David van der Spoel [Thu, 27 Dec 2012 12:31:52 +0000 (13:31 +0100)]
Fixes #994 confusion in atomprop.
The atomprop code modified the contents of the atom
database files by turning everything into uppercase.
This caused confusion between elements and protein
or nucleic acid atom names.
Change-Id: Ia0ac4636471b7051bf38a714ed16e299bf3d64ab
Roland Schulz [Fri, 11 Jan 2013 02:00:05 +0000 (03:00 +0100)]
Merge "Handle compiler flags more flexibly" into release-4-6
Christoph Junghans [Fri, 11 Jan 2013 00:05:06 +0000 (01:05 +0100)]
Merge "Remove incorrect assert added by
05f9a740" into release-4-6
Erik Lindahl [Mon, 7 Jan 2013 00:19:15 +0000 (01:19 +0100)]
Fixed flop-accounting for periodic improper dihedrals
Flops were incorrectly assigned as proper dihedrals.
Fixes #632.
Change-Id: Ifda09b9a0e6575c5f6f19f3c55979804fe1dc2eb
Mark Abraham [Thu, 10 Jan 2013 22:04:17 +0000 (23:04 +0100)]
Merge "Revert default rlist/rvdw/rcoulomb to valid values of 1.0" into release-4-6
Mark Abraham [Thu, 10 Jan 2013 22:00:48 +0000 (23:00 +0100)]
Merge "fixed bug with Verlet + DD + bonded atom communication" into release-4-6
Roland Schulz [Thu, 10 Jan 2013 21:28:51 +0000 (16:28 -0500)]
Remove incorrect assert added by
05f9a740
Change-Id: I39c3ba9135e44112fe54523e4cbf8125410b238c
Roland Schulz [Thu, 10 Jan 2013 16:23:31 +0000 (11:23 -0500)]
Handle compiler flags more flexibly
Flags aren't cached anymore. This prevents all problems with
caching dependent variables. It is the approached taken by other
projectes (VTK,libssh,...). The cached CMAKE_C*_FLAGS* only contain
the user provided flags. The user can add flags by setting the
variables directly or by setting environment variables.
All flags added by Gromacs are only added to the uncached version
with the same name. For the user to overwrite flags the new option
GMX_SKIP_DEFAULT_CFLAGS is added. This option gives the user total
control. Gromacs doesn't add any flags automatically and instead
shows which flags would be added. The user can manually add those
flags she wants.
Fixes #1038, #1040.
Change-Id: I8655f93fac60bce2c9a35152937d672b3786ff32
Erik Lindahl [Thu, 10 Jan 2013 00:12:41 +0000 (01:12 +0100)]
Disallow the use of Clang to compile AVX_128_FMA
Clang apparently produces buggy code both for verlet kernels
and group kernels when the AVX_128_FMA acceleration is enabled.
Since it happens in two places it is unlikely to be a minor
bug, and since it covers versions up to the currently
released one, we don't have much choice but to disallow this
combination for now.
Fixes #1099.
Change-Id: If8346fa0a58f51a0ef6ac16e4801fe98ad1c73c9
Roland Schulz [Thu, 10 Jan 2013 18:51:02 +0000 (19:51 +0100)]
Merge "Move Windows shared/static options to later point" into release-4-6
Roland Schulz [Thu, 10 Jan 2013 18:50:25 +0000 (19:50 +0100)]
Merge "Remove workaround" into release-4-6
Berk Hess [Thu, 10 Jan 2013 16:08:44 +0000 (17:08 +0100)]
fixed bug with Verlet + DD + bonded atom communication
Atoms communicated for bonded interactions can be beyond the cut-off
distance. Such atoms are now put placed in an extra row in the grid.
Fixes #1114
Also improved the performance of the nbnxn grid sorting, especially
for inhomogeneous systems.
Change-Id: Ibe5ba24af95959f5dadd89584e2315da60b55091
Roland Schulz [Wed, 9 Jan 2013 17:52:08 +0000 (12:52 -0500)]
Move Windows shared/static options to later point
No need to do early and now is together with where those flags
are handled for Unix
Also warn if BUILD_SHARED_LIBS and GMX_PREFER_STATIC_LIBS don't
agree. And undo MD MT replacement if user changes
GMX_PREFER_STATIC_LIBS.
Change-Id: I66a165a7d3aebb31350bb13d19392d3f3935e54b
Roland Schulz [Wed, 9 Jan 2013 17:06:52 +0000 (12:06 -0500)]
Remove workaround
Fixed in 2.8.9. Given that earlier version only have a warning
not an error no need to clutter CMakeLists.txt.
Change-Id: I11410c92f160ba846a9591e670bb7757a5e31bf3
Erik Lindahl [Fri, 28 Dec 2012 19:26:57 +0000 (20:26 +0100)]
Remove broken g_dih tool
Per the redmine discussion for #1094, g_dih was broken
due to hardcoded atom names while the documentation
claimed dihedrals were assigned from the topology.
For now it is better to use g_angle and manually define
the dihedrals. We plan to reimplement g_dih from scratch
for 5.0. Fixes #1094.
Change-Id: I57e0614e4d98bb5d4bbb3aaa1d3ba4377a93f988
Mark Abraham [Thu, 10 Jan 2013 15:30:03 +0000 (16:30 +0100)]
Merge "Fixes SSE/AVX compilation under Windows" into release-4-6
Erik Lindahl [Mon, 7 Jan 2013 00:06:06 +0000 (01:06 +0100)]
Revert default rlist/rvdw/rcoulomb to valid values of 1.0
This reverts the part of commit
103d98cf31f064cce7c6ec14fcccd081aa2bbfac
where the default values for rlist, rvdw, and rcoulomb were set
to -1 to enable automatic optimization with verlet kernels and "force
the user to think about the cutoff".
The main reason is that this change breaks the default grompp files
from working, which means it was no longer possible to use an empty
mdp file for quick tests. However, I also think it is against the
idea that the default values should be reasonable first tries - otherwise
we might as well change every single default value in the mdp file to
be invalid to force users to think.
Change-Id: I1c40ea5fefc31c6635f21ceefe4da5c1c350b755
Erik Lindahl [Fri, 28 Dec 2012 18:40:53 +0000 (19:40 +0100)]
Fixes SSE/AVX compilation under Windows
- 32-bit MSVC cannot handle more than 3 xmm/ymm register
arguments due to stack alignment, so some group kernel
routines have been copied into optional macros. These are
only used for 32-bit MSVC compiles; other alternatives including
icc on windows use the normal functions that are easier to debug.
- Since the windows compilers control 32 vs 64 bit with flags, a
new log file entry has been added to show whether the present
build is a 32 or 64 bit one.
- Minor fixes to enable double precision AVX_128_FMA builds on
windows.
- Replace use of explicit binary constants with _MM_SHUFFLE()
macro in nbnxn kernels to make it compile under windows.
With these fixes, both SSE2, SSE4, and AVX256 group kernels pass
regressiontests in single and double with MSVC2010, MSVC2012, and
icc 2013.1 used with visual studio 2012. The nbnxn kernels pass
all tests with the exception of 32-bit double precision AVX_256
where all three compilers still fail (Refs #1097).
Fixes #1092, #1093, #1068.
Change-Id: I6807b102af1db01cafba26a45284f5c38c7498fd
Erik Lindahl [Wed, 9 Jan 2013 22:04:22 +0000 (23:04 +0100)]
Merge "Corrected gmxcheck output for Gromos96 bonds." into release-4-6
Justin Lemkul [Wed, 9 Jan 2013 16:09:04 +0000 (11:09 -0500)]
Corrected gmxcheck output for Gromos96 bonds.
There was a small output bug since Gromos96 bonds are modified to have
the reference value stored as (b0)^2 rather than just b0.
Fixes #1109.
Change-Id: Ie4516515f7cacb35d262c2059b5e461962340fec
Roland Schulz [Wed, 9 Jan 2013 15:33:43 +0000 (16:33 +0100)]
Merge "Added work-around for gcc bug in AVX intrinsincs formal parameter" into release-4-6
Roland Schulz [Wed, 9 Jan 2013 06:02:39 +0000 (07:02 +0100)]
Merge "Add check to remove zero Charmm dihedrals" into release-4-6
Roland Schulz [Wed, 9 Jan 2013 03:40:02 +0000 (04:40 +0100)]
Merge "[tools] g_sans - add trajectory avereging" into release-4-6
Erik Lindahl [Thu, 20 Dec 2012 18:18:04 +0000 (19:18 +0100)]
Added work-around for gcc bug in AVX intrinsincs formal parameter
Many relatively recent gcc versions (4.5.2, possibly 4.6.0) use incorrect
formal parameters for maskload and maskstore intrinsics. This patch
detects the bug during configuration and works around it with a define.
Refs #1058, and fixes it at least from gcc-4.5.2.
Change-Id: I447a968d2153f5acf59ad170ace69ad1b6b3f24d
Erik Lindahl [Sun, 6 Jan 2013 23:54:27 +0000 (00:54 +0100)]
Add check to remove zero Charmm dihedrals
Proper torsions where the force constant is zero
in both A and B states are now removed. We also
check for other angle, torsion, and restraint
functional types, and if all parameters are zero
for these the interaction is not added. This will
not change any results, but increase performance
slightly by not calculating unnecessary interactions.
Fixes #810.
Change-Id: I37ecd06d0641008593edab29e5b08433bde7b6cc
Erik Lindahl [Thu, 27 Dec 2012 15:04:33 +0000 (16:04 +0100)]
Do not always add -msse2 to release flags for icc
At least on Windows, this flag will override the -msse4.1 or -mavx
flags added to the main C flags. Since we already add -msse2 in
the same place when using SSE2, I see no reason why it should be
added to the release flags separately.
Change-Id: I933f5b1d5e4e4ead1635ec47b5272a0f6f69da67
Roland Schulz [Tue, 8 Jan 2013 03:05:03 +0000 (04:05 +0100)]
Merge "Reduce use of monolithic sets of compiler flags" into release-4-6
Roland Schulz [Mon, 7 Jan 2013 22:54:27 +0000 (23:54 +0100)]
Merge "fixed nbnxn AVX-256 Ewald table pointer alignment" into release-4-6
Mark Abraham [Thu, 13 Dec 2012 21:58:33 +0000 (22:58 +0100)]
Reduce use of monolithic sets of compiler flags
This prepares to fix the Redmine issue below (but perhaps could
be folded into it).
Refs #1038
Change-Id: I6407dbbd331e58c30ab1b275748a211040c9c414
Roland Schulz [Mon, 7 Jan 2013 22:14:27 +0000 (23:14 +0100)]
Merge "cmake: remove double-negative quotes logic" into release-4-6
Berk Hess [Thu, 3 Jan 2013 12:24:03 +0000 (13:24 +0100)]
fixed nbnxn AVX-256 Ewald table pointer alignment
This could lead to access violations, but up till now
this was only observed with 32-bit MSVC builds.
Fixes #1097
Also added more documentation to nbnxn_kernel_simd_utils.h,
renamed macro variables and added minor table optimization
by replacing shuffle with movelh or unpack.
Change-Id: I9df2131cbabb0e6cb86f7224a5fd238acb2e7681
Roland Schulz [Mon, 7 Jan 2013 19:15:55 +0000 (20:15 +0100)]
Merge "Ignore bool cast warning for MSVC and C++" into release-4-6
David van der Spoel [Mon, 7 Jan 2013 13:39:04 +0000 (14:39 +0100)]
Merge "Removed reference to nonexistent file in g_helix." into release-4-6
Christoph Junghans [Wed, 19 Dec 2012 17:50:27 +0000 (10:50 -0700)]
cmake: remove double-negative quotes logic
Change-Id: I75b3a45a4f0fbbff6300a6317126c5b0cc302b86
Roland Schulz [Mon, 7 Jan 2013 01:21:49 +0000 (02:21 +0100)]
Merge "improved reporting of failed affinity setting" into release-4-6
Roland Schulz [Mon, 7 Jan 2013 01:21:37 +0000 (02:21 +0100)]
Merge "Fixed format error in online manual." into release-4-6
Roland Schulz [Mon, 7 Jan 2013 01:21:24 +0000 (02:21 +0100)]
Merge "Fixed a bug that with multiple exchanges" into release-4-6
Roland Schulz [Mon, 7 Jan 2013 01:21:10 +0000 (02:21 +0100)]
Merge "Essential dynamics: fixed restarts when ED group has > 1 molecule" into release-4-6
Roland Schulz [Mon, 7 Jan 2013 01:20:47 +0000 (02:20 +0100)]
Merge "minor speed-up and code clean-up in nbnxn kernels" into release-4-6
Christoph Junghans [Mon, 7 Jan 2013 01:06:32 +0000 (02:06 +0100)]
Merge "Make gmx_cpuid.h self-standing." into release-4-6
Justin Lemkul [Sat, 5 Jan 2013 23:09:27 +0000 (18:09 -0500)]
Removed reference to nonexistent file in g_helix.
For many years, g_helix has referred to a file called n-ahx.xvg, but
no released version of Gromacs has ever produced it. Being that its contents
are largely reproduced by do_dssp, there is no need to introduce this
functionality and thus the easiest solution is to remove the reference
to this file.
Fixes #1103.
Change-Id: I2b87eed44d9d4c174d3772a39abf24827f63202d
Teemu Murtola [Fri, 4 Jan 2013 19:48:12 +0000 (20:48 +0100)]
Merge "Minor fixes to g_angle help description." into release-4-6
Mark Abraham [Tue, 18 Dec 2012 23:20:04 +0000 (00:20 +0100)]
Set CMake module search path at a better time
This needs to be set before project() in order that
toolchain files for cross compilling can use the same
search path. Otherwise, the users has to specify
fully-qualified toolchain files.
Refs #1064
Change-Id: I1f1fb4803c9f0dd2b95d236da1c1858c5ea382f9
Teemu Murtola [Fri, 4 Jan 2013 12:23:58 +0000 (13:23 +0100)]
Merge "add an option to not build the template" into release-4-6
Teemu Murtola [Fri, 4 Jan 2013 12:23:37 +0000 (13:23 +0100)]
Merge "Add missing defines to PKG_CFLAGS" into release-4-6
Teemu Murtola [Fri, 4 Jan 2013 12:22:26 +0000 (13:22 +0100)]
Merge "Fixed error message for zwitterion residues" into release-4-6
Christoph Junghans [Fri, 21 Dec 2012 18:23:14 +0000 (11:23 -0700)]
add an option to not build the template
Change-Id: Ia85fc9dfbd191ac66cfff2d7b7c815620d800afe
Christoph Junghans [Wed, 19 Dec 2012 23:03:37 +0000 (16:03 -0700)]
Add missing defines to PKG_CFLAGS
Change-Id: I7e4234cf194f10aba1a16cfa81774b8f1941ca76
Roland Schulz [Thu, 3 Jan 2013 18:20:29 +0000 (19:20 +0100)]
Merge "Fixed GMXRC so we are not polluting standard shell variables" into release-4-6
Justin Lemkul [Thu, 3 Jan 2013 14:52:43 +0000 (09:52 -0500)]
Fixed format error in online manual.
The .gro format indicated a right-aligned residue name, but in
reality the residue name is left-aligned and the atom name in the
next column is right-aligned. The online manual now reflects this.
Change-Id: I610392c692bf31f962ad069c23d7e55196b64b53
Christoph Junghans [Thu, 3 Jan 2013 02:53:53 +0000 (03:53 +0100)]
Merge "Remove non-functional PowerPC invsqrt." into release-4-6
Berk Hess [Wed, 2 Jan 2013 10:42:50 +0000 (11:42 +0100)]
minor speed-up and code clean-up in nbnxn kernels
Clusters without LJ now use the half-LJ instead of the full-LJ
plus Coulomb kernels. This gives a few percent speed-up for water.
Also updated some kernel comments and macros.
Change-Id: Ifa6072561a7042d9d0602ec7d84bc667361951e4
Szilard Pall [Wed, 2 Jan 2013 18:19:36 +0000 (19:19 +0100)]
improved reporting of failed affinity setting
Change-Id: I8a10c524b9d168c29ca587d6328b8d246d287c47
Michael Shirts [Tue, 1 Jan 2013 06:43:55 +0000 (01:43 -0500)]
Fixed a bug that with multiple exchanges
Fixed a very subtle bug with multiple exchanges: with multiple
exchanges, Swapping states and swapping configurations are NOT
equivalent, for the same reason that the cycles 1->2->3->1 and
1->3->2->1 are not equivalent. Also added a number of comments
to help explain the code more.
Change-Id: I52b4543d5b6e1b035d8d6225df3388d0f07cd76f
Erik Lindahl [Sun, 30 Dec 2012 11:28:52 +0000 (12:28 +0100)]
Fixed GMXRC so we are not polluting standard shell variables
csh/tcsh is now detected by looking for the lower-case $shell
variable, which seems to work on all recent platforms, instead
of using the 'set' command (which affected $* and $@ in bash).
Fixes #1044.
Change-Id: I852d075c80e2bf8f81a02932432dd31b3bab7f09
Erik Lindahl [Sun, 30 Dec 2012 18:29:53 +0000 (19:29 +0100)]
Merge "Thread-MPI fixes for i386 llvm & simplification of atomics" into release-4-6
Teemu Murtola [Sun, 30 Dec 2012 06:42:32 +0000 (08:42 +0200)]
Remove non-functional PowerPC invsqrt.
Also remove remaining Power6-related CMake code now that there is no
Power6 CPU acceleration option.
Fixes #947, see that issue for justification.
Change-Id: I6466f3ca7297f96757097119ee7b10e7e467bfe7
Christoph Junghans [Fri, 28 Dec 2012 22:11:31 +0000 (15:11 -0700)]
cmake: add option to install libmd as libgmxmd
Change-Id: I984494e843a344f50ecec8789e4e535ed6ce3c61
Sander Pronk [Sat, 29 Dec 2012 17:29:23 +0000 (18:29 +0100)]
Thread-MPI fixes for i386 llvm & simplification of atomics
llvm on 32-bit x86 now uses the gcc-style intrinsics rather than
inline assembly; this fixes http://redmine.gromacs.org/issues/1098
Also, atomics use in thread-MPI is simplified to use only add-return
rather than fetch-add and add-return.
Change-Id: Id7edba926957b0d708e59ffd42db7c2b38edbdfc
Fixes: 1098
Erik Lindahl [Thu, 27 Dec 2012 11:42:21 +0000 (12:42 +0100)]
Fixed error message for zwitterion residues
Previously, pdb2gmx complained that the residue was
not available as a 'starting' terminus for isolated
residues (usually zwitterions). This is really confusing
when starting terminus residuetypes ARE available. Now
we properly explain there is no type to use the residue
isolated.
Change-Id: I0c9c8328f12e75a5a7ffaa8ea894ff46f8fdfe75
Justin Lemkul [Thu, 27 Dec 2012 05:06:50 +0000 (00:06 -0500)]
Minor fixes to g_angle help description.
A few grammatical tweaks and removal of an ambiguous sentence to make
the help description somewhat clearer and more generally applicable.
Change-Id: Ibd2e8a9f43fd81cc1905f06f075f2e43b68bebab
Alexey Shvetsov [Mon, 14 May 2012 17:01:39 +0000 (21:01 +0400)]
[tools] g_sans - add trajectory avereging
This change adds
1. trajectory averaging for s(q) and p(r)
2. can compute s(q) and p(r) for each frame
Change-Id: Ieb421a8b5ae06b72442bbe5fbae4231a7fa9c980
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Mark Abraham [Wed, 19 Dec 2012 21:16:21 +0000 (22:16 +0100)]
New beta release: 4.6-beta3
Change-Id: Ibee5545fa0c45cf97486ca25ff7449b9ee0c0d3a
Christoph Junghans [Mon, 17 Dec 2012 18:47:39 +0000 (11:47 -0700)]
cmake: mark FFTW_HAVE_{SIMD,AVX} as advanced
Change-Id: Id31f15e4a92722daa3b59fbbc909b8ac6ddc38ce
Roland Schulz [Fri, 21 Dec 2012 04:26:01 +0000 (23:26 -0500)]
Add missing visibility exports
For template and for double
Also: fix define symbol for gpu libs
declare of MPI_Wtime
Change-Id: Iba1a0c6e5ec74739c00b20d43a577813228e3f2d
Christoph Junghans [Fri, 21 Dec 2012 17:45:29 +0000 (18:45 +0100)]
Merge "Remove non-functional compiler override for MacOSX." into release-4-6
Erik Lindahl [Thu, 20 Dec 2012 14:41:19 +0000 (15:41 +0100)]
Fixed gmx_cpuid not working on non-x86
Added x86-specific #ifdefs around calls to x86-specific routines.
The cpuid calls should now correctly return 'unknown' for everything
on other platforms. Fixes #1075.
Change-Id: Id0dfcb2fd944ea37b176efb9978ccedfc00e06e9
Teemu Murtola [Thu, 20 Dec 2012 20:42:35 +0000 (22:42 +0200)]
Make gmx_cpuid.h self-standing.
The header should now compile irrespective of include order.
Change-Id: I0358b818cdb02ee8a948abc57eed5c4b1a8fdf3c
Roland Schulz [Fri, 21 Dec 2012 06:34:09 +0000 (01:34 -0500)]
Ignore bool cast warning for MSVC and C++
We have been ignoring this warning for C++ in master for a while.
No need for it for the GPU code either.
Change-Id: Ib76541d344dc520d5a14da241b29d92362311980
Teemu Murtola [Fri, 21 Dec 2012 05:38:41 +0000 (07:38 +0200)]
Remove non-functional compiler override for MacOSX.
As discussed in #1021, at least with CMake 2.8.9 this does not work, so
it only causes confusion. A better solution can be implemented if
identified in #1021 discussion.
Related to #1021.
Change-Id: Iec704dcae65cd7a213cf31861a262ac0b2763474
Szilard Pall [Thu, 20 Dec 2012 23:36:31 +0000 (00:36 +0100)]
fix incorrect gmx_fatal argument order
The format specifiers did not match the argument order.
Change-Id: Ib58892f4b0e09d7c3d3442a88f0bda98ea4b54b9
Erik Lindahl [Thu, 20 Dec 2012 22:29:27 +0000 (23:29 +0100)]
Merge "cmake: added option to disable quotes" into release-4-6
Erik Lindahl [Thu, 20 Dec 2012 22:28:37 +0000 (23:28 +0100)]
Merge "Small fix for g_tune_pme" into release-4-6
Erik Lindahl [Thu, 20 Dec 2012 22:26:49 +0000 (23:26 +0100)]
Merge "Fixes for andersen temperature control" into release-4-6
Erik Lindahl [Thu, 20 Dec 2012 22:25:59 +0000 (23:25 +0100)]
Merge "Fixes for expanded ensemble and HREPEX" into release-4-6
Christoph Junghans [Thu, 20 Dec 2012 21:07:45 +0000 (22:07 +0100)]
Merge "Fixed AVX256 double-precision kernels for gcc" into release-4-6
Christoph Junghans [Wed, 19 Dec 2012 17:50:27 +0000 (10:50 -0700)]
cmake: added option to disable quotes
Change-Id: Ia1793f3d3dddb3a08012723c2279cab51fa1eafa
Michael Shirts [Sat, 15 Dec 2012 16:50:52 +0000 (11:50 -0500)]
Fixes for andersen temperature control
First, fixes a bug introduced in the merge that
caused the same random seed being used on all nodes, resulting
in correlated velocities in the kinetic energy, and thus an
incorrect distribution of total kinetic energy because of correlations
between particles.
Also fixed another bug caused during merge that resulted in andersen
not being applied when there were no constraints.
Change-Id: If6b857bf3d3b9345c18d0680fdba0f65a4860a7e
Michael Shirts [Mon, 10 Dec 2012 02:50:10 +0000 (21:50 -0500)]
Fixes for expanded ensemble and HREPEX
Various other fixes broke expanded ensemble and Hamiltoian
replica exchange. These changes restore functionality.
Change-Id: Iae9def3838a5b90f1efee1fb0598441e0af6cce3
Erik Lindahl [Thu, 20 Dec 2012 14:05:42 +0000 (15:05 +0100)]
Fixed AVX256 double-precision kernels for gcc
Gcc is pickier with memory alignment and implicit conversions than
either clang or icc. This patch makes sure we align tables to 32-byte
boundaries (16 before), and uses explicit casts to make gcc happy.
Fixes redmine #1074.
Change-Id: I613d49dad74597ce6167e18fd3a048254bc1b859
Michael Shirts [Sat, 1 Dec 2012 19:55:47 +0000 (14:55 -0500)]
Fix for the pressure in MTTK with constraints + dispersion
Fix for pressure in MTTK - broken at some point in the
merge process. The MTTK+constraints code definitely needs to
be simplified for 5.0, it's too easy to break on code rearrangements
right now!
Testing with simple systems over long time shows that the pressure is
unbiased, while the PR pressure is off by a factor of 1/N (which is totally
fine for most realistic systems).
Fixes redmine bug #1061
Change-Id: Ie82cf8d6bdeb3e47db044ae34fc42c077ad73c75
Carsten Kutzner [Thu, 20 Dec 2012 12:20:28 +0000 (13:20 +0100)]
Small fix for g_tune_pme
Setting the "-err" command line flag in g_tune_pme would, in combination with the "-launch" flag
prevent a proper launch of mdrun after tuning since "-err" would also appear on the mdrun
command line. This patch removes the "-err" switch from the mdrun arguments list.
Change-Id: Idb2e3cf2e4eca587180b932faccc227be171b3d7
Carsten Kutzner [Tue, 18 Dec 2012 15:55:49 +0000 (16:55 +0100)]
Essential dynamics: fixed restarts when ED group has > 1 molecule
To ensure proper restarts when the ED group consists of more than a
single molecule, the PBC-correct positions of the ED group are now
stored in the checkpoint file.
Change-Id: Id87bee610ad248f8695927d0027254e7d6d4c677
Berk Hess [Thu, 20 Dec 2012 09:09:59 +0000 (10:09 +0100)]
fixed recent bugs in LINCS for derivatives
The LINCS projection code, do_lincsp, working on derivatives
got OpenMP parallelization in
6585fa01, but this introduced bugs.
The constraining of derivatives of the coordinates has now been fixed
and the lambda derivatives have been added again.
Also constraining of forces now works with OpenMP.
Change-Id: Idc5516ec0e9d994a86cf8acdc7480502c8dcac1d
Mark Abraham [Wed, 19 Dec 2012 17:47:27 +0000 (18:47 +0100)]
Merge "Remove the rest of the fortran/power6 acceleration" into release-4-6
Mark Abraham [Wed, 19 Dec 2012 17:30:20 +0000 (18:30 +0100)]
Merge "Always build template program" into release-4-6
Mark Abraham [Wed, 19 Dec 2012 14:10:56 +0000 (15:10 +0100)]
Fix Reference build type
This typo led to the Reference build claiming it was not building
for thread-MPI, but actually it did. Pity we don't have a CMake
syntax checker.
Change-Id: I932794145471451e09028297cfbffa4a72e96f39
Szilárd Páll [Wed, 19 Dec 2012 14:38:23 +0000 (15:38 +0100)]
Merge "Avoid using undefined CMake variables" into release-4-6
Szilárd Páll [Wed, 19 Dec 2012 14:10:05 +0000 (15:10 +0100)]
Merge "Removed orphan file" into release-4-6
Roland Schulz [Wed, 19 Dec 2012 13:54:49 +0000 (14:54 +0100)]
Merge "Fix license text printed by programs." into release-4-6
Roland Schulz [Wed, 19 Dec 2012 13:49:59 +0000 (14:49 +0100)]
Merge changes Idc652236,If03cf569 into release-4-6
* changes:
renamed gmx_x86_simd_macros.h to gmx_simd_macros.h
implemented nbnxn AVX-256 2x(N+N) kernels
Roland Schulz [Wed, 19 Dec 2012 13:16:08 +0000 (14:16 +0100)]
Merge "issue error if GPU ID is provided with GPU acc. off" into release-4-6
Mark Abraham [Wed, 19 Dec 2012 12:19:51 +0000 (13:19 +0100)]
Removed orphan file
The use of this check was removed long ago, the bug report that
it cites is invalid, and its detection functionality is duplicated
in gmxGetCompilerInfo.
Change-Id: I8478e155376930c27d259214e13d9b1e6e7a9cca
Mark Abraham [Wed, 19 Dec 2012 12:04:52 +0000 (13:04 +0100)]
Avoid using undefined CMake variables
C_COMPILER_VERSION is not defined before CMake 2.8.8, so the logic
and reporting was wrong. However, we already have a work-around.
Change-Id: If34deadf3a912d48e204d80cc5be7718c151e39d
Christoph Junghans [Tue, 18 Dec 2012 23:22:23 +0000 (00:22 +0100)]
Merge "Fixes redmine issue #1071" into release-4-6
Szilard Pall [Mon, 17 Dec 2012 21:28:28 +0000 (22:28 +0100)]
issue error if GPU ID is provided with GPU acc. off
Manually setting the GPU IDs is an implicit "GPU on" request from the
user, so we need to fail if mdrun in compiled without GPU support.
Additionally, added hint to what content is expected in the GPU ID
string to the respective errors and changed an incorrect collective
fatal.
Change-Id: Iebce58c0626889d047eebebd8e4547d4f1e9ff26
Berk Hess [Wed, 12 Dec 2012 15:25:08 +0000 (16:25 +0100)]
renamed gmx_x86_simd_macros.h to gmx_simd_macros.h
This is in preparation for non-x86 SIMD acceleration.
Change-Id: Idc652236f4b2e0f48e759d579c798c1b0dc6944f
Berk Hess [Mon, 10 Dec 2012 17:20:24 +0000 (18:20 +0100)]
implemented nbnxn AVX-256 2x(N+N) kernels
With AVX-256 nbnxn kernels are faster with 2x(4+4)=4x4 than 4x8.
To reduce the number of nbnxn kernels, there are no longer both
simd128 and simd256 kernels, but simd_4xn and for AVX-256 additionally
simd_2xnn kernels. The nbnxn search code is simplified significantly,
as it no longer has 128-bit and 256-bit simd simultaneously.
The SIMD pair-search and kernel configuration is now separated from
the SSE SIMD bounding box code configuration.
Additionally the label x86_simd in all nbnxn files is replaced by simd
only, in prepartion for non-x86 SIMD acceleration.
Change-Id: If03cf569cf918dcec675fbcb43e1ff3a30528f74
Szilárd Páll [Mon, 17 Dec 2012 22:43:00 +0000 (23:43 +0100)]
Merge "reduced PLINCS communication with H-bond constraints" into release-4-6
Teemu Murtola [Mon, 17 Dec 2012 15:51:09 +0000 (17:51 +0200)]
Fix license text printed by programs.
Since source files are now licensed under LGPL, it doesn't make much
sense for the programs to indicate they are still under GPL.
Follow-up to I1c507b3, which seems to have missed this.
Part of #818.
Change-Id: I44ffcf75f4840326d09f924249619077ea5a1013