Mark Abraham [Mon, 31 Mar 2014 14:28:36 +0000 (16:28 +0200)]
Fix bug accumulating nrank_pp_intranode on PME ranks
The old code led to cr->nrank_pp_intranode=zero on PME ranks, which
meant that a command line of mpirun -np 4 mdrun -npme 2 on a two-GPU
node would fail, because gmx_select_gpu_ids() runs on all ranks, and
it calls limit_num_gpus_used() which thinks 0 PP ranks and 2 GPUs is
silly. Adding -gpu_id 01 works, of course, but that takes a different
code path in gmx_select_gpu_ids().
Change-Id: Iecd43ef9b71e2cc0339e93724b6b1071f0a159f6
Berk Hess [Tue, 3 Dec 2013 08:54:35 +0000 (09:54 +0100)]
Added LJ-PME and LJ Pot-switch to PME load estimate
Change-Id: I7f032fffb0a26d40914740c1180c4137c0b95653
Mark Abraham [Mon, 31 Mar 2014 16:11:33 +0000 (18:11 +0200)]
Re-use gmx_greatest_common_divisor()
Change-Id: Iee3a7b3bc339639360eed3498769efe64dd7dbf8
Teemu Murtola [Mon, 31 Mar 2014 18:20:05 +0000 (21:20 +0300)]
Move smalloc.h to utility/
One common header away from legacyheaders/.
Mostly mechanical replacement for the include paths, but removed a few
instances where the header was included more than once. Also, reordered
the headers a bit, mainly in C++ files.
Part of #1415.
Change-Id: Ic438d501ebf5eccc285655a9e8f2f625eb12f1d1
Teemu Murtola [Mon, 31 Mar 2014 17:26:26 +0000 (20:26 +0300)]
Remove #include <...> for local files in gmx-view
There were only a few remaining, and those don't seem to be necessary
for the headers that were including them.
Change-Id: I99c6663edc0e608fe349206d9a9ecdd2d61faea2
David van der Spoel [Mon, 31 Mar 2014 19:52:36 +0000 (21:52 +0200)]
Fixed compilation issue in fgrid.cpp due to int/enum
gcc 4.8 is somewhat more picky about enums, and this
patch fixes an issue where an enum variable was used
outside of the defined range.
Change-Id: Ibfd7720d1d3e575c45bc1d5dbd30daad6391400c
Mark Abraham [Mon, 31 Mar 2014 14:04:14 +0000 (16:04 +0200)]
Remove quote
"No gentleman wears a beard" would be ridiculous, and so is
the quote removed here.
Change-Id: Iac8aec72776dfe0147db15c32e7170004b168cab
Rossen Apostolov [Wed, 5 Mar 2014 16:12:05 +0000 (17:12 +0100)]
Added CMake support for Extrae.
Website of the project is http://www.bsc.es/computer-sciences/extrae
Change-Id: Ifc71637ae7fbe855f3879b19f0968e929a92daf0
Teemu Murtola [Sun, 30 Mar 2014 04:05:34 +0000 (07:05 +0300)]
Clean up smalloc.h
- Remove unused maxavail() and memavail().
- Remove unused scalloc().
- Remove srealloc(), which was only used in gmx_bar.c, and even there
incorrectly.
- Move scoped_ptr_sfree to a separate header (this also potentially
postpones issues that boost causes in CUDA code, since this is the
only part that currently was pulling boost into CUDA).
- Convert all documentation to Doxygen.
- Fix some system header dependencies that were previously covered
transitively, and fix some stylistic issues in the touched files.
Preparation for moving smalloc.h from legacyheaders/.
Change-Id: I89d6445799d818ccdb2bd93b6592eff1ccc618a7
Carsten Kutzner [Fri, 28 Mar 2014 14:23:35 +0000 (15:23 +0100)]
Fix documentation of swap/enums.h
Another issue picked up by the doxygen documentation checker.
Change-Id: Ieaad04e713bb045a018823d26983dea1d52b202f
Teemu Murtola [Thu, 27 Mar 2014 04:12:48 +0000 (06:12 +0200)]
Move some math headers away from legacyheaders/
- Move nrjac.* to linearalgebra/
- Move do_fit.* to math/
Also some minor associated clean-up.
Change-Id: I11943d5c9a0150133ca0a0d9bc36aceb06fb8bca
Roland Schulz [Thu, 6 Mar 2014 22:30:48 +0000 (17:30 -0500)]
Disable shared libraries by default for mdrun-only
Shared libraries don't have any advantage for mdrun-only
build.
Also, add warning that someone re-using a normal build tree for a
subsequent mdrun-only build may want to manage this aspect explicitly.
Documented all this behaviour in the install guide.
Change-Id: I65fad0df8e54003599544903276a2be0ac61bbc2
Teemu Murtola [Thu, 27 Mar 2014 04:22:49 +0000 (06:22 +0200)]
Remove dependency on commandline/ from oenv.cpp
This was unnecessary, and this simplifies the module dependency graph.
With some simple changes, oenv only needs to use
utility/programcontext.h.
Change-Id: I794b15cee88bf49379fd8c783672df5f57628c97
Teemu Murtola [Sat, 29 Mar 2014 13:20:49 +0000 (15:20 +0200)]
Clean up string2.h-related includes
- Remove unused split().
- Remove string2.h includes from files that were not using any function
from there.
- Remove unnecessary system headers from string2.h, and add them to
files where they are needed. Some transitive dependencies can be
left, since some headers actually require string.h etc.
- Add/remove ctype.h such that exactly those files that use functions
from it actually include it.
There can be a few files now that use ctype.h without including
string2.h, which may trigger warnings on Cygwin, but those can be fixed
if we get around to properly supporting and testing Cygwin.
Preparation for moving string2.h from legacyheaders/.
Change-Id: Id9c441d2159ac3f06e088d6d7e0f05ffadb450cb
Christian Wennberg [Tue, 11 Mar 2014 14:44:45 +0000 (15:44 +0100)]
Free-energy support for LJ-PME
Free energy calculations is now supported together with
LJ-PME.
Change-Id: I8f30bbf565d06bb10a5b6be37a3680fbd5cef6af
Teemu Murtola [Wed, 26 Mar 2014 04:35:44 +0000 (06:35 +0200)]
Optimize intermodule dependencies
- Move genconf from gmxana to gmxpreprocess. sortwater.* is used by
genconf and grompp, so moving them to the same place allows moving
these files as well, removing all dependencies between gmxana and
gmxpreprocess.
- Move utility/path.* to fileio/. This removes a cyclic dependency
between utility and fileio modules. Can be moved back if #950 gets
resolved such that nothing in path.h no longer depends on futil.h.
Change-Id: Ia81173d4845143dc3cc94e0c200cab96c87308a5
Teemu Murtola [Wed, 26 Mar 2014 19:44:26 +0000 (21:44 +0200)]
Improve version information handling
- Always use the same mechanism (a generated source file) to communicate
the version information from the build system to the source, even when
not using git to generate the info. This allows removing several
variables from config.h.
- Rename the generated file from gitversion.c to baseversion-gen.c to
better reflect its new role. Rename the header correspondingly.
- Add utility/baseversion.h to provide functions to access the version
information, and use the new functions in a few places that were using
copyrite.cpp only for GromacsVersion(). This removes some cyclic
dependencies and warnings from the new Doxygen checker.
- Make checkpoint.c use the full version string in the checking instead
of VERSION, which is now removed from config.h. It is anyways
checking also the build time, so it doesn't hurt even if the version
string is more specific.
Change-Id: Ie85bab434a5e8c7e4e1a72b0af726ea4ea1f8d6f
Teemu Murtola [Sat, 22 Mar 2014 20:16:51 +0000 (22:16 +0200)]
Better include dependency graph generator
Rewrite the include dependency graph generator to use the scripts used
for the doc-check target. Most of the graph generation code is still
the same as in the old includedeps.py (except for some renaming and
other cleanup), but it now uses the data structures in gmxtree.py as
input instead of custom parsing. Only real differences in the output
for now:
- The module graph colors nodes based on the group they are documented
in. All modules that don't have explicit documentation are now
marked as "legacy".
- The file graphs don't use clusters for subdirectories, but instead
only color tests differently. Not sure which one is clearer; the
answer may even depend on the module.
However, the new code is much cleaner and easier to extend than the old
one was, so improving the graphs further should be much easier now.
The generated graph is also laid out differently, but that may just be
by chance; because of existing cyclic dependencies, dot doesn't produce
stable layouts, and the layout can depend on the order of things in the
generated graph. Since the internal data structures are now mainly
dicts, stuff is likely in a different order than what it used to be.
doxygen.md now also has a bit more documentation for the graphs.
Change-Id: I0530c8e4278890fdb5b5d874bda6fef3521a704e
Carsten Kutzner [Fri, 28 Mar 2014 13:32:57 +0000 (14:32 +0100)]
Fix documentation issues for interactive MD module.
This patch fixes three warnings reported by Teemu's doxygen documentation
checker (gerrit.gromacs.org/#/c/3213/13). I additionally added a
\libinternal to the module_imd in imd.h to suppress an (empty) IMD module
from occurring in the user documentation.
Change-Id: I01324ec17692419274a605745716f25321d5d729
Christian Wennberg [Fri, 13 Dec 2013 10:49:56 +0000 (11:49 +0100)]
New VDW kernel flavour for LJ-PME and updated group kernels
Group-scheme LJ-PME now calculates the same properties as Verlet-scheme
The previous group kernels implemented the non-bonded interactions
as described in J. Chem. Theory Comput., 2013, 9 (8), pp 3527–3537,
These are now updated to subtract the grid contribution in real
space, which corrects for any difference in the reciprocal-space
part from the use of approximate LJ parameters.
Group kernels + LJ-PME now supports modifiers
Added a new interaction type "LJEwald" which is used in the
group scheme for simulations with LJ-PME.
Change-Id: I4c9394381bf813082afe1fdbc168659de2412da6
Teemu Murtola [Thu, 20 Mar 2014 18:21:32 +0000 (20:21 +0200)]
Move include dependency checks to doc-check
The new doc-check target now contains all the checks that were
previously in depcheck and doccheck. Remove the old targets.
Update the documentation to describe the new checker.
Change-Id: I3cd6b916507a9d21318914dbf88a8431b2a12149
Teemu Murtola [Mon, 3 Mar 2014 19:06:37 +0000 (21:06 +0200)]
Better automated Doxygen documentation checker
Add a completely rewritten checker to replace 'make doccheck'.
This is based on first generating and then parsing the Doxygen XML
output. It is somewhat slower than the old approach, but more robust
(exact format of the comments no longer matters) and allows relatively
easily checking all the documentation. As a side effect, the XML
extraction also makes Doxygen parse those comments that appear in
undocumented files, so that at least syntax errors in them can be
spotted from warnings (the checker can also check them otherwise, and
even warn about them getting ignored).
The new check can be run with 'make doc-check'. Not all functionality
from the old checker is available; documentation of the new checks in
doxygen.md follows when that is done, as well as some additional cleanup
of the code.
Currently, the new checker produces some warnings, which are suppressed
using suppressions.txt.
Short-term, this could be used to check for most common issues like
missing brief descriptions.
Medium-term, we could implement our own logic for enforcing what needs
to be documented, and disable all Doxygen-provided warnings about
undocumented members (by turning HIDE_UNDOC_MEMBERS=ON). This would
remove the need for most \cond directives.
Long-term, we could even consider generating some extra member listings
or such from the XML output, and/or use it to patch the HTML pages
generated by Doxygen such that they would be more useful for our uses.
Change-Id: I25262b28699e10547e2116a50d3a9d8d5aa966a6
Teemu Murtola [Tue, 25 Mar 2014 20:13:01 +0000 (22:13 +0200)]
Misc. Doxygen fixes
- Fix some issues in Doxygen-formatted comments that are currently
ignored by Doxygen. These were still causing warnings in XML
extraction.
- Document pargs.h, and make one function from there static as it is no
longer used outside the source file.
- Fix some other issues that the new Doxygen checker complains about.
Change-Id: I611ee3f9dbaf8a4406b4cba1f8b29aee5b5a4843
Teemu Murtola [Tue, 25 Mar 2014 04:10:31 +0000 (06:10 +0200)]
Move thread_mpi to src/external/
Now that thread-MPI headers are no longer installed, the whole thing can
be easily moved to src/external/, which better resembles its status
until it is decided what we really want to do with it. There, it is
excluded from checks that are done for other parts of the source, as
well as from Doxygen, removing the need to treat it specially in all
these cases.
This also removes a large number of headers from legacyheaders/ with a
relatively simple change, advancing this effort.
Related to #1411.
Change-Id: I64d202eb61dc2c61668ad5858d551add6578cb97
Mark Abraham [Wed, 26 Mar 2014 21:22:00 +0000 (22:22 +0100)]
Fix use of inline in IMD
Change-Id: I2390f7df2becb260d1a4f8c4ad74676c997e9437
Daniel Landau [Mon, 24 Mar 2014 16:01:22 +0000 (11:01 -0500)]
Add Cray compiler support
* Add support for SIMD intstructions with the Cray compiler with
-hgnu. This is a general GNU compatibility mode so there
also has to be a guard in the atomics section in threadMPI.
* Add support for atomics with the Cray compiler.
* Add Cray compiler support for cycle counting.
* OpenMP detection for the Cray compiler in CMake before
version 3.0 is broken, so refuse to proceed with that
combination.
Change-Id: I1209f3a61ed1d4d49e56dacbb315235088c5eea6
Carsten Kutzner [Tue, 25 Mar 2014 16:56:36 +0000 (17:56 +0100)]
Documentation house-keeping in file swapcoords.c
Modified Doxygen documentation of functions such that they now have
\brief descriptions. This way, Teemu's automated Doxygen documentation
checker won't complain about many missing brief descriptions in that
file. I am not making this patch dependent on the documentation
checker (gerrit issue #3213) because the brief descriptions should be
there anyway.
Change-Id: I4fc2c9de17b5ce8e9abdcd8fc51d002a245fbf2a
Martin Hoefling [Thu, 7 Jun 2012 11:07:21 +0000 (13:07 +0200)]
Interactive Molecular Dynamics (IMD)
IMD allows to interact with and to monitor a running molecular dynamics
simulation. The protocol goes back to 2001 ("A system for interactive
molecular dynamics simulation", JE Stone, J Gullingsrud, K Schulten,
P Grayson, in: ACM symposium on interactive 3D graphics, Ed. JF Hughes
and CH Sequin, pp. 191--194, ACM SIGGRAPH). The user can watch the
running simulation (e.g. using VMD) and optionally interact with
it by pulling atoms or residues with a mouse or a force-feedback
device.
Communitcation between GROMACS and VMD is achieved via TCP sockets
and thus enables controlling an mdrun locally or one running on a
remote cluster. Every N steps, mdrun receives the applied forces from
the VMD client and sends the new positions to VMD.
Other features:
- correct PBC treatment, molecules of a (parallel) simulation are made
whole (with respect to the configuration found in the .tpr file)
- in the .mdp file, one can define an IMD group (including the protein
but not the water for example is useful). Only the coordinates of
atoms belonging to this group are then transferred between mdrun and
VMD. This can be used to reduce the performance impact to an almost
negligible level.
- adds only two single-line function calls in the main MD loop
- and mdrun test fixture checks whether grompp and mdrun understand
the IMD options
Change-Id: I235e07e204f2fb77f05c2f06a14b37efca5e70ea
Teemu Murtola [Mon, 24 Mar 2014 15:44:30 +0000 (17:44 +0200)]
Remove gmxpreprocess from include path
One step closer to the final goal of only having src/ there.
This wasn't even necessary except for a few rare cases.
Also cleaned up the cppcheck rules slightly.
Change-Id: Ifc65fbb48699d0e4bb5c55b90a2c41b0255d353d
Mark Abraham [Sat, 22 Mar 2014 17:21:15 +0000 (18:21 +0100)]
Keep CMake quiet about non-detection of optional stuff
Repeated calls to cmake would otherwise warn every time that these
optional things were not detected. That lack is only rarely a problem
that needs solving, so they should not be emitting status messages all
the time.
Change-Id: Iad6f0bdf72ba7848bcc819db6937b70b37900148
Mark Abraham [Sun, 23 Mar 2014 11:00:07 +0000 (12:00 +0100)]
Merge branch release-4-6
Change-Id: Ie4431fb0002cd36799c8e664dcf4e096e66bc0ea
Berk Hess [Mon, 17 Mar 2014 15:48:53 +0000 (16:48 +0100)]
Fixed bug in parallel v/f constraining
Constraining v or f with 3 or more decomposition domains in one
or more dimensions could lead to modification of communicated
v and f components by the box size for inter charge-group constraints.
Fixes #1462
Change-Id: Idece9d2d0d8f48e65a654d5c2892fbe1ff836ba0
Berk Hess [Wed, 12 Mar 2014 07:23:19 +0000 (08:23 +0100)]
CUDA cut-off kernels now shift exclusion energies
This is to make the GPU kernels consistent with the CPU nbnxn
kernels, which for eeltype=cut-off modifier=potential-shift
effectively do reaction-field with epsilon_rf=1.
Also implemented shifting of the Coulomb potential for the group
cut-off scheme for non-excluded pairs only.
The manual now explains these details.
Also fixed the generic group kernel with an exact cutoff for
either Coulomb or VdW. I think this was supposed to not be supported
but neither grompp nor mdrun checked for this. The fix is trivial.
Change-Id: I48bff73587e43338162f90fa7d526e1909ce5ad1
Mark Abraham [Sat, 15 Mar 2014 09:40:32 +0000 (10:40 +0100)]
Fix print_date_and_time
The old call signature and lack of documentation of this function made
it easy to misuse, and (e.g.) mdrun was reporting the same initial and
final time stamp. Fixed signature and documented.
Change-Id: Ib4d9a07bc6e1165affa3bfdf7cd3b54c615d4765
Roland Schulz [Fri, 7 Mar 2014 00:28:39 +0000 (19:28 -0500)]
Fix dependencies on config.h for typedefs.h
The include in simple.h hid other dependencies and was only
used for gmx_inline and gmx_restrict. Defining those
in just one place simplifies it.
Also fix missing includes in public headers.
All public headers should be able to be compiled by themselfes
and shouldn't rely on other headers aready being included.
Also fixes that math module headers were installed to maths.
thread-mpi headers and commrec.h are not installed anymore.
The installed headers have no dependency on GMX_LIB_MPI and
GMX_THREAD_MPI anymore.
Change-Id: Ie1f26913739d3e42d653a51fa2c2d71e6ea3ef7a
Mark Abraham [Wed, 12 Mar 2014 15:19:14 +0000 (16:19 +0100)]
Revert "Added new amber99sb-ildn-bsc0 force field."
This reverts commit
3f7bdff15b41f7e0ffbfd0bf86b9c677ae51db77.
This is a temporary measure, pending testing of this variant
that is comparable with that for other AMBER forcefields, and/or
resolution of questions raised on gmx-developers.
Also removed line from the manual that was generated when this force
field was in the repo.
Change-Id: I1c2269d2ed554b827fb183d54f1db789a5762a8f
Christian Wennberg [Thu, 13 Mar 2014 16:31:53 +0000 (17:31 +0100)]
Renaming in PME-routines
Fixes naming issues in PME-routines by renaming variables
and functions to be more general, and not using names specific
to electrostatics
Fixes #1459
Change-Id: I7abb624b9f3d31e247404007dbe5d9c4e475687e
Christian Wennberg [Wed, 12 Mar 2014 14:27:21 +0000 (15:27 +0100)]
Bugfix in LJ-PME without electrostatics
Simulations using cut-off for electrostatics, and
PME for LJ resulted in segfault since pme.c tried
to access non-existing grids.
Change-Id: Ic32c8cd2eb6afb3e49265d6c9a7da81418b18dca
Mark Abraham [Tue, 11 Mar 2014 08:37:20 +0000 (09:37 +0100)]
Removed more stuff related to gmx.ff and gmx2.ff
Code and documentation no longer refers to these force fields. There
are corresponding changes to examples in the manual.
Updated list of force fields in the manual, plus minor correction
to description of CHARMM27 there and in the forcefield.doc.
It would be nice to leave gmx2?.ff/forcefield.itp intact with an error
message, but this means gmx pdb2gmx continues to show these force
fields. Instead, I made a README to note that these force fields have
gone.
Change-Id: I10480a0fad169493d13a743c43e8b2321128155d
Teemu Murtola [Fri, 14 Mar 2014 18:19:55 +0000 (20:19 +0200)]
Remove interactive help from core selection parser
The help is now handled in the loop that processes user input, and it
never gets into the parser itself. This removes several special cases
from the parser and simplifies it.
Add a few string utilities and tests for them to make it easy to handle
the help commands.
Change-Id: Ida58bccd3b9ced4b7060485cc2f064b73796c996
Teemu Murtola [Wed, 12 Mar 2014 19:47:42 +0000 (21:47 +0200)]
Improve interactive selection input
- Print the static index groups always at the start of the prompt.
- Add a hint for that an empty line provides information about the
available index groups.
- Print the whole prompt again after an empty input line.
- Print only the selections from the current interactive prompt in the
output. This makes the listing clearer for commands like
gmx sasa -surface -output
when providing the latter set of selections interactively.
- Print the number of selections still required after the above list.
- Work better (on Unix) if stdin is from a pipe (using the same
mechanism that was there in 4.5 and 4.6).
Change-Id: I38152fb4fccd142aeee318739ab3782fa6a775d8
Rossen Apostolov [Fri, 7 Mar 2014 18:14:03 +0000 (19:14 +0100)]
Cleaned up endif/else-s in CMakeLists.txt and *.cmake files
Removed FindBLAS/LAPACK.cmake files which come anyway with
CMake > 2.8.8. Included properly the licenses in some of the
BlueGene*.cmake files.
Change-Id: I69d68566865facf0af759526a579f32c5c444464
Mark Abraham [Mon, 17 Mar 2014 17:46:59 +0000 (18:46 +0100)]
House-keeping for MTTK
Leapfrog + MTTK silently produced a .tpr that is probably broken;
certainly the documentation only states support for Velocity-verlet
integrators.
Added note about deprecation and planned removal of MTTK + constraints.
Refs #1292
Change-Id: Iec2cf0dd866242735ce04a954e585b2461f6e701
Mark Abraham [Mon, 17 Mar 2014 17:06:04 +0000 (18:06 +0100)]
Merge "Merge branch release-4-6"
Mark Abraham [Fri, 14 Mar 2014 18:08:48 +0000 (19:08 +0100)]
Merge branch release-4-6
Conflicts:
src/gromacs/pulling/pull_rotation.c
Adopted the bugfixes from release-4-6
Uncrustified incoming code
Change-Id: I7d90bb49ef83750b9607f677e97a94f2b5793eeb
Mark Abraham [Sun, 16 Mar 2014 12:05:28 +0000 (13:05 +0100)]
Fix perturbation to Verlet scheme when not perturbing
A .top that has B-state parameters for non-bonded interactions
should run the same with free-energy = no as a .top that has no
B-state parameters. Renamed variable to better reflect its use,
and used it to correctly trigger the FEP code path.
Change-Id: I47656b29ef4ca2462af0fb587e0424d0eab3d5c4
Teemu Murtola [Sat, 15 Mar 2014 05:00:41 +0000 (07:00 +0200)]
Update manual analysis section
- Reference tools as 'gmx <tool>' instead of the old names.
- Expand the section on selections now that there actually are some
tools that can use the full power.
- Rewrite sections that were referencing obsolete tools (g_bond and
g_sgangle).
- Remove references to tools that aren't there.
Change-Id: Iee99f69e2d4effa585d98930ef1d78c1367e2ec0
Erik Lindahl [Sun, 16 Mar 2014 09:13:11 +0000 (10:13 +0100)]
Use a constant instead of sizeof(int) for SSE2 immediate constant.
Apparently gcc-4.8.2 was not able to evaluate sizeof(int) to the
constant 4 at compile time, but thought it was either a 64-bit
value or a non-const value. Since the register sizes are fixed
we simply hardcode the value 4 bytes instead.
Change-Id: If739b733727b032eb7e5b7fa0a75e7cd51989a0b
Carsten Kutzner [Wed, 12 Mar 2014 15:14:04 +0000 (16:14 +0100)]
Avoid cross product with zero vector in rotational pulling.
Fixes #1431 (rotation/flex-t regression test failing on BG/Q)
In do_flex_lowlevel() we checked (by mistake!) for xj-xcn being
zero, although we need to check for yj0-ycn being zero, since
we use yj0-ycn in a cross product in the following lines of code.
I now also replaced the direct check (0 == norm(...)) by checking
what gmx_numzero(norm(...)) returns. The latter replacement
was also applied in the do_flex2_lowlevel() routine. Note that there
the check for small xj-xcn was and is actually correct.
Change-Id: I972b6d67a81e30f297db286cd2224f66753a20aa
Carsten Kutzner [Fri, 14 Mar 2014 10:27:36 +0000 (11:27 +0100)]
The van der Waals radius must equal the Coulomb radius with Verlet
This patch fixes an issue that can occur when using g_tune_pme
with a Verlet pair-list .tpr input file. If the .tpr itself has
large cutoffs (e.g. 1.2 nm) and one asks g_tune_pme to scale
_down_ the Coulomb radius, the van der Waals radius is not
scaled down with the Coulomb radius (only upscaling worked).
One ends up with an unusable .tpr file because rVdW != rCoul.
This patch ensures that van der Waals and Coulomb radii
are always equal with Verlet pair-lists. Fixes #1460. Thanks
to Joao Rodrigues for reporting the issue!
Change-Id: I5ef30e71a35cd83838040057e16e52e09ea82e9a
Christoph Junghans [Tue, 11 Mar 2014 16:31:22 +0000 (10:31 -0600)]
Install enums.h
Related to #1452
Change-Id: I94db8d0f9661b7398e5924f4adefbfdcc82da483
Mark Abraham [Thu, 6 Mar 2014 17:42:31 +0000 (18:42 +0100)]
Fix MKL linking
Setting the same for CMAKE_STATIC_LINKER_FLAGS broke because that
variable got applied to calls to ar for linking libgmock.a. Probably
not important because Intel probably encourages shared linking for
MKL.
Change-Id: I6816d8ba318c704a0efad7659f5afecaeb48b092
Mark Abraham [Wed, 26 Feb 2014 14:58:50 +0000 (15:58 +0100)]
Avoid array-bounds warnings with gcc 4.8.2
The asserts fix RelWithAssert build and for Relase
build the warning is suppressed.
Change-Id: I0a7e6576014bd32648a1e2f08d88e1f2eef3335e
Rossen Apostolov [Thu, 20 Feb 2014 15:48:29 +0000 (16:48 +0100)]
Removed .itp files from top level directory.
There is no need for these files, the water models
should be included from the corresponding .ff directory.
Since many users are likely to still use those files,
an error message is printed.
Also re-added ions.itp and treated it similarly.
Also update an integration test that was using a one of the top-level
water .itp files that is now removed.
Change-Id: I599e203329340587afa7fc5efced485d09b9ce1c
Roland Schulz [Sat, 1 Mar 2014 06:43:37 +0000 (01:43 -0500)]
Simplify gmxTestLibXml2
Change-Id: Ia652633f529cc1cf6ba09e29159025ff762efad2
Berk Hess [Fri, 28 Feb 2014 22:03:09 +0000 (23:03 +0100)]
PME load balancing now works with LJ-PME
PME load balancing only works with LJ-PME when PME is also used
for electrostatics.
Change-Id: I7145b242fd5dd00690e6b789b9cc6f3e147d430b
Teemu Murtola [Sat, 8 Mar 2014 11:10:34 +0000 (13:10 +0200)]
Fix misc. Doxygen issues
- Fix some missing brief descriptions.
- Fix some function definitions so that Doxygen correctly pairs them
with the corresponding declarations.
- Fix some documentation visibility issues. Not all these are strictly
required, in particular in the SIMD parts, where \cond is used to
exclude full classes. But the presence of \cond is
difficult/expensive to test automatically.
- Also some misc. other fixes.
- Document some of these issues better on the Doxygen page.
- Exclude parser.h from Doxygen, since it doesn't contain any meaningful
comments, and confuses Doxygen at least with the XML output.
Also, explicitly list input file extensions for Doxygen.
This excludes some random Python files from the documentation. At least
for now, we probably want to keep the documentation such that it applies
mainly to the C/C++ code, and not bother how to also document Python
code in a Doxygen-compatible way.
CUDA files are still left out, as they were previously, since they
currently produce several warnings.
Most of these were found by the current work-in-progress checker script.
After these, the checker mainly complains about a lot of missing brief
descriptions in thread-MPI headers and in swapcoords.c.
Change-Id: Ib8a492fde6327ce3d814a23d887b05323bd6d334
Roland Schulz [Fri, 7 Mar 2014 08:38:35 +0000 (03:38 -0500)]
Don't disable MSVC warnings in config.h
All other warning flags are passed as compiler flags, thus this
was inconsistent. Also didn't work correctly if source file
doesn't include config.h.
Also makes ICC warning flags consistent between Linux and
Windows.
Change-Id: Ic52f6eb3c2dc5751b8aac1bba836ad5ff7d7c3cf
Roland Schulz [Sun, 9 Mar 2014 01:00:49 +0000 (20:00 -0500)]
Fix CheckCXXCompilerFlag
ICC on Windows was always failing the CheckCXXCompilerFlag.
This was caused by the warning:
LINK : warning LNK4224: /INCREMENTAL:YES is no longer supported; ignored
being matched by the compiler fail_regex for aix because of a missing
escale for the semicolon. A single escape isn't sufficient. Using double
escape ("\\\;") doesn't produce this problem, but I'm not sure whether it
always matches correctly thus instead a "." is used (works because it is
a regex). This fix doesn't address either the fact that the deprecated
linker flag is used nor does it address the problem that if incorrect
flags are somehow added (either by cmake or the user), this macro
fails without a diagnosible error message or fatal error (to notice it).
Change-Id: Ia45d6cd4fbf4f464bcb03e0d945085987a97aaad
Szilárd Páll [Fri, 28 Feb 2014 12:21:39 +0000 (13:21 +0100)]
Bump required CUDA version to 4.0
- Added warning with CUDA 4.0;
- Fixed some typos in comments;
- Fixed the comment referring to GPU code generation with CUDA v5.0+.
Fixes #1382
Change-Id: Iee182ace765022fc6a179531d42e965594cff104
Roland Schulz [Fri, 7 Mar 2014 06:06:41 +0000 (01:06 -0500)]
Replace inline with gmx_inline
We always try to avoid defining std names in our headers.
Thus we shouldn't define inline for those C compilers (=MSCC)
which don't have it.
Change-Id: Ia2023435c916892cdaf2ce97905b55ec10cd1a08
Mark Abraham [Sun, 9 Mar 2014 21:02:30 +0000 (22:02 +0100)]
Fix dependency on swapcoords enums
state.h needs these enums, but it seems wrong to introduce
a header dependency on the whole enums.h, when so few places need
these enums at all.
Change-Id: Ia8f080d5c0dc73b19a54f5ff77fbf7ef76f16139
Teemu Murtola [Sat, 8 Mar 2014 11:27:59 +0000 (13:27 +0200)]
Remove some unnecessary declarations
- topexcl.h was an outdated copy of gpp_nextnb.h, and wasn't used
anywhere. Rename the source file to gpp_nextnb.c to match the header.
- Remove one declaration from gpp_nextnb.h, which wasn't used outside
the source file. Make it static in the source file.
- Remove duplicate declarations of (init|done)_top().
- Remove unused create_visibility() from src/programs/view/.
Change-Id: I87982e5581aff8caca3dc753492e01ee457ab694
Roland Schulz [Thu, 6 Mar 2014 07:46:51 +0000 (02:46 -0500)]
Remove KERNEL_WIDTH
Wasn't used anywhere
Change-Id: I579297d71225ba3c0360f8419856b0f5e72a4b5a
Rossen Apostolov [Thu, 20 Feb 2014 15:34:45 +0000 (16:34 +0100)]
Removed the deprecated gmx.ff and gmx2.ff.
There are still a few places in the manual that need to be fixed.
Change-Id: I5c265470c1b73cb755918c5a000208da3d1e7b22
Mark Abraham [Thu, 6 Mar 2014 13:51:16 +0000 (14:51 +0100)]
Fix formatting in install guide
Change-Id: I28833dee21220aacbf06ccc7d06f8f5e6a328352
Mark Abraham [Tue, 4 Mar 2014 15:18:48 +0000 (16:18 +0100)]
Fix CMake syntax error
Change-Id: I8a39e50a741a23da3640fe7ccbcd83c844bf0d69
Roland Schulz [Wed, 5 Mar 2014 06:34:53 +0000 (01:34 -0500)]
Use gmx_int64_t for gmx_off_t
We anyhow require 64-bit file support and 64-bit integer
support. Thus the defintion of gmx_off_t can be dont
trivially.
Partial fix for #1452
Change-Id: I6ae70454cfa8ace3ca84a047149b6f4648e84b00
Berk Hess [Tue, 4 Mar 2014 12:01:19 +0000 (13:01 +0100)]
Fixed exit with FEP with PME nodes without LJ-PME
With FEP runs with separate PME nodes without LJ-PME, mdrun would
exit with a gmx_incons.
Reorganized the PME some flags and conditionals for clarity.
Change-Id: I04513a2d84682617b36c0c8ad4afe632ce3f7ee1
ngoga [Tue, 25 Feb 2014 16:27:29 +0000 (17:27 +0100)]
Martini CG - Combined angle-torsion potentials
- Potential important for Martini
- Most Important diffence: bondfree.c
- Rest of files: definition of types
- Different MD groups want to have it
- Avoid the numerical instabilities
of having three beads in a row and
therefore an undefined dihedral
angle. This might not happen easily
at the atomistic level, but for coarse-grain
models this is a real pain.
- Paper at
http://md.chem.rug.nl/~monica/Bulacu_Marrink_2013.pdf
Adopted new tpx_version scheme.
Paper published.
Change-Id: I8ed470c464d843eb0218c87aeea3a44c3a1f64f8
David van der Spoel [Wed, 5 Mar 2014 20:08:18 +0000 (21:08 +0100)]
Six new quotes from classic literature.
Change-Id: Id881baea8d6eeedc70dec3975a4c3e20e788285a
Roland Schulz [Sun, 2 Mar 2014 19:40:47 +0000 (14:40 -0500)]
Add RelWithAssert build type
Works mostly like Release just without -DNDEBUG.
Also generalized some machinery for managing compiler/linker flags so
that we can have an easier time later when we reconsider how to manage
all of our build types.
Also minor corrective changes to the behaviour of other build types.
Change-Id: I70283cb6069cb772c287c0aef329d95b8eacd987
Roland Schulz [Wed, 5 Mar 2014 07:34:17 +0000 (02:34 -0500)]
Remove dependency on TNG in trxio.h
Partial fix for #1452
Change-Id: I59474ea08d40362fa9d10745a5fb1d4e12254b68
Roland Schulz [Thu, 27 Feb 2014 06:41:41 +0000 (01:41 -0500)]
Report MIC SIMD correctly
Avoid cmake warning because SIMD cannot be detected. And
avoid that version information prints "None". This is
needed because MIC doesn't use GMX_SIMD so that the same
setting (__MIC__) can be used both for native and (future)
offload.
Also added installguide section.
Change-Id: I4af3b13678aa5c3c69c60bda499c3691ac83dc53
Mark Abraham [Wed, 5 Mar 2014 06:23:00 +0000 (07:23 +0100)]
Merge "Merge release-4-6 into master"
Berk Hess [Fri, 28 Feb 2014 11:37:29 +0000 (12:37 +0100)]
Buffer estimate now works with rvd-switch=0
With rvdw-switch=0, the Verlet buffer estimation code would divide
by 0. The estimate for vdw-switch functions now use the exact 3rd
derivative of the potential at the cut-off iso estimating the 2nd.
grompp now prints a note with rvdw-switch < 0.5*rvdw.
Updated estimate formula in the manual and added a missing factor
of 2 (the code did use the factor of 2).
Change-Id: Ia259d703515f69b0ed3390e2f7be671e0a15bd5f
Roland Schulz [Thu, 27 Feb 2014 05:53:18 +0000 (00:53 -0500)]
Check zlib can actually be linked
Only use zlib compression in tng if zlib can really be linked.
This is equivalent to
ee26e1264 for libxml2.
It is slightly simpler than the approach in gmxTestLibXml2
and CheckLibraryExists could be used there too.
This does not detect potential linking errors with shared
libraries similar to those solved in #740 for FFTW.
Fixes #1435
Change-Id: I5009e50b6caf810a12e71ecd83bde2edb21a2b32
Roland Schulz [Mon, 3 Mar 2014 23:22:31 +0000 (18:22 -0500)]
Avoid segfault when comparing tpr
Segfault was possible if number of idef didn't match
Change-Id: I62315e3340eec8acf14c01d14917392bc63e46e0
Mark Abraham [Sun, 2 Mar 2014 16:53:40 +0000 (17:53 +0100)]
Add enum and docs for using tpx_version
Documented procedure for having hassle-free feature branches and
ensuring merges into main branch cannot silently cause problems.
Added an enum to make the process work smoothly.
Change-Id: I69b87f9bac0b51784e70f8a618808ef086951343
Roland Schulz [Mon, 3 Mar 2014 20:31:54 +0000 (15:31 -0500)]
Merge release-4-6 into master
Conflicts:
admin/installguide/installguide.tex
3643d2a Add fatal error for Andersen+constraints+DD ignored
because already in master.
Change-Id: I6b3346503036e5b31bcc929daa5bcc9a04dde3bc
Mark Abraham [Mon, 3 Mar 2014 16:34:53 +0000 (17:34 +0100)]
Fix calling SIMD group kernels
The #define of GMX_SIMD*_OR_HIGHER takes place in simd.h, which got
changed late in the evolution of the recent SIMD-module patch, in
order to reduce unwanted module dependencies. However, the explicit
dependency of the group kernel setup code on the SIMD module was not
added. (It seems that the dependency on the old SIMD macros.h was been
satisfied transitively.) In effect, this turned off group-scheme SIMD,
but the silent fallback to C kernels meant there was no red flag until
we got around to measuring performance.
Change-Id: I78842cb191f6188fe4188800399efd2ed99e5543
Teemu Murtola [Fri, 28 Feb 2014 04:33:59 +0000 (06:33 +0200)]
Fix incorrect grid cell size in g_sas -nopbc
Fixes #1445
Change-Id: I798fc8fe96608633f26d9a3500f83f39b44af008
Teemu Murtola [Sun, 12 Jan 2014 18:37:08 +0000 (20:37 +0200)]
Move default library path search to program context
The default library path search is now implemented in
CommandLineProgramContext, and accessible through the generic interface.
This provides the following benefits:
- All the magic for finding stuff from the binary path is in a single
place, under the commandline/ module, where it belongs.
- Code using the library path is now in C++, fixing some potential
buffer overruns and removing the need for some utility code.
- Programs using the Gromacs library can customize how the library data
files are found.
- PATH_SEPARATOR is no longer exposed outside path.cpp, encapsulating
this detail.
- The library path is only searched once during the execution of the
binary, reducing the amount of file I/O done if multiple data files
are accessed.
- The library path is printed in the startup header, making it explicit
where they are read (helpful in particular if there are problems with
it, or the user may have multiple installations). The GMXLIB
override doesn't currently affect this printout; maybe it should, but
I don't want to put the environment variable (and the support for
multiple directories) into the program context.
Change-Id: I4d099215ef7e1f269d4c7a42989835d980bc1566
Mark Abraham [Mon, 24 Feb 2014 16:31:07 +0000 (17:31 +0100)]
Add fatal error for Andersen+constraints+DD
This combination produced a temperature that was 6.5 degrees higher
than the same with one domain, for a 1ns PME lysozyme in water
simulation.
Change-Id: I9f80276c47de955a5053bcabb6fe7c9bfdceaf0e
Christoph Junghans [Mon, 3 Feb 2014 20:52:32 +0000 (13:52 -0700)]
switch ld_seed from int to gmx_int64_t
* allows more than 4,294,967,295 different seeds for ld
* tpx version bumped, used new style for magic version constants
* changed printf format strings to conform to new type
Change-Id: Id661ca331a100dc942ac978cc1b50cfdade09731
Szilard Pall [Tue, 25 Feb 2014 20:39:07 +0000 (21:39 +0100)]
Added CUDA LJ-PME nbnxn kernels
This change implements CUDA non-bonded kernels for LJ-PME introduced
in the Verlet scheme with 99029d.
The CUDA kernels implement geometric as well as Lorentz-Berthelot (LB)
combinations rules (unlike the CPU SIMD) mostly because even though PME
is very slow with LB, it is still beneficial to let the user offload the
non-bondeds to a GPU and potentially bump up the cut-off to further
reduce the CPU PME load.
Note that as now we have 120 kernels compiled for up to four different
target architectures, the nbnxn_cuda module takes a very long time to
build and can become the bottleneck during compilation. We will deal
with this later.
Change-Id: I819b59a8948da0c8492eac6a43d4a7fb6dc98354
Magnus Lundborg [Sat, 1 Mar 2014 11:39:22 +0000 (12:39 +0100)]
Bumped TNG to latest version.
Change-Id: Id3ca6c18c1f51640997829bd8ad251a7ca91d04f
Szilard Pall [Fri, 28 Feb 2014 21:11:08 +0000 (22:11 +0100)]
Improved CUDA non-bonded kernel performance
Some old tweak which was supposed to improve performance had in fact
the opposite effect. Removing this tweak and with it eliminating
shared memory bank conflicts it caused improved performance by up
to 2.5% in the force-only CUDA kernel.
Change-Id: I7fcb24defed2c68627457522c39805afc83b3276
Teemu Murtola [Mon, 27 Jan 2014 18:55:00 +0000 (20:55 +0200)]
Residual SIMD Doxygen improvements
- Add a link to the overview documentation from the module page.
- Remove some trailing spaces.
Some issues noted, but not fixed here:
- \nosubgrouping would make the file pages look more consistent, if it
worked for files...
- Some of the SIMD routines are not included in any named group, making
them appear separately at the end of the documentation.
- The list of members on the SIMD module page is exceedingly long,
making it hard to find things there. Would require some thinking on
how to best solve this.
Change-Id: I628f321172a3c3e8f4874e166c48e12763d1490e
Teemu Murtola [Mon, 27 Jan 2014 18:55:00 +0000 (20:55 +0200)]
Misc. Doxygen configuration changes
- Adjust Doxygen preprocessor behavior such that it actually parses
#ifdefs in the code. Otherwise, some parts of the SIMD code seemed to
get ignored.
- Extract static functions on all levels of documentation for
consistency (and we may end up with some static inline members in
public headers; currently at least vec.h qualifies).
- Remove unnecessary excludes now that VERBATIM_HEADERS=NO already
excludes the unwanted files.
- Some other minor cleanup.
- Move member groups higher up in the layouts, since they generally are
the most interesting part.
Change-Id: Iea04772628716ed12f44cd4465c2027f4670bfae
Teemu Murtola [Sat, 26 Oct 2013 05:25:28 +0000 (08:25 +0300)]
Convert gmx-sas to the C++ framework
An example of converting a non-trivial analysis tool to the new
framework. Most functionality is intact, but the command-line interface
is changed a bit. Changes in behavior:
- Writing a position restraint file is not implemented. Would not be
very difficult to add.
- Solvation free energy estimates are written into a separate file
instead of the main output file, and only if requested with an -odg
option.
- The calculation group is specified as a selection with -surface.
Can be a dynamic selection. The total area of this group is always
written out.
- There can be 0..* extra output groups, specified as selections with
-output. All can be dynamic, and must always be a subset of the
calculation group.
- There is no longer a separate concept of hydrophilic and hydrophobic
surface area. The user can trivially calculate such things by
providing two different output groups. The old hydrophobicity
definition is easily expressed as "... and charge {-0.2 to 0.2}".
- tpr file is no longer required for most of the output.
- Output precision is different from the old tool. The current
precision (fixed to three decimal places) should be sufficient for
most uses, but it could be considered to use %g for formatting like
the old tool if really necessary.
Future TODOs:
- Consider if the legends on the plots could be improved.
- Add unit tests for the actual surface area calculation routine.
Part of #665.
Change-Id: Iee60c13b927b3b63b6e218164cd961971f2f3fce
Teemu Murtola [Thu, 27 Feb 2014 05:02:02 +0000 (07:02 +0200)]
Add support for non-uniform X axis in array data
It is now possible to construct AnalysisArrayData objects that have a
non-uniform X axis. AnalysisDataAverageModule can use this to provide a
more meaningful X axis in the output plot in case the values correspond
to, e.g., a set of atoms.
Change-Id: I578f6944d4ff51c315d068b011b705be2a4be00a
Teemu Murtola [Wed, 26 Feb 2014 09:55:03 +0000 (11:55 +0200)]
Improve support for data sets in C++ tools
- If a data set does not set the number of columns, the framework now
leaves it uninitialized (does not call startData() etc.), and the tool
can check this when processing the frame.
- Make it possible to specify an output file in a tool unit test without
actually testing the contents of the file. This supports testing
tools that only produce data in response to certain output options
being set.
- Add support for specifying a comparison tolerance for a data set in a
unit test.
Change-Id: I49794c93336c22c07f1a745d28d1b4f6f856b25b
Szilard Pall [Fri, 10 Jan 2014 11:46:15 +0000 (12:46 +0100)]
CUDA kernels for switched LJ
This change adds CUDA GPU kernels for force and potential switching,
implemented in the Verlet scheme for CPUs in f3acaf.
Change-Id: I73a83d352924379d9005104fa59f3478d3e684b0
Teemu Murtola [Sun, 23 Feb 2014 19:42:17 +0000 (21:42 +0200)]
Improve floating point comparisons in unit tests
Improve basic floating point comparison support:
- Replace EXPECT_NEAR_TOL with a more flexible alternative that allows
specifying various tolerances.
- Some Doxygen improvements in testasserts.h.
Additionally, make the reference data framework use the new approach:
- Add a tolerance setting to the reference data framework, and make the
default tolerance a lot stricter.
- Store the reference data with enough precision to allow lossless
roundtrips. This makes them more difficult to inspect visually with
the XSLT files, but that can be addressed separately.
- Run FFT tests with GMX_FFT_FLAG_CONSERVATIVE to make the results with
FFTW have less variance. The 3D FFT tests were already using this,
but others weren't. Set the tolerance for the FFT tests based on a
bit of testing of what works. It should now pass even without the
conservative flag, at least most of the time. The tolerance is still
lower than what it was earlier even for single, and a lot stricter for
double.
- Regenerated all reference values from a double-precision build.
For the FFT tests, used fftpack without optimizations.
Change-Id: I187dd9be20fd17cc8b3e779dcd9dbad34043bb00
Roland Schulz [Wed, 26 Feb 2014 22:26:26 +0000 (17:26 -0500)]
Remove Cygwin+MingW from installguide
MingW was never supported (#448). And Cygwin is currently
not working. Until/Unless it is working the guide shouldn't
claim support.
Change-Id: I6558b95bc47b80f7d97a7960587e83e959682990
Berk Hess [Tue, 26 Nov 2013 07:52:16 +0000 (08:52 +0100)]
Free-energy now works with the Verlet scheme
Implemented perturbed non-bonded interactions with the Verlet
by masking them from the nbnxn pair lists and storing them in an
old-fashioned group neighbor list. This way we keep a single
free energy kernel.
The free energy kernel uses OpenMP atomic for reductions.
Also fixed grompp setting nstcalcenergy=0 with nstenergy=0.
Change-Id: I5a6a7e84b46e06250d141e2e08cb3a11077cddab
Alexey Shvetsov [Fri, 29 Nov 2013 18:54:50 +0000 (22:54 +0400)]
Fix -Wmaybe-uninitialized warnings in some files
Also clean-up and clarification of clean_vsite_dihs.
Change-Id: Ica4b1d17039e23bc2274a20fe5abca18295a7593
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Teemu Murtola [Wed, 26 Feb 2014 05:08:53 +0000 (07:08 +0200)]
Misc. Doxygen build system improvements
- Check Doxygen version when running one of the Doxygen targets, and
produce a note that states the expected version if there is a
mismatch.
- Check the result of the Doxygen process and fail the build if the
program returns an error code.
- Add a tag to all warnings that identify the type of documentation that
produces them. This should make it easier to understand the Jenkins
warnings in the case not all documentation types produce a certain
warning.
Change-Id: I030c0b2c69958fe41f0b964399cb1c2e1b250e77
Erik Lindahl [Mon, 24 Feb 2014 23:06:24 +0000 (00:06 +0100)]
Added message to warn that group kernels are deprecated.
Nothing will change for now, but both grompp and mdrun now
warn that we will remove the support for group kernels in
a future version when all interaction forms are supported by
the verlet cutoff scheme (tentatively a year from now).
Change-Id: Id00a67e44e60818cb0e6f1897d6939f53ea01540