+++ /dev/null
- Welcome to GROMACS!
-
-*Note*: Detailed, step-by-step installation instructions
-are available on the website
-http://www.gromacs.org/Downloads/Installation_Instructions.
-
-*Note*: If you want to use automake for building look at INSTALL.
- However, automake will be deprecated in releases after 4.5
-
-
-
-Cmake (cross-platform make) is a relatively new build system that
-is gaining in popularity. One of the biggest selling points is
-compatibility with MS Windows. Starting with the 4.5 release,
-it is possible to configure and compile the source code with it.
-
-GETTING CMAKE
-
-Packages for various platforms can be found on the project's download page.
-Most of the Linux distributions come with packages available through the
-corresponding package manage. Make sure the installed version is 2.6 or later.
-Using CMake
-
-Please read carefully the documentation on the CMake website. Developers
-may look at some of the online tutorials.
-
-CONFIGURING WITH DEFAULTS SETTINGS
-
-It is advisable that the configuration and the build of the binaries are done
-outside of the source tree. On Linux/Mac, the following will configure
-the build with the default settings:
-
-$ tar xvfz gromacs-4.5.tar.gz
-$ ls
-gromacs-4.5
-$ mkdir build
-$ cd build
-$ cmake ../gromacs-4.5
-$ make
-
-On multi-core CPU systems (very likely nowadays), the parallel make will do the job much faster:
-
-$ make -j 4
-$ make install
-
-Substitute 4 with the number of available cores.
-
-CONFIGURING WITH CUSTOM OPTIONS
-
-Custom options can be set in a few different ways.A list of the more commonly
-used ones can be found at http://www.gromacs.org/Developer_Zone/Cmake/Custom_options.
-
- *command line flag
-
-The values of custom options are supplied with the -D flag. Note that the source path should
-be the last argument (otherwise remove the space between -D and the option)!
-
-$ cmake -D GMX_DOUBLE=ON ../gromacs-4.5
-
- *interactive CMake session
-
-$ cmake -i ../gromacs-4.5
-
- *curses cmake interface (ccmake)
-
-$ ccmake ../gromacs-4.5
-
- *CMake GUI
-
-$ cmake-gui ../gromacs-4.5
-
-Explanation about the different options will be presented when using any of the
-interactive, curses or gui methods.
-
-All configure options are saved in the CMakeCache.txt file in the build directory.
-The file can be edited using a text editor, but after that cmake should be run again.
-
-$ vim CMakeCache.txt
-$ cmake ../gromacs-4.5
Welcome to the official version of GROMACS!
-If you are familiar with unix, it should be fairly trivial to compile and
-install GROMACS. Installation instructions for CMake are available in the
-INSTALL.* files (the use of autotools is no longer available). A more
-extended step-by-step guide can be found on our website http://www.gromacs.org.
+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!
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 modified must be licensed
-under GPL, and 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.
+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!
* * * * *
* 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 (2013)
+ DOI: 10.1093/bioinformatics/btt055
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 GPL and can be redistributed freely) or
+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 at gromacs@gromacs.org if you are interested.
+++ /dev/null
-
-To support special compiler and OS combinations like the Portland
-compilers on Linux/x86, Compaq compilers on Linux/Alpha, and enable
-shared libraries when using wrapper scripts like mpcc we are using
-a prerelease version of libtool (1.4e), and the libtool.m4 script has been
-patched and included at the end of acinclude.m4.
-
-PLEASE NOTE - You NEVER have to install libtool, and autoconf/automake
-are only necessary for developers who change the Makefile.in's. You can
-find the software at ftp.gromacs.org/developers.
-
-This file summarizes the patches/extensions we made so we can check it
-if we ever update the files in GROMACS:
-
-
-
-**********************************************************************
-
-B. Changes in libtool-1.4e:
- All these changes should go in libtool.m4. This file is included
- in the GROMACS acinclude.m4 to make sure we use the right version.
-
-1. I have implemented Fortran 77 support in libtool, which hopefully
- will make its way into the main distribution. This involves
- the AC_LIBTOOL_LANG_F77_CONFIG macro, and all supporting routines
- with "F77" in the name :-)
- Since a couple of f77 compilers (ibm xlf notably) dont accept -DPIC
- I also separated the compiler flag test into one for -fPIC and
- a separate one for -DPIC.
- I have changed echo to printf for the lt_simple.. variables, to
- get the fortran formatting right.
-
- There is one specific Gromacs-related change that won't be a
- part of the main libtool distribution:
-
- I removed the --with-tags argument from _LT_AC_TAGCONFIG,
- to fix libtool always creating the F77 and CXX macros,
- and replaced it with a check for ac_cv_prog_**_g to determine
- whether we should use CXX and/or F77. Don't care about GCJ...
- To avoid AC_PROG_CXX always being expanded, I introduced the macro
- inside an always-false test in our configure.ac.
-
-2. To support dynamic libraries on Alpha/Linux with the Compaq Compilers,
- I have added some flag specifications in the non-gcc compiler section
- of the AC_LIBTOOL_PROG_COMPILER_PIC macro. I added the linux*) case:
-
-=============================================================
- irix5* | irix6* | nonstopux*)
- _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
- # PIC (with -KPIC) is the default.
- _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
- ;;
-
-+ linux*)
-+ # Check flags for non-gnu compilers on Linux
-+ case "$host_cpu" in
-+ alpha*)
-+ # The only non-gnu compiler on Linux/Alpha is the Compaq one:
-+ _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
-+ _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
-+ ;;
-+
-+ i?86)
-+ # Intel icc compiler
-+ if $CC -V 2>&1 | grep 'Intel Corporation' > /dev/null 2>&1; then
-+ _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption,link,'
-+ _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static'
-+ else
-+ _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
-+ fi
-+ ;;
-+
-+ ia64)
-+ # Intel icc compiler
-+ if $CC -V 2>&1 | grep 'Intel Corporation' > /dev/null 2>&1; then
-+ _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption,link,'
-+ _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static'
-+ else
-+ _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
-+ fi
-+ ;;
-+
-+ *)
-+ _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
-+ ;;
-+ esac
-+ ;;
-
- newsos6)
- _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
- _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
- ;;
-
-
-=====================================================================
-The intel compilers echoes stupid stuff to stderr, which is interpreted
-as errors when libtool checks for supported flags. As a workaround we
-only grep for the actual flag tried, or the words "flag" or "option".
-The modified versions of the macros are:
-
-
-# AC_LIBTOOL_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
-# [OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
-# ----------------------------------------------------------------
-# Check whether the given compiler option works
-AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION],
-[AC_CACHE_CHECK([$1], [$2],
- [$2=no
- ifelse([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
- save_CFLAGS="$CFLAGS"
- CFLAGS="$CFLAGS $3"
- printf "$lt_simple_compile_test_code" > conftest.$ac_ext
- if (eval $ac_compile 2>conftest.err) && test -s $ac_outfile; then
- # Modified by Erik Lindahl:
- # Some compilers (icc, pgcc) echo stupid stuff to stderr.
- # To avoid this being interpreted as errors we check the output
- # and only fail the test if the option is present, or one of the
- # words 'option' or 'flag'.
- if test -n "$3" && grep "$3" conftest.err > /dev/null 2>&1 || grep "option" conftest.err > /dev/null 2>&1 || grep "flag" conftest.err > /dev/null 2>&1 ; then
- # Append any errors to the config.log.
- cat conftest.err 1>&AS_MESSAGE_LOG_FD
- else
- $2=yes
- fi
- fi
- $rm conftest*
- CFLAGS="$save_CFLAGS"
-])
-
-if test x"[$]$2" = xyes; then
- ifelse([$5], , :, [$5])
-else
- ifelse([$6], , :, [$6])
-fi
-])# AC_LIBTOOL_COMPILER_OPTION
-
-
-# AC_LIBTOOL_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
-# [ACTION-SUCCESS], [ACTION-FAILURE])
-# ------------------------------------------------------------
-# Check whether the given compiler option works
-AC_DEFUN([AC_LIBTOOL_LINKER_OPTION],
-[AC_CACHE_CHECK([$1], [$2],
- [$2=no
- save_LDFLAGS="$LDFLAGS"
- LDFLAGS="$LDFLAGS $3"
- printf "$lt_simple_link_test_code" > conftest.$ac_ext
- if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
- # The compiler can only warn and ignore the option if not recognized
- # So say no if there are warnings
- if test -n "$3" && grep "$3" conftest.err > /dev/null 2>&1 || grep "option" conftest.err > /dev/null 2>&1 || grep "flag" conftest.err > /dev/null 2>&1 ; then
- # Append any errors to the config.log.
- cat conftest.err 1>&AS_MESSAGE_LOG_FD
- else
- $2=yes
- fi
- fi
- $rm conftest*
- LDFLAGS="$save_LDFLAGS"
-])
-
-if test x"[$]$2" = xyes; then
- ifelse([$4], , :, [$4])
-else
- ifelse([$5], , :, [$5])
-fi
-])# AC_LIBTOOL_LINKER_OPTION
-
-
-
-===============================================================
-
-That's it. I've submitted most patches and extensions to
-automake/libtool mailing lists, so hopefully the next release will be
-easier if they are included in future versions :-)
-
-Erik Lindahl <lindahl@gromacs.org>, 2002-01-23
-
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biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff