.
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2015,2016, 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.
#