Alan Gray [Thu, 24 Jan 2019 15:31:21 +0000 (07:31 -0800)]
Position buffer ops in CUDA
On all but search steps the buffer ops transform can now be done on a
CUDA GPU. If PME runs on the same GPU the already uploaded coordinates
will be used as input.
Activate with GMX_USE_GPU_BUFFER_OPS env variable.
Note:
- waits for X copy on the PME stream to finish, need to implement sync
point between PME and NB streams (in follow-up).
Implements part of #2817
Change-Id: Ib87dabd74a02727898681249691ac9786b8ac65c
Paul Bauer [Tue, 12 Mar 2019 11:06:48 +0000 (12:06 +0100)]
Remove more manual memory management
Changed another virtual site preprocessing type to std::container and
added some documentation for types.
Refs #2833
Change-Id: I24e84bdb18e46f2cff710a1ca2cb0e1d4b80e633
M. Eric Irrgang [Tue, 2 Apr 2019 15:57:39 +0000 (18:57 +0300)]
More Python testing infrastructure for gmxapi.
* Add and improve test fixtures.
* Generate MD input files for tests.
Refs: #2756
Refs: #2896
Change-Id: I15ac8e44844cbf699cfe362e2fa443d07a355b3d
M. Eric Irrgang [Wed, 8 May 2019 12:23:50 +0000 (15:23 +0300)]
Add gmxapi._logging submodule.
To rearrange import statements and module initialization code,
a private _logging module is introduced to initialize the
Python logging module and to provide gmxapi.logger.
Change-Id: Ifc13db35df300d10500d4ced80fc84684bea2c0c
M. Eric Irrgang [Tue, 2 Apr 2019 11:23:45 +0000 (14:23 +0300)]
Update I/O handling in gmxapi.commandline.
Change-Id: Ic0506ac3df91b7a5e234242fb6dfdd0ce4796027
M. Eric Irrgang [Tue, 7 May 2019 20:32:02 +0000 (23:32 +0300)]
Expand gmxapi.operation tools to support the data flow constraints.
Achieves functional requirements 1, 2, and 3 as described
in the documentation submitted under #2893.
Updates some acceptance tests duplicated in a companion change.
Fixes: #2894
Change-Id: I26b1413c83e3ad176f2fd70f93e8b8e1033667ae
M. Eric Irrgang [Wed, 8 May 2019 12:30:58 +0000 (15:30 +0300)]
Fix formatting and typos.
Resolve some typos from earlier rebase.
Rearrange imports, dunders, and white space for better PEP8 compliance.
Change-Id: I14319b7882e17937f92951339a5caf9bc454cf4d
M. Eric Irrgang [Wed, 10 Apr 2019 14:32:00 +0000 (17:32 +0300)]
Support basic command line wrapper in gmxapi
Introduces gmxapi.commandline module and updates gmxapi.operation
to support gmxapi.commandline.cli() operation.
Ref: #2894
Change-Id: I9f6c113f21d3a1ce97184a1e48b8bd4856c5c924
Mark Abraham [Tue, 7 May 2019 13:20:14 +0000 (15:20 +0200)]
Provide hook for forks of GROMACS to describe themselves
This will help everybody understand which version of GROMACS is being
used because a description ends up in the log file.
Change-Id: I2ddd4def5b2a3768174a6b0ccc284cbc118906a1
Mark Abraham [Tue, 7 May 2019 08:08:55 +0000 (10:08 +0200)]
Provide better help for using libc++
This is now the actual cmake option required
Refs #2842
Change-Id: I1ab4676b0e01d65ba8df736b78eeb3c676cdc4ea
Artem Zhmurov [Fri, 3 May 2019 16:31:31 +0000 (18:31 +0200)]
Fixing minor memory issues in MDLib
1. Changed to PaddedVector in SETTLE test
2. Added GPU memory deallocation in CUDA versions of
LINCS and SETTLE.
Change-Id: I3dc8207f8e84f52bfde3f99b144cc44f91f65ee5
Mark Abraham [Thu, 2 May 2019 15:39:52 +0000 (17:39 +0200)]
Improve how mdrun -noappend names output files
Fixes a bug that could lead to names like md.part0001.part0002.log
Change-Id: Ic8f16f7f77e98e1506d7eec2dfc336e808c2d00c
Berk Hess [Tue, 16 Apr 2019 08:54:54 +0000 (10:54 +0200)]
Remove PME exclusion correction
Now the group scheme has been removed, ewald_LRcorrection() no longer
needs to correct for exclusions, which simplifies the code.
Also restructured the conditionals for the PME calls in
do_force_lowlevel().
Change-Id: I518f7929460e7209780b967bd612e4b83c14831d
Mark Abraham [Tue, 30 Apr 2019 15:14:35 +0000 (17:14 +0200)]
More tests for how mdrun -cpi restarts handle files
These tests clarify the behaviour of mdrun -cpi -noappend. It should
append ".partNNNN" to output files, but it is currently possible to
produce output files named like md.part0001.part0002.log
Added some unit tests around the string-handling behaviour that needs
fixing and left TODO comments to show what issues need fixing.
Reduced use of the deprecated mdrun -nsteps option
Refs #2804, #2829
Change-Id: I7e370b835d6fd3512fcaac575d0ff627b33c6e47
Paul Bauer [Thu, 30 Aug 2018 13:28:27 +0000 (15:28 +0200)]
Add outputadapters (2/3)
Add outputadapters based on IOutputAdapter that can be used to set the
box information in the t_trxframe, and toggle the settings for including
forces and velocities into the t_trxframe.
Change-Id: I13c637ab5e6f7e008a971798a5573f8ee1314667
Paul Bauer [Tue, 2 Apr 2019 10:36:58 +0000 (12:36 +0200)]
Replace t_grps with std::vector
Refs #2833
Change-Id: Ia1f156fec4c6c24f4c29a792e384668d835416f0
Berk Hess [Wed, 17 Apr 2019 16:50:38 +0000 (18:50 +0200)]
Convert manage_threading_t and gmx_enerdata_t to C++
Change-Id: I75fd6e0b8f217461f328690d168f61d5b45239cf
Paul Bauer [Thu, 30 Aug 2018 13:23:49 +0000 (15:23 +0200)]
Add outputadapters (1/3)
Add outputadapters based on IOutputAdapter that can be used to set the
number of atoms written to disk and control the addition of the t_atoms
information to the processed t_trxframe.
Change-Id: I0084a1566024f0a56f72eab031f927d342f42b30
M. Eric Irrgang [Fri, 29 Mar 2019 12:23:39 +0000 (15:23 +0300)]
Infrastructure updates for dependent changes.
* Introduce gmxapi.exceptions.ProtocolError.
* Add some pytest configuration and helpers.
* Update some comments.
Refs: #2893
Change-Id: I71030c3b552d568df7263115430631208812b9dc
Artem Zhmurov [Mon, 29 Apr 2019 13:33:34 +0000 (15:33 +0200)]
Use test with parameters for EnergyOutput
Some of the energy terms are printed out only if the specific
combination of thermostat/barostat/integrator is enabled. The
output also considerably different if it is from a rerun. This
commit changes the tests so that several possible combinations
of input parameters are tested.
This commit also fixes a possible bug when having more
acceleration groups than temperature coupling groups would
lead to under-allocation of temporary variable tmp_v.
Change-Id: Icc08e49a428b14ffd62d251662eb96184564b2c4
Paul Bauer [Tue, 9 Oct 2018 12:52:46 +0000 (14:52 +0200)]
Add builder for TrajectoryFileWriter
Adds builder method and storage for requirements on how to build an
object with its outputadapter methods.
Change-Id: I1b52e0cbb0bc39d8d1a78087a0526dcee8f8c289
Berk Hess [Tue, 30 Apr 2019 07:07:24 +0000 (09:07 +0200)]
Change nbnxm FEP pointer to unique_ptr
This fixes an incorrect delete issue in free energy runs.
Change-Id: Ib247c6eaa98807fe3abe2fcefd09d8509d6b8598
Mark Abraham [Tue, 30 Apr 2019 15:03:53 +0000 (17:03 +0200)]
Enhance path search functions
Extracted common implementation functions based on compat::string_view
and simplified the uses of them. Some temporary strings are no longer
created. Added, updated, and corrected Doxygen. Removed comments about
dot and dot-dot special directories, as the code does not do anything
about them. Moved some naming in the direction of C++17
std::filesystem::path.
Added new tests to cover the changes. Used namespaces better in the
test file. Used reference data for the tests.
Eliminated getParentPathAndBasename as redundant.
Change-Id: I11a1a25a257da753ca83f5bdd09d06b11c76cec5
Artem Zhmurov [Wed, 27 Feb 2019 15:38:42 +0000 (16:38 +0100)]
CUDA version of SETTLE algorithm with basic tests
CUDA-based GPU implementation of SETTLE. This is a part of
all-GPU loop. Can work isolated from other parts of the code
since coordinates are copied to (from) device before (after)
SETTLE kernel call. The velocity update as well as virial
evaluations can be enabled.
To enable, set GMX_SETTLE_GPU environment variable.
Limitations:
1. Does not work when domain decomposition is enabled.
2. Projection of the derivative is not implemented.
3. Not fully integrated/unified with the CPU version.
TODOs:
1. Multi-GPU case.
2. Better virial reduction. This is a more general feature,
not only related to constraints.
5. More cleanup in constr.cpp needed.
6. Better unit tests.
Refs #2816, #2886
Change-Id: I218e1bf1f86a2351e189e3c27f950f45c06135a4
Mark Abraham [Wed, 17 Apr 2019 06:35:11 +0000 (08:35 +0200)]
Test the output of "gmx mdrun help"
As we migrate mdrun to use the gmx::Options framework, several chunks
of text and many option descriptions will move to their respective
modules. However users would prefer the output of "gmx mdrun help" to
only change in ways that we as developers expect.
This will also provide a stable path towards e.g. implementing gmx
minimize, gmx tpi, gmx rerun, etc. and having the help text relevant
only to that runner. It may also be useful if in future we structure
mdrun modules to write their help via e.g. "gmx help mdrun pulling".
Change-Id: Iccd07f797004d8ff24eb56ca528a3fe9148b6749
Berk Hess [Thu, 28 Feb 2019 12:40:27 +0000 (13:40 +0100)]
Add con/destructor for t_forcetable
This avoids the need for sfree calls in C++ objects that use this.
Change-Id: I21d6867a9e3c84929ecf472e65ee97b3cf7c4846
Berk Hess [Wed, 27 Feb 2019 08:58:37 +0000 (09:58 +0100)]
Convert DispersionCorrection to a class
This change is only refactoring.
Change-Id: Ic6d90a26b485ab1546706bf8f419d7a297c7c7b5
Artem Zhmurov [Mon, 29 Apr 2019 15:42:48 +0000 (17:42 +0200)]
Fix for the CUDA version of LINCS
This fixes a couple of Jenkins Post-submit failures:
1. Clang warnings in the CUDA portion of code.
2. New CUDA LINCS failure on the host with CUDA, but without
capable GPU.
Also done is minor renaming and typo correction.
Change-Id: I4f1d89d4bf5a6f3f0083186cb67787cdf6536bb9
Artem Zhmurov [Wed, 20 Feb 2019 14:30:29 +0000 (15:30 +0100)]
CUDA version of LINCS constraints.
Implementation of the LINCS constraints for NVIDIA GPUs.
Currently works isolated from the other parts of the code:
coordinates and velocities are copied to and from GPU on
every integration timestep. Part of the GPU-only loop.
Loosely based on change 9162 by Alan Gray. To enable,
set the environmental variable GMX_LINCS_GPU.
Limitations:
1. Works only if the constraints can be split in short
uncoupled groups (currently < 256, designed for H-bonds
constraints).
2. Does not change the matrix inversion order for costraints
triangles.
3. Does not support free energy computations.
4. Assumes no communications between domains (i.e. assumes that
there is no constraints connecting atoms from two different
domains).
5. Number of thread per blocks should be a power of 2 for
reduction of virial to work.
TODOs:
1. Move more data from the global memory to local.
2. Change .at() to []
3. Add sorting by the number of coupled constraints to decrease
warp divergencies.
4. numAtoms should be changeable (for multi-GPU case).
Refs #2816, #2885
Change-Id: I3c975cf898053b7467bcd30459e60ce2c8852be6
Christian Blau [Wed, 17 Apr 2019 13:50:35 +0000 (15:50 +0200)]
mrc density map reading/writing
Add a class that combines header and mrc data handling for float values
to enable reading and writing of mrc files.
refs #2282
Change-Id: Idd84ab2628a52a2fcafb6121ad66f62e88235c74
Christian Blau [Tue, 23 Apr 2019 13:03:52 +0000 (15:03 +0200)]
Three dimensional coordiante transformation.
Introduce class that transforms three dimensional coordiantes via scaling and translation.
Change-Id: Ic433400cf42c33d7eadd4a17020d0486542b8542
Paul Bauer [Tue, 9 Oct 2018 12:35:12 +0000 (14:35 +0200)]
Add C++ coordinate file writing method.
TrajectoryFileWriter also allows the chaining of modules derived from
IOutputAdapter together to perform actions that modify the meta
information contained in a t_trxframe before writing the information to
disk.
IOutputAdapter can be used to communicate what requirements a specific
file writing method has on the meta information contained in t_trxframe,
with modules being able to proclaim those and TrajectoryFileWriter checking
them against the requested file types before accepting the addition of a
module to the processing chain.
The TrajectoryFileWriter object needs a builder method to construct itself that will
be added in a child change.
Change-Id: I1c29701b4ce788918cb6b3a47ca9277898a7bff4
Szilárd Páll [Thu, 25 Apr 2019 12:20:04 +0000 (14:20 +0200)]
Fix clang warning about NULL use
Change-Id: Ia34e401bf04f1743419898fdb60671d3f066992f
Szilárd Páll [Wed, 24 Apr 2019 10:36:02 +0000 (12:36 +0200)]
Avoid using AtomLocality::Count as a valid value
Change-Id: I740eef01e679f085a9f73c60a67377e0122daba4
Christian Blau [Tue, 16 Apr 2019 12:04:13 +0000 (14:04 +0200)]
density fitting forces
Evaluate forces on atoms that increase a measure of the goodness of fit to a reference density.
The density fitting forces are evaluated as the gradient of the goodness of fit of a comparison density is generated from atoms by spreading on a grid via a Gaussian kernel to the reference density.
Applying the chain rule for this gradient yields the density fitting force as the inner product of the derivative of the comparison density to reference density goodness-of-fit function at all density values and the gradient of the spreading kernel used to simulate the density.
This patch assumes that the comparison density to reference density goodness of fit derivative density is given, methods that aid the evaluation of this derivative density are part of a child patch.
refs #2282
Change-Id: I4d93fffbdb41753f9a0a4af921011aca02ade69c
Artem Zhmurov [Fri, 12 Apr 2019 15:49:22 +0000 (17:49 +0200)]
Improvements for energy output test.
EnergyOutput handles outputs to the text log file
as well as to the binary edr file with the number of
the printed energy terms determined by the simulation
setup. This commit adds the tests for the binry output
and increases the number of tested energy terms.
TODO Proper fix for memory leak in energy output.
Change-Id: I670b168a83c0a1883b821a4b317c0df3055183e8
Paul Bauer [Tue, 13 Nov 2018 10:36:33 +0000 (11:36 +0100)]
Add Interface to change coordinate file info
Adds the IOutputAdapter interface to organize coordinate output file
writing, as well as enum flags to communicate requirements between output
modules and output filetypes, as well as the outputadaptercontainer storage
object to keep track of modules derived from the IOutputAdapter
interface.
IOutputAdapter can be used to communicate what requirements are specific
file writing method has on the meta information contained in t_trxframe.
Change-Id: I0011c852eb54bd551230dd8c4971292dd4edc7e5
Mark Abraham [Thu, 25 Apr 2019 08:04:02 +0000 (10:04 +0200)]
Update style guide about class enums
Change-Id: Icf6ddde8ce030bd5ed737152a8c58daad87ff991
Szilárd Páll [Fri, 15 Feb 2019 17:34:52 +0000 (18:34 +0100)]
Fix CUDA fallback shmem gather reduction
Fixed some shmem races and an intra-warp WAR hazard.
Change-Id: Ic02874f147e1c3a0dad1b67a6464ede453f77c47
Mark Abraham [Wed, 17 Apr 2019 09:24:00 +0000 (11:24 +0200)]
Clarify pushing of interaction types
gcc was warning about possibly pushing atomNumber to a vector when its
value was not defined. That was impossible because of the gmx_incons
earlier, but we can express the validity of the code much more clearly
to the reader/compiler.
Fixes CMAP implementation also
Extracted the common code to a function.
Change-Id: I74be61b125e05ff5505162440349fcef4ea50fdb
Mark Abraham [Wed, 17 Apr 2019 12:31:44 +0000 (14:31 +0200)]
Updated clang -Weverything checks to clang-7
This is supposed to be used with the latest tested clang
compiler. That is now clang 7, but the logic is hard-coded to clang 6,
which is why some things only failed in post-submit testing where we
have such a compiler for the clang-cuda build.
Fixed issues only found with clang -Weverything.
Also fixed those found with clang-8, but as we do not yet use that in
Jenkins, they're commented out for now.
Change-Id: I83be1cb770d486cc81a453d4911361f06a056ce3
Christian Blau [Wed, 10 Apr 2019 13:58:46 +0000 (15:58 +0200)]
Three dimensional gauss transform
Added class that adds gaussians functions with specified
amplitudes and coordinates onto a three-dimensional scalar field.
Change-Id: I07ea2cdd219b34afc402975a0b0e8a52eb71acaf
refs: #2282
Christian Blau [Wed, 10 Apr 2019 13:52:48 +0000 (15:52 +0200)]
One dimensional Gaussian function on lattice.
Evaluate a Gaussian of width sigma in one dimension on lattice points with unit spacing.
refs #2282
Change-Id: I57a513f05af44323e7109c4560438dc023793c4c
Berk Hess [Thu, 21 Mar 2019 21:09:30 +0000 (22:09 +0100)]
Remove nbnxm kernel type from pairlist generation
The type of kernel for computing distances between atom clusters pairs
is no longer set directly by the non-bonded interaction kernel type.
A new type is added for this, although the actual choice of cluster
distance kernel type has actually not changed.
Also moved the declaration of PairlistType to pairlistparams.h.
Change-Id: Iaf38ca7804eed75295e6cb0e1176a23d620c6f0c
Berk Hess [Tue, 16 Apr 2019 14:19:01 +0000 (16:19 +0200)]
Remove charge groups from domdec and localtop
Code explicitly handling charge groups has been removed in the domdec
module. Removed the charge groups from gmx_localtop_t.
Changed cginfo in forcerec to std::vector, which propagates into
the nbnxm module.
Parts of the TPI code are now commented out until reimplemented.
Change-Id: I9d3bffe26e34ebbb8e31ef97a9a7f1e0bea92306
Todo: Change naming from charge group to atom.
Todo: Remove duplicate counters for atoms and charge groups.
Szilárd Páll [Mon, 15 Apr 2019 16:24:42 +0000 (18:24 +0200)]
Fix warnings & consolidate declarations
- Unused variables warnings with cuda 10.1
- Early declaration of kernel pointers eliminated
Change-Id: I7c8ca06322a3da9c948cc19d6b0b0f6a53f16beb
Mark Abraham [Fri, 8 Feb 2019 15:55:27 +0000 (16:55 +0100)]
Create gmx::compat::optional
This C++17 std component is an extremely useful vocabulary type that
has a straightforward implementation in C++14. Having it available is
likely to mean we can write simpler, less buggy code in less developer
time. It should be used in cases where the absence of a proper value
has an obvious natural interpretation, e.g. the type of the return
value of a function that parses an integer value from a string, or
searching for a matching element in a range, or optionally naming
a residue type.
Updated developer guide and COPYING file accordingly.
Used compat::optional for some aspects of residue handling. This
simplifies some code, and sometimes avoids needing to make a dummy
residue name string that then needs to be compared with other strings.
Let .clang-tidy file's header management apply to source fields for
test binaries.
Excluded the external code from Doxygen checking. Noted where to go
for documentation in the file Doxygen.
Fixes #2861
Change-Id: Ife34983f234549702902a0ea45dc3592098e377d
Mark Abraham [Sun, 14 Apr 2019 19:45:53 +0000 (21:45 +0200)]
Move pull work struct out of inputrec
Its lifetime is now managed by runner. This will make high-level
organization more comprehensible, and permit more meaningful
const-correctness of t_inputrec.
Change-Id: I66bf765ad7235d84184227325eb52afd58146b72
Mark Abraham [Sat, 13 Apr 2019 14:46:20 +0000 (16:46 +0200)]
Improve swapcoords session lifetime management
This is no longer stored in the inputrec (which is now more
const-correct), and it is also now be cleaned up in one place.
Change-Id: I4d3c3ebb8124849cf7e13334759fda731370c1bc
Paul Bauer [Fri, 5 Apr 2019 08:22:49 +0000 (10:22 +0200)]
Update clang-tidy to check for dangling references
Change-Id: I4a720ee29dddcb0778f88aaa3b1057c61d319036
Berk Hess [Sat, 13 Apr 2019 10:00:06 +0000 (12:00 +0200)]
Fix pdb-related issues
In editconf, if a PDB input was read, chain IDs are known, and should
be written if the output is also PDB. This now works again, after
being broken in commit
8dd3c9ae88004054b3.
This required adding missing tpr support to readConfAndAtoms(), which
also fixes that pdb2gmx, insert-molecules, and solvate could not read
tpr files. Those are the only tools that directly or indirectly called
readConfAndAtoms with a .tpr file.
Fix in master also closes memory leaks.
Refs #2900
Change-Id: I883777be945023a7e69260b22e76df54477828ee
Berk Hess [Wed, 17 Apr 2019 09:35:59 +0000 (11:35 +0200)]
Remove group scheme search code
This also required removing the generic group kernel code.
Removed domdec group scheme sorting code.
Also removed the nbnxm grid size call from the domdec module off it
turned out the results were not used.
Change-Id: I1a49967bbeca33dcd62834e8a244aaf02e80a95e
Berk Hess [Tue, 16 Apr 2019 20:59:03 +0000 (22:59 +0200)]
Simplify vsite PBC handling
Since we no longer support charge groups, removed the (complex)
vsite pbc tracking code.
Also changed the inter charge group vsite counting to inter update
groups counting, so we can avoid PBC calculation with update groups.
Change-Id: Iebaee9a25e761d38c571563fd0814b57e15c7e5f
Prashanth Kanduri [Fri, 29 Mar 2019 16:15:32 +0000 (17:15 +0100)]
Move shellfc code to the mdrun module
This code was previously in mdlib and made use of the force
calculation routines. The introduction of the forceschedules
module (Patch 9363) introduces a cyclic dependency.
Therefore, this clean up is important to ensure that all
users of the Force Schedules are present in a single module.
Related: #2574, #2774
Change-Id: I19563f0f6e7985d198a2497a799c5377b24a1419
Paul Bauer [Fri, 5 Apr 2019 15:41:55 +0000 (17:41 +0200)]
Enable printing of known issues in commandline
Showcase in gmx dump.
Added test for it.
Change-Id: If1e70cc3b1a9c73a9483ba643a979edb2838d6a5
Paul Bauer [Wed, 3 Apr 2019 13:38:44 +0000 (15:38 +0200)]
Create gmx::compat::string_view
This part of the C++-17 std will likely help in cases we want objects to
store views to std::strings instead of performing a copy of them.
Updated COPYING instructions and developer guide.
Excluded the external code from Doxygen checking.
Noted where to go for documentation in the file Doxygen.
Change-Id: Ibc75f32929d385159d27d0b7ba87f2133995e915
Mark Abraham [Wed, 17 Apr 2019 05:06:54 +0000 (07:06 +0200)]
Fix post-submit
Change-Id: I203647ed9ac70c99d188d29223a3a4141d3d4533
Berk Hess [Fri, 12 Apr 2019 12:43:34 +0000 (14:43 +0200)]
Reduce nbnxm CPU kernel arguments
The number of output arguments for nbnxm CPU kernel functions
ave been reduced to one.
Change-Id: I4d69d848b490dced6007400f8f8fae0ff0638f63
Berk Hess [Fri, 12 Apr 2019 12:17:37 +0000 (14:17 +0200)]
Simplify nbnxm shift force handling
Now thread 0 also stores the shift forces in the out thread buffer
of nbnxn_atomdata_t instead of using the global fshift buffer.
Change-Id: I8c850ffc2d55db1cd7b34c1a18977f73e5cb77b0
Szilárd Páll [Mon, 15 Apr 2019 23:32:27 +0000 (01:32 +0200)]
Move functions operating on enerdata out of force.cpp
Change-Id: I20165ac5b2a34fcb80db8c7624adb57b4b542df6
Berk Hess [Fri, 12 Apr 2019 09:26:33 +0000 (11:26 +0200)]
Simplify nbnxm buffer clearing
We should not pass both the output index and the buffer to the clearing
function.
Also templated the flagged clearing in preparation for use for clearing
other buffers.
Change-Id: I0fdb8eb0ba9ab5766e9d6ba57804783a87163cd4
Berk Hess [Tue, 16 Apr 2019 08:05:59 +0000 (10:05 +0200)]
Remove RF_excl_correction()
Was only used with the group scheme. The RF correction is computed
along with the non-bonded interactions in the nbnxm kernels.
Change-Id: I1451493faa7fafb7cddf508d396b0bd06cf70272
Szilárd Páll [Mon, 15 Apr 2019 22:23:18 +0000 (00:23 +0200)]
Remove "coarse load balancing vars" from forcerec
Legacy timing code dropped during cleanup.
Change-Id: I4a3d0f69d926973c6269df15eea8b448539c54d4
Paul Bauer [Tue, 12 Mar 2019 11:17:11 +0000 (12:17 +0100)]
Refactor t_pindex
Also change naming of containers for interaction types to better reflect
what is actually stored in the container.
Refs #2833
Change-Id: I581fb2a436528c00770b98ba6e5d45af7c7d9a0c
Szilárd Páll [Mon, 15 Apr 2019 19:02:17 +0000 (21:02 +0200)]
Group scheme related cleanup
Removed:
- SR force calculation invocation
- LR correction invocations
- SR free energy component accumulation
Minor cleanup.
Refs #1852
Change-Id: I4e22986279039a0f49a5a8be3c447f4115308492
Mark Abraham [Sat, 13 Apr 2019 14:55:39 +0000 (16:55 +0200)]
Removed mdrun -gcom
This was previously deprecated, and is now removed to make the
behaviour of mdrun simpler to understand and implement.
Renamed a function whose job was previously not to check a thing,
and is now clearly to compute something
Noted several TODOs to clean up behaviour related to nstcomm.
Refs #1925
Change-Id: I0b3a803fb209148e865957f796c871caef2f1fea
Szilárd Páll [Mon, 15 Apr 2019 19:15:05 +0000 (21:15 +0200)]
Remove Group scheme neighbor search wrapper
Change-Id: Id89aa1b7b38c918a120385d4f1a2c7bdba82fa7b
Artem Zhmurov [Mon, 15 Apr 2019 17:41:56 +0000 (19:41 +0200)]
Fix for the memory access error in constraints test.
When SIMD enabled, some memory accesses can fall outside
the allocated memory space. Hence, padding was added for
coordinates and velocities.
Change-Id: I95fa496d398fef85c62aa0ee7e90ecda4dbb8daf
ejjordan [Mon, 15 Apr 2019 19:11:55 +0000 (21:11 +0200)]
Die with helpful note in case of incorrect input to editconf with -conect
Previously editconf would give a cryptic error message
Assertion failed:
Condition: fio->xdr != nullptr
Implementation error: NULL XDR pointers
if -conect was specified and a tpr was not supplied.
This is now replaced by a fatal error
Change-Id: I69efc6d36c8dd8314b2656e88407e8ba00915fd7
ejjordan [Mon, 15 Apr 2019 18:34:08 +0000 (20:34 +0200)]
fix formatting of editconf note
Change-Id: I628fc820a176fdc4b019e5819e6fa650842024d4
Mark Abraham [Sun, 31 Mar 2019 16:42:04 +0000 (18:42 +0200)]
Start making IMD and swap model IMDModule
Moved MDModules to mdrun code module (to relieve cyclic dependency
that would otherwise result), because it is a very high level thing
that is intended to be aware of very many components.
Refs #2877
Change-Id: Ia7d1422bab887f768f8abed01edcbc4fb290dfeb
M. Eric Irrgang [Fri, 15 Mar 2019 11:24:53 +0000 (14:24 +0300)]
Add GROMACS library dependency to gmxapi package.
The `gmxapi` Python package has a C++ extension module configured and
built through CMake. This change links the C++ extension module to the
GROMACS library external interface.
No new code is introduced. This change just establishes that a Python
package can be built, installed, and imported with dynamic linking to
an installed GROMACS library.
Ref: #2912
Change-Id: I1c992c30132df25cf6a91902611cb201962649af
M. Eric Irrgang [Wed, 27 Feb 2019 07:46:51 +0000 (10:46 +0300)]
Use pybind11 to make a minimal C++ Python extension.
* Bundle pybind11 2.2.4 headers
* Create the `gmxapi._gmxapi` submodule as a C++ extension module.
Ref: #2912
Change-Id: Iadc8645906c2b89d98fae57b891deac80793b050
Mark Abraham [Wed, 10 Apr 2019 05:51:00 +0000 (07:51 +0200)]
Reuse rvecs_differ in InteractiveMD module
Change-Id: I5dfbfc0c0934dc734045f41db8075ad5f1a0b635
Mark Abraham [Sun, 31 Mar 2019 12:29:20 +0000 (14:29 +0200)]
Make ImdSession into a Pimpl-ed class with factory function
This prepares to make IMD into a proper module. No
functionality changes in this commit.
Replaced gmx_bool with bool
Used fast returns when IMD is inactive, for better
readability of code.
Refs #2877
Change-Id: Ibbe8c452f6f480e9a357fe1b87da3ab0ae166317
Mark Abraham [Fri, 29 Mar 2019 13:54:36 +0000 (14:54 +0100)]
Reform IMD module
Remove GMX_HAVE_WINSOCK which was synonymous with Windows
support. Because that is somewhat risky, introduced CMake variable to
turn off IMD support. Reduced a lot of config.h dependency in
headers. Moved portability constructs to imdsocket source file.
Expanded testing coverage to be of both a minimizer and a dynamical
integrator. Switched the test case to be one that has some
interactions (because steep segfaults otherwise), and updated the mdp
settings to continue to work given the likely future directions of
mdrun.
Removed an unused method
Moved the ownership of the IMD session data structure out of inputrec
and its point of construction out of minimizers and do_md. This is now
done in runner.cpp, alongside other such construction. This prepares
for more use of MDModules. Set up the default period between IMD steps
in a different but equivalent way (since it works differently for
minimization).
Separated the inputrec boolean for whether IMD connections are
supported by the input from the run-time boolean of whether the mdrun
command-line arguments require IMD connections to be possible. Now the
inputrec is logically const with IMD.
Used logging framework for reporting, and noted future improvements as
TOD items. Improved reporting in some cases where IMD sessions are
impossible.
Note TODOs for future improvements for renaming and restructuring.
Removed some useless inclusion of imd.h
Fixes #2913
Change-Id: I2b13dcdd9a0e69caba697f9dd2c928d94e1fb80c
M. Eric Irrgang [Fri, 29 Mar 2019 12:59:54 +0000 (15:59 +0300)]
Introduce gmxapi operations and basic data model.
Ref: #2894
Change-Id: I4e899e63287370fd2fdde89ddc1b2ea39c3fe67d
M. Eric Irrgang [Tue, 19 Mar 2019 14:58:03 +0000 (17:58 +0300)]
gmxapi 2019 Q1/Q2 project roadmap.
Lay out project goals, functional requirements, and testing plans.
Provides roadmap.rst and pytest acceptance tests
expressing the required functionality of the Python package.
Ref: #2893
Change-Id: I71ec79eb5d8a6e4d61fb5d7d6e20176c9c07a6af
M. Eric Irrgang [Mon, 8 Apr 2019 15:23:40 +0000 (18:23 +0300)]
Remove stale "TODO".
Refs #2839
Change-Id: I927ee73fc9c6ffa423d37fd4606654392cb8a1b8
Paul Bauer [Thu, 4 Apr 2019 14:31:03 +0000 (16:31 +0200)]
Remove t_topology from two preprocess tools
Refs #2833
Change-Id: Ic842305579986910db8cc30313f74278239640bc
Christian Blau [Thu, 21 Mar 2019 15:48:04 +0000 (16:48 +0100)]
densityfitting - MDModule declaration
Declaring the infrastructure for running molecular dynamics simulations with
addional forces that are derived from densities.
Adds a IForceProvider for density fitting simulation that is set up with
its DensityFittingParameters that are in turn built from DensityFittingOptions.
refs #2282 #2901
Change-Id: I0732a78747582a6e23bba1e141d73c4cda421011
Szilárd Páll [Thu, 4 Apr 2019 16:59:29 +0000 (18:59 +0200)]
Revert "Temporarily disable ARM HPC compiler in post-submit"
This reverts commit
d8d9b66ca33e423ca09079e5f9294ca872d61ca5.
Reason for revert: build slave software issues resolved.
Change-Id: I9f7c904152e4be951199c9fcdba00bd9d928f33b
Carsten Kutzner [Thu, 4 Apr 2019 14:36:50 +0000 (16:36 +0200)]
Early exit from mdrun if group scheme is detected in .tpr
Fixes #2918
Change-Id: I37566623c3ed4613f8b4e69f9f74882656772d1d
Artem Zhmurov [Mon, 1 Apr 2019 09:48:05 +0000 (11:48 +0200)]
Remove isPressureCouplingStep(...)
The isPressureCouplingStep(..) subroutine is called from places,
where the type of barostat is already known and then checks for it
again. Removing this subroutine eliminates the double-checks and
improves readability of the code.
Change-Id: I5bbb0706432e16414097e87e4e0d302f669ab83f
Paul Bauer [Thu, 4 Apr 2019 09:59:27 +0000 (11:59 +0200)]
Update developer guide for changes to Gerrit
Change-Id: I2fad9ad5dfd0fb4536520529706d6dbaaca5d5d9
Artem Zhmurov [Mon, 1 Apr 2019 09:24:23 +0000 (11:24 +0200)]
Remove isTemperatureCouplingStep(...)
This subroutine hides the checks on whether the temperature
coupling should be updated, making it harder to read the
sequence of events in the main loop. Also, the subroutine is
used only twice and both times some of the conditionals are
double checked (e.g. is Velocity-Verlet integrator is in use).
Change-Id: Idb4196c2f81095c09426b2798e79d2beea4f306e
Mark Abraham [Wed, 3 Apr 2019 13:58:39 +0000 (15:58 +0200)]
Initial deactivation of group scheme.
mdrun now gives a fatal error with a group-scheme .tpr, so anybody
using one won't get a segfault.
do_force now only has one implementation, which suits those working
on improved force calculations.
More removal of inactive code will follow later. Noted TODO to fix the
release notes properly in such a commit.
Refs #1852
Change-Id: I3b13135565951f4d7f872ddf3b8518860eccfdb0
Paul Bauer [Wed, 3 Apr 2019 08:47:02 +0000 (10:47 +0200)]
Fix post submit
Change-Id: Ia45a8e1154c0d5ddd94155ddb7907c0290d13866
Paul Bauer [Tue, 12 Mar 2019 15:28:44 +0000 (16:28 +0100)]
Refactor gpp_bond_atomtype
Refs #2833
Change-Id: Id17a93c9cc4a66b0bf89c465d2d44601fe2c523d
Paul Bauer [Fri, 15 Mar 2019 11:26:38 +0000 (12:26 +0100)]
Add std::string case insensitive compare
Add another function for std::string case insensitive
comparison over a user specified length instead of
comparing the full string.
Added tests for functionality.
Showcase in preprocessing.
Change-Id: I1f117261ce56ad7c6bc5e5113da1fef705cf8aa6
Paul Bauer [Thu, 14 Mar 2019 11:21:55 +0000 (12:21 +0100)]
Refactor gmx_group_t to SimulationAtomGroups
Change allocation on type to std::container, but did not touch to
underlying t_grps datastructure yet.
Change-Id: I3858e650a31764b3ab83090eaa0653fc579a8af1
Paul Bauer [Tue, 19 Mar 2019 09:46:06 +0000 (10:46 +0100)]
Fix simulated annealing and add test
Refs #2871
Change-Id: Ibde5226a664d3d4d5558477fdf9b81e1219a5295
Szilárd Páll [Mon, 1 Apr 2019 19:52:26 +0000 (21:52 +0200)]
Temporarily disable ARM HPC compiler in post-submit
Change-Id: Ib59a495f70d073f13c08a55344b6323dd163d8b1
Mark Abraham [Thu, 14 Mar 2019 16:40:23 +0000 (17:40 +0100)]
Move MDModules initialization earlier
This will permit extending the functionality to also provide
command-line options and help descriptions for gmx tools.
Moved more functionality into Mdrunner::Builder
It also permits the Mdrunner constructor that is normally used to
prompt the construction of a properly formed MDModules. Removed a
comment about default initialization that is a normal fact of life
with constructors. Updating it would be wordy and no real value.
Refs #2877
Change-Id: I70126f297422a9076484083d461b0b003ae2e23b
Mark Abraham [Sun, 31 Mar 2019 16:52:05 +0000 (18:52 +0200)]
Move enerdata ownership to mdrunner
All the things managed by runner need a gmx_enerdata_t, so consolidate
the management of its lifetime. This prepares for modularization of
code that requires one of these.
Change-Id: Ibbf03c17beecb53039bb50a5ef6462925d777b52
David van der Spoel [Sun, 31 Mar 2019 18:17:26 +0000 (20:17 +0200)]
Removed confusing gpp_atomtype functions.
For some reason there were functions to extract the massB
and chargeB from atomtypes, however atomtypes do only have
a single charge or mass.
Change-Id: Iddcbeb57e4fa7fd905f5969447f14faf6d626ff0
M. Eric Irrgang [Wed, 27 Feb 2019 08:08:05 +0000 (11:08 +0300)]
Plumbing for gmxapi 2019 Q1/Q2 project roadmap.
Provide infrastructure so that dependent change can focus on content
of project plan.
Ref: #2893
Change-Id: Idd72e9ede890f7fc97a680c5a5bffe97499eaaf5
Berk Hess [Wed, 27 Mar 2019 13:16:47 +0000 (14:16 +0100)]
Simplify nbnxm final force reduction
Change-Id: I66485bfe1c056db82492b531b266de1071aeb12c
Berk Hess [Tue, 26 Mar 2019 13:37:53 +0000 (14:37 +0100)]
Move early return for nbnxm force reduction
To reduce dependencies and code complexity, the early return for
avoiding overhead of a force reduction reducing no forces at all
has been moved from nonbonded_verlet_t to atomdata.cpp. The check
has been changed from no non-local work to no non-local atoms, which
should not affect performance much.
Change-Id: I3315699e15918482b321b702f6ba24209aa3a6b2
Berk Hess [Mon, 18 Mar 2019 15:25:26 +0000 (16:25 +0100)]
Move PairlistSet declaration
Moved the declaration of PairlistSet to pairlistset.h.
Also completed the documentation.
Change-Id: I0cac4bbf1919b4a2f39d8ead63aa75f112ab60c7