commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2020-08-01 12:31:52 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new.3592 (New) Package is "gromacs" Sat Aug 1 12:31:52 2020 rev:46 rq:822970 version:2019.6 Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2020-03-04 09:47:46.774192978 +0100 +++ /work/SRC/openSUSE:Factory/.gromacs.new.3592/gromacs.changes 2020-08-01 12:32:12.786514956 +0200 @@ -1,0 +2,5 @@ +Mon Jul 27 09:08:28 UTC 2020 - Michel Normand + +- Increase default disk size from 3 to 6GB in _constraints file + +--- Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.HrU9YE/_old 2020-08-01 12:32:14.942516974 +0200 +++ /var/tmp/diff_new_pack.HrU9YE/_new 2020-08-01 12:32:14.946516978 +0200 @@ -1,7 +1,7 @@ # # spec file for package gromacs # -# Copyright (c) 2019 SUSE LLC +# Copyright (c) 2020 SUSE LLC # Copyright (c) 2015-2019 Christoph Junghans # # All modifications and additions to the file contributed by third parties ++ _constraints ++ --- /var/tmp/diff_new_pack.HrU9YE/_old 2020-08-01 12:32:14.974517004 +0200 +++ /var/tmp/diff_new_pack.HrU9YE/_new 2020-08-01 12:32:14.978517008 +0200 @@ -5,7 +5,7 @@ 2 - 3 + 6 kvm
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2020-03-04 09:47:34
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new.26092 (New)
Package is "gromacs"
Wed Mar 4 09:47:34 2020 rev:45 rq:781240 version:2019.6
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2019-12-24
14:30:32.554592572 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new.26092/gromacs.changes
2020-03-04 09:47:46.774192978 +0100
@@ -1,0 +2,13 @@
+Fri Feb 28 18:14:42 UTC 2020 - Christoph Junghans
+
+- - version bump to 2019.6 details here:
+ http://manual.gromacs.org/documentation/2019.6/release-notes/2019/2019.6.html
+ Hightlights:
+ - Actually fix PME forces with FE without perturbed q/LJ
+ - Avoid overzealous program abort with orientation restraints
+ - Calculate Coulomb and LJ reciprocal terms in rerun
+ - Added check for inconsistent input of distance restraint labels in gmx
disre.
+ - Fix compiler errors with Intel compiler
+ - Avoid cryptic GPU detection errors when devices are unavailable or out of
memory
+
+---
Old:
gromacs-2019.5.tar.gz
manual-2019.5.pdf
regressiontests-2019.5.tar.gz
New:
gromacs-2019.6.tar.gz
manual-2019.6.pdf
regressiontests-2019.6.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.kVrMsx/_old 2020-03-04 09:47:57.134199187 +0100
+++ /var/tmp/diff_new_pack.kVrMsx/_new 2020-03-04 09:47:57.138199190 +0100
@@ -35,7 +35,7 @@
%endif
Name: gromacs
-Version:2019.5
+Version:2019.6
Release:0
%define uversion %{version}
%define sover 4
++ gromacs-2019.5.tar.gz -> gromacs-2019.6.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-2019.5.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new.26092/gromacs-2019.6.tar.gz differ:
char 5, line 1
++ manual-2019.5.pdf -> manual-2019.6.pdf ++
(binary differes)
++ regressiontests-2019.5.tar.gz -> regressiontests-2019.6.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/regressiontests-2019.5.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new.26092/regressiontests-2019.6.tar.gz
differ: char 18, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2019-12-24 14:30:22
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new.6675 (New)
Package is "gromacs"
Tue Dec 24 14:30:22 2019 rev:44 rq:759039 version:2019.5
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2019-11-15
22:40:28.736472729 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new.6675/gromacs.changes
2019-12-24 14:30:32.554592572 +0100
@@ -1,0 +2,17 @@
+Mon Dec 23 18:17:04 UTC 2019 - Christoph Junghans
+
+- version bump to 2019.5 details here:
+ http://manual.gromacs.org/documentation/2019.5/release-notes/2019/2019.5.html
+ Hightlights:
+ - Fix use of uninitialized data on PME only ranks
+ - Fix out of range memory access with free-energy calculations
+ - Fix error with intermolecular interactions and domain decomposition
+ - Fix issues with AWH with pull-geometry ‘direction’ to be periodic
+ - Remove assertion failure with AWH when not using the initial stage
+ - Fix dihedral angle calculation near 180 degree boundary
+ - Remove problematic output of gmx angle tool
+ - Check that libhwloc headers and runtime match
+ - Fix .gro file formatting with large boxes
+ - Fix duplicate PDB CONECT record output
+
+---
Old:
gromacs-2019.4.tar.gz
manual-2019.4.pdf
regressiontests-2019.4.tar.gz
New:
gromacs-2019.5.tar.gz
manual-2019.5.pdf
regressiontests-2019.5.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.JbHNfa/_old 2019-12-24 14:30:41.402596853 +0100
+++ /var/tmp/diff_new_pack.JbHNfa/_new 2019-12-24 14:30:41.450596876 +0100
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2019 SUSE LLC
# Copyright (c) 2015-2019 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
@@ -16,6 +16,7 @@
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
+
# Build with OpenMPI
%if 0%{?sle_version} == 0
%define mpiver openmpi2
@@ -34,14 +35,14 @@
%endif
Name: gromacs
-Version:2019.4
+Version:2019.5
Release:0
%define uversion %{version}
%define sover 4
Summary:Molecular Dynamics Package
-License:GPL-2.0-or-later and Apache-2.0
+License:GPL-2.0-or-later AND Apache-2.0
Group: Productivity/Scientific/Chemistry
-Url:http://www.gromacs.org
+URL:http://www.gromacs.org
Source0:ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{uversion}.tar.gz
Source1:ftp://ftp.gromacs.org/pub/manual/manual-%{uversion}.pdf
Source2:
http://gerrit.gromacs.org/download/regressiontests-%{uversion}.tar.gz
@@ -143,6 +144,11 @@
%build
source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh
+# save some memory
+%ifarch ppc64le
+%global _smp_mflags -j1
+%endif
+
%ifarch %x86 x86_64
#increse to SSE4.1, AVX_128_FMA, AVX_256 when possible
%define acce SSE2
++ _constraints ++
--- /var/tmp/diff_new_pack.JbHNfa/_old 2019-12-24 14:30:41.702596998 +0100
+++ /var/tmp/diff_new_pack.JbHNfa/_new 2019-12-24 14:30:41.710597002 +0100
@@ -5,7 +5,7 @@
2
- 2
+ 3
kvm
++ gromacs-2019.4.tar.gz -> gromacs-2019.5.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-2019.4.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new.6675/gromacs-2019.5.tar.gz differ: char
5, line 1
++ manual-2019.4.pdf -> manual-2019.5.pdf ++
(binary differes)
++ regressiontests-2019.4.tar.gz -> regressiontests-2019.5.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/regressiontests-2019.4.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new.6675/regressiontests-2019.5.tar.gz
differ: char 18, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2019-11-15 22:40:01
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new.26869 (New)
Package is "gromacs"
Fri Nov 15 22:40:01 2019 rev:43 rq:748954 version:2019.4
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2019-06-19
20:57:08.973917513 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new.26869/gromacs.changes
2019-11-15 22:40:28.736472729 +0100
@@ -1,0 +2,20 @@
+Fri Nov 15 14:57:22 UTC 2019 - Christoph Junghans
+
+- version bump to 2019.4 details here:
+ http://manual.gromacs.org/documentation/2019.4/release-notes/2019/2019.4.html
+ Hightlights:
+ - Fix incorrect pressure when atoms in CMAP cross a box boundary
+ - Fix incorrect LJ cut-off on GPU when rvdw < rcoulomb
+ - Fix (unlikely) missing bonded forces with CUDA GPUs and domain
decomposition
+ - Fix incorrect reporting of final kinetic energy and temperature
+ - Fix segmentation fault in grompp and mdrun with cosine COM pulling
+ - Fix grompp not adding angle constraints between constraints
+ - Fix gmx wham with angle and dihedral geometries
+ - Fix bug in gmx xpm2ps
+ - Fix bug in gmx anaeig
+ - Fix issue with demux.pl script
+ - Fixed writing of gro files with index groups
+ - Made gmx make_ndx keep chain IDs
+ - Fixes that affect portability
+
+---
Old:
gromacs-2019.2.tar.gz
manual-2019.2.pdf
regressiontests-2019.2.tar.gz
New:
gromacs-2019.4.tar.gz
manual-2019.4.pdf
regressiontests-2019.4.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.ewNVgA/_old 2019-11-15 22:40:32.984470738 +0100
+++ /var/tmp/diff_new_pack.ewNVgA/_new 2019-11-15 22:40:32.988470736 +0100
@@ -16,20 +16,25 @@
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
-
# Build with OpenMPI
+%if 0%{?sle_version} == 0
+%define mpiver openmpi2
+Obsoletes: gromacs-openmpi < %{version}
+%else
%if 0%{?sle_version} <= 120300
%define mpiver openmpi
%else
+Obsoletes: gromacs-openmpi < %{version}
%if 0%{?sle_version} <= 15
%define mpiver openmpi2
%else
%define mpiver openmpi3
%endif
%endif
+%endif
Name: gromacs
-Version:2019.2
+Version:2019.4
Release:0
%define uversion %{version}
%define sover 4
++ gromacs-2019.2.tar.gz -> gromacs-2019.4.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-2019.2.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new.26869/gromacs-2019.4.tar.gz differ:
char 5, line 1
++ manual-2019.2.pdf -> manual-2019.4.pdf ++
(binary differes)
++ regressiontests-2019.2.tar.gz -> regressiontests-2019.4.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/regressiontests-2019.2.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new.26869/regressiontests-2019.4.tar.gz
differ: char 28, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2019-06-19 20:56:48
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new.4811 (New)
Package is "gromacs"
Wed Jun 19 20:56:48 2019 rev:42 rq:701640 version:2019.2
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2018-11-13
17:13:00.282630762 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new.4811/gromacs.changes
2019-06-19 20:57:08.973917513 +0200
@@ -1,0 +2,42 @@
+Wed May 8 15:07:49 UTC 2019 - Christoph Junghans
+
+- version bump to 2019.2 details here:
+ http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html
+ Hightlights:
+ - Fix L-BGFS minimizer
+ - Disallow pull geometry direction-periodic with AWH
+ - Fixed mdrun -nsteps option
+ - gmx cluster -clndx indices now correct
+ - gmx editconf -f in.pdb -o out.pdb again preserves chain IDs
+ - Tools again accept .tpr files as input
+ - Fix segmentation fault when preparing simulated annealing inputs
+ - Fix error in AVX 512 detection code
+ - Added warning with the use of GROMOS force fields
+ - Prevented internal build of FFTW with clang and AVX-512 SIMD
+ - Updated performance guide for recent Intel processors with AVX512
instruction support
+
+---
+Tue Feb 26 10:48:25 UTC 2019 - Klaus Kämpf
+
+- add fdupes
+
+---
+Mon Feb 25 17:51:49 UTC 2019 - Christoph Junghans
+
+- version bump to 2019.1 details here:
+ http://manual.gromacs.org/documentation/2019.1/release-notes/2019/2019.1.html
+ Hightlights:
+ - Fix error with 2D/3D dynamic load balancing
+ - Fix incorrect LJ repulsion force switching on GPUs
+ - Fix segmentation fault in mdrun with domain decomposition
+ - Fix segmentation fault with energy minimization with the group scheme
+ - Correct free-energy Delta H output with mass lambda’s
+ - Prevent mdrun -rerun from writing incorrect free-energy output
+ - Fix possible division by zero in enforced-rotation code
+ - Fix trjconv -ndec
+ - Fix using index file groups when .tpr file not supplied
+ - Fix tune_pme
+ - Fixes that affect portability
+ - Explicitly require 64-bit platforms for OpenCL
+
+---
Old:
gromacs-2018.4.tar.gz
manual-2018.4.pdf
regressiontests-2018.4.tar.gz
New:
gromacs-2019.2.tar.gz
manual-2019.2.pdf
regressiontests-2019.2.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.jxStw2/_old 2019-06-19 20:57:18.997925862 +0200
+++ /var/tmp/diff_new_pack.jxStw2/_new 2019-06-19 20:57:19.001925865 +0200
@@ -1,8 +1,8 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany.
-# Copyright (c) 2015-2018 Christoph Junghans
+# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2015-2019 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -13,27 +13,41 @@
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
-# Please submit bugfixes or comments via http://bugs.opensuse.org/
+# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
+# Build with OpenMPI
+%if 0%{?sle_version} <= 120300
+%define mpiver openmpi
+%else
+ %if 0%{?sle_version} <= 15
+ %define mpiver openmpi2
+ %else
+ %define mpiver openmpi3
+ %endif
+%endif
+
Name: gromacs
-Version:2018.4
+Version:2019.2
Release:0
+%define uversion %{version}
+%define sover 4
Summary:Molecular Dynamics Package
-License:GPL-2.0-or-later
+License:GPL-2.0-or-later and Apache-2.0
Group: Productivity/Scientific/Chemistry
Url:http://www.gromacs.org
-Source0:ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
-Source1:ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf
-Source2:
http://gerrit.gromacs.org/download/regressiontests-%{version}.tar.gz
+Source0:ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{uversion}.tar.gz
+Source1:ftp://ftp.gromacs.org/pub/manual/manual-%{uversion}.pdf
+Source2:
http://gerrit.gromacs.org/download/regressiontests-%{uversion}.tar.gz
+BuildRequires: %{mpiver}
+BuildRequires: %{mpiver}-devel
BuildRequires: cmake >= 2.8.8
BuildRequires: fdupes
BuildRequires: gcc-c++
BuildRequires: ocl-icd-devel
BuildRequires: opencl-headers
-BuildRequires: ope
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2018-11-13 17:02:47
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Tue Nov 13 17:02:47 2018 rev:41 rq:648638 version:2018.4
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2018-07-31
15:57:04.787310602 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2018-11-13
17:13:00.282630762 +0100
@@ -1,0 +2,45 @@
+Tue Nov 13 01:10:07 UTC 2018 - Christoph Junghans
+
+- version bump to 2018.4 details here:
+ http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html
+ Highlights:
+ - Correct PME forces with free energy without perturbed charges/LJ
+ - Add constraint contribution to foreign Hamiltonian differences
+ - Add mass contribution to foreign Hamiltonian differences
+ - Work around bugs with expanded ensemble runs
+ - Checkpoint continuations require suitable .tpr files
+ - Fix mindist output file checks
+ - Fix gmx helix segmentation faults
+ - Fix bug in entropy calculation in gmx anaeig
+ - Fixed an issue where the log file could sometimes report an incorrect
initial dynamic load balancing state
+ - Fix Bromine parameters in amber forcefield files
+ - Made normal-mode analysis work for more than one molecule
+ - Disallow rerun using same filename as output file
+ - Fix issue when building GROMACS without TNG
+
+---
+Wed Nov 7 16:16:25 UTC 2018 - Christoph Junghans
+
+- version bump to 2018.3 details here:
+ http://manual.gromacs.org/documentation/2018.3/release-notes/2018/2018.3.html
+ Highlights:
+ - Multi-domain GPU runs can no longer miss pair interactions
+ - Fix Conjugate Gradient assertion failure at end of minimization
+ - Multi-domain Conjugate Gradient minimimization no longer segfaults.
+ - Fix pairlist buffer with Brownian Dynamics
+ - Avoid “atom moved to far” errors
+ - grompp now checks that pull groups are not close to half the box size
+ - Fixed segmentation fault in mdrun with QM/MM ONIOM scheme
+ - Fixed syntax error in make_gromos_rtp.py
+ - Fix gmx solvate topology updating
+ - Fix bfactor output error caused by fix for Issue 2511
+ - Made sure that gmx rms can skip values
+ - Fix trjconv when not providing structure file
+ - Fix enforced rotation energy output
+ - Fix nvcc host compiler check triggering
+ - Report up to date hwloc version information
+ - Disable single compilation unit with CUDA 9.0
+ - Avoid aborting mdrun when GPU sanity check detects errors
+ - Improve OpenCL kernel performance on AMD Vega GPUs
+
+---
@@ -5 +50 @@
- http://manual.gromacs.org/documentation/2018.1/release-notes/2018/2018.2.html
+ http://manual.gromacs.org/documentation/2018.2/release-notes/2018/2018.2.html
Old:
gromacs-2018.2.tar.gz
manual-2018.2.pdf
regressiontests-2018.2.tar.gz
New:
gromacs-2018.4.tar.gz
manual-2018.4.pdf
regressiontests-2018.4.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.QDrKHG/_old 2018-11-13 17:14:30.766511937 +0100
+++ /var/tmp/diff_new_pack.QDrKHG/_new 2018-11-13 17:14:30.766511937 +0100
@@ -18,7 +18,7 @@
Name: gromacs
-Version:2018.2
+Version:2018.4
Release:0
Summary:Molecular Dynamics Package
License:GPL-2.0-or-later
@@ -136,6 +136,9 @@
# gromacs' cmake has too much rpath auto-magic, just
# force to skip it (CMAKE_SKIP_RPATH=1) and use
# LD_LIBRARY_PATH for checks below
+
+# regression are currently broken on i686,
https://redmine.gromacs.org/issues/2584
+# and cannot be used with GMX_BUILD_MDRUN_ONLY=ON
%{cmake} \
-DCMAKE_INSTALL_PREFIX=%{_prefix} \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
@@ -151,7 +154,9 @@
%endif
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
+%ifnarch i586
-DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \
+%endif
-DGMX_LIB_INSTALL_DIR=%{_lib} ../../
make %{?_smp_mflags}
@@ -174,7 +179,6 @@
%endif
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
- -DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \
-DGMX_LIB_INSTALL_DIR=%{_lib} ../../
make %{?_smp_mflags}
++ gromacs-2018.2.tar.gz -> gromacs-2018.4.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-2018.2.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2018.4.tar.gz differ: char 5,
line 1
++ manual-2018.2.pdf -> manual-2018.4.pdf ++
(binary differes)
++ regressiontests-2018.2.tar.gz -> regressiontests-2018.4.tar.gz ++
/work/SRC/op
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2018-07-31 15:56:46 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) Package is "gromacs" Tue Jul 31 15:56:46 2018 rev:40 rq:624642 version:2018.2 Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2018-04-20 17:25:56.870202641 +0200 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2018-07-31 15:57:04.787310602 +0200 @@ -1,0 +2,11 @@ +Sat Jul 21 00:11:15 UTC 2018 - jungh...@votca.org + +- version bump to 2018.2 details here: + http://manual.gromacs.org/documentation/2018.1/release-notes/2018/2018.2.html + Highlights: + - Prevented OpenCL timing memory leak + - Fixed MPI error after constraint failure during energy minimization + - Fixed moving frozen atoms with constraints + - Fixed COM removal moving frozen atoms + +--- Old: gromacs-2018.1.tar.gz manual-2018.1.pdf regressiontests-2018.1.tar.gz New: gromacs-2018.2.tar.gz manual-2018.2.pdf regressiontests-2018.2.tar.gz Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.b6TKfl/_old 2018-07-31 15:57:10.979321081 +0200 +++ /var/tmp/diff_new_pack.b6TKfl/_new 2018-07-31 15:57:10.979321081 +0200 @@ -18,7 +18,7 @@ Name: gromacs -Version:2018.1 +Version:2018.2 Release:0 Summary:Molecular Dynamics Package License:GPL-2.0-or-later ++ gromacs-2018.1.tar.gz -> gromacs-2018.2.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/gromacs-2018.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2018.2.tar.gz differ: char 5, line 1 ++ manual-2018.1.pdf -> manual-2018.2.pdf ++ (binary differes) ++ regressiontests-2018.1.tar.gz -> regressiontests-2018.2.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-2018.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-2018.2.tar.gz differ: char 28, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2018-04-20 17:25:50
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Fri Apr 20 17:25:50 2018 rev:39 rq:593844 version:2018.1
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2018-01-21
15:49:20.436875516 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2018-04-20
17:25:56.870202641 +0200
@@ -1,0 +2,22 @@
+Wed Apr 4 16:07:40 UTC 2018 - jungh...@votca.org
+
+- version bump to 2018.1 details here:
+ http://manual.gromacs.org/documentation/2018.1/release-notes/2018/2018.1.html
+ Highlights:
+ - Fixed leap-frog integrator with Nose-Hoover T coupling and
Parrinello-Rahman P coupling
+ - Used SIMD bondeds without perturbed interactions
+ - Fixed bonds whose displacement was zero
+ - Fixed centre-of-mass motion removal on part of the system
+ - Fixed multi-simulations with multiple ranks per simulation
+ - Improved inter-simulation signalling implementation
+ - Fixed FEP calculations with SHAKE
+ - Fixed handling of mdp define statement assigning preprocessor values
+ - Prevented log file energy average printing dividing by zero
+
+---
+Fri Mar 23 08:53:36 UTC 2018 - guillaume.gar...@opensuse.org
+
+- Add _constraints file to avoid build failure and timeout on tests
+ for slow CPU workers
+
+---
Old:
gromacs-2018.tar.gz
manual-2018.pdf
regressiontests-2018.tar.gz
New:
_constraints
gromacs-2018.1.tar.gz
manual-2018.1.pdf
regressiontests-2018.1.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.7uWQ7r/_old 2018-04-20 17:26:05.457891236 +0200
+++ /var/tmp/diff_new_pack.7uWQ7r/_new 2018-04-20 17:26:05.457891236 +0200
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2017-2018 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany.
# Copyright (c) 2015-2018 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
@@ -18,10 +18,10 @@
Name: gromacs
-Version:2018
+Version:2018.1
Release:0
Summary:Molecular Dynamics Package
-License:GPL-2.0+
+License:GPL-2.0-or-later
Group: Productivity/Scientific/Chemistry
Url:http://www.gromacs.org
Source0:ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
@@ -31,11 +31,11 @@
BuildRequires: cmake >= 2.8.8
BuildRequires: fdupes
BuildRequires: gcc-c++
+BuildRequires: ocl-icd-devel
+BuildRequires: opencl-headers
BuildRequires: openmpi-devel
BuildRequires: pkg-config
BuildRequires: pkgconfig(fftw3)
-BuildRequires: opencl-headers
-BuildRequires: ocl-icd-devel
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
++ _constraints ++
1500
2
kvm
SLOW_CPU
++ gromacs-2018.tar.gz -> gromacs-2018.1.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-2018.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2018.1.tar.gz differ: char 5,
line 1
++ manual-2018.pdf -> manual-2018.1.pdf ++
(binary differes)
++ regressiontests-2018.tar.gz -> regressiontests-2018.1.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/regressiontests-2018.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-2018.1.tar.gz differ:
char 18, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2018-01-21 15:49:18
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Sun Jan 21 15:49:18 2018 rev:38 rq:567816 version:2018
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2017-11-07
09:58:14.689765431 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2018-01-21
15:49:20.436875516 +0100
@@ -1,0 +2,14 @@
+Fri Jan 19 18:46:11 UTC 2018 - jungh...@votca.org
+
+- version bump to 2018 details here:
+ http://manual.gromacs.org/documentation/2018/ReleaseNotes/index.html
+ Highlights:
+- A new dual-list dynamic-pruning algorithm for the short-ranged
interactions
+- PME long-ranged interactions can now run on a single GPU
+- AWH (Accelerated Weight Histogram) method is now supported
+- A physical validation suite is added, which runs a series of short
simulations
+- Conserved quantities are computed and reported for more integration
schemes
+- disable GPU on ppc64le, build error
+- use internal tinyxml2 as tinxml-6 is broken with gromacs, only testing is
build it anyhow
+
+---
Old:
gromacs-2016.4.tar.gz
manual-2016.4.pdf
regressiontests-2016.4.tar.gz
New:
gromacs-2018.tar.gz
manual-2018.pdf
regressiontests-2018.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.uO28ZP/_old 2018-01-21 15:49:28.628491132 +0100
+++ /var/tmp/diff_new_pack.uO28ZP/_new 2018-01-21 15:49:28.632490945 +0100
@@ -1,8 +1,8 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany.
-# Copyright (c) 2015-2017 Christoph Junghans
+# Copyright (c) 2017-2018 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2015-2018 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -18,7 +18,7 @@
Name: gromacs
-Version:2016.4
+Version:2018
Release:0
Summary:Molecular Dynamics Package
License:GPL-2.0+
@@ -34,7 +34,6 @@
BuildRequires: openmpi-devel
BuildRequires: pkg-config
BuildRequires: pkgconfig(fftw3)
-BuildRequires: pkgconfig(tinyxml2)
BuildRequires: opencl-headers
BuildRequires: ocl-icd-devel
BuildRoot: %{_tmppath}/%{name}-%{version}-build
@@ -60,11 +59,11 @@
This package contains development libraries and header for GROMACS
-%package -n libgromacs2
+%package -n libgromacs3
Summary:Libraries for Gromacs
Group: System/Libraries
-%description -n libgromacs2
+%description -n libgromacs3
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
@@ -147,10 +146,11 @@
-DGMX_SIMD=%{acce} \
-DGMX_MPI=OFF \
-DGMX_THREAD_MPI=ON \
+%ifnarch ppc64le
-DGMX_GPU=ON -DGMX_USE_OPENCL=ON \
+%endif
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
- -DGMX_EXTERNAL_TINYXML2=ON \
-DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \
-DGMX_LIB_INSTALL_DIR=%{_lib} ../../
make %{?_smp_mflags}
@@ -169,10 +169,11 @@
-DGMX_BUILD_MDRUN_ONLY=ON \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_MPI=ON \
+%ifnarch ppc64le
-DGMX_GPU=ON -DGMX_USE_OPENCL=ON \
+%endif
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
- -DGMX_EXTERNAL_TINYXML2=ON \
-DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \
-DGMX_LIB_INSTALL_DIR=%{_lib} ../../
make %{?_smp_mflags}
@@ -199,8 +200,8 @@
LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/openmpi/%{_lib}'
make -C openmpi/build %{?_smp_mflags} check
%endif
-%post -n libgromacs2 -p /sbin/ldconfig
-%postun -n libgromacs2 -p /sbin/ldconfig
+%post -n libgromacs3 -p /sbin/ldconfig
+%postun -n libgromacs3 -p /sbin/ldconfig
%files
%defattr(-,root,root,-)
@@ -208,10 +209,12 @@
%{_bindir}/*.pl
%dir %{_datadir}/gromacs
%{_datadir}/gromacs/top
+%ifnarch ppc64le
%{_datadir}/gromacs/opencl
+%endif
%{_mandir}/man1/*
-%files -n libgromacs2
+%files -n libgromacs3
%defattr(-,root,root,-)
%{_libdir}/lib*.so.*
++ gromacs-2016.4.tar.gz -> gromacs-2018.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-2016.4.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2018.tar.gz differ: char 5,
line 1
++ manual-2016.4.pdf -> manual-2018.pdf ++
(binary differes)
++ regressiontests-2016.4.tar.gz -> regressiontests-2018.ta
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2017-11-07 09:58:02
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Tue Nov 7 09:58:02 2017 rev:37 rq:538872 version:2016.4
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2017-10-25
17:48:56.447417867 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2017-11-07
09:58:14.689765431 +0100
@@ -1,0 +2,5 @@
+Sat Nov 4 00:30:29 UTC 2017 - jungh...@votca.org
+
+- enable GPU support via OpenCL
+
+---
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.RusLLg/_old 2017-11-07 09:58:18.901612631 +0100
+++ /var/tmp/diff_new_pack.RusLLg/_new 2017-11-07 09:58:18.901612631 +0100
@@ -35,6 +35,8 @@
BuildRequires: pkg-config
BuildRequires: pkgconfig(fftw3)
BuildRequires: pkgconfig(tinyxml2)
+BuildRequires: opencl-headers
+BuildRequires: ocl-icd-devel
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
@@ -145,6 +147,7 @@
-DGMX_SIMD=%{acce} \
-DGMX_MPI=OFF \
-DGMX_THREAD_MPI=ON \
+ -DGMX_GPU=ON -DGMX_USE_OPENCL=ON \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
-DGMX_EXTERNAL_TINYXML2=ON \
@@ -166,6 +169,7 @@
-DGMX_BUILD_MDRUN_ONLY=ON \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_MPI=ON \
+ -DGMX_GPU=ON -DGMX_USE_OPENCL=ON \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
-DGMX_EXTERNAL_TINYXML2=ON \
@@ -204,6 +208,7 @@
%{_bindir}/*.pl
%dir %{_datadir}/gromacs
%{_datadir}/gromacs/top
+%{_datadir}/gromacs/opencl
%{_mandir}/man1/*
%files -n libgromacs2
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2017-10-25 17:48:55
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Wed Oct 25 17:48:55 2017 rev:36 rq:536517 version:2016.4
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2017-09-17
22:38:15.937187368 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2017-10-25
17:48:56.447417867 +0200
@@ -1,0 +2,5 @@
+Wed Oct 25 11:40:37 UTC 2017 - kkae...@suse.com
+
+- adapt to new openlmi package - source mpivars.h during build
+
+---
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.ju6QZq/_old 2017-10-25 17:49:00.843211554 +0200
+++ /var/tmp/diff_new_pack.ju6QZq/_new 2017-10-25 17:49:00.843211554 +0200
@@ -1,8 +1,8 @@
#
# spec file for package gromacs
#
+# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany.
# Copyright (c) 2015-2017 Christoph Junghans
-# Copyright (c) 2013,2014 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
@@ -16,6 +16,7 @@
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
+
Name: gromacs
Version:2016.4
Release:0
@@ -27,9 +28,9 @@
Source1:ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf
Source2:
http://gerrit.gromacs.org/download/regressiontests-%{version}.tar.gz
-BuildRequires: gcc-c++
BuildRequires: cmake >= 2.8.8
BuildRequires: fdupes
+BuildRequires: gcc-c++
BuildRequires: openmpi-devel
BuildRequires: pkg-config
BuildRequires: pkgconfig(fftw3)
@@ -120,6 +121,8 @@
tar -xzf %{S:2}
%build
+source %{_libdir}/mpi/gcc/openmpi/bin/mpivars.sh
+
%ifarch i386 x86_64
#increse to SSE4.1, AVX_128_FMA, AVX_256 when possible
%define acce SSE2
@@ -228,3 +231,5 @@
%files bash
%defattr(-,root,root,-)
%config %{_sysconfdir}/bash_completion.d/gromacs
+
+%changelog
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2017-09-17 22:38:04 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) Package is "gromacs" Sun Sep 17 22:38:04 2017 rev:35 rq:526433 version:2016.4 Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2017-08-10 14:13:28.492865191 +0200 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2017-09-17 22:38:15.937187368 +0200 @@ -1,0 +2,27 @@ +Fri Sep 15 16:20:29 UTC 2017 - jungh...@votca.org + +- version bump to 2016.4 details here: + http://manual.gromacs.org/documentation/2016.4/ReleaseNotes/index.html + Highlighs: + - Disabled PME tuning with the group scheme + - Fixed value of Ewald shift + - Fixed orientation restraint reference + - Fixed bugs with setup for orientation restraints + - Worked around missing OpenMP implementation in orientation restraints + - Enable group-scheme SIMD kernels on recent AVX extensions + - Fix FEP state with rerun + - Fixed COM pull force with SD + - Fix PBC bugs in the swap code + - Fixed flat-bottomed position restraints with multiple ranks + - Fixed null pointer print in DD + - Improved the “files not present” error message + - Fixed LJ-PME + switch grompp error + - Fixed unused SIMD PME table kernel + - Fixed bugs in most double-precision Simd4 implementations + - Avoid inf in SIMD double sqrt() + - Fix NVML error messages + - Fixed IMD interface malfunctions + - Fixed initial temperature reporting + - Fix exception in SIMD LJ PME solve + +--- Old: gromacs-2016.3.tar.gz manual-2016.3.pdf regressiontests-2016.3.tar.gz New: gromacs-2016.4.tar.gz manual-2016.4.pdf regressiontests-2016.4.tar.gz Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.mINubO/_old 2017-09-17 22:38:24.264016634 +0200 +++ /var/tmp/diff_new_pack.mINubO/_new 2017-09-17 22:38:24.264016634 +0200 @@ -17,7 +17,7 @@ # Name: gromacs -Version:2016.3 +Version:2016.4 Release:0 Summary:Molecular Dynamics Package License:GPL-2.0+ ++ gromacs-2016.3.tar.gz -> gromacs-2016.4.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/gromacs-2016.3.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2016.4.tar.gz differ: char 5, line 1 ++ manual-2016.3.pdf -> manual-2016.4.pdf ++ (binary differes) ++ regressiontests-2016.3.tar.gz -> regressiontests-2016.4.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-2016.3.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-2016.4.tar.gz differ: char 18, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2017-08-10 14:06:06
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Thu Aug 10 14:06:06 2017 rev:34 rq:515274 version:2016.3
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2017-05-16
14:44:36.539734203 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2017-08-10
14:13:28.492865191 +0200
@@ -1,0 +2,5 @@
+Tue Aug 8 23:24:41 UTC 2017 - jungh...@votca.org
+
+- Fix build on Factory
+
+---
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.DupOKH/_old 2017-08-10 14:13:30.896526751 +0200
+++ /var/tmp/diff_new_pack.DupOKH/_new 2017-08-10 14:13:30.908525061 +0200
@@ -189,7 +189,7 @@
#s390x is too slow for tests
%ifnarch s390x
LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C nompi/build %{?_smp_mflags}
check
-LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C openmpi/build %{?_smp_mflags}
check
+LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/openmpi/%{_lib}'
make -C openmpi/build %{?_smp_mflags} check
%endif
%post -n libgromacs2 -p /sbin/ldconfig
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2017-05-16 14:43:27
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Tue May 16 14:43:27 2017 rev:33 rq:494476 version:2016.3
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2017-03-16
09:51:37.365046526 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2017-05-16
14:44:36.539734203 +0200
@@ -1,0 +2,6 @@
+Mon May 8 16:28:38 UTC 2017 - jungh...@votca.org
+
+- __builddir is not overwritable on SLE-12, so use subdirs
+- disable test on s390x (too slow)
+
+---
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.7IwuO3/_old 2017-05-16 14:44:39.723286884 +0200
+++ /var/tmp/diff_new_pack.7IwuO3/_new 2017-05-16 14:44:39.727286321 +0200
@@ -126,7 +126,8 @@
%else
%define acce None
%endif
-%define __builddir nompi
+mkdir nompi
+cd nompi
# note about rpath
# gromacs' cmake has too much rpath auto-magic, just
# force to skip it (CMAKE_SKIP_RPATH=1) and use
@@ -144,12 +145,13 @@
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
-DGMX_EXTERNAL_TINYXML2=ON \
- -DREGRESSIONTEST_PATH="$PWD/../regressiontests-%{version}" \
- -DGMX_LIB_INSTALL_DIR=%{_lib}
+ -DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \
+ -DGMX_LIB_INSTALL_DIR=%{_lib} ../../
make %{?_smp_mflags}
-cd ..
-%define __builddir openmpi
+cd ../..
+mkdir openmpi
+cd openmpi
%{cmake} \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
@@ -164,13 +166,13 @@
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
-DGMX_EXTERNAL_TINYXML2=ON \
- -DREGRESSIONTEST_PATH="$PWD/../regressiontests-%{version}" \
- -DGMX_LIB_INSTALL_DIR=%{_lib}
+ -DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \
+ -DGMX_LIB_INSTALL_DIR=%{_lib} ../../
make %{?_smp_mflags}
%install
-make -C nompi install DESTDIR=%{buildroot}
-make -C openmpi install DESTDIR=%{buildroot}
+make -C nompi/build install DESTDIR=%{buildroot}
+make -C openmpi/build install DESTDIR=%{buildroot}
%fdupes %{buildroot}%{_prefix}
#no need when installed in /usr
@@ -184,8 +186,11 @@
cp %{S:1} %{buildroot}%{_datadir}/gromacs
%check
-LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C nompi %{?_smp_mflags} check
-LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C openmpi %{?_smp_mflags} check
+#s390x is too slow for tests
+%ifnarch s390x
+LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C nompi/build %{?_smp_mflags}
check
+LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C openmpi/build %{?_smp_mflags}
check
+%endif
%post -n libgromacs2 -p /sbin/ldconfig
%postun -n libgromacs2 -p /sbin/ldconfig
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2017-03-16 09:42:41 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) Package is "gromacs" Thu Mar 16 09:42:41 2017 rev:32 rq:479436 version:2016.3 Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2016-11-10 13:19:00.0 +0100 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2017-03-16 09:51:37.365046526 +0100 @@ -1,0 +2,31 @@ +Tue Mar 14 15:11:23 UTC 2017 - jungh...@votca.org + +- version bump to 2016.3 details here: + http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/index.html +- Highlights: + - Made distance restraints work with threads and DD + - Fixed Ewald surface+3DC corrections + - Fixed opening of wall table files + - Fixed bug in gmx insert-molecules. + - Made virial reproducible + - Updated to support FFTW 3.3.5 + - Permitted automatic load balancing to disable itself when it makes the run slower + - Improved the accuracy of timing for dynamic load balancing with GPUs + - Corrected kernel launch bounds for Tesla P100 GPUs + - Improved logic handling if/when the run is terminated for SETTLE warnings + - Fixed bug in gmx wham for reading pullx files. + - Fixed ouput bug in gmx wham + - Fixed deadlock with thread-MPI + - Made error reporting in grompp more user friendly + - Fixed SIMD suggestion for VMX + - Fixed script xplor2gmx.pl to work with GMXDATA + - Fixed default nice level in mdrun-only build + - Fixed math-test false positive + - Improved documentation + - OpenCL error string are now written, instead of cryptic error codes + - Fixed build with GMX_USE_TNG=off + - Removed variable-precision .gro writing + - Fixed BG/Q platform files and install guide + - Reduced the memory required for free-energy simulations + +--- Old: gromacs-2016.1.tar.gz manual-2016.1.pdf regressiontests-2016.1.tar.gz New: gromacs-2016.3.tar.gz manual-2016.3.pdf regressiontests-2016.3.tar.gz Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.od2Vam/_old 2017-03-16 09:51:40.632583783 +0100 +++ /var/tmp/diff_new_pack.od2Vam/_new 2017-03-16 09:51:40.632583783 +0100 @@ -1,7 +1,7 @@ # # spec file for package gromacs # -# Copyright (c) 2015,2016 Christoph Junghans +# Copyright (c) 2015-2017 Christoph Junghans # Copyright (c) 2013,2014 SUSE LINUX Products GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties @@ -17,7 +17,7 @@ # Name: gromacs -Version:2016.1 +Version:2016.3 Release:0 Summary:Molecular Dynamics Package License:GPL-2.0+ ++ gromacs-2016.1.tar.gz -> gromacs-2016.3.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/gromacs-2016.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2016.3.tar.gz differ: char 5, line 1 ++ manual-2016.1.pdf -> manual-2016.3.pdf ++ (binary differes) ++ regressiontests-2016.1.tar.gz -> regressiontests-2016.3.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-2016.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-2016.3.tar.gz differ: char 12, line 1
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2016-11-10 13:18:58 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) Package is "gromacs" Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2016-09-01 14:02:36.0 +0200 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2016-11-10 13:19:00.0 +0100 @@ -1,0 +2,28 @@ +Sat Nov 5 18:27:42 UTC 2016 - jungh...@votca.org + +- version bump to 2016.1 details here: + http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html +- Highlights: + - Made distance restraints work with threads and DD + - Fixed Ewald surface+3DC corrections + - Fixed opening of wall table files + - Fixed bug in gmx insert-molecules. + - Made virial reproducible + - Permitted automatic load balancing to disable itself when it makes the run slower + - Improved the accuracy of timing for dynamic load balancing with GPUs + - Corrected kernel launch bounds for Tesla P100 GPUs + - Improved logic handling if/when the run is terminated for SETTLE warnings + - Fixed bug in gmx wham for reading pullx files. + - Fixed ouput bug in gmx wham + - Fixed deadlock with thread-MPI + - Made error reporting in grompp more user friendly + - Fixed SIMD suggestion for VMX + - Fixed script xplor2gmx.pl to work with GMXDATA + - Fixed default nice level in mdrun-only build + - Fixed math-test false positive + - Improved documentation + - Fixed build with GMX_USE_TNG=off + - Removed variable-precision .gro writing + - Reduced the memory required for free-energy simulations + +--- @@ -4 +32 @@ -- version bump to 2015 details here: +- version bump to 2016 details here: Old: gromacs-2016.tar.gz manual-2016.pdf regressiontests-2016.tar.gz New: gromacs-2016.1.tar.gz manual-2016.1.pdf regressiontests-2016.1.tar.gz Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.RYSha5/_old 2016-11-10 13:19:07.0 +0100 +++ /var/tmp/diff_new_pack.RYSha5/_new 2016-11-10 13:19:07.0 +0100 @@ -17,7 +17,7 @@ # Name: gromacs -Version:2016 +Version:2016.1 Release:0 Summary:Molecular Dynamics Package License:GPL-2.0+ ++ gromacs-2016.tar.gz -> gromacs-2016.1.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/gromacs-2016.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2016.1.tar.gz differ: char 5, line 1 ++ manual-2016.pdf -> manual-2016.1.pdf ++ (binary differes) ++ regressiontests-2016.tar.gz -> regressiontests-2016.1.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-2016.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-2016.1.tar.gz differ: char 12, line 1
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2016-09-01 14:02:34
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2015-10-20
00:05:19.0 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2016-09-01
14:02:36.0 +0200
@@ -1,0 +2,17 @@
+Wed Aug 24 15:24:30 UTC 2016 - jungh...@votca.org
+
+- version bump to 2015 details here:
+ http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html
+- Highlights:
+ - As always, we’ve got several useful performance improvements, with or
without GPUs. CPU-side SIMD and threading enhancements will make
GPU-accelerated simulations faster even if we’d left the GPU code alone! Thanks
to these and additional GPU kernel improvements, in GPU-accelerated runs expect
around 15% improvement in throughput. (And not just for plain vanilla MD,
either... the pull code now supports OpenMP threading throughout, and
multi-simulations have less coupling between simulations.)
+ - We have a new C++11 portability layer permitting us to accelerate in SIMD
on the CPU lots of minor routines. These will also often improve runs that use
accelerators or many nodes through better load balancing. POWER8, ARM64, AVX512
(KNL), and more are fully SIMD accelerated now because they are supported in
the new portability layer!
+ - We made further SIMD acceleration of bonded interactions which reduces
their calculation time by about a factor of 2. This improves load balance at
high parallelization by a factor of 2, and shows significantly better scaling.
+ - Similarly, SIMD acceleration of SETTLE reduces the time for constraints by
a factor of 3 to 5 - which has a strong effect for GPU runs.
+ - OpenCL GPU support is now available with all combinations of MPI,
thread-MPI and GPU sharing (ie. the same as CUDA). Kernel performance has
improved by up to 60%. AMD GPUs benefit the most, OpenCL on NVIDIA is generally
still slow.
+ - Tools in the new analysis framework can handle trajectories that are
subsets of the simulation system.
+ - New pull coordinate geometries angle-axis, dihedral, and normal angle.
+ - Checkpoint restarts work only in the cases where the implementation can
always do what the user wants.
+ - The version numbering has changed to be the year of the release, plus (in
future) a patch number. GROMACS 2016 will be the initial release from this
branch, then GROMACS 2016.1 will have the set of bugs that have been fixed in
GROMACS 2016, etc.
+
+
+---
@@ -8 +24,0 @@
-
Old:
gromacs-5.1.tar.gz
manual-5.1.pdf
regressiontests-5.1.tar.gz
New:
gromacs-2016.tar.gz
manual-2016.pdf
regressiontests-2016.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.PLO56N/_old 2016-09-01 14:02:42.0 +0200
+++ /var/tmp/diff_new_pack.PLO56N/_new 2016-09-01 14:02:42.0 +0200
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2015 Christoph Junghans
+# Copyright (c) 2015,2016 Christoph Junghans
# Copyright (c) 2013,2014 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
@@ -17,7 +17,7 @@
#
Name: gromacs
-Version:5.1
+Version:2016
Release:0
Summary:Molecular Dynamics Package
License:GPL-2.0+
@@ -31,12 +31,9 @@
BuildRequires: cmake >= 2.8.8
BuildRequires: fdupes
BuildRequires: openmpi-devel
-%if %{defined fedora}
-BuildRequires: pkgconfig
-%else
BuildRequires: pkg-config
-%endif
BuildRequires: pkgconfig(fftw3)
+BuildRequires: pkgconfig(tinyxml2)
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
@@ -60,6 +57,19 @@
This package contains development libraries and header for GROMACS
+%package -n libgromacs2
+Summary:Libraries for Gromacs
+Group: System/Libraries
+
+%description -n libgromacs2
+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 libraries for Gromacs
+
%package bash
Summary:Bash completion for Gromacs
Group: Productivity/Other
@@ -116,13 +126,12 @@
%else
%define acce None
%endif
-mkdir nompi openmpi
-cd nompi
+%define __builddir nompi
# note about r
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2015-10-19 22:51:24
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2014-10-16
18:16:57.0 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2015-10-20
00:05:19.0 +0200
@@ -1,0 +2,9 @@
+Wed Oct 14 16:08:31 UTC 2015 - jungh...@votca.org
+
+- version bump to 5.1 details here:
+ http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html
+- html documentation is gone
+- devel package now includes cmake macros and config files
+
+
+---
Old:
gromacs-5.0.2.tar.gz
manual-5.0.2.pdf
regressiontests-5.0.2.tar.gz
New:
gromacs-5.1.tar.gz
manual-5.1.pdf
regressiontests-5.1.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.aKuKn7/_old 2015-10-20 00:05:25.0 +0200
+++ /var/tmp/diff_new_pack.aKuKn7/_new 2015-10-20 00:05:25.0 +0200
@@ -1,6 +1,7 @@
#
# spec file for package gromacs
#
+# Copyright (c) 2015 Christoph Junghans
# Copyright (c) 2013,2014 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
@@ -16,7 +17,7 @@
#
Name: gromacs
-Version:5.0.2
+Version:5.1
Release:0
Summary:Molecular Dynamics Package
License:GPL-2.0+
@@ -187,16 +188,13 @@
%{_bindir}/*
%exclude %{_bindir}/*_mpi
%{_datadir}/gromacs
-%exclude %{_datadir}/gromacs/html
%exclude %{_datadir}/gromacs/template
%exclude %{_datadir}/gromacs/*.pdf
%{_libdir}/lib*.so.*
%{_mandir}/man1/*
-%{_mandir}/man7/*
%files doc
%defattr(-,root,root,-)
-%doc %{_datadir}/gromacs/html
%doc %{_datadir}/gromacs/*.pdf
%files openmpi
@@ -206,6 +204,7 @@
%files devel
%defattr(-,root,root)
%{_datadir}/gromacs/template
+%{_datadir}/cmake
%{_includedir}/gromacs/
%{_libdir}/*.so
%{_libdir}/pkgconfig/*
++ gromacs-5.0.2.tar.gz -> gromacs-5.1.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-5.0.2.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new/gromacs-5.1.tar.gz differ: char 5, line
1
++ manual-5.0.2.pdf -> manual-5.1.pdf ++
(binary differes)
++ regressiontests-5.0.2.tar.gz -> regressiontests-5.1.tar.gz ++
/work/SRC/openSUSE:Factory/gromacs/regressiontests-5.0.2.tar.gz
/work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-5.1.tar.gz differ: char
13, line 1
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2014-10-16 18:14:57 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) Package is "gromacs" Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2014-09-08 21:29:56.0 +0200 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2014-10-16 18:16:57.0 +0200 @@ -1,0 +2,6 @@ +Wed Oct 8 14:22:10 UTC 2014 - jungh...@votca.org + +- version bump to 5.0.2 +- Details: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x + +--- Old: gromacs-5.0.1.tar.gz manual-5.0.1.pdf regressiontests-5.0.1.tar.gz New: gromacs-5.0.2.tar.gz manual-5.0.2.pdf regressiontests-5.0.2.tar.gz Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.BqPj80/_old 2014-10-16 18:17:02.0 +0200 +++ /var/tmp/diff_new_pack.BqPj80/_new 2014-10-16 18:17:02.0 +0200 @@ -16,7 +16,7 @@ # Name: gromacs -Version:5.0.1 +Version:5.0.2 Release:0 Summary:Molecular Dynamics Package License:GPL-2.0+ ++ gromacs-5.0.1.tar.gz -> gromacs-5.0.2.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/gromacs-5.0.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/gromacs-5.0.2.tar.gz differ: char 5, line 1 ++ manual-5.0.1.pdf -> manual-5.0.2.pdf ++ (binary differes) ++ regressiontests-5.0.1.tar.gz -> regressiontests-5.0.2.tar.gz ++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-5.0.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-5.0.2.tar.gz differ: char 215, line 1 -- To unsubscribe, e-mail: opensuse-commit+unsubscr...@opensuse.org For additional commands, e-mail: opensuse-commit+h...@opensuse.org
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2014-09-08 21:28:55
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2014-02-11
11:19:38.0 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2014-09-08
21:29:56.0 +0200
@@ -1,0 +2,6 @@
+Sat Sep 6 16:16:42 UTC 2014 - jungh...@votca.org
+
+- version bump to 5.0.1
+- Details: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x
+
+---
@@ -9 +15 @@
-- version bumped to 4.5.6
+- version bumped to 4.6.5
Old:
gromacs-4.6.5.tar.gz
manual-4.6.5.pdf
regressiontests-4.6.5.tar.gz
New:
gromacs-5.0.1.tar.gz
manual-5.0.1.pdf
regressiontests-5.0.1.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.LlPjZm/_old 2014-09-08 21:30:06.0 +0200
+++ /var/tmp/diff_new_pack.LlPjZm/_new 2014-09-08 21:30:06.0 +0200
@@ -16,7 +16,7 @@
#
Name: gromacs
-Version:4.6.5
+Version:5.0.1
Release:0
Summary:Molecular Dynamics Package
License:GPL-2.0+
@@ -24,8 +24,10 @@
Url:http://www.gromacs.org
Source0:ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
Source1:ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf
-Source2:
https://gromacs.googlecode.com/files/regressiontests-%{version}.tar.gz
-BuildRequires: cmake
+Source2:
http://gerrit.gromacs.org/download/regressiontests-%{version}.tar.gz
+
+BuildRequires: gcc-c++
+BuildRequires: cmake >= 2.8.8
BuildRequires: fdupes
BuildRequires: openmpi-devel
%if %{defined fedora}
@@ -115,19 +117,24 @@
%endif
mkdir nompi openmpi
cd nompi
+# note about rpath
+# gromacs' cmake has too rpath much auto-magin, just
+# force to skip it (CMAKE_SKIP_RPATH=1) and use
+# LD_LIBRARY_PATH for make check
cmake \
- -DCMAKE_INSTALL_PREFIX=/usr \
+ -DCMAKE_INSTALL_PREFIX=%{_prefix} \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \
-DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \
- -DCMAKE_SKIP_INSTALL_RPATH=ON \
- -DGMX_CPU_ACCELERATION=%{acce} \
+ -DCMAKE_SKIP_RPATH=1 \
+ -DGMX_SIMD=%{acce} \
-DGMX_MPI=OFF \
-DGMX_THREAD_MPI=ON \
+ -DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
-DREGRESSIONTEST_PATH="$PWD/../regressiontests-%{version}" \
- -DGMXLIB=%{_lib} \
+ -DGMX_LIB_INSTALL_DIR=%{_lib} \
..
make %{?_smp_mflags}
cd ../openmpi
@@ -142,26 +149,27 @@
-DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \
-DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \
-DCMAKE_SKIP_RPATH=1 \
- -DGMX_CPU_ACCELERATION=%{acce} \
+ -DGMX_SIMD=%{acce} \
+ -DGMX_BUILD_MDRUN_ONLY=ON \
-DGMX_MPI=ON \
+ -DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
- -DGMXLIB=%{_lib} \
+ -DGMX_LIB_INSTALL_DIR=%{_lib} \
..
-#only mdrun uses mpi, change for gromacs>=5.0
-make %{?_smp_mflags} mdrun
+make %{?_smp_mflags}
%install
make -C nompi install DESTDIR=%{buildroot}
-make -C openmpi install-mdrun DESTDIR=%{buildroot}
+make -C openmpi install DESTDIR=%{buildroot}
%fdupes %{buildroot}%{_prefix}
#not need when installed in /usr
rm -f %{buildroot}%{_bindir}/GMXRC*
# Move bash completion file to correct location
mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d
-cp %{buildroot}%{_bindir}/completion.bash
%{buildroot}%{_sysconfdir}/bash_completion.d/gromacs
-#TODO make a csh and zsh completion in the future maybe
-rm -f %{buildroot}%{_bindir}/completion.*
+#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
+cat %{buildroot}%{_bindir}/gmx-completion{,?*}.bash >
%{buildroot}%{_sysconfdir}/bash_completion.d/gromacs
+rm -f %{buildroot}%{_bindir}/gmx-completion*
cp %{S:1} %{buildroot}%{_datadir}/gromacs
@@ -169,12 +177,10 @@
%if %{defined fedora}
%{_openmpi_unload}
%endif
-make -C nompi check
+LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C nompi %{?_smp_mflags} check
%post -p /sbin/ldconfig
%postun -p /sbin/ldconfig
-%post openmpi -p /sbin/ldconfig
-%postun openmpi -p /sbin/ldconfig
%files
%defattr(-,root,root,-)
@@ -185,7 +191,6 @@
%exclude %{_datadir}/gromacs/template
%exclude %{_datadir}/gromacs/*.pdf
%{_libdir}/lib*.so.*
-%exclude %{_libdir}/lib*_mpi.so.*
%{_mandir}/man1/*
%{_mandir}/man7/*
@@ -197,7 +202,6 @@
%files openmpi
%defattr(-,root,root,-)
%{_bindir}/*_mpi
-%{_libdir}/lib*_mpi.so.*
%files devel
%defattr(-,root,root
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2014-02-11 11:19:37
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs"
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2013-03-06
09:36:01.0 +0100
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2014-02-11
11:19:38.0 +0100
@@ -1,0 +2,13 @@
+Mon Feb 10 16:47:31 UTC 2014 - jungh...@votca.org
+
+- added %check
+
+---
+Sun Feb 9 16:23:45 UTC 2014 - jungh...@votca.org
+
+- version bumped to 4.5.6
+- fix GMX_CPU_ACCELERATION to SSE2 for older i386 machines
+- added openmpi package
+- split doc, bash-completion into separate packages
+
+---
Old:
gromacs-4.6.1.tar.bz2
New:
gromacs-4.6.5.tar.gz
manual-4.6.5.pdf
regressiontests-4.6.5.tar.gz
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.WJpow6/_old 2014-02-11 11:19:41.0 +0100
+++ /var/tmp/diff_new_pack.WJpow6/_new 2014-02-11 11:19:41.0 +0100
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2013 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2013,2014 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
@@ -15,106 +15,197 @@
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
-
Name: gromacs
-Version:4.6.1
+Version:4.6.5
Release:0
-%define srcversion 4.6.1
Summary:Molecular Dynamics Package
License:GPL-2.0+
Group: Productivity/Scientific/Chemistry
Url:http://www.gromacs.org
-Source0:gromacs-%{srcversion}.tar.bz2
+Source0:ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
+Source1:ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf
+Source2:
https://gromacs.googlecode.com/files/regressiontests-%{version}.tar.gz
BuildRequires: cmake
BuildRequires: fdupes
-BuildRequires: fftw3-devel
-BuildRequires: gcc-c++
-BuildRequires: libstdc++-devel
-BuildRequires: libxml2-devel
-BuildRequires: xorg-x11-devel
+BuildRequires: openmpi-devel
+%if %{defined fedora}
+BuildRequires: pkgconfig
+%else
+BuildRequires: pkg-config
+%endif
+BuildRequires: pkgconfig(fftw3)
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
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 version has the
-dynamic libs and executables; to hack new utility programs you also
-need the headers and static libs in gromacs-dev. Linux kernel 2.4 or
-later is STRONGLY recommended on Pentium III and later processors since
-GROMACS then can use assembly loops with SSE instructions.
-
+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.
%package devel
Summary:Molecular dynamics package
-Group: Productivity/Scientific/Chemistry
+Group: Development/Libraries/C and C++
Requires: %{name} = %{version}
-Requires: fftw3-devel
-Requires: glibc-devel
-Requires: xorg-x11-devel
%description devel
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 version has the
-dynamic libs and executables; to hack new utility programs you also
-need the headers and static libs in gromacs-dev. Linux kernel 2.4 or
-later is STRONGLY recommended on Pentium III and later processors since
-GROMACS then can use assembly loops with SSE instructions.
+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 dev
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2013-03-06 09:35:59 Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) Package is "gromacs", Maintainer is "kkae...@suse.com" Changes: --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2013-02-04 20:16:50.0 +0100 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2013-03-06 09:36:01.0 +0100 @@ -1,0 +2,33 @@ +Tue Mar 5 21:02:02 UTC 2013 - kkae...@suse.com + +- Update to 4.6.1 + Bugfix release + - increased shared object major version to 8, #1147 + - updates to HTML manual, install guide, PDF manual, shell completions +copious minor bug fixes + - various build system upgrades and fixes #1143 + - new and enhanced error messages + - fixes for AdResS bugs (neighbour list construction, flop accounting, +multiple tf tables) + - fixed PME timing counter issues #1125 + - fixed PME load balance reporting + - fixed forcerec to work with tools like genion and g_disre #1136 + - various GPU performance enhancements + - fixed sd integrator with OpenMP threading #1138 + - various minor fixes for interacting with CUDA for GPUs + - fixes for g_tune_pme to cope with new mdrun behaviour and changed +command-line options (for both g_tune_pme and mdrun) + - more checks for system support for setting thread affinities + - removed inter-flag dependency in g_order + - fixed issues with free-energy pertubation soft-core and cut-offs #1146 + - fixed issues with md-vv + nose-hoover + (nstcalcenergy > nsttcouple) +#1129 + - incorporated new changes from release 4.5.x branch + - prevented building with icc 11.1 and SSE4.1 because of known problems +#1126 + - adding warning about not building with icc version < 12 #1126 + - fixed bug sorting atoms with GPUs introduced since 4.6 #1153 + - fixed issues with automated download of regression tests #1150 + - fixed bug with DD cut-off check and PME dynamic load balancing #1169 + +--- Old: gromacs-4.6.tar.bz2 New: gromacs-4.6.1.tar.bz2 Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.Z2mhmK/_old 2013-03-06 09:36:15.0 +0100 +++ /var/tmp/diff_new_pack.Z2mhmK/_new 2013-03-06 09:36:15.0 +0100 @@ -17,9 +17,9 @@ Name: gromacs -Version:4.6 +Version:4.6.1 Release:0 -%define srcversion 4.6 +%define srcversion 4.6.1 Summary:Molecular Dynamics Package License:GPL-2.0+ Group: Productivity/Scientific/Chemistry ++ gromacs-4.6.tar.bz2 -> gromacs-4.6.1.tar.bz2 ++ 15839 lines of diff (skipped) -- To unsubscribe, e-mail: opensuse-commit+unsubscr...@opensuse.org For additional commands, e-mail: opensuse-commit+h...@opensuse.org
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2013-02-04 20:16:48
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs", Maintainer is "kkae...@suse.com"
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2012-09-14
12:26:01.0 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2013-02-04
20:16:50.0 +0100
@@ -1,0 +2,41 @@
+Mon Feb 4 09:20:09 UTC 2013 - kkae...@suse.com
+
+- Update to 4.6
+ New features
+
+ - New Verlet non-bonded scheme which, by default, uses exact cut-off's
+and a buffered pair-list.
+ - Multi-level hybrid parallelization (MPI + OpenMP + CUDA):
+full OpenMP multithreading with the Verlet scheme;
+ - OpenMP mulitthreading for PME-only nodes with the group scheme;
+native GPU acceleration using CUDA (supporte NVIDIA hardware).
+ - New x86 SIMD non-bonded kernels for the usual cut-off scheme, called
+group scheme and the new verlet scheme, use x86 SIMD intrinsics (no
+more assembly code):
+SSE2
+SSE4.1
+AVX-128-FMA (for AMD Bulldozer/Piledriver)
+AVX-256 (for Intel Sandy/Ivy Bridge)
+ - Automated OpenMP thread count choice to use all available cores.
+ - Automated CPU affinity setting: locking processes or threads to cores.
+ - Automated PP-PME (task) load-balancing: balancing non-bonded force and
+PME mesh workload when the two are executed on different
+compute-resources (i.e CPU and GPU or different CPUs). This enables
+GPU-CPU and PP-PME process load balancing by shifting work from the
+mesh to the non-bonded calculation.
+ - PPPM/P3M with analytical derivative at the same cost and with the same
+features as PME.
+ - New, advanced free energy sampling techniques.
+ - AdResS adaptive resolution simulation support.
+ - Enforced rotation ("rotational pulling")
+ - Build configuration now uses CMake, configure+autoconf/make no longer
+supported. (The CMake build system features with a lot of automation
+and cleverness under the hood and we know that the it might not always
+prove to be as rock-solid as the old one. However, far more advanced
+and complex, so bear with us while we iron out issues that come up
+along the way.)
+ - g_hbond now utilizes OpenMP.
+
+ Plus plenty of bug fixes.
+
+---
Old:
gromacs-4.5.5.tar.bz2
New:
gromacs-4.6.tar.bz2
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.ErKEnp/_old 2013-02-04 20:16:51.0 +0100
+++ /var/tmp/diff_new_pack.ErKEnp/_new 2013-02-04 20:16:51.0 +0100
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2012 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2013 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
@@ -15,21 +15,23 @@
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
+
Name: gromacs
-Version:4.5.5
-Release:1
+Version:4.6
+Release:0
+%define srcversion 4.6
Summary:Molecular Dynamics Package
-Url:http://www.gromacs.org
License:GPL-2.0+
Group: Productivity/Scientific/Chemistry
-Source0:gromacs-%{version}.tar.bz2
+Url:http://www.gromacs.org
+Source0:gromacs-%{srcversion}.tar.bz2
BuildRequires: cmake
+BuildRequires: fdupes
BuildRequires: fftw3-devel
BuildRequires: gcc-c++
-BuildRequires: libxml2-devel
BuildRequires: libstdc++-devel
+BuildRequires: libxml2-devel
BuildRequires: xorg-x11-devel
-BuildRequires: fdupes
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
@@ -45,10 +47,12 @@
%package devel
-License:GPL-2.0+
Summary:Molecular dynamics package
Group: Productivity/Scientific/Chemistry
-Requires: %{name} = %{version} fftw3-devel glibc-devel xorg-x11-devel
+Requires: %{name} = %{version}
+Requires: fftw3-devel
+Requires: glibc-devel
+Requires: xorg-x11-devel
%description devel
GROMACS is a versatile and extremely well optimized package to perform
@@ -62,7 +66,7 @@
GROMACS then can use assembly loops with SSE instructions.
%prep
-%setup -q
+%setup -q -n %{name}-%{srcversion}
%build
%if 0%{?fedora}
++ gromacs-4.5.5.tar.bz2 -> gromacs-4.6.tar.bz2 ++
/work/SRC/openSUSE:Factory/gromacs/gromacs-4.5.5.tar.bz2
/work/SRC/openSUSE:Factory/.gromacs.new/gromacs-4.6.tar.bz2 differ: char
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2012-09-14 12:25:55
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs", Maintainer is "kkae...@suse.com"
Changes:
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2011-09-23
02:02:01.0 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2012-09-14
12:26:01.0 +0200
@@ -1,0 +2,5 @@
+Mon Jun 4 16:09:35 UTC 2012 - toddrme2...@gmail.com
+
+- Clean up spec file
+
+---
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.8ysBEJ/_old 2012-09-14 12:26:02.0 +0200
+++ /var/tmp/diff_new_pack.8ysBEJ/_new 2012-09-14 12:26:02.0 +0200
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2011 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2012 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
@@ -15,15 +15,7 @@
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
-
-
Name: gromacs
-BuildRequires: cmake fftw3-devel libxml2-devel xorg-x11-devel
-BuildRequires: gcc-c++ libstdc++-devel
-%if 0%{?suse_version} > 1010
-BuildRequires: fdupes
-%endif
-
Version:4.5.5
Release:1
Summary:Molecular Dynamics Package
@@ -31,6 +23,13 @@
License:GPL-2.0+
Group: Productivity/Scientific/Chemistry
Source0:gromacs-%{version}.tar.bz2
+BuildRequires: cmake
+BuildRequires: fftw3-devel
+BuildRequires: gcc-c++
+BuildRequires: libxml2-devel
+BuildRequires: libstdc++-devel
+BuildRequires: xorg-x11-devel
+BuildRequires: fdupes
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
@@ -62,13 +61,12 @@
later is STRONGLY recommended on Pentium III and later processors since
GROMACS then can use assembly loops with SSE instructions.
-
%prep
%setup -q
%build
%if 0%{?fedora}
-export RPM_OPT_FLAGS="$RPM_OPT_FLAGS -DFEDORA"
+export RPM_OPT_FLAGS="%{optflags} -DFEDORA"
%endif
mkdir build
cd build
@@ -76,8 +74,8 @@
-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_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \
+ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \
-DCMAKE_SKIP_RPATH=1 \
-DPACKAGE_ARCHITECTURE=uname -m \
-DLIB=%{_lib} \
@@ -88,37 +86,31 @@
%install
cd build
-make DESTDIR=${RPM_BUILD_ROOT} install
-%{__rm} -f %{buildroot}%{_libdir}/*.la
-%if 0%{?suse_version} > 1010
+%makeinstall
+rm -f %{buildroot}%{_libdir}/*.la
%fdupes %{buildroot}/usr/share/gromacs
-%endif
%post -p /sbin/ldconfig
-
%postun -p /sbin/ldconfig
%files
%defattr(-,root,root)
%{_bindir}/*
-%dir %{_datadir}/gromacs
-%{_datadir}/gromacs/top
-%{_datadir}/gromacs/tutor
-%docdir %{_datadir}/gromacs/html
-%{_datadir}/gromacs/html/
-%{_mandir}/man1/*
-%{_mandir}/man7/*
+%{_datadir}/gromacs/
+%exclude %{_datadir}/gromacs/template
+%doc %{_datadir}/gromacs/html/
%{_libdir}/libgmx.so.*
%{_libdir}/libgmxana.so.*
%{_libdir}/libmd.so.*
%{_libdir}/libgmxpreprocess.so.*
+%{_mandir}/man1/*
+%{_mandir}/man7/*
%files devel
%defattr(644,root,root,755)
%{_datadir}/gromacs/template
+%{_includedir}/gromacs/
%{_libdir}/*.so
-%dir %{_includedir}/gromacs
-%{_includedir}/gromacs/*
%{_libdir}/pkgconfig/*
%changelog
--
To unsubscribe, e-mail: opensuse-commit+unsubscr...@opensuse.org
For additional commands, e-mail: opensuse-commit+h...@opensuse.org
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked
in at 2011-12-06 18:16:21
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
Package is "gromacs", Maintainer is "kkae...@suse.com"
Changes:
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.1zJ67e/_old 2011-12-06 18:25:08.0 +0100
+++ /var/tmp/diff_new_pack.1zJ67e/_new 2011-12-06 18:25:08.0 +0100
@@ -28,7 +28,7 @@
Release:1
Summary:Molecular Dynamics Package
Url:http://www.gromacs.org
-License:GPLv2+
+License:GPL-2.0+
Group: Productivity/Scientific/Chemistry
Source0:gromacs-%{version}.tar.bz2
BuildRoot: %{_tmppath}/%{name}-%{version}-build
@@ -46,7 +46,7 @@
%package devel
-License:GPLv2+
+License:GPL-2.0+
Summary:Molecular dynamics package
Group: Productivity/Scientific/Chemistry
Requires: %{name} = %{version} fftw3-devel glibc-devel xorg-x11-devel
--
To unsubscribe, e-mail: opensuse-commit+unsubscr...@opensuse.org
For additional commands, e-mail: opensuse-commit+h...@opensuse.org
commit gromacs for openSUSE:Factory
Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory
checked in at Thu Sep 22 10:46:07 CEST 2011.
--- gromacs/gromacs.changes 2011-03-22 09:39:20.0 +0100
+++ /mounts/work_src_done/STABLE/gromacs/gromacs.changes2011-09-21
15:56:44.0 +0200
@@ -1,0 +2,20 @@
+Wed Sep 21 13:32:02 UTC 2011 - kkae...@suse.com
+
+- Clean up spec file
+
+- Update to 4.5.5
+ - Improved pdb2gmx -chainsep option and reintroduced the -merge option.
+ - Fixed mdrun file appending truncating files to 0 bytes when
+continuation runs stopped before writing new output.
+ - Fixed COM pulling with multiple constraints checking the
+convergence of one constraint instead of all.
+ - Fixed some dihedrals in sugars in Gromos53a5/6 working on the
+wrong atoms.
+ - AmberGS force field is now based on Amber94 instead of Amber96.
+ - Moved hydrogens in Charmm27 protein termini to separate charge
+groups and added ACE and CT3 residue types.
+ - Many small fixes which avoid termination with fatal errors or
+crashes in mdrun and tools.
+ - Many small updates to the manual pages of programs.
+
+---
@@ -15 +34,0 @@
-
calling whatdependson for head-i586
Old:
gromacs-4.5.4.tar.bz2
New:
gromacs-4.5.5.tar.bz2
Other differences:
--
++ gromacs.spec ++
--- /var/tmp/diff_new_pack.uUYT3m/_old 2011-09-22 10:46:04.0 +0200
+++ /var/tmp/diff_new_pack.uUYT3m/_new 2011-09-22 10:46:04.0 +0200
@@ -1,7 +1,7 @@
#
-# spec file for package gromacs (Version 4.5.4)
+# spec file for package gromacs
#
-# Copyright (c) 2010 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2011 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
@@ -15,7 +15,6 @@
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
-# norootforbuild
Name: gromacs
@@ -25,13 +24,12 @@
BuildRequires: fdupes
%endif
-Version:4.5.4
+Version:4.5.5
Release:1
Summary:Molecular Dynamics Package
Url:http://www.gromacs.org
License:GPLv2+
Group: Productivity/Scientific/Chemistry
-AutoReqProv:on
Source0:gromacs-%{version}.tar.bz2
BuildRoot: %{_tmppath}/%{name}-%{version}-build
@@ -47,13 +45,6 @@
GROMACS then can use assembly loops with SSE instructions.
-
-Authors:
-
-David van der Spoel
-Berk Hess
-Erik Lindahl
-
%package devel
License:GPLv2+
Summary:Molecular dynamics package
@@ -72,13 +63,6 @@
GROMACS then can use assembly loops with SSE instructions.
-
-Authors:
-
-David van der Spoel
-Berk Hess
-Erik Lindahl
-
%prep
%setup -q
@@ -97,6 +81,7 @@
-DCMAKE_SKIP_RPATH=1 \
-DPACKAGE_ARCHITECTURE=uname -m \
-DLIB=%{_lib} \
+ -DGMXLIB=%{_lib} \
..
make
@@ -109,9 +94,6 @@
%fdupes %{buildroot}/usr/share/gromacs
%endif
-%clean
-rm -rf $RPM_BUILD_ROOT
-
%post -p /sbin/ldconfig
%postun -p /sbin/ldconfig
++ gromacs-4.5.4.tar.bz2 -> gromacs-4.5.5.tar.bz2 ++
gromacs/gromacs-4.5.4.tar.bz2
/mounts/work_src_done/STABLE/gromacs/gromacs-4.5.5.tar.bz2 differ: char 11,
line 1
Remember to have fun...
--
To unsubscribe, e-mail: opensuse-commit+unsubscr...@opensuse.org
For additional commands, e-mail: opensuse-commit+h...@opensuse.org
commit gromacs for openSUSE:Factory
Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at Mon Sep 19 21:22:57 CEST 2011. --- gromacs/gromacs.changes 2010-11-10 09:44:15.0 +0100 +++ /mounts/work_src_done/STABLE/gromacs/gromacs.changes2011-03-22 09:39:20.0 +0100 @@ -1,0 +2,16 @@ +Tue Mar 22 08:37:59 UTC 2011 - kkae...@novell.com + +- Update to 4.5.4 + - Fixed pdb2gmx picking up force field from local instead of +library directory + - Made pdb2gmx vsite generation work again for certain His +namings. + - Fixed incorrect virial and pressure averages with certain +nst... values (instantaneous values correct) + - Fixed incorrect cosine viscosity output + - New -multidir alternative for mdrun -multi option + - Several minor fixes in analysis tools + - Several updates to the program documentation + + +--- calling whatdependson for head-i586 Old: gromacs-4.5.3.tar.bz2 New: gromacs-4.5.4.tar.bz2 Other differences: -- ++ gromacs.spec ++ --- /var/tmp/diff_new_pack.k8x6WB/_old 2011-09-19 21:22:50.0 +0200 +++ /var/tmp/diff_new_pack.k8x6WB/_new 2011-09-19 21:22:50.0 +0200 @@ -1,5 +1,5 @@ # -# spec file for package gromacs (Version 4.5.3) +# spec file for package gromacs (Version 4.5.4) # # Copyright (c) 2010 SUSE LINUX Products GmbH, Nuernberg, Germany. # @@ -25,7 +25,7 @@ BuildRequires: fdupes %endif -Version:4.5.3 +Version:4.5.4 Release:1 Summary:Molecular Dynamics Package Url:http://www.gromacs.org ++ gromacs-4.5.3.tar.bz2 -> gromacs-4.5.4.tar.bz2 ++ gromacs/gromacs-4.5.3.tar.bz2 /mounts/work_src_done/STABLE/gromacs/gromacs-4.5.4.tar.bz2 differ: char 11, line 1 Remember to have fun... -- To unsubscribe, e-mail: opensuse-commit+unsubscr...@opensuse.org For additional commands, e-mail: opensuse-commit+h...@opensuse.org
