[gromacs] Update to 4.6 series.
Susi Lehtola
jussilehtola at fedoraproject.org
Sun Dec 23 22:58:11 UTC 2012
commit e48395bb088dbf01a37b4938a4262e32b2219949
Author: Jussi Lehtola <jussilehtola at fedoraproject.org>
Date: Mon Dec 24 00:58:00 2012 +0200
Update to 4.6 series.
gromacs-4.5.1-gmxrc.patch | 160 -----------------
gromacs-GMXRC.patch | 32 ----
gromacs-README.fedora | 9 +-
gromacs-gmxdemo.patch | 320 ----------------------------------
gromacs-template-makefile-double | 13 --
gromacs-template-makefile-mpi-double | 13 --
gromacs-template-makefile-mpi-single | 13 --
gromacs-template-makefile-single | 13 --
gromacs.spec | 92 +++++------
9 files changed, 43 insertions(+), 622 deletions(-)
---
diff --git a/gromacs-README.fedora b/gromacs-README.fedora
index 7c10055..b06ec76 100644
--- a/gromacs-README.fedora
+++ b/gromacs-README.fedora
@@ -1,5 +1,5 @@
-Fri May 22 2009
-Jussi Lehtola
+Thu Dec 20 2012
+Susi Lehtola
Some notes about the GROMACS Fedora package:
@@ -17,8 +17,3 @@ precision.
both single and double precision versions. Single precision
versions have _mpi suffix, double precisin versions _mpi_d suffix.
For instance g_mdrun_mpi and g_mdrun_mpi_d.
-
-- Debug versions are available of all libraries and binaries with the
-_debug suffix. For instance the debug version of g_mdrun_mpi_d is
-g_mdrun_mpi_d_debug. The debug versions have been compiled without assembly
-loops, so they are much slower than the normal versions.
diff --git a/gromacs.spec b/gromacs.spec
index 6f2505b..016ae32 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -5,34 +5,28 @@
%endif
Name: gromacs
-Version: 4.5.5
-Release: 3%{?dist}.1
+Version: 4.6
+Release: 0.1.beta3%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
Group: Applications/Engineering
License: GPLv2+
URL: http://www.gromacs.org
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
-Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
+#Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
+Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}-beta3.tar.gz
# File gotten from
# http://www.gromacs.org/@api/deki/files/152/=manual-4.5.4.pdf
-Source1: manual-4.5.4.pdf
-Source2: gromacs-template-makefile-single
-Source3: gromacs-template-makefile-double
-Source4: gromacs-template-makefile-mpi-single
-Source5: gromacs-template-makefile-mpi-double
+#Source1: manual-4.5.4.pdf
+Source1: ftp://ftp.gromacs.org/pub/manual/gromacs-manual-4.6-beta1.pdf
Source6: gromacs-README.fedora
-# Add shebangs to scripts
-Patch0: gromacs-GMXRC.patch
-# Patch gmxdemo for new filenames
-Patch1: gromacs-gmxdemo.patch
-
BuildRequires: cmake
BuildRequires: atlas-devel
BuildRequires: fftw-devel
BuildRequires: gsl-devel
BuildRequires: libxml2-devel
BuildRequires: libX11-devel
+BuildRequires: lesstif-devel
# To get rid of executable stacks
BuildRequires: prelink
@@ -66,6 +60,8 @@ Group: Applications/Engineering
BuildArch: noarch
# Due to switch to noarch package
Obsoletes: gromacs-common < 4.0.7-1
+# No more tutor package
+Obsoletes: gromacs-tutor < 4.6-1
%description common
GROMACS is a versatile and extremely well optimized package to perform
@@ -220,6 +216,18 @@ and solid state physics.
This package contains development libraries for GROMACS MPICH2.
You may need it if you want to write your own analysis programs.
+%package ngmx
+Summary: GROMACS X11 visualization program
+Group: Applications/Engineering
+
+%description ngmx
+GROMACS is a versatile and extremely well optimized package to perform
+molecular dynamics computer simulations and subsequent trajectory analysis.
+It is developed for biomolecules like proteins, but the extremely high
+performance means it is used also in several other field like polymer chemistry
+and solid state physics.
+
+This package contains ngmx, the X11 visualization program.
%package bash
@@ -280,27 +288,10 @@ and solid state physics.
This package provides scripts needed to run GROMACS with csh and a completion
script.
-%package tutor
-Summary: GROMACS tutorial files
-Group: Applications/Engineering
-Requires: gromacs-common = %{version}-%{release}
-BuildArch: noarch
-# Due to switch to noarch package
-Obsoletes: gromacs-tutor < 4.0.7-1
-
-%description tutor
-GROMACS is a versatile and extremely well optimized package to perform
-molecular dynamics computer simulations and subsequent trajectory analysis.
-It is developed for biomolecules like proteins, but the extremely high
-performance means it is used also in several other field like polymer chemistry
-and solid state physics.
-
-This package provides tutorials for the use of GROMACS.
-
%prep
-%setup -q
-%patch0 -p1 -b .gmxrc
-%patch1 -p1 -b .gmxdemo
+%setup -q -n %{name}-%{version}-beta3
+#patch0 -p1 -b .gmxrc
+#patch1 -p1 -b .gmxdemo
# Fix incorrect permission
#chmod a-x src/tools/gmx_xpm2ps.c
@@ -319,13 +310,18 @@ export CFLAGS="%optflags -Wa,--noexecstack -fPIC"
export LIBS="-L%{_libdir}/atlas -lblas -llapack"
# Default options, used for all compilations
-export DEFOPTS="-D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=%{_lib}"
+export DEFOPTS="-D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=%{_lib} -DGMX_X11=ON"
export SINGLE="-D GMX_DOUBLE=OFF" # Single precision
export DOUBLE="-D GMX_DOUBLE=ON" # Double precision
export MPI="-D GMX_MPI=ON"
-# Add this to the configure options if you want to build a debug version
-export NOASM="-D GMX_ACCELERATION=OFF"
+# Acceleration flag
+export CPUACC="None"
+# .. but on x86_64 we know that SSE2 is available always, so
+%ifarch x86_64
+export CPUACC="SSE2"
+%endif
+export DEFOPTS+=" -DGMX_CPU_ACCELERATION=${CPUACC}"
# Single precision
mkdir single
@@ -450,17 +446,9 @@ cd ..
## Now, the rest of the necessary stuff
# Install manual & packager's note
-install -cpm 644 %{SOURCE1} .
+install -cpm 644 %{SOURCE1} manual.pdf
install -cpm 644 %{SOURCE6} README.fedora
-# Remove broken makefiles generated by build process
-rm -rf %{buildroot}%{_datadir}/%{name}/template/Makefil*
-# Install template makefiles
-install -cpm 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/template/Makefile.single
-install -cpm 644 %{SOURCE3} %{buildroot}%{_datadir}/%{name}/template/Makefile.double
-install -cpm 644 %{SOURCE4} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.single
-install -cpm 644 %{SOURCE5} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.double
-
# Fix GMXRC file permissions
chmod a+x %{buildroot}%{_bindir}/GMXRC %{buildroot}%{_bindir}/GMXRC.*
@@ -515,16 +503,19 @@ rm -rf %{buildroot}
%defattr(-,root,root,-)
%{_bindir}/g_*
+%files ngmx
+%defattr(-,root,root,-)
+%{_bindir}/ngmx*
+
%files common
%defattr(-,root,root,-)
-%doc AUTHORS COPYING README manual-4.5.4.pdf README.fedora
+%doc AUTHORS COPYING README manual.pdf README.fedora
%{_bindir}/GMXRC
%{_bindir}/GMXRC.bash
%{_mandir}/man1/*
%{_mandir}/man7/gromacs.*
%{_datadir}/%{name}/
%exclude %{_datadir}/%{name}/template/
-%exclude %{_datadir}/%{name}/tutor/
%files libs
%defattr(-,root,root,-)
@@ -592,12 +583,11 @@ rm -rf %{buildroot}
%doc completion.csh
%{_bindir}/GMXRC.csh
-%files tutor
-%defattr(-,root,root,-)
-%{_datadir}/%{name}/tutor/
-
%changelog
+* Mon Dec 24 2012 Susi Lehtola <jussilehtola at fedoraproject.org> - 4.6-0.1.beta3
+- Update to 4.6 beta 3.
+
* Fri Nov 02 2012 Jussi Lehtola <jussilehtola at fedoraproject.org> - 4.5.5-3.1
- Bump due to MPICH2 update.
More information about the scm-commits
mailing list