Mailinglist Archive: opensuse-commit (1023 mails)

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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@xxxxxxxxxx
+
+- 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@xxxxxxxxxxxx
+
+- 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@xxxxxxxxxxx>
 
 %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


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



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