commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory
checked in at Tue Nov 2 16:16:34 CET 2010.
--------
--- gromacs/gromacs.changes 2009-06-20 14:07:18.000000000 +0200
+++ /mounts/work_src_done/STABLE/gromacs/gromacs.changes 2010-10-20 16:19:50.000000000 +0200
@@ -1,0 +2,60 @@
+Thu Oct 7 07:24:01 UTC 2010 - kkaempf@novell.com
+
+- Update to 4.5.1
+ - fix bnc#642828 (CVE-2010-4001: Insecure use of LD_LIBRARY_PATH)
+ See http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5
+ for a full list of changes
+
+ - 2D decomposition support for PME: improved load balancing with
+ up to 40% overall performance improvement for large systems.
+ - Memory usage is improved for very large systems, allowing
+ simulations of >100 million atoms.
+ - Running on multi-core nodes now automatically uses thread-
+ based parallelization.
+ - GPU computing support
+ - Check-pointing is made more secure:MD5sum are used to verify
+ that all files are correctly in-place before a simulation is
+ appended. Output file appending at continuation is turned on
+ by default
+ - Full Cmake support. Autoconf/automake will be deprecated after
+ the final 4.5 release!
+ - Full support for 7 AMBER force fields
+ - Support for CHARMM27, including cmap for dihedrals
+ - Efficient Generalized-Born implicit solvent support including
+ the Still/HCT/OBC-models to compute the Born radii, a novel way
+ of tabulating the generalized Born-interaction formula for
+ greater speed, and optimized SSE-routines for both cut-off and
+ all-vs-all simulations.
+ - Support for nucleic acid simulations
+ - Support for Velocity-Verlet integrators for reversible T- and
+ P-coupling; MTTK pressure control integrators; Nose-Hoover
+ chains
+ - Support for Bennett acceptance ratio (BAR) free energy
+ calculations
+ - Decoupling group setup for free energy
+ - File formats: All GROMACS tools can now read any VMD supported
+ trajectory format, without converting trajectory first. (VMD
+ is required)
+ - g_rdf was a little bit enhanced that structure factors can be
+ calculated for any system, by supplying the necessary data via
+ sfactor.dat. Most of the common atomtypes are already contained,
+ but everybody who needs more freedom can enhance the table
+ - Library support for "dynamic index groups" based on textual
+ selections (experimental feature). See the tool g_select, the
+ included template.c, or Doxygen documentation for information on
+ how to write analysis tools using the library. Existing tools
+ have not (yet) been converted.
+ - g_tune_pme: For a given number of processes or threads this tool
+ systematically times mdrun with various numbers of PME-only nodes
+ and determines which setting is fastest. It also checks whether
+ performance can be enhanced by shifting load between the real and
+ the reciprocal space part of the Ewald sum.
+ - g_membed: a very convenient utility for embedding membrane
+ proteins into equilibrated lipid bilayers
+
+-------------------------------------------------------------------
+Sat May 22 19:29:07 UTC 2010 - cristian.rodriguez@opensuse.org
+
+- read "/dev/urandom" instead of /dev/random
+
+-------------------------------------------------------------------
calling whatdependson for head-i586
Old:
----
gromacs-3.3.1.dif
gromacs-3.3.1.tar.bz2
New:
----
avoid_empty_elements_in_ld_library_path.patch
cmake_lib64.patch
gromacs-4.5.1.tar.bz2
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ gromacs.spec ++++++
--- /var/tmp/diff_new_pack.v2592s/_old 2010-11-02 16:16:19.000000000 +0100
+++ /var/tmp/diff_new_pack.v2592s/_new 2010-11-02 16:16:19.000000000 +0100
@@ -1,7 +1,7 @@
#
-# spec file for package gromacs (Version 3.3.1)
+# spec file for package gromacs (Version 4.5.1)
#
-# Copyright (c) 2009 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2010 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -19,16 +19,18 @@
Name: gromacs
-BuildRequires: fftw3-devel xorg-x11-devel
-Version: 3.3.1
-Release: 166
+BuildRequires: cmake fftw3-devel libxml2-devel xorg-x11-devel
+BuildRequires: gcc-c++ libstdc++-devel
+Version: 4.5.1
+Release: 1
Summary: Molecular Dynamics Package
Url: http://www.gromacs.org
-License: GPL v2 or later
+License: GPLv2+
Group: Productivity/Scientific/Chemistry
AutoReqProv: on
Source0: gromacs-%{version}.tar.bz2
-Patch: gromacs-%{version}.dif
+Patch: avoid_empty_elements_in_ld_library_path.patch
+Patch1: cmake_lib64.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
@@ -51,7 +53,7 @@
Erik Lindahl
participants (1)
-
root@hilbert.suse.de