Mark Abraham [Tue, 20 Dec 2016 12:03:37 +0000 (23:03 +1100)]
Merge branch release-2016
No conflicts
Change-Id: I175809e0b4f6ebf7dbbe668de66c47c318954b55
M. Eric Irrgang [Wed, 14 Dec 2016 00:21:24 +0000 (19:21 -0500)]
Fix syntax in cmake status message
Change-Id: I9ab793fe7d11e979fbc1cbd5ab3ec8ed6189dbb8
Roland Schulz [Fri, 25 Nov 2016 06:04:08 +0000 (22:04 -0800)]
Add create_unique_with_deleter
A more flexible alternative to unique_cptr. Takes also
non-void deleter functions or lambdas as argument.
Change-Id: I25c1d7d9ed63556cc42230f3da578dc449116d78
Roland Schulz [Thu, 24 Nov 2016 02:02:45 +0000 (18:02 -0800)]
Replace scoped_cptr with unique_cptr
scoped_cptr only exists for historic reasons
Change-Id: Ie77ce22855cbd440bc51d31cf9c1d5d5b30e10eb
Vedran Miletić [Mon, 12 Dec 2016 18:40:57 +0000 (19:40 +0100)]
Improve include sorter error reporting
Change-Id: I5fe5d1ad6a4001cff6ae8a2b109e831c5e3eb433
Mark Abraham [Sat, 10 Dec 2016 03:59:27 +0000 (14:59 +1100)]
Removed support for multiple entries in mdp files
This was never used.
Refs #2074
Change-Id: If97800cc75b809080abb407ec3f9a885c8f95b5c
Mark Abraham [Mon, 12 Dec 2016 03:28:35 +0000 (14:28 +1100)]
Handle warninp correctly in xpm2ps and membed
The code should not (over)write the output file before checking for
errors. For membed, it is useful to require the user to fix issues in
their input file before we unilaterally over-write it.
Called done_warning where it was omitted, which in the case of membed
meant that errors were not fatal when they should be.
Change-Id: I3c87f6bd99691b12d66906df3cc9980373429439
Mark Abraham [Tue, 13 Dec 2016 22:11:00 +0000 (09:11 +1100)]
Fix misleading parallelization docs for gmx wham
Change-Id: I5bbadc4fc9b9af6bcd2a6ea1a848eae262e4fd8c
Berk Hess [Thu, 8 Dec 2016 11:20:23 +0000 (12:20 +0100)]
Add bonded #thread runtime check
Replaced a debug assertion on the number of OpenMP threads not being
larger than GMX_OPENMP_MAX_THREADS by fatal error.
But since the listed forces reduction is actually not required with
listed forces, these are now conditional and mdrun can run with more
than GMX_OPENMP_MAX_THREADS threads.
Fixes #2085.
Change-Id: I7a6049d727924cd0b4df10a3525f9e7aec49c3dc
Teemu Murtola [Mon, 12 Dec 2016 19:39:12 +0000 (21:39 +0200)]
Merge branch release-2016
Conflicts:
cmake/gmxVersionInfo.cmake
Add a suppression for Intel compiler warning in generated code in
scanner.cpp.
Change-Id: I3a6310c433a50202fbc76e53570a491bd3d06544
Teemu Murtola [Sun, 20 Nov 2016 08:02:25 +0000 (10:02 +0200)]
Minor CMake cleanup & modernization
- Our minimum CMake version now supports BYPRODUCTS for
add_custom_target(), which allows simplification of
gmxCustomCommandUtilities.cmake.
- Specify USES_TERMINAL for targets that provide status output for nicer
usability with Ninja.
- Rely on add_custom_command() automatically marking its outputs as
generated.
- Update the minimum required version for building the template to match
the main project.
- Do not unnecessarily put regressiontests MD5 to the cache.
- Fix the branch used for regression tests download for git builds.
Change-Id: Iee9a7e67d694724ad79cce9801bea670ef2f94c8
Teemu Murtola [Thu, 1 Dec 2016 19:18:53 +0000 (21:18 +0200)]
Build scripts for improved release workflow
Add build scripts to support extracting version info from
gmxVersionInfo.cmake, and to update the regressiontests MD5.
Part of #2066
Change-Id: I916439c1be26823b4e366aea4e7fcded6de21659
Mark Abraham [Thu, 8 Dec 2016 16:47:09 +0000 (03:47 +1100)]
Fix logic of TRR reading
Commit
f7d4d019 introduced a bug where TRR reading reaching the end of
the file was indistinguishable from a reading error or a magic-number
error. This is now fixed, restoring the end-of-file behaviour that
existed before
f7d4d019, while retaining the wrong-magic-number
behaviour that it introduced.
Refs #1926
Change-Id: Ic8540846c481f022bc6ae7b774794792c8c7a523
Mark Abraham [Fri, 9 Dec 2016 18:48:26 +0000 (05:48 +1100)]
Remove nxframe from t_trxstatus
This is unused. Probably xframe can go too, once the long-deprecated
read_firstx/read_next_x functions are removed.
Change-Id: Ibf6a4fc3c6e4d598383a1d85baf6303b2944749d
Szilárd Páll [Wed, 2 Nov 2016 23:52:32 +0000 (00:52 +0100)]
Turn off hwloc support when static lib found
Hwloc dependencies are not resolved at CMake time when static
libwloc.a is detected and in most of these cases link-time
errors will prevent building GROMACS. As it is hard for a user to know
how to solve such cryptic errors and hwloc is not a required dependency,
we turn off hwloc support when a static lib is detected. The user can
override this on the cmake command line.
Refs #1919
Change-Id: Ic3917e2e59ee4c291b78ee47150e513ae77ced85
Teemu Murtola [Tue, 6 Dec 2016 19:19:54 +0000 (21:19 +0200)]
Fix and clean up handling of some linking
Split GMX_EXTRA_LIBRARIES to several lists, depending on the intended
use of those libraries. Some of these also need to be linked by code
other than libgromacs, either because they are required by the public
headers (mostly -lm), or because also code outside libgromacs directly
references those libraries (e.g., MPI).
Should fix #2087.
Change-Id: Ie0e211b8f77a932ccd63017ee0743b78361624c4
Berk Hess [Thu, 24 Nov 2016 07:43:17 +0000 (08:43 +0100)]
Made mdrun -pforce terminate with non-finite forces
The mdrun option -pforce would print non-finite forces, but would
not terminate the run if any were found. Now a fatal error is issued.
Change-Id: Ie126904bd45acee4e5999db77e02fbe8b6b39226
Teemu Murtola [Sat, 3 Dec 2016 08:50:56 +0000 (10:50 +0200)]
Fix possible memory error with long selections
If a selection was more than 1000 characters long and there was a
whitespace exactly at the 1000 point, a buffer overflow could occur.
Replaced the buffer with std::string, simplifying the code
significantly. Update the generated code to use a newer flex, which
also removes the need for some suppressions.
Should fix #2086.
Change-Id: I56513bcf5ee99f05ce144461740d0f868be10186
Mark Abraham [Sat, 19 Nov 2016 16:46:56 +0000 (17:46 +0100)]
Consolidate files supporting TNG file I/O
The distinction between mdrun and tools in supporting TNG file formats
isn't useful, and makes it difficult to implement a wrapper type that
will mean GROMACS code depends on tng_trajectory_t only in one
source file.
Change-Id: Iea0d337b6f11599a33c6c8ba3857a31a839f8d59
Mark Abraham [Wed, 7 Dec 2016 04:16:48 +0000 (15:16 +1100)]
Merge branch release-2016
Ignored fix to zlib management for GMX_EXTERNAL_TNG=on because that
was already a feature of the refactoring of TNG management in master
branch.
Change-Id: I8bc7ce196fb0d64685c6957b5055d73ff093d864
David van der Spoel [Mon, 28 Nov 2016 20:12:24 +0000 (21:12 +0100)]
Couple of new quotes
Change-Id: Idf02358ec11092e9d6e3c7e58397ad57bb94f00e
Teemu Murtola [Mon, 5 Dec 2016 19:26:27 +0000 (21:26 +0200)]
Fix use of position variables with plus/merge
If a selection contained a position variable (e.g., 'com of ...') that
was used more than once, and at least one of those uses was with
plus/merge, there were out-of-bounds memory writes. This was caused by
the internal position structure not getting fully initialized.
Incomplete initialization happens in all contexts with such variables,
but only plus/merge (and possibly permute) actually use the values that
remained uninitialized, which caused them to incorrectly compute the
amount of memory required to store the result.
Fixes part of #2086.
Change-Id: I016e796db268a11d557309935c02cbd1bc79a83c
Mark Abraham [Mon, 5 Dec 2016 22:54:01 +0000 (23:54 +0100)]
Fix memory handling in gmx dump of TNG files
Calling code in dump.cpp did not free the memory used in each loop
over different TNG data blocks. This is also more efficiently and
simply done with srenew, along with a final sfree.
Change-Id: I0fbfdc9acf3bc5f498ec3ec9b15da1c59bf4c271
Aleksei Iupinov [Mon, 5 Dec 2016 17:11:54 +0000 (18:11 +0100)]
Stop including parallel_3dfft.h in headers
Change-Id: I21565f240f892e8fa9596675795e47e1f7cd7087
Mark Abraham [Mon, 5 Dec 2016 13:25:54 +0000 (14:25 +0100)]
Remove undue narrowing of integer in TNG reading
This compromised the reading of TNG trajectories with sufficiently
large numbers of frames. Both types are 64-bit integers so we should
just do the obvious thing.
Change-Id: Id8dcaacc35231c6b4737d9924f70da3ac29e7408
Mark Abraham [Mon, 24 Oct 2016 15:45:24 +0000 (17:45 +0200)]
Add INSTALL-dev to aid people doing unusual builds
Occasionally it is useful to build GROMACS other than from an official
release tarball, e.g. when testing a new feature. The contents of this
file will help such people to find the right documentation, without
compromising clarity for normal installations from the tarball.
Change-Id: I38d957fe0d1ca2ba1e509ed30bb93a100f018306
Aleksei Iupinov [Fri, 28 Oct 2016 11:09:51 +0000 (13:09 +0200)]
Move GPU assignment functions into a separate file
2 GPU assignment functions (gmx_select_gpu_ids() and set_gpu_ids())
are moved from detecthardware.cpp to a new file hardwareassign.cpp
to separate the GPU scheduling from GPU detection. They are also renamed
for clarity: set_gpu_ids() to assign_rank_gpu_ids(),
gmx_select_gpu_ids() to gmx_select_rank_gpu_ids().
Related deprecated function print_gpu_detection_stats() is also moved,
and changed to only print errors in case of heterogenous MPI configurations,
like it was intended to.
sprint_gpus() is refactored.
Change-Id: Ieef402954194e747e4c6dc5535e0652b5f862e28
Mark Abraham [Thu, 1 Dec 2016 00:24:48 +0000 (01:24 +0100)]
Fix minor trjconv bug
gmx trjconv -novel -f in.pdb -o out.pdb did not work as was probably
intended, because ftpin had an excessive large scope plus a default
value, and was only set by the -vel path (which fortunately is the
default).
Minimized scope of ftp while I was there.
Change-Id: I6b7dadc109834384f6cfb19f61258fa30d52ef80
Teemu Murtola [Sat, 26 Nov 2016 05:07:00 +0000 (07:07 +0200)]
Additional selection help
- Explain resindex and resnr keywords in selection help.
- Explain how selection-enabled tools treat -s and -f input files.
Fixes #2083
Change-Id: I93e38c46a2bdb35f057688cf29fb3392712c2443
Berk Hess [Tue, 11 Oct 2016 12:16:22 +0000 (14:16 +0200)]
Change spline moduli calculation to double
Even though single precision seems enough, since the spline moduli
are only calculated once per grid, we should do this in double.
Also simplified the code by using the actual spline order, changing
and merged loops and removing a lot of unused variables.
Change-Id: If1bd3741a3efca14e6fefe1f80aa10cc31f84e42
Berk Hess [Fri, 14 Oct 2016 20:12:54 +0000 (22:12 +0200)]
Convert energyhistory_t to use std::vector
This change converts energyhistory_t and its child struct
delta_h_history_t to classes that use std::vector. Thus the init
and done routines and energyhistory.cpp are removed.
Part of #2059.
Change-Id: Ieb1f43d18187d4f8de5a21d043bcddcf6686280d
Berk Hess [Mon, 17 Oct 2016 12:29:52 +0000 (14:29 +0200)]
Use templating in checkpoint.cpp
The low level int, real and double writing routines have been
converted to a single template function. The listing functionality
has been moved to a separate function. Added functions for processing
more std::vector types.
Also fixes a bug causing memory corruption in gmx dump -cp.
Part of #2059.
Change-Id: Ia48e57841c7a2dfaa3aefd1f43f0cdc9c0034119
Mark Abraham [Thu, 17 Nov 2016 23:31:21 +0000 (00:31 +0100)]
Stop including tng_io_fwd.h
The two header files in GROMACS associated with TNG support only need
a forward declaration of the tng_trajectory type, and the typedef
tng_trajectory_t. For a build without TNG, that is all that is
required, because the pointer is never dereferenced. For a build that
uses TNG (whether bundled with GROMACS or installed on the systm), if
TNG no longer declares a type of that name, then compilation will fail
with or without this change.
Thus there is no change in quality of support of TNG from this change.
However, it does avoid a build configuration that does not use TNG
needing to be able to find one. This will be convenient for static
analysis support.
Also removed a useless include of tngio_for_tools.h.
Change-Id: I3438d3e1b0c38a62afec4ea3a7f6e977d6602d96
Aleksei Iupinov [Thu, 10 Nov 2016 12:34:46 +0000 (13:34 +0100)]
Move hardcoded PME grid indexing constants into header
Moved the table size factor of 5 to pme-grid.h as a constexpr.
Also changed the spread code that use the table to use a constexpr
for the offset, which in turn determines the table size.
Change-Id: Ief524e9510c0406f60973800f2e110c361128ef5
David van der Spoel [Thu, 18 Aug 2016 08:04:33 +0000 (10:04 +0200)]
Added first tests of bonded force functions.
Tests for bond_angle and dih_angle functions.
Some tests for bondeds, angles and dihedrals.
Part of #2034
Change-Id: I53835ff6fea98e8163505126d347150b64262770
Mark Abraham [Mon, 7 Nov 2016 16:54:49 +0000 (17:54 +0100)]
Enhanced ArrayRef
Added a non-explicit constructor also for std::array, so we can
use ArrayRef more often as a view of memory.
Most clients need to know that the storage has a starting pointer, is
contiguous, and has a given size, but doesn't care e.g. whether it can
be resized or inserted into. The interface for such clients should
express that, so we avoid ripples all over the code base when someone
finds a reason to switch between std::vector, std::array or perhaps
something custom.
Change-Id: I98d96281ab324f2c0d3d3188810295d0027e5fe5
Mark Abraham [Mon, 7 Nov 2016 15:58:42 +0000 (16:58 +0100)]
Created paddedvector.h
This permits forcerec.h to not depend on state.h, and creates a stable
location in which to implement e.g. PaddedRVecVector. There are now
about 25 fewer source files that depend on state.h.
Change-Id: I07c443dea45b394773d60f74b036584af5920cf8
Mark Abraham [Wed, 16 Nov 2016 15:33:05 +0000 (16:33 +0100)]
Remove unimplemented gmx trjcat -vel
Change-Id: Iae2e46c43b01d46fb0c6f0734c2de309a5395564
Carsten Kutzner [Tue, 15 Nov 2016 14:13:41 +0000 (15:13 +0100)]
Fixed typo in membed.cpp
Fixes #2076
Change-Id: Idcebb45ee85b478d7863ac55eb5cef62a2109bb8
Christoph Junghans [Thu, 3 Nov 2016 18:12:17 +0000 (12:12 -0600)]
cmake: fix build with GMX_EXTERNAL_TNG=ON
tng_set_source_properties is not defined in case of GMX_EXTERNAL_TNG=ON
due to the fact that BuildTNG.cmake never gets included. Also this
call isn't really needed tng doesn't get compile when external anyway.
Change-Id: Id3c7e0da55ce9ef8cf43d2aecaa187e965bf6ad2
Dan Horák [Tue, 8 Nov 2016 10:38:42 +0000 (11:38 +0100)]
Fix x86 conditional
The CpuInfoTest.SupportLevel testcase fails on s390x because wrong
condition in src/gromacs/hardware/tests/cpuinfo.cpp is used. Fixed
this by setting GMX_TARGET_X86 to 0 or 1 in all cases, both for
GROMACS CMake detection and GROMACS build.
Fixes: https://bugzilla.redhat.com/show_bug.cgi?id=
1390149
Refs #2072
Change-Id: Id50fd65c6228a25f2bb2eca684d680a2b34d2263
Teemu Murtola [Sat, 4 Jun 2016 18:09:22 +0000 (21:09 +0300)]
Add selection-enabled gmx traj
For now, this tool only plots coordinates, velocities, and forces for
selections, so it should provide a full replacement for -ox, -ov, -of,
-com, and -mol from gmx traj.
Clean up implementation in other tools noticed while touching them.
Change-Id: Ia3b0e77353d9183ffc049d1e1fb0253e30332664
Roland Schulz [Fri, 21 Oct 2016 19:25:32 +0000 (12:25 -0700)]
Supress ICC 16 on Windows false postives
Change-Id: I7ef020d12a7f0dbbb9e0ddf60bdc6b8a671652b4
Aleksei Iupinov [Mon, 31 Oct 2016 16:29:41 +0000 (17:29 +0100)]
Remove imatrix type and related unused/erroneous code
Change-Id: I7fd80b7b05cbd3206668168964501856246de0b4
Szilárd Páll [Tue, 1 Nov 2016 11:28:17 +0000 (12:28 +0100)]
Merge "Merge branch release-2016"
Berk Hess [Tue, 1 Nov 2016 11:05:07 +0000 (12:05 +0100)]
Fix time label print in gmx vanhove
Change-Id: Ibf668e46622c2739ae44f950d1bbfadbbb67b276
Mark Abraham [Mon, 31 Oct 2016 11:39:40 +0000 (12:39 +0100)]
Merge branch release-2016
Trivial conflicts for version number and the fix for gmx
wham that was duplicated in each branch.
Change-Id: I0ba030398cc2d3679841000a40db6e8a3f7b68cb
Mark Abraham [Mon, 31 Oct 2016 11:39:40 +0000 (12:39 +0100)]
Merge branch release-2016
Trivial conflicts for version number and the fix for gmx
wham duplicated in each branch.
Change-Id: I0ba030398cc2d3679841000a40db6e8a3f7b68cb
Teemu Murtola [Wed, 26 Oct 2016 18:44:12 +0000 (21:44 +0300)]
Support normalizing values in KeyValueTree
Make it possible to normalize values stored in a KeyValueTree to match
an Options structure. This makes the types etc. consistent in the tree.
This is mainly useful for reducing variability in tpr files for better
forward/backward compatibility management, but can also be nice for
producing consistent mdp output files from grompp (if we want to keep
that feature).
Change-Id: Ib5ea03faaa690c84076c1ada0c0a08ddf9a1a128
Roland Schulz [Fri, 21 Oct 2016 10:17:38 +0000 (03:17 -0700)]
Replace qsort/bsearch with std::sort/lower_bound
Change-Id: Ic8dc3d86f9738751e463065a012ff1adc02bdf7c
Berk Hess [Tue, 21 Jun 2016 10:00:24 +0000 (12:00 +0200)]
Add gmx dump option for printing parameters
For comparing topologies of the same system with different force
fields it can be very useful to print bonded parameters instead
of the parameter type index.
Change-Id: I06a3b65b695ace4de1491f2d58abb6b7e752693d
Mark Abraham [Fri, 28 Oct 2016 21:18:02 +0000 (23:18 +0200)]
Bumped version to prepare for next patch release
Change-Id: I5f72d87d3b0ed4c06edade7188471ea12ed31046
Mark Abraham [Tue, 25 Oct 2016 09:35:54 +0000 (11:35 +0200)]
Version 2016.1
Bumped regressiontests hash and minor soversion as usual.
Change-Id: I339d70a29553be8662a2a5d3ebb1a11d8361af34
Berk Hess [Tue, 11 Oct 2016 20:08:02 +0000 (22:08 +0200)]
DLB can now turn off, when slower
Under certain conditions, especially with (shared) GPUs, DLB can
decrease the performance. We now measure the cycles per step before
turning on DLB. When the running average of cycles per step with DLB
gets above the average without DLB, we turn off DLB. We then measure
again without DLB. DLB can then turn on again. If we turn on DLB of
DLB multiple times in close succesion and we measure performance loss,
we keep DLB off for the remainder of the run. This procedure ensures
that the performance will never deteriorate due to DLB.
Updated and expanded the DLB section in the manual.
Change-Id: I6e0291c1a41adf6da94fae46d36e0fcb95585a02
Szilárd Páll [Tue, 25 Oct 2016 17:33:30 +0000 (19:33 +0200)]
GPU-related additions to the install/user guide
Additions:
- clarification of OpenCL compile- and run-time dependencies;
- rewrote info about OpenCL-enabled run requirements / peculiarities;
- added section on reducing overheads in GPU runs (related to both
CUDA and OpenCL).
Change-Id: I310ab5605b46b4ed90db87d4ce022005c9b26419
Berk Hess [Tue, 4 Oct 2016 07:39:37 +0000 (09:39 +0200)]
Fix DLB timing with CUDA and OpenCL
With OpenCL the time for the local non-bonded to finish on the GPU
was ignored in the dynamic load balancing. This change lets OpenCL
take the same code path as CUDA.
Also the cycle wait limit of 50 Kcycles was far too small for both
CUDA and OpenCL. It now 2 Mcyles, based on measurements.
Note that with OpenCL we should have access to accurate host and
device timing (unlike with CUDA), but we will not use that in
a release branch.
Change-Id: I5b401fdeae7ab0b426a33baf01a3dbeb7d0d924e
Szilárd Páll [Tue, 25 Oct 2016 23:29:01 +0000 (01:29 +0200)]
Make -cl-fast-relaxed-math default
The change makes fastmath default and changes the previous env-var
trigger to GMX_OCL_DISABLE_FASTMATH to allow disabling it for testing.
It is known to be faster on all supported platforms (and we use it in
CUDA too) and it has been planned to be enabled for the r'16 release.
Change-Id: I8d196c9a14785ff43aae144ed95c3cb29241c83b
Szilárd Páll [Tue, 25 Oct 2016 22:52:37 +0000 (00:52 +0200)]
Add GMX_DISABLE_GPU_TIMING env var
It disables timing for both CUDA and OpenCL so on the long run
it can replace both.
Change-Id: I3556d87c135eba2e24935e77a0d608b72219b284
Teemu Murtola [Fri, 30 Sep 2016 19:17:22 +0000 (22:17 +0300)]
Electric field mdp parsing using options
Make the module declare a structured set of options, as well as a
transform from a flat mdp structure to this set of options.
Use these for assigning the input values, instead of passing t_inpfile
directly.
There is one regression introduced here: values not specified in the mdp
file are no longer automatically inserted with defaults, and comments
related to the electric field input values are lost. With just the
electric field affected, this should not be a big deal, but that can
limit adoption of this approach until we can solve it (preferably, by
changing the mdp format to something where it is easier).
Change-Id: Ic71275f3533f06ce6fee64983c7e1686b782fb9b
Teemu Murtola [Fri, 21 Oct 2016 14:17:32 +0000 (17:17 +0300)]
Support for default values from Options to KeyValueTree
Make it possible to copy default values from an Options structure to a
KeyValueTreeObject for values that are not present in the original tree.
Also, sort the tree values in the order they are present in the Options
object.
Basic things work, but this will require some generalization in the
future.
Change-Id: If1dd59a11d34af19e16712de12fee705c9b814f2
Aleksei Iupinov [Mon, 24 Oct 2016 10:58:27 +0000 (12:58 +0200)]
Treat CUDA files as C++ during cppcheck
CUDA sources (*.cu) were treated as plain C for cppcheck purposes,
but should be treated as C++.
Some outdated CUDA suppressions removed.
Change-Id: I26fb768464660da1e569dda6d844a63ee2823313
Mark Abraham [Fri, 21 Oct 2016 21:12:04 +0000 (23:12 +0200)]
Update install guide
Some recent traffic on gmx-users suggested some
improvements.
Change-Id: Iaaf116ebf582755a466048aed1cd30bc123dc817
Teemu Murtola [Thu, 20 Oct 2016 16:04:15 +0000 (19:04 +0300)]
Clean up option (default) value access
Currently, the only user for valueCount() and formatValue() in
OptionInfo was actually interested in the default values, and limiting
access to the default values only makes the responsibilities clearer.
So replace both methods with a single method that returns just the
default values. The internal implementation currently places some
limitations on when this can actually be called, but that should not be
a problem for current or future uses.
Change-Id: I3e68ce397ec3f40f62ececad4ee6b87d0ecc790e
Roland Schulz [Fri, 21 Oct 2016 14:06:08 +0000 (07:06 -0700)]
Suppress cppcheck warning
Change-Id: I7b212df760c3dfb0020c41f9050e70d8c4be7b48
Mark Abraham [Tue, 18 Oct 2016 15:32:06 +0000 (17:32 +0200)]
Update cppcheck support to 1.76.1
Suppressed some classes of warnings where cppcheck was systematically
failing (for at least some source files). Added assert statements
to cover others.
Propagated some const correctness.
Replaced some block_* macros with templated functions in a header
that we re-use in a few places.
The gmx_arpack and lapack issues were inherited from the original
FORTRAN.
The simd/support.cpp issue is a bug that is fixed in release-2016.
Removed some unnecessary stderr output.
Noted TODOs for further cleanup.
Change-Id: Ia93690e3dbd529ef27e5b7f8331d12a2f7d34766
Teemu Murtola [Mon, 10 Oct 2016 15:59:13 +0000 (18:59 +0300)]
Serialization support for KeyValueTree
Implement serialization of KeyValueTree objects to xdr files for use in
storing inputrec values using this format.
There is a C++ ISerializer interface in between to support testing, but
in the future, this could possibly be replaced with more direct xdr
serialization. However, our current gmx_system_xdr.cpp does not support
in-memory serialization, which would be a requirement for broadcasting
the data structure, so the ISerializer can provide a useful abstraction
also for this.
Change-Id: I6836d8e7f725c364336e09745052521eccf331ce
Mark Abraham [Sun, 16 Oct 2016 21:58:10 +0000 (23:58 +0200)]
Upgrade coverage matrix.
Add support for CUDA 8.0, and migrate responsibilities. This will have
the side effect of actually using bs_nix1204 again for testing master,
because it is the only GPU slave that currently has CUDA
8.0. bs_nix1310 still has the CUDA 6.5 job, and some non-GPU jobs.
Removed specification of cmake-3.5.2 which isn't necessary to be
sure that we check in pre-submit testing.
Change-Id: I559189e74f366fa1523fa6a8ad650471df4fcfb3
Mark Abraham [Tue, 18 Oct 2016 15:16:02 +0000 (17:16 +0200)]
Fix SIMD suggestion for VMX
Change-Id: Iebf55611512bf02d2a1a5780a1d6c05ce4b16023
Erik Lindahl [Sun, 21 Feb 2016 21:31:01 +0000 (22:31 +0100)]
New classes for spline interpolation tables
Quadratic and cubic spline tables can be constructed either
from analytical functions or numerical vector input, and they
can contain an arbitrary number of functions as multi-tables.
Spacing is optimized to achieve the requested precision.
To make the class more generic it works with functions and
derivatives, and avoids worrying about swapping signs to get
forces. The interpolation functions are templated and will also
work with SIMD, without exposing any table internals.
Change-Id: If75f52b0601ad4b396d3cef74b5bbbe81ba91753
Teemu Murtola [Wed, 12 Oct 2016 17:09:26 +0000 (20:09 +0300)]
Support option assignment from different precision
Make it possible to assign a value from float to DoubleOption and from
double to FloatOption. This is needed to support tpr serialization for
cases where the code reading the file is different precision than what
wrote it.
Change-Id: Ib2268b343e4abbe70868d0d60b66559b8052c239
Teemu Murtola [Sun, 9 Oct 2016 18:33:06 +0000 (21:33 +0300)]
Add support for reading values from refdata
This is the easiest way to support tests in child changes for
serialization. Some alternative approach may be possible in the future,
when the serialization approach matures, but I seem to recall there have
been requests for this functionality also in other contexts. There is
some less-than-ideal behavior (in particular, a newly created test fails
if it uses this functionality, and only succeeds when you actually
create the reference data).
Also add support for a separate type of unsigned char reference values,
to support serialization tests.
Change-Id: I35ee9d43a0737a342f756cda0e7a789273ce1d9e
Teemu Murtola [Sun, 2 Oct 2016 18:26:16 +0000 (21:26 +0300)]
Improved error handling for KeyValueTree operations
Support an error handler for operations involving KeyValueTrees to allow
for better error messages during mdp parsing.
Change-Id: I3738b956baafe7a4ecb96ec6f9e4729541d74bf8
Berk Hess [Sat, 15 Oct 2016 08:52:06 +0000 (10:52 +0200)]
Move energyhistory_t out of t_state
We have three different types of states in mdrun:
1) the microstate of the system we are simulating
2) history information for output
3) the state of the simulation machinery in mdrun
The struct energyhistory_t clearly belongs to 2) and is therefore
moved out of t_state, which should eventually only contain 1).
TODO: Consider what to do with the other structs in t_state that
(also) store history rather than the state of the simulated system.
Note: reverts recent commit
ec827264
Part of #2059.
Change-Id: Ie84a19efcd0a170c0aaafe18c06275b7fb15244a
Teemu Murtola [Tue, 12 Apr 2016 17:53:43 +0000 (20:53 +0300)]
Improved address sanitizer support
Use support in CTest 3.1+ for parsing ASAN output. Work around various
bugs in CTest to make this actually work. Remove an OS X workaround,
since it does not appear necessary with a recent XCode toolchain.
Use newer clang to get LeakSanitizer.
Change-Id: I37002bffd653e04b52ba340a97d2806851f692b8
Teemu Murtola [Sat, 15 Oct 2016 03:11:17 +0000 (06:11 +0300)]
Work around memory leak in t_state
Use std::shared_ptr for t_state.enerhist, which should have the same
semantics as the earlier plain pointer, but ensure that the memory gets
eventually freed.
Change-Id: Ibe291261eb4997035a5165130ee01d309a1dc395
Teemu Murtola [Fri, 14 Oct 2016 18:32:35 +0000 (21:32 +0300)]
Fix most memory leaks recently introduced
- Do not overwrite memory allocated in init_mtop() when creating
molecules in selection tests.
- Add function to properly deallocate t_topology and gmx_mtop_t when
gmx_mtop_t_to_t_topology(..., false) has been called.
- Free all memory in done_mtop().
These should be enough to (again) make the unit tests free of memory
leaks, except that t_state.enerhist is leaked in a few places. That
requires more complicated handling.
Change-Id: I84b853b9cb8a11c0458ea4f29316a83a41d7ae22
Berk Hess [Thu, 18 Aug 2016 20:40:48 +0000 (22:40 +0200)]
Apply Berendsen P-couple at nstpcouple steps
Berendsen pressure coupling was applied at step%nstpcouple=1. Since
there is no need for this, this is changed to step%nstpcouple=0.
This also simplifies the P-coupling management.
Note that this change prevents continuation from old checkpoint files
for Berendsen P-couple runs, since the step-1 pressure is removed.
Change-Id: I5e2e6b1a1d5cb347ebdd6c1a402b41280bedff68
David van der Spoel [Fri, 14 Oct 2016 06:41:25 +0000 (08:41 +0200)]
Fixes some memory leaks associated with testing applied forces
Fixes memory leaks associated with the electric
field test. Implemented a done_commrec function.
There may be need for a done_domdec as well but
that falls outside the scope of this patch.
Change-Id: Ib86629bb7959b064b6ac3a57d4bb96e2dd3bfe94
Teemu Murtola [Thu, 29 Sep 2016 18:44:49 +0000 (21:44 +0300)]
Use gmx_mtop_t in selections, part 3
Convert remainder of the selection code to use gmx_mtop_t.
Part of #1862.
Change-Id: Icb1c4a30cc5456e64ed2d73f93ca4a7d6dbfbfbd
Teemu Murtola [Tue, 21 Jun 2016 18:42:59 +0000 (21:42 +0300)]
Use gmx_mtop_t in selections, part 2
Use gmx_mtop_t throughout low-level selection routines, i.e.,
centerofmass.cpp, poscalc.cpp, and indexutil.cpp. Adapt test code,
which is now using gmx_mtop_t throughout as well.
In places where gmx_mtop_t is actually accessed, the changes are as
local as possible. In most cases, some additional restructuring could
give better performance and/or much clearer code, but that is outside
the scope of this change.
Part of #1862.
Change-Id: Icc99432bddec04a325aef733df56571d709130fb
Teemu Murtola [Tue, 21 Jun 2016 18:42:59 +0000 (21:42 +0300)]
Use gmx_mtop_t in selections, part 2
Use gmx_mtop_t throughout low-level selection routines, i.e.,
centerofmass.cpp, poscalc.cpp, and indexutil.cpp. Adapt test code,
which is now using gmx_mtop_t throughout as well.
In places where gmx_mtop_t is actually accessed, the changes are as
local as possible. In most cases, some additional restructuring could
give better performance and/or much clearer code, but that is outside
the scope of this change.
Part of #1862.
Change-Id: Icc99432bddec04a325aef733df56571d709130fb
Berk Hess [Thu, 13 Oct 2016 12:28:36 +0000 (14:28 +0200)]
Extend mtop_lookup.h
Added three lookup functions that will be used in the selection code.
Harmonized the functions by making all functions that look up
a single object return a reference.
Replaced uses of mtopGetAtomParameters() that only used the mass
(which is nearly all) by mtopGetAtomMass().
Change-Id: Ibbe9729502038cd1f863433ce03a80dc544e4003
Teemu Murtola [Sun, 2 Oct 2016 04:58:38 +0000 (07:58 +0300)]
Add back-mapping to KeyValueTreeTransform
Add ability to map paths from the output structure of the transform back
to the original structure, which will be useful for error messages.
Change-Id: I9dded5a517fa72177219294596e5c23bec7785ce
Teemu Murtola [Thu, 15 Sep 2016 19:08:02 +0000 (22:08 +0300)]
Update bundled TNG
This commit bundles
6e41191016 from the TNG repo.
Required TNG 1.7.10 in future, which is the first version to include
support for the build system features used here.
Update the build system to use imported targets and interface properties
that TNG now provides. Add support for building TNG that also bundles
zlib, which reduces the dependency footprint of GROMACS, which is
important for portability and ease of installation.
Refs #1908.
Change-Id: Ibc94d5a9470136331045738f105634ec95fdb455
Teemu Murtola [Sun, 2 Oct 2016 05:20:12 +0000 (08:20 +0300)]
Getter for mapped paths from KeyValueTreeTransform
This allows identifying which values the transform will use. In the
long run, this may be replaced with another mechanism (or removed
altogether), but for now, this makes it easier to do piecewise
transition from old mdp parsing to using KeyValueTree and options.
Currently, the values are returned in alphabetical order, but subsequent
work may need this in the order the rules are added. That will be easy
to change internally to the transform.
Change-Id: I3f225ce4f693644e5ac17685f0a887eec02807a8
James W. Barnett [Tue, 11 Oct 2016 13:09:55 +0000 (08:09 -0500)]
Set maxwarn to INT_MAX if GMX_MAXCONSTRWARN < 0
maxwarn is set to the value of the environmental variable
GMX_MAXCONSTRWARN, and we tell users to set that variable to -1 to have
no maximum. This condition was not being checked, so when set to -1 just
1 SETTLE warning was enough to halt the program. This commit fixes
that behavior by setting maxwarn to INT_MAX if GMX_MAXCONSTRWARN is -1
(or any other negative number).
Fixes #2058.
Change-Id: Ie6e2cb57f8402dd9a327f72f7fad36db19b8bb68
Teemu Murtola [Mon, 20 Jun 2016 17:59:30 +0000 (20:59 +0300)]
Use gmx_mtop_t in selections, part 1
Make the C++ analysis framework (and insert-molecules, which is also
using selections) use a gmx_mtop_t as the initial internal format to
load the topology, and make SelectionCollection::setTopology() use an
mtop. Adapt tests. One test is disabled as it is much easier to
re-enable it after the next step in the conversion process than in this
intermediate state.
Internally, the mtop structure is still converted to t_topology for use
in lower levels and in the tool code.
This change also makes it possible to convert the analysis tools and gmx
insert-molecules to use gmx_mtop_t independently from changes in the
selection code.
Part of #1862.
Change-Id: I3ce03c6524b27f0f44168890ac1a4a491da52a4c
Teemu Murtola [Fri, 17 Jun 2016 05:49:40 +0000 (08:49 +0300)]
Wrap sel. method evaluation parameters to struct
This removes about 1/3 of t_topology instances in the selection code,
reducing the number of lines that need to be changed when switching to
gmx_mtop_t.
Also make most of the contents const.
Related to #1862.
Change-Id: Idcd71bc578a6daa4644f049a31f84e74717c258a
Mark Abraham [Wed, 12 Oct 2016 12:01:18 +0000 (14:01 +0200)]
Make regressiontests updater build work for master branch
Forgot to resolve this TODO in the merge.
Change-Id: I5ec487e5335ca34509ee1c0fc5f8b841d1718d0d
Berk Hess [Wed, 12 Oct 2016 14:35:21 +0000 (16:35 +0200)]
Fixed exception in usused result
Change
f2854f89 introduced an code path in NPT_energy() of which
the result is, as of yet, unused. Here MassQ->Winv was uninitialized.
This could cause tests to fail with a floating point exception.
Change-Id: I7973336fb34ed50e7eb87da63af964058fd1aef0
Berk Hess [Mon, 10 Oct 2016 07:08:05 +0000 (09:08 +0200)]
Fixed print bug in gmx wham
Change-Id: I1957d1213498c25dff0f9257a51aa89af8cf03b8
Berk Hess [Mon, 15 Aug 2016 09:51:56 +0000 (11:51 +0200)]
Refactor NPT energy calculation
The NPT conserved energy quantity calculation is now managed by
a single function with separate functions for each thermo- and
barostat.
Change-Id: Id7cf431e4da78bffe33caaddb0a7c806c9c29091
Berk Hess [Mon, 14 Dec 2015 14:18:40 +0000 (15:18 +0100)]
Restructure leap-frog integrators
There are now 2 template function for MD leap-frog integration
instead of 4 branches in multiple functions.
In addition to invmass, mdatoms now contains invMassPerDim.
invMassPerDim is set to zero for encode frozen dimensions, so LF
update functions no longer need to check the freeze groups.
Also removed the conditionals for vsites and shells in the LF update
functions. Their velocities are now set to zero at startup.
A template function for the most common leap-frog integrator setups
allows for full SIMD acceleration, at least for AVX with gcc5.
Changed dt from double to real in the update, since we need far less
than real precision.
Changed calculation of alpha for VV to real, as it is passed as real.
Fixed multiple time stepping with Parrinello-Rahman and Nose-Hoover.
Fixes #2031.
Fixes #2032.
Change-Id: Iae5e787f1338b99c2338c9d0c1f14e90393e9252
James W. Barnett [Tue, 11 Oct 2016 16:07:36 +0000 (11:07 -0500)]
fix typo
Change-Id: Iee8170173b5c4f02361e588260985d7ddf24f198
Mark Abraham [Sat, 8 Oct 2016 23:35:10 +0000 (01:35 +0200)]
Update for FFTW 3.3.5
The auto-download now gets FFTW 3.3.5 and builds it properly,
including with --enable-vsx when GMX_SIMD is set to VSX, i.e. for
Power8, and --enable-avx512 when GMX_SIMD is any of the AVX flavours
(which is safe on non-512 now, works on KNL, and is presumed useful
for future AVX512 architectures).
Note that 3.3.5 does not automatically add avx and sse support if
configured with --enable-avx2, so changed the documentation
accordingly.
Change-Id: I2a48ec1cb4f812dcae18870e0afcaf1120da251b
Teemu Murtola [Mon, 20 Jun 2016 17:55:59 +0000 (20:55 +0300)]
Support concurrent t_topology and gmx_mtop_t use
Make gmx_mtop_t_to_t_topology() take a boolean flag that specifies
whether to free memory from mtop or not. This makes it possible to
convert an mtop to a t_topology and then use both in subsequent code.
This in turn makes a piecewise conversion from t_topology to gmx_mtop_t
possible.
Using these two concurrently currently always leads to memory leaks, but
these should mostly be temporary during the conversion, and can be
sorted out separately if necessary.
Part of #1862.
Change-Id: Iccd6039c2226d1dc617963878e5640bb53f09ad6
Teemu Murtola [Wed, 15 Jun 2016 17:26:14 +0000 (20:26 +0300)]
Check atom mass availability in selections
Check for the availability of atom masses before using them in
selections, and give fatal errors early instead of asserts when
accessing the masses. Try to load the masses on demand if not
available.
Change-Id: If288d2b3920b92c6994aee8b7ff96c85ce3f6cb8
Berk Hess [Tue, 27 Sep 2016 12:50:05 +0000 (14:50 +0200)]
Speed up mtop_util atom lookup
The lookup of atom indices and properties on global atom index have
been sped up by moving functions to a new header file mtop_lookup.h
and by storing start and end global atom indices in gmx_mtop_t.
Another performance improvement is that the previous molblock index is
used as starting value for the next search.
The atom+residue lookup function now also returns the reside index.
This change also simplifies the code, since we no longer need a lookup
data structure.
A large number of files are touched because the t_atom return pointer
is changed to const also in the atomloop functions.
Change-Id: I185b8c2e614604e9561190dd5e447077d88933ca
Mark Abraham [Mon, 10 Oct 2016 22:49:37 +0000 (00:49 +0200)]
Merge "Merge branch release-2016"
Aleksei Iupinov [Mon, 10 Oct 2016 10:28:54 +0000 (12:28 +0200)]
Fix trivial PME memory leaks
This fixes still not all, but most of the memory leaks.
Change-Id: Iccd4ec5432df845665fedad411ac8fc83898c767