Merge branch 'release-4-6'
authorMark Abraham <mark.j.abraham@gmail.com>
Fri, 20 Sep 2013 12:35:43 +0000 (14:35 +0200)
committerMark Abraham <mark.j.abraham@gmail.com>
Fri, 20 Sep 2013 12:50:40 +0000 (14:50 +0200)
commit866f5c8724ac624a06aee106b43289760ae6c1a0
tree548e3422e37c93d5d5025bf178278cc407e49aad
parentdd08732c88487572bfe26be61dd8b76c127b4912
parente6728b964ccebb501b24d59b87001a2efc5db21b
Merge branch 'release-4-6'

Conflicts:
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_includes.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_inner.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_outer.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn.c
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_includes.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_inner.h
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_outer.h
src/mdlib/CMakeLists.txt
src/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c
src/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_inner.h
src/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_outer.h
src/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn.c
src/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_inner.h
src/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_outer.h
src/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
src/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h
src/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
src/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
src/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h
src/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
All resolved in favour of release-4-6, per I0da1faf351def

There was no merge conflict in
src/gromacs/gmxlib/nonbonded/nb_free_energy.c, but Ic7ba3cc26be and
Ia8202ee90 had duplicated the same clean-up of doubly assigned
variables (e.g. Vc), but in different ways. The version in Ia8202ee90
has been retained.

Change-Id: Ia0ec22b7fc16b2be6817b007e52c8b4832549360
118 files changed:
CMakeLists.txt
src/gromacs/gmxana/gmx_tune_pme.c
src/gromacs/gmxlib/checkpoint.c
src/gromacs/gmxlib/nonbonded/nb_free_energy.c
src/gromacs/gmxlib/nonbonded/nb_free_energy.h
src/gromacs/gmxlib/typedefs.c
src/gromacs/legacyheaders/gmx_math_x86_avx_256_double.h
src/gromacs/legacyheaders/gmx_math_x86_avx_256_single.h
src/gromacs/mdlib/CMakeLists.txt
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/make_verlet_simd_kernel_files.py
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_2xnn_kernel.c.pre
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_4xn_kernel.c.pre
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_ewald_twin_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_rf_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_tab_twin_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_ewald_twin_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_rf_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_comb_none_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_geom_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_geom_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_geom_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_lb_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_lb_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_lb_noener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_none_ener.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_none_energrp.c
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_tab_twin_comb_none_noener.c
src/gromacs/mdlib/sim_util.c
src/programs/gmx/grompp.c
src/programs/mdrun/runner.c