BioD PNPI Git Repos - alexxy/gromacs.git/commit

Merge branch release-4-6 into master

Conflicts:
CMakeLists.txt
admin/installguide/installguide.tex
cmake/gmxDetectAcceleration.cmake
cmake/gmxSetBuildInformation.cmake
Resolved generally in favour of release-4-6, but some changes in
master branch associated with new CMake functionality was kept in the
expected way. Behaviour detecting hardware (particularly on non-x86
platforms) is not optimal in this commit, but is fixed in
I94e0756856e7.

src/gromacs/gmxlib/checkpoint.c
src/gromacs/legacyheaders/typedefs.h
src/gromacs/mdlib/expanded.c
Resolved in favour of release-4-6 (expanded ensemble fixes)

src/gromacs/mdlib/pme.c
Resolved in favour of release-4-6 (SIMD generalization)

src/gromacs/mdlib/pme_sse_single.h
Deleted (superseded by src/gromacs/mdlib/pme_simd4.h)

src/mdlib/CMakeLists.txt
Relocated new comment to correct place in src/gromacs/CMakeLists.txt
(BUILD_OWN_FFTW fixing)

src/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
Replaced src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h with this file,
but preserved corrected comments from master branch

src/gromacs/legacyheaders/mdrun.h
src/programs/mdrun/md.c
Resolved in trajectory_writing.c (removed df_history parameter that is
now useless)

Change-Id: I44ffdc7eb15039b98910f6b3f32252f5849ecfce

author	Mark Abraham <mark.j.abraham@gmail.com>
	Tue, 22 Oct 2013 16:42:04 +0000 (18:42 +0200)
committer	Mark Abraham <mark.j.abraham@gmail.com>
	Wed, 23 Oct 2013 15:24:43 +0000 (17:24 +0200)
commit	75679bb9641b3db017c2dab928c622e9f1fc5f2a
tree	52e96d930c7b8ddd24b9de10414922d551fe8142	tree \| snapshot
parent	805b9f1b00b6c8024670149c8447d253025d2810	commit \| diff
parent	6aeb9d180579594a7ad5da0261fb44ce172fd698	commit \| diff

CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
admin/installguide/installguide.tex	diff1 \|	diff2 \|	blob \| history
cmake/gmxDetectAcceleration.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxGetCompilerInfo.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxManageBlueGene.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxManageNvccConfig.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxSetBuildInformation.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxTestInlineASM.cmake	diff1 \|	diff2 \|	blob \| history
src/config.h.cmakein	diff1 \|	diff2 \|	blob \| history
src/gromacs/CMakeLists.txt	diff1 \|	\|	blob \| history
src/gromacs/fft/fft5d.cpp	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_cluster.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_membed.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_spatial.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_vanhove.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/bondfree.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/checkpoint.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gmx_cpuid.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gmx_thread_affinity.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/network.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_free_energy.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/typedefs.c	diff1 \|	\|	blob \| history
src/gromacs/gmxpreprocess/readir.c	diff1 \|	\|	blob \| history
src/gromacs/gmxpreprocess/toppush.c	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_simd4_macros.h	\|	diff2 \|	blob \| history
src/gromacs/legacyheaders/gmx_simd4_ref.h	\|	diff2 \|	blob \| history
src/gromacs/legacyheaders/gmx_simd_macros.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_simd_ref.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/legacyheaders/mdrun.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/network.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/thread_mpi/atomic/gcc_x86.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/legacyheaders/typedefs.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/inputrec.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/nb_verlet.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/nbnxn_pairlist.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/state.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/domdec.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/expanded.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/forcerec.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/init.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/md_support.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_atomdata.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_legacy.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_internal.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ibm_qpx.h	\|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ref.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128d.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256d.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256s.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/nbnxn_search.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search_simd_2xnn.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search_simd_4xn.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/ns.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/pme.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/pme_simd4.h	\|	diff2 \|	blob \| history
src/programs/mdrun/md.c	diff1 \|	\|	blob \| history
src/programs/mdrun/runner.c	diff1 \|	\|	blob \| history
src/programs/mdrun/trajectory_writing.c	diff1 \|	\|	blob \| history