Berk Hess [Wed, 27 Mar 2013 09:19:41 +0000 (10:19 +0100)]
corrected log file wall time breakdown
The recent commit
873b9854 doubled the wall times in the breakdown
table in the log file when not using separate PME nodes.
Note that this didn't affect cycle count or total timing prints.
Fixes #1210
Change-Id: Ia2b1d5e6c21543990465b7c7a4a8a1e687c41528
Christoph Junghans [Tue, 19 Mar 2013 17:42:28 +0000 (18:42 +0100)]
Merge "Essential dynamics: fixed legend in ED .xvg output file" into release-4-6
Mark Abraham [Tue, 12 Mar 2013 17:36:44 +0000 (18:36 +0100)]
Merge "fix broken things in mkhtml" into release-4-6
Mark Abraham [Mon, 11 Mar 2013 11:10:49 +0000 (12:10 +0100)]
Merge "Fixes linkage with FFTW + MKL for BLAS/LAPACK" into release-4-6
Carsten Kutzner [Fri, 8 Mar 2013 16:07:26 +0000 (17:07 +0100)]
Essential dynamics: fixed legend in ED .xvg output file
If one performs flooding only and none of the standard essential dynamics
protocols are turned on, the .xvg output file did still print ED legends.
I moved the bNeedDoEdsam check from init_edi() to write_edo_legend(), so
that already here we can check whether ED or only flooding is performed.
Change-Id: Ic3a784b63b335059c17aed852d1b4a4f3126841a
Roland Schulz [Wed, 6 Mar 2013 04:57:14 +0000 (05:57 +0100)]
Merge "fixed PME time print with -ntomp_pme != -ntomp" into release-4-6
Mark Abraham [Fri, 15 Feb 2013 23:05:48 +0000 (00:05 +0100)]
New patch release 4.6.1
Change-Id: I60998e3be8c0c7289d0aa5279e554cc79fb74310
Mark Abraham [Tue, 5 Mar 2013 15:56:34 +0000 (16:56 +0100)]
Fix automated regression testing GMXLIB value
Change-Id: I3030a85df4d649106f4620b48374ee41a9bdebc9
Berk Hess [Thu, 28 Feb 2013 17:10:34 +0000 (18:10 +0100)]
fixed bug with DD cut-off check and PME DLB
During the initial stage of PME DLB, the cut-off limit check for the
DD DLB was not checked correcty. This reduced the effectiveness of
both DD and PME DLB and could lead to missing interactions during
a very limited number of steps.
Fixes #1169
Change-Id: I0b0cac22d4abbe8a9b0c16488aeb662d7d4d9bcc
Mark Abraham [Wed, 27 Feb 2013 15:29:42 +0000 (16:29 +0100)]
Fix regressiontests automated download
Refs #1150
Change-Id: I7ba82b22a75532516f481dcb5e4a870047c0bfe8
Berk Hess [Wed, 20 Feb 2013 09:41:38 +0000 (10:41 +0100)]
fixed recent bug with sorting atoms for GPUs
The sort buffer in the nbnxn gridding for GPUs was made too small
in
8d6cc146. This led to inconsistency errors (not incorrect output).
This is fixed and the sort_atoms call is now made simpler and
multiple consistency checks are now always on in debug builds.
Fixes #1153
Change-Id: Ifcdf45bb4de88e7584628d3ed2699e2fd469d5c6
Mark Abraham [Wed, 20 Feb 2013 10:04:48 +0000 (11:04 +0100)]
Update shell completions
There's some strange changes of what completions are being generated
for inputs that take multiple files when generated by different 4.6.x
versions, but nobody seems to know what is going on. Also, those
problems do not have a large impact.
Refs #1159
Change-Id: Ib4b1ad4999e1b68904d46b0d01c2a5dd07507fd7
Mark Abraham [Fri, 15 Feb 2013 22:54:38 +0000 (23:54 +0100)]
Update outdated admin things
* remove outdated CMake installation guide
* updated the bootstrap script
* remove outdated admin/README.patches
* update README, including adding reference to
GROMACS 4.5 paper and DOIs for old papers
Change-Id: I9a55126049806ca67f6ad846cdbd67cc530c7db0
Roland Schulz [Tue, 5 Mar 2013 09:15:01 +0000 (04:15 -0500)]
Fixes linkage with FFTW + MKL for BLAS/LAPACK
The order of linking was incorrect, when using both mkl and fftw
causing the mkl fftw wrapper to be used instead of fftw itself.
Removes all unnecessary transitive libraries (cmake adds those
automatically). Simplifies the target_link_libraries lines, and
makes it much easier to change the fft/blas link order.
Only remaining transitive libraries are gmx/md for binaries. This
is required because OpenMP_LINKER_FLAGS needs to be at the end
but transitive libraries are added at the end. Thus without listing
gmx/md manually the order is incorrect.
Also fixes that nbnxn_cuda has cuda_tools listed as library
dependency. Was prior working without it but now is needed and is
also anyhow the more corect way to do it.
Fixes #1067
Change-Id: I639b16f1460d27a15eb72cc00674c041266f6624
Justin Lemkul [Fri, 8 Feb 2013 20:40:53 +0000 (15:40 -0500)]
Fixes for install guide page.
Editorial fixes to rename GMX_LIBS_SUFFIX and provide an example
of proper usage of adding suffixes. These edits now keep the .tex
file in sync with the edits manually made to the wiki page.
Change-Id: Iba5b4c66ad3d0d84ddb06591d4681ff48e4de2ee
Mark Abraham [Wed, 20 Feb 2013 11:35:46 +0000 (12:35 +0100)]
Updated install guide
* bumped some versions for 4.6.1
* reviewed various promises about 4.6.1
Change-Id: I6d8549e1f47c53367db275c3091b02556af3b8d8
Mark Abraham [Tue, 5 Mar 2013 14:02:23 +0000 (15:02 +0100)]
Warn if X11 was not found and the user wanted it
Also, removed unused HAVE_X11 variable.
Change-Id: I581b2036f9de27a02c034230f2d1212b9814ffbb
Mark Abraham [Tue, 5 Mar 2013 13:45:56 +0000 (14:45 +0100)]
fix broken things in mkhtml
Change-Id: Ifb9aa694eddd4bffe457674265a2b17093182c50
Christoph Junghans [Sat, 2 Mar 2013 23:01:24 +0000 (00:01 +0100)]
Merge "Uncrustified code changes since 4.6" into release-4-6
Peter Kasson [Thu, 28 Feb 2013 01:32:07 +0000 (17:32 -0800)]
Declaration-definition consistency nbxn_cuda_wait_gpu.
Changed float->real in nbnxn_cuda_wait_gpu() for consistency between
function declaration and function definition. Added note that this is
only implemented for single-precision at the moment. CMake will
complain if GMX_GPU and GMX_DOUBLE are both set.
Addresses Bug #1157.
Change-Id: Ide495cbaba6d120d91f106c6a87ca04e46a2f5a8
Berk Hess [Tue, 26 Feb 2013 19:29:54 +0000 (20:29 +0100)]
fixed PME time print with -ntomp_pme != -ntomp
Fixes #1158
Change-Id: I9028e6309b8802125e91935e87d96b341ec30f77
Mark Abraham [Fri, 15 Feb 2013 23:15:20 +0000 (00:15 +0100)]
Uncrustified code changes since 4.6
The group kernel python scripts have changed slightly to emit
code that uncrustify won't want to change. Group kernel
generation and uncrustify are now mutual null operations.
Recent changes to the declarations in gmx_order in
baa65b60
may have exposed a possible bug in uncrustify. Those declarations
have been simplified so that there will be no future issue from
that possible bug.
Refs #845
Change-Id: I33495d57ca37317cef4bf12707fd77d67309d292
Michael Shirts [Mon, 25 Feb 2013 04:03:05 +0000 (23:03 -0500)]
fix imcompatibility with tpr vers<64 with free energy option
should fix to redmine #1156
Change-Id: I6e60f1efbb03bf460009b8bc59f80f2e0e15bf44
Christoph Junghans [Fri, 15 Feb 2013 17:29:46 +0000 (10:29 -0700)]
Bump shared object version to 8
libs are not compatible with the ones from Gromacs 4.5.x, which had so
version 6 through 4.5.6, and now so version 7 for 4.5.7.
Fixes #1147
Change-Id: If96fd044b00a99eb4ba8376ffa0a2ecbea37894a
Berk Hess [Fri, 8 Feb 2013 12:43:57 +0000 (13:43 +0100)]
fixed issues with FEP soft-core and cut-off's
Now the cut-off is applied to the PME mesh correction for perturbed
pairs with soft-core. Now the cut-off is applied to VdW with soft-core.
Fixes possible NaN in free energy kernel with r close to 0.
Replaced a confusing grompp warning with PME and soft-core by a note.
Removed an invalid grompp warning about soft-core and twin-range.
Fixes #1146
Change-Id: I79a06b20158df2bce575808b6e31e660163bd307
Mark Abraham [Tue, 19 Feb 2013 13:01:57 +0000 (14:01 +0100)]
Merge release-4-5-patches into release-4-6
Avoided the 4.5.6 release patch by using
git merge -s ours
10b109beb3ffa95e37386d38140d2c0fd7769f20
git merge release-4-5-patches
tree=$(git log -1 HEAD --pretty=%T)
git reset --hard $(git cat-file commit HEAD | sed '1,/^$/d' | \
git commit-tree $tree -p
2b05689 -p
8d6cc14)
Conflict resolution was straightforward, except that the vsite
code was somewhat reorganized in the meantime.
Conflicts:
Makefile.am
src/contrib/Makefile.am
src/contrib/addquote.c
src/gmxlib/copyrite.c
src/mdlib/vsite.c
Change-Id: Ib90ac4e55fac308c433b15c344caf5ee41f0146c
Berk Hess [Thu, 14 Feb 2013 21:27:17 +0000 (22:27 +0100)]
fixed GPU particle gridding performance issue
The scaling factor for the grid binning for the GPU pair search
was set incorrectly, which made the binning 50% slower.
Change-Id: I146592c37094a3d81a7ae50b3903fcc615e748d5
Carsten Kutzner [Fri, 15 Feb 2013 10:51:09 +0000 (11:51 +0100)]
Made g_tune_pme work with 4.6 if user sets "-p" command line option
Added "-p" (performance statistics log file) to the list of files that
must not appear on the mdrun command line at launch time. (This would lead
mdrun to refuse to launch due to an unknown command line option.)
Change-Id: I268bbf6513709866b9a6a8d81c97706ccc832988
Mark Abraham [Sat, 9 Feb 2013 16:35:11 +0000 (17:35 +0100)]
Fix CMake namespace pollution
When gmxManageMPI finds MPI and CMake version is less than 2.8.10,
the variable file_cmd ends up in the non-advanced CMake namespace.
Made it advanced in those cases.
Change-Id: I79fd46e1b66d6c5ab008973e654092939eeae4dc
Roland Schulz [Mon, 21 Jan 2013 22:58:46 +0000 (17:58 -0500)]
Issue errors/warnings for ICC before 12.0.0
ICC 11.1 with SSE4.1 gives incorrect results, so CMake will
refuse to build with that minor version. Given that we
currently don't know anything specific and 11 is old, we
warn with any version older than 12.0.0. If more information
is available later, this warning can be made more specific.
Fixes #1126
Change-Id: I3c37844c69ce34769187f288c43cd8aef4086c53
Michael Shirts [Thu, 14 Feb 2013 03:01:14 +0000 (22:01 -0500)]
bugfix for md-vv + nose-hoover + (nstcalcenergy > nsttcouple)
Need global communication the step befre nsttcouple
in order to get the kinetic energy right, because
of the offsets velocity verlet from leapfrog.
Fixes redmine #1129
Change-Id: Ia6157db8304cc4fb8cccbda0ac3b949e800efeb5
Mark Abraham [Tue, 29 Jan 2013 13:29:28 +0000 (14:29 +0100)]
Use explicit kernel pointer typecasts
Some compilers don't like implicit casts from function pointers
to void*, so if we're going to be dirty, dirty people, we may
as well come clean about it.
Change-Id: Ia071c6a10a4ec20b83ddb13e4f0cd2a7b139264f
Mark Abraham [Fri, 15 Feb 2013 22:32:16 +0000 (23:32 +0100)]
Merge "Minor fixes to Verlet kernels" into release-4-6
Mark Abraham [Fri, 15 Feb 2013 18:29:33 +0000 (19:29 +0100)]
Merge "improved PME load balancing reporting" into release-4-6
Mark Abraham [Fri, 15 Feb 2013 16:51:47 +0000 (17:51 +0100)]
Merge "Re-generated group kernels" into release-4-6
Mark Abraham [Fri, 15 Feb 2013 14:54:21 +0000 (15:54 +0100)]
Merge "Unwinds flag dependencies in g_order." into release-4-6
David van der Spoel [Fri, 15 Feb 2013 12:41:47 +0000 (13:41 +0100)]
Merge "Fixed an initialization issue in gmx_dipoles." into release-4-6
Mark Abraham [Fri, 15 Feb 2013 12:38:24 +0000 (13:38 +0100)]
Merge "use legacy CUDA non-bonded kernels only on Fermi" into release-4-6
Mark Abraham [Fri, 15 Feb 2013 12:38:05 +0000 (13:38 +0100)]
Merge "More descriptive Verlet kernel macro parameter names" into release-4-6
Sander Pronk [Fri, 15 Feb 2013 12:12:53 +0000 (13:12 +0100)]
Fixed an initialization issue in gmx_dipoles.
This fixes a warning in gcc 4.7
Change-Id: Ief8a057dff24c9a61c20301215a7009c2a16e74a
Berk Hess [Tue, 5 Feb 2013 11:55:52 +0000 (12:55 +0100)]
improved PME load balancing reporting
With the group cut-off scheme, rlist was reported incorrectly.
Added a note in log and stderr when PME load balancing increases
the non-bonded workload by more than 50%.
Change-Id: I7d46f5a110b24cbb40b6b9cb53a1d90715c7c5ec
Mark Abraham [Mon, 28 Jan 2013 15:48:08 +0000 (16:48 +0100)]
Minor fixes to Verlet kernels
* clarified some comments
* documented use of nbfp_s4 better
Change-Id: I0848f2e570daef881368a45d4a429a3f80fde81b
Peter Kasson [Tue, 22 Jan 2013 20:18:43 +0000 (12:18 -0800)]
Unwinds flag dependencies in g_order.
A feature added a while back to g_order had a flag dependency
(-calcdist forced -radial). This patch attempts to unwind that
dependency and allow -calcdist independent of -radial.
Fixed help message for -calcdist
Change-Id: I8c368f9109ee305d79a3c0c1b6838439598a4e89
Mark Abraham [Fri, 15 Feb 2013 08:41:16 +0000 (09:41 +0100)]
Merge "Fix and add Verlet kernel error messages" into release-4-6
Sander Pronk [Wed, 13 Feb 2013 21:24:25 +0000 (22:24 +0100)]
Merge "Fix code bug with thread-MPI on PowerPC with xlc" into release-4-6
Roland Schulz [Wed, 13 Feb 2013 21:24:19 +0000 (22:24 +0100)]
Merge "Fixed the MPI recognition string in g_tune_pme" into release-4-6
Roland Schulz [Wed, 13 Feb 2013 21:22:49 +0000 (22:22 +0100)]
Merge "improve setup of multiple tf tables" into release-4-6
David van der Spoel [Sat, 15 Dec 2012 10:11:43 +0000 (11:11 +0100)]
Plain text quotes.
And removed 5 gurgles and 2 bromacses - replaced the bromacses
by new and exciting ones.
Change-Id: Ibdad70d6ceb0caa52be351762704a677e9dddba8
Mark Abraham [Tue, 29 Jan 2013 12:37:30 +0000 (13:37 +0100)]
Fix code bug with thread-MPI on PowerPC with xlc
Change-Id: I8254ae915fdd24e02cf8f07789c69c3d4b35525e
Mark Abraham [Sun, 3 Feb 2013 10:40:06 +0000 (11:40 +0100)]
More descriptive Verlet kernel macro parameter names
Also more consistent with SIMD kernel usage
Change-Id: Ia8dd723075b5c289d0171e3d34ecd51a0fc152f4
Mark Abraham [Sat, 2 Feb 2013 11:53:19 +0000 (12:53 +0100)]
Fix and add Verlet kernel error messages
Handles default cases better
Change-Id: I45d8ebd73184630180e6ed87d54c3a8fc3cbef73
Mark Abraham [Wed, 13 Feb 2013 15:07:33 +0000 (16:07 +0100)]
Re-generated group kernels
This should be a null operation, but I had to fix copyright
years in python scripts and it had the following effects:
* removed some debugging printf statements in GB C kernels
* minor whitespace change now consistent between template and output
Change-Id: I3c3fe9be625ca4f7ade6871fc105fd80899e5a70
Sander Pronk [Wed, 13 Feb 2013 14:24:22 +0000 (15:24 +0100)]
Added extra check in for setaffinity support.
The Linux version of tMPI_Thread_setaffinity_support() did not check
whether pthread_setaffinity_np() would actually work on the system
it's running on. It now checks by running pthread_getaffinity_np()
and checking its return value.
This is relevant for, for example, Bluegene systems which don't
support explicit affinity setting.
Change-Id: I4833e7384067f897013d6fa4d0b35963ae740fcf
Carsten Kutzner [Wed, 13 Feb 2013 11:41:46 +0000 (12:41 +0100)]
Fixed the MPI recognition string in g_tune_pme
Since the identifying string "NNODES="is not printed any more by MPI-enabled
mdrun, we now use the "MPI library:" string instead.
Change-Id: Ibbcc0678a7c89057743129aa664fad8bb68f1941
Roland Schulz [Wed, 13 Feb 2013 01:15:23 +0000 (02:15 +0100)]
Merge "Updated FindGSL.cmake to version written by me." into release-4-6
Mark Abraham [Tue, 12 Feb 2013 19:58:14 +0000 (20:58 +0100)]
Merge "PME-only counters are now reset with -maxh -resethway" into release-4-6
Christoph Junghans [Wed, 16 Jan 2013 21:25:52 +0000 (14:25 -0700)]
Updated FindGSL.cmake to version written by me.
relates to #815
Change-Id: I323f113b4016ef232124fcdcc985d0526bc8a880
Mark Abraham [Tue, 12 Feb 2013 19:56:14 +0000 (20:56 +0100)]
Merge "fixed bug with sd integrator and OpenMP threading" into release-4-6
Mark Abraham [Tue, 12 Feb 2013 19:43:02 +0000 (20:43 +0100)]
Merge "Fix CUDA_HOST_COMPILER flag name" into release-4-6
Szilárd Páll [Wed, 16 Jan 2013 20:05:28 +0000 (21:05 +0100)]
use legacy CUDA non-bonded kernels only on Fermi
This solves a remainig todo as well as clarifies some variable naming
and documentation.
Change-Id: Ifad80cb7e740d1329a9c84df992d899400efeca2
Roland Schulz [Sat, 9 Feb 2013 18:18:10 +0000 (19:18 +0100)]
Merge "Typo fix" into release-4-6
Mark Abraham [Sat, 9 Feb 2013 17:20:36 +0000 (18:20 +0100)]
Typo fix
Change-Id: Id5bb7297adbc38909aa184b6d6a222aa719f90be
Roland Schulz [Fri, 8 Feb 2013 20:09:06 +0000 (15:09 -0500)]
Fix CUDA_HOST_COMPILER flag name
Fixes #1143
Change-Id: If34f27aa8fa73420ac85d4ec6997e8ebe78261d4
Mark Abraham [Fri, 8 Feb 2013 15:16:30 +0000 (16:16 +0100)]
Merge "added back cuda.h includes to fix missing CUDA_VERSION" into release-4-6
Mark Abraham [Fri, 8 Feb 2013 15:16:17 +0000 (16:16 +0100)]
Merge "Fixed flop counting for generic cg/adress kernels" into release-4-6
Mark Abraham [Fri, 8 Feb 2013 15:16:05 +0000 (16:16 +0100)]
Merge "cmake: fixed typo in template CMakeLists.txt" into release-4-6
Berk Hess [Wed, 6 Feb 2013 15:21:24 +0000 (16:21 +0100)]
fixed bug with sd integrator and OpenMP threading
This could cause small error in the integration or a segv.
This bug was introduced with
d120c370
Fixes #1138
Change-Id: I4ae2c0c857cb68e796d01c5b2e0ea42beaf13d4a
Christoph Junghans [Tue, 5 Feb 2013 23:52:49 +0000 (00:52 +0100)]
Merge "Documented what GMX_CPU_ACCELERATION really means" into release-4-6
Christoph Junghans [Wed, 23 Jan 2013 20:57:13 +0000 (13:57 -0700)]
improve setup of multiple tf tables
* buffer string was not initialized
* put tf table info in log instead of on the screen
Change-Id: I11ecdcd8c9a18a8931dbccef528ff02a74959ee1
Mark Abraham [Tue, 5 Feb 2013 19:27:04 +0000 (20:27 +0100)]
Merge "improved load balancing on the GPU" into release-4-6
Mark Abraham [Tue, 5 Feb 2013 19:00:46 +0000 (20:00 +0100)]
Documented what GMX_CPU_ACCELERATION really means
Discussion arose in I0848f2e570daef881368a45d4a429a3f80fde81b
Change-Id: Ib99ab86ff7d8acf913121decb00756f47327f046
Berk Hess [Fri, 1 Feb 2013 09:22:09 +0000 (10:22 +0100)]
improved load balancing on the GPU
For the GPU, small pair list entries are now sorted to the end.
The improves performance by 5 to 20%.
Change-Id: I25e5efeb813ad5dde48f0955366519db699f21a2
Berk Hess [Mon, 4 Feb 2013 12:44:31 +0000 (13:44 +0100)]
fixed segv in init_forcerec with fr->hwinfo=NULL
This caused genion and g_disre to segv with the Verlet scheme.
Fixes #1136
Change-Id: I9059b0e108c80ea86567a568e9f488b4db500eee
Christoph Junghans [Sat, 2 Feb 2013 03:02:04 +0000 (20:02 -0700)]
Fixed flop counting for generic cg/adress kernels
Change-Id: I95f2a68a0de64f479820143fdba09ea09805fa93
Christoph Junghans [Sat, 2 Feb 2013 01:46:46 +0000 (18:46 -0700)]
cmake: fixed typo in template CMakeLists.txt
* prevented build after make clean, when build was used before
Change-Id: I0ba88b36752801c3d492d46c71327fb966edb508
Berk Hess [Wed, 30 Jan 2013 09:57:51 +0000 (10:57 +0100)]
PME-only counters are now reset with -maxh -resethway
Fixes #1125
For clarity gmx_pme_recv_q_x now returns and enum
and gmx_pme_send_switch is renamed to gmx_pme_send_switchgrid.
Change-Id: I21952780f0b719378d947a79324c844ccde7160a
Sebastian Fritsch [Mon, 28 Jan 2013 19:49:40 +0000 (20:49 +0100)]
AdResS: fixes bug in the neighbour list routine
* coarse-grained interactions were not excluded in the all-atom region
* Some atomistic interactions were not excluded in the coarse-grained region
Change-Id: Ib4ac145722367cf139ad3d23b86f0de1ca9d6caf
Christoph Junghans [Fri, 18 Jan 2013 21:46:05 +0000 (14:46 -0700)]
fixed copyright of adress kernel
Change-Id: I21816431b4f77210a93dedc7a265c10f074502c4
Christoph Junghans [Fri, 25 Jan 2013 21:06:55 +0000 (22:06 +0100)]
Merge "Moved a few comments back into position" into release-4-6
Han Wang [Wed, 23 Jan 2013 21:02:22 +0000 (14:02 -0700)]
fix invalid read in construct_vsites
* aj is not available in the F_VSITEN case hence cannot be read in
the common part of the function
Change-Id: Ic98dfb91eb095aea933abc3dbfb4f5cc10bf4166
Szilard Pall [Thu, 24 Jan 2013 01:27:09 +0000 (02:27 +0100)]
added back cuda.h includes to fix missing CUDA_VERSION
nvcc doesn't define its version identity macro, CUDA_VERSION, by default,
but this needs to be pulled in through cuda.h. Quite weird and
non-standard behavior, but as swithing to legacy kernels and certain
kernel optimizations are broken now, to fix these we need to include
cuda.h.
Change-Id: I4836335e97a287e18e595c160819db2e46a8d798
Mark Abraham [Tue, 22 Jan 2013 18:17:52 +0000 (19:17 +0100)]
Merge "Illegal acceleration defaulted to QPX" into release-4-6
Mark Abraham [Tue, 22 Jan 2013 16:41:00 +0000 (17:41 +0100)]
Merge "Re-licenced FindGROMACS.cmake (was written by me)" into release-4-6
Roland Schulz [Mon, 21 Jan 2013 21:34:35 +0000 (16:34 -0500)]
Illegal acceleration defaulted to QPX
Change-Id: I1bfd9c7bc7bac68944fd912bda84e8bd03af1fbc
Mark Abraham [Tue, 22 Jan 2013 16:40:12 +0000 (17:40 +0100)]
Merge "Fix TOUPPER usage" into release-4-6
Mark Abraham [Tue, 22 Jan 2013 16:39:55 +0000 (17:39 +0100)]
Merge "Updated html manual to 4.6" into release-4-6
Mark Abraham [Tue, 22 Jan 2013 15:31:01 +0000 (16:31 +0100)]
Merge "added missing cleanup of some nbnxn_cuda data" into release-4-6
Roland Schulz [Mon, 21 Jan 2013 21:12:52 +0000 (16:12 -0500)]
Fix TOUPPER usage
The last argument is the variable name, thus it shouldn't be ${..}.
Caused compile error when setting accleration to sse2, because
TOUPPER wasn't done correctly.
Change-Id: I0087a6cf3c9a160862757f561b5782c0ac253df8
Roland Schulz [Sun, 20 Jan 2013 00:51:02 +0000 (19:51 -0500)]
Updated html manual to 4.6
Change-Id: I2d66c41c56a44fddc31bba823a264795c07d078a
Carsten Kutzner [Tue, 22 Jan 2013 12:00:50 +0000 (13:00 +0100)]
Moved a few comments back into position
No code changes whatsoever - just formatted some multi-line comments
which uncrustify could not understand.
Change-Id: I85e2f58681c61be937315414dc2a708974b027f8
Christoph Junghans [Mon, 21 Jan 2013 20:44:02 +0000 (21:44 +0100)]
Merge "Set version info for 4.6.x release series" into release-4-6
Christoph Junghans [Fri, 18 Jan 2013 21:00:56 +0000 (14:00 -0700)]
Re-licenced FindGROMACS.cmake (was written by me)
Change-Id: If6a94c561933cbc6db9d47d5a364f75e7fdf5e13
Roland Schulz [Sat, 19 Jan 2013 06:42:22 +0000 (01:42 -0500)]
Fix AVX double compile error
Introduced by
fa181964de6c9
Note that this change will be included in the 4.6 release, therefore
this commit will effectively be the one that the 4.6 release is made
from instead of the parent.
Change-Id: Ieeede7d15109f2c44fcd2e0ef59eff2944206eab
Roland Schulz [Sat, 19 Jan 2013 06:08:57 +0000 (01:08 -0500)]
Add fftpack to EXTRA_DIST
The new fftpack files added by
51c2f6c are only compiled if
fftpack is used. Thus "make dist" does not included those
by default.
Change-Id: Id51bba3c622a7087f35e74f7c499b066f095fd0d
Roland Schulz [Sat, 19 Jan 2013 03:35:35 +0000 (22:35 -0500)]
Release 4.5.6
- Updated the version to 4.5.6 in CMakeLists.txt, configure.ac
and gromacs.7
- Regenerated man-pages and completions
Change-Id: I7692220dfe20248b4cdbdd1ed242d1d97f56fda5
Mark Abraham [Wed, 16 Jan 2013 01:08:33 +0000 (02:08 +0100)]
Set version info for 4.6.x release series
Change-Id: I31378a7ef5d9b7333aa91f076c2a792072d304f9
Mark Abraham [Wed, 16 Jan 2013 01:06:19 +0000 (02:06 +0100)]
New major release: 4.6
* note -dev gets stripped off by the release manager by hand before
building tarballs
Change-Id: I36fe0b8ec18c7d6f09da852e216fdf6d0a250bb7
Michael Shirts [Wed, 16 Jan 2013 14:03:30 +0000 (09:03 -0500)]
Addendum for expanded ensemble options plus formatting fixes.
Change-Id: I4547fe74064593c939fcb292ccee056b49b292af
Roland Schulz [Fri, 18 Jan 2013 20:25:05 +0000 (15:25 -0500)]
Merge release-4-5-patches into release-4-6
Conflicts:
src/gmxlib/confio.c (whitespace only)
286575f0cd68 commit is not needed and is ignored
by this merge.
Change-Id: I7c4aabd918384aadbf6108501023ca77e019d6c1
Roland Schulz [Fri, 18 Jan 2013 05:12:58 +0000 (00:12 -0500)]
Fix typo
Change-Id: Iba23e5cea570b2a283a19290774fe21b0e625cab