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 <lindahl@gromacs.org> %package devel -License: GPL v2 or later +License: GPLv2+ Summary: Molecular dynamics package Group: Productivity/Scientific/Chemistry Requires: %{name} = %{version} fftw3-devel glibc-devel xorg-x11-devel @@ -77,19 +79,31 @@ %prep %setup -q -%patch +%patch -p1 +%patch1 -p1 %build -autoreconf --force --install -%{?suse_update_config:%{suse_update_config -f}} -export CFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" -export CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" -%configure --disable-static --with-pic --enable-shared --without-motif-libraries -%{__make} %{?jobs:-j%jobs} +%if 0%{?fedora} +export RPM_OPT_FLAGS="$RPM_OPT_FLAGS -DFEDORA" +%endif +mkdir build +cd build +cmake \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_VERBOSE_MAKEFILE=TRUE \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_C_FLAGS_RELEASE:STRING="$RPM_OPT_FLAGS -fno-strict-aliasing" \ + -DCMAKE_CXX_FLAGS_RELEASE:STRING="$RPM_OPT_FLAGS" \ + -DCMAKE_SKIP_RPATH=1 \ + -DPACKAGE_ARCHITECTURE=uname -m \ + -DLIB=%{_lib} \ + .. + +make %install +cd build make DESTDIR=${RPM_BUILD_ROOT} install -mv ${RPM_BUILD_ROOT}/usr/share/man/man1/disco.1 ${RPM_BUILD_ROOT}/usr/share/man/man1/g_disco.1 %{__rm} -f %{buildroot}%{_libdir}/*.la %clean @@ -108,9 +122,11 @@ %docdir %{_datadir}/gromacs/html %{_datadir}/gromacs/html/ %{_mandir}/man1/* +%{_mandir}/man7/* %{_libdir}/libgmx.so.* %{_libdir}/libgmxana.so.* %{_libdir}/libmd.so.* +%{_libdir}/libgmxpreprocess.so.* %files devel %defattr(644,root,root,755) @@ -118,5 +134,6 @@ %{_libdir}/*.so %dir %{_includedir}/gromacs %{_includedir}/gromacs/* +%{_libdir}/pkgconfig/* %changelog ++++++ avoid_empty_elements_in_ld_library_path.patch ++++++ diff -wruN -x '*~' ../orig-gromacs-4.5.1/scripts/GMXRC.bash.cmakein ./scripts/GMXRC.bash.cmakein --- ../orig-gromacs-4.5.1/scripts/GMXRC.bash.cmakein 2010-08-23 19:58:30.000000000 +0200 +++ ./scripts/GMXRC.bash.cmakein 2010-10-07 09:05:23.000000000 +0200 @@ -8,8 +8,12 @@ tmppath="" for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do if test "$i" != "$GMXLDLIB"; then + if test ${tmppath} == ""; then + tmppath=$i + else tmppath=${tmppath}:$i fi + fi done LD_LIBRARY_PATH=$tmppath diff -wruN -x '*~' ../orig-gromacs-4.5.1/scripts/GMXRC.csh.cmakein ./scripts/GMXRC.csh.cmakein --- ../orig-gromacs-4.5.1/scripts/GMXRC.csh.cmakein 2010-08-23 19:58:30.000000000 +0200 +++ ./scripts/GMXRC.csh.cmakein 2010-10-07 09:09:17.000000000 +0200 @@ -16,7 +16,13 @@ # remove previous gromacs part from ld_library_path set tmppath = "" foreach i ( `echo $LD_LIBRARY_PATH | sed "s/:/ /g"` ) - if ( "$i" != "$GMXLDLIB" ) set tmppath = "${tmppath}:$i" + if ( "$i" != "$GMXLDLIB" ) then + if ("${tmppath}" == "") then + set tmppath = "$i" + else + set tmppath = "${tmppath}:$i" + endif + endif end setenv LD_LIBRARY_PATH $tmppath diff -wruN -x '*~' ../orig-gromacs-4.5.1/scripts/GMXRC.zsh.cmakein ./scripts/GMXRC.zsh.cmakein --- ../orig-gromacs-4.5.1/scripts/GMXRC.zsh.cmakein 2010-08-23 19:58:30.000000000 +0200 +++ ./scripts/GMXRC.zsh.cmakein 2010-10-07 09:06:27.000000000 +0200 @@ -8,8 +8,12 @@ tmppath="" for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do if test "$i" != "$GMXLDLIB"; then + if test ${tmppath} == ""; then + tmppath=$i + else tmppath=${tmppath}:$i fi + fi done LD_LIBRARY_PATH=$tmppath ++++++ cmake_lib64.patch ++++++ diff -wruN -x '*~' ../orig-gromacs-4.5.1/CMakeLists.txt ./CMakeLists.txt --- ../orig-gromacs-4.5.1/CMakeLists.txt 2010-09-02 12:39:25.000000000 +0200 +++ ./CMakeLists.txt 2010-10-07 09:44:36.000000000 +0200 @@ -642,7 +642,17 @@ ######################################################################## # Specify install locations and which subdirectories to process # ######################################################################## -set(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib) +# Library path (lib / lib64 ) + +IF ( DEFINED LIB ) + SET ( LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${LIB}" ) +ELSE ( DEFINED LIB ) + IF (CMAKE_SIZEOF_VOID_P MATCHES "8") + SET( LIB_SUFFIX "64" ) + ENDIF(CMAKE_SIZEOF_VOID_P MATCHES "8") + SET ( LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}" ) +ENDIF ( DEFINED LIB ) +MESSAGE(STATUS "Libraries will be installed in ${LIB_INSTALL_DIR}" ) set(BIN_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/bin) set(DATA_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/gromacs) set(MAN_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/man) ++++++ gromacs-3.3.1.tar.bz2 -> gromacs-4.5.1.tar.bz2 ++++++ gromacs/gromacs-3.3.1.tar.bz2 /mounts/work_src_done/STABLE/gromacs/gromacs-4.5.1.tar.bz2 differ: char 11, line 1 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Remember to have fun... -- To unsubscribe, e-mail: opensuse-commit+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-commit+help@opensuse.org