Aleksei Iupinov [Mon, 5 Dec 2016 16:36:09 +0000 (17:36 +0100)]
PME spline+spread CUDA kernel and unit tests
The CUDA implementation of PME spline computation and charge spreading
for PME order 4 is added in pme-spread.cu.
The unit tests for PME CPU spline/spread stages
(
e8cf7c0) are also extended to work with
the PME CUDA kernel, using the same reference data.
The tests iterate over all CUDA GPUs which are compatible with Gromacs.
Refs #2054, #2092.
Change-Id: If5ec49f030b9b94395db28fa454ea25c3efb05d1
Mark Abraham [Tue, 12 Sep 2017 09:34:54 +0000 (11:34 +0200)]
Use clang-5 in Jenkins
Change-Id: Ibff723750ff66629da5066c4de43ed3de1198f19
Berk Hess [Mon, 9 Oct 2017 12:07:10 +0000 (14:07 +0200)]
Disable ARM Neon native rsqrt iteration
Fixes #2261
Change-Id: Iebcdb3f85506b8159c06d9a9a5cb5f5c81ba11c9
Aleksei Iupinov [Mon, 9 Oct 2017 10:47:26 +0000 (12:47 +0200)]
Remove some unnecessary includes from PME
Change-Id: I16da782c6c889fdde6ed81044803edfb367624b3
Aleksei Iupinov [Mon, 26 Sep 2016 10:53:29 +0000 (12:53 +0200)]
PME GPU/CUDA data framework.
This patch adds most of the PME GPU data handling routines
(pme.h and pme-gpu.cpp / pme.cu(h) / pme-gpu-internal.h/cpp),
data structures used on host and on device
(pme-gpu-types.h / pme.cuh).
The PME GPU kernels and their host code will live in separate files.
There is also cuFFT code (pme-3dfft.cu(h)) and
optional CUDA timing events (pme-timings.cu(h)) included.
Currently this is a dead code, PME GPU is not actually getting initialized
as the corresponding enum is always set for CPU path, which is asserted.
Change-Id: I9b03f54a2412885e25ea27f17bf2dca1b01f9f78
Mark Abraham [Sat, 7 Oct 2017 12:57:56 +0000 (14:57 +0200)]
Tell cppcheck that .cpp and .cu files are c++
This will avoid known strange behavior with .cu files.
Fixes #2265
Change-Id: I06850509afa11a531fe9b7063368614c81f4a7d1
Roland Schulz [Fri, 22 Sep 2017 17:05:02 +0000 (10:05 -0700)]
Refactor load+SimdLoad*ProxyInternal to reduce duplication
A child patch requires both the const and non-const version.
This would increase the duplication per (un/)aligned load/proxy
from 3 to 6. To avoid this, refactor here to remove the duplication.
Also remove GMX_DISALLOW_COPY_AND_ASSIGN because child patch requires it
to be copyable and macro doesn't work with templated class.
Change-Id: Ib0f6867d2ef75132a1dfa28ea761633adf7d1e8d
Berk Hess [Tue, 3 Oct 2017 11:44:37 +0000 (13:44 +0200)]
Add acceleration correction VCM mode
Minor refactoring in vcm.cpp using templating to reduce code
duplication and improve performance.
Change-Id: I560027fe6f315eede0d7aa573bc22bf12eba4c5d
Berk Hess [Fri, 6 Oct 2017 10:21:13 +0000 (12:21 +0200)]
Fix max_size() in allocator.h
Change-Id: I2d3c0bf2782b59d25f987ed0522d98fd1dc61e15
Berk Hess [Wed, 5 Jul 2017 09:44:42 +0000 (11:44 +0200)]
Add SIMD intrinsics version of simple update
To get better performance in cases where the compiler can't vectorize
the simple leap frog integrator loop and to reduce cache pressure of
the invMassPerDim, introduced a SIMD intrinsics version of the simple
leap-frog update without pressure coupling and one T-scale factor.
To achieve this md->invmass now uses the aligned allocation policy
and is padded by GMX_REAL_MAX_SIMD_WIDTH elements.
Asserts have been added to check for the padding.
Change-Id: I98f766e32adc292403782dc67f941a816609e304
Berk Hess [Wed, 4 Oct 2017 07:36:40 +0000 (09:36 +0200)]
Improve PaddedRVecVector resizing
PaddedRVecVector is now resized with paddedRVecVectorSize() instead
of the using natoms+1 in several places in the code.
In preparation for a SIMD intrinsics version of the integrator,
PaddedRVecVector now uses the aligned allocator and has padding
for GMX_REAL_MAX_SIMD_WIDTH width at the end.
do_force() checks for padding of coordinates and forces.
Also extended ArrayRef to allow for different allocators.
Fixes a potential nullptr issue in doPaddedRvecVector().
Change-Id: Ifb8dacf4f41b755b9981e936e462fa5823cff1d8
Aleksei Iupinov [Thu, 28 Sep 2017 13:08:50 +0000 (15:08 +0200)]
Add timing accumulation capability into GpuRegionTimer
Added a TODO to deprecate NB timing structures in favor of new
functionality.
Change-Id: Idb78e5a36a7f372f01378a580a05b928bd728c57
Berk Hess [Thu, 5 Oct 2017 16:31:58 +0000 (18:31 +0200)]
Make SIMD ambiguous test work with float/double only
Fixes #2262
Change-Id: I612aea147a7808a72aa05dca44f588a60c27eea0
Szilárd Páll [Mon, 2 Oct 2017 23:55:09 +0000 (01:55 +0200)]
Refactor scaled box handling for PME/Ewald
The box scaling code for Ewald and related logic is now encapsulated in
new box scaler class. This also allows box scaling moving box scaling
it further down the call chain so that logic is reduced in do_force.
Change-Id: Ic5071b825b9d36daca5f49d6f7c6c50261af1e1b
Szilárd Páll [Thu, 5 Oct 2017 01:20:10 +0000 (03:20 +0200)]
Fix pair list array assertion
Was caught by the clang CUDA build.
Refs #2259
Change-Id: I8633e48ea5c33225829f92f60c2c785f16e17aca
Szilárd Páll [Thu, 5 Oct 2017 00:53:15 +0000 (02:53 +0200)]
Avoid -Wmissing-prototypes warnings in clang CUDA builds
Fixes #2259 partially
Change-Id: Ib47530c89cf4b3af5c2b65cfcfa39b9dfe0148b4
Roland Schulz [Wed, 4 Oct 2017 00:32:25 +0000 (17:32 -0700)]
Make ConstArrayRef alias to ArrayRef<const T>
Removes code duplication and makes it easier to extend.
Change-Id: I4ac01e3be89bb9f2ad92937ce19e436ac7f1178b
Mark Abraham [Mon, 2 Oct 2017 16:19:05 +0000 (18:19 +0200)]
Continue removing -nb gpu_cpu
Now that hybrid mode is gone, both local and non-local Verlet-scheme
groups use the same kernel_type and thus both nbat pointers were
always the same. Thus, there's no reason to maintain two of them.
This simplifies and slightly optimizes nbnxn_atomdata_set().
Also fixed some other docs, comments, and logic that were either
already wrong, or are useless with hybrid mode gone.
Change-Id: Id02a11a00553b1df151a1e15b934611e0e15b9f7
Roland Schulz [Wed, 27 Sep 2017 22:15:46 +0000 (15:15 -0700)]
Fix that exp(load(x)) is ambiguous
Because of the template argument added by
e34ead15, exp(float) was
preferred over exp(SimdFloat). This causes code which is ambiguous
to compile and creates unintuitive behavior.
Also:
- Add compile tests that these functions don't compile when they
are used ambiguously.
- Add sqrt to scalar_math which was missing
Change-Id: Ic7582764f1fa9b644d4608536100004e5f737462
Roland Schulz [Tue, 3 Oct 2017 19:40:09 +0000 (12:40 -0700)]
Allow non-const access for const ArrayRef
const ArrayRef<T> should not mean that the data contained in the range
is const. If it were used that way, it behave very purely as a const
object because if it is copied it looses its const. Instead
ConstArrayRef<T> (or potentially ArrayRef<const T>) should be used
consistently. This makes having const versions of operator[]/at and
begin/end/front/back confusing and inconsistent. The meaning of
const ArraryRef should be that reassigning a new range to the ref
is not allowed. To be consistent, even for a const ArrayRef non-const
access to the data should be allowed.
Change-Id: I7e921c1a5562889bfd26eb0688b475406c87857c
Aleksei Iupinov [Thu, 28 Sep 2017 13:22:55 +0000 (15:22 +0200)]
Remove GPU timing functions superseded by GpuRegionTimer
Change-Id: I451fdd9263e87a567c8b4942a041de6950c75921
Berk Hess [Fri, 29 Sep 2017 10:36:28 +0000 (12:36 +0200)]
Remove a force buffer argument from IForceProvider
For the foreseeable future force providers will produce forces that
should not go into the coord x force type virial calculation.
Therefore the old force argument is now removed and the old f_novirsum
argument is renamed to force. Also removed the confusingly named
withoutVirialContribution_ container (because providers should actually
provide the virial contributions).
Change-Id: I580ac2cef31da6c191a0852c1f3be0c9e09ea1b0
Mark Abraham [Sat, 15 Jul 2017 07:09:08 +0000 (09:09 +0200)]
Enable group-scheme SIMD with GMX_SIMD=AVX2_128
The group-scheme kernels can can use AVX instructions from either the
AVX_128_FMA and AVX_256 extensions. But hardware that supports the new
AVX2_128 extensions also supports AVX_256, so we those extensions
for the group-scheme kernels.
Change-Id: I7728e1d97998509368dfc456dc9c33489b6dfee5
Aleksei Iupinov [Fri, 16 Jun 2017 16:04:51 +0000 (18:04 +0200)]
Add GpuRegionTimer class
GpuRegionTimer class is implemented in CUDA/OpenCL to help timing
regions of GPU code. For CUDA, it contains pair of CUDA start/stop events;
for OpenCL, it contains fixed-size array of OpenCL events, which are
passed manually into OpenCL calls within region.
Using this class, cu/cl_timers_t structures and the GPU timing code
are made a bit more uniform.
Change-Id: I8fcd7568653c5bcf3496a2bee227ae03f14a756a
Szilárd Páll [Tue, 3 Oct 2017 14:04:46 +0000 (16:04 +0200)]
Move Ewald splitting-related code to ewald-utils
This code used to be under gromacs/math, but it is an Ewald-only
functionality, so it belongs to the Ewald module.
Change-Id: Ib2d7def243a88b09f328a8ea1bafe27dd7a783d5
Aleksei Iupinov [Tue, 3 Oct 2017 14:43:07 +0000 (16:43 +0200)]
Bring CUDA texture getters documentation up-to-date
Change-Id: Id2b588129287a0e2372fd3564f8a24513ae89e0e
Aleksei Iupinov [Fri, 22 Sep 2017 13:35:28 +0000 (15:35 +0200)]
Template/move CUDA texture cleanup code from NB CUDA module to cudautils.cu
Noted TODO: easy transformation into a GPU table class.
Change-Id: I20d684221fa8304d01ab7fd4a19f2c4469110142
Szilárd Páll [Wed, 25 Jan 2017 01:53:17 +0000 (02:53 +0100)]
Enable compiling CUDA device code with clang
clang can be used as a device compiler by setting GMX_CLANG_CUDA=ON. A
CUDA toolkit (>=7.0) is also needed. Workarounds required:
- texture operations are not supported, use the LDG/direct load-based
fallback in such cases;
- CMake does not support natively clang for CUDA, but it's easy to
convince it by setting CXX as compiler and few extra flags for *.cu.
Note that clang support is experimental and it is aimed at improving
portability and to allow using clang sanitizers without hassle in
CUDA builds.
TODO/investigate:
- CMake seems to not track some files properly with clang, changes
to nbnxn_cuda_kernel{,_fermi}.cuh do not trigger a recompile (likely
due to the indirect include through a macro in nbnxn_cuda_kernels.cuh).
- Full rebuild is triggered even if only CUDA compile flags are changed.
Change-Id: I3543469d9f0fda37c186ba8bb474980018bd5c54
Berk Hess [Thu, 28 Sep 2017 21:01:14 +0000 (23:01 +0200)]
Move calling of special force functions
All special force provider algorithm functions are now collected
in computeSpecialForces(). This function is now called before
the wait for non-bondeds on the GPU. This allows for more overlap.
The only cost is potentially one extra force buffer reduction at
steps where the virial is needed, but with PME we already do that.
To achieve this, f->f_novirsum is now always set, as the
documentation already (incorrectly) stated.
This change also simplifies both do_force routines and clarifies
where special algorithms can be called, which could now actually
be anywhere in do_force().
Change-Id: I0711a379ed3c31838ede9e55c4cd5d0a95e967fd
Aleksei Iupinov [Wed, 20 Sep 2017 13:45:13 +0000 (15:45 +0200)]
Add WinAPI page size query for allocator purposes
Change-Id: I4c1e534a4b950bc38d45c40ad5598cabb2045ede
Magnus Lundborg [Tue, 13 Jun 2017 15:04:10 +0000 (17:04 +0200)]
Write atom masses and partial charges to TNG
B states of molecules are not yet written. Data blocks for that
must be added to TNG first.
'gmx dump' will print atom masses and partial charges along
with the molecule, if the data is available. No other utilities
use the data yet.
Refs #2188.
Change-Id: I7dd80d7b6281b2c3710fb541fa3cee6fbdcb2256
Mark Abraham [Mon, 3 Jul 2017 17:40:10 +0000 (19:40 +0200)]
Introduce and use AlignedAllocationPolicy
This permits the allocators to be specialised with a policy class that
can vary (and report on) the alignment.
Change-Id: I875548ac325edcf07074ad35f9d90cdf561ea750
Berk Hess [Wed, 9 Aug 2017 12:06:01 +0000 (14:06 +0200)]
Remove hybrid gpu+cpu nonbonded mode
This mode was not very useful, since it ran the non-local non-bonded
interactions on the CPU. The fraction of non-local interaction is set
by the domain decomposition, so this is not flexible.
Also this mode is not being tested.
Amended docs to remove ambiguous reference to hybrid mode
Change-Id: I8cdd31f228e2c0104527f66265fd06a5e971b9da
Szilárd Páll [Thu, 28 Sep 2017 14:22:17 +0000 (16:22 +0200)]
Correct misplaced CUDA timing event record
The event record happens after a cudaStreamWaitEvent is placed in the
non-local stream and therefore, in that stream it would include the wait
time in the measurement. However, as with DD / two streams timing can
not be performed due to the limitations of CUDA events, in practice this
was never an issue.
Change-Id: I2ca89c7acd461e480a324d40911dd4c6f5aac478
tomaskubar [Mon, 18 Sep 2017 16:57:19 +0000 (18:57 +0200)]
QM/MM: remove optimization and trans. state search
These functionalities used to only work with old versions of Orca,
had very limited use and will possibly not work any longer now.
The possibility of optimization with QM/MM using the Gromacs drivers
(steep, cg, lbfgs) has been already tested,
and it will be added in a follow-up commit.
Transition state search functionality will not be available however.
This is a beginning of an attempt to clean up the QM/MM code.
A version that works with Verlet nblists is already prepared,
and will follow also.
Change-Id: Ice166dad0d4080821f1a20671fe698d549b3ce99
Aleksei Iupinov [Fri, 22 Sep 2017 12:41:02 +0000 (14:41 +0200)]
Move CUDA texture setup code from NB CUDA module to cudautils.cu
Change-Id: I7e47a65866c29be06ce522572e90a17c775157ab
Szilárd Páll [Thu, 21 Sep 2017 14:13:43 +0000 (16:13 +0200)]
Rename GPU launch/wait cycle counters
In preparation for the PME GPU task and GPU launch overhead to be
counted together in the same counter for all GPU tasks, the current main
counters have been renamed to be more general. The label of GPU waits in
the performance table have also been renamed to reflect the task name.
Additionally a non-bonded specific sub-counter is been added.
Change-Id: I65a15b0090c1ccebb300cf425c7b3be4100e17a0
Berk Hess [Sat, 23 Sep 2017 09:28:01 +0000 (11:28 +0200)]
Put rerun state preparation in a function
This is only code motion and some variable renaming.
Note that the vsite construction now constructs in the global state
pointer, but the old code asserted that this was identical to
the local state pointer.
Change-Id: I81d0bad0650eb781b68816e917814b2f97e2d529
Berk Hess [Wed, 6 Sep 2017 13:48:04 +0000 (15:48 +0200)]
Set global state on master rank only
The global state class was initialized on the master rank
and broadcasted over all ranks. This lead to unnecessary communication
and it was difficult to know what part of the global state was up to
date at different points in the code.
Now only the master rank has a global state object.
This change requires conditional access to the global state pointer
for the few algorithms that use it.
Replaced bcast_state() by a function that only broadcasts x and box.
Also made the box pointer constant in domdec initialization.
Change-Id: I924487863abe096eeb0b3cbc944b4ba32898ef03
Aleksei Iupinov [Thu, 21 Sep 2017 16:31:48 +0000 (18:31 +0200)]
Template the CUDA texture setup code on raw value type T
Change-Id: I252e1d68d263f4aca15f00863e9ed67213fdb22f
Aleksei Iupinov [Thu, 21 Sep 2017 15:51:49 +0000 (17:51 +0200)]
Eliminate unused Coulomb correction table size coulomb_tab_size
Change-Id: I35df7fc0590e12de8ad44791bce26cac1193065a
Aleksei Iupinov [Thu, 21 Sep 2017 15:43:17 +0000 (17:43 +0200)]
Eliminate duplicate CUDA texture setup code
init_ewald_coulomb_force_table() now uses initParamLookupTable(),
which is moved higher in the file.
Change-Id: I2cb799f1b4b78c650282be37b125b3da88e98f6c
Berk Hess [Tue, 12 Sep 2017 11:21:50 +0000 (13:21 +0200)]
Change nbnxn indexing to templates
Replaced the index lookup functions for SIMD pair list generation
with templates.
The last remaining ci_to_cj function and call will be removed in
a follow-up change.
Change-Id: I3222e616ac60f846d7c1e85685f915fba014290f
Roland Schulz [Fri, 15 Sep 2017 21:47:37 +0000 (14:47 -0700)]
ICC: Disable include path warning
Under certain circumstances MKL and PSTL can cause spurious
warnings. Unlikely for warning to be important.
Change Icdb24d0fed4060 previously removed this flag for C++.
Change-Id: I828c73c7139532dca6ee2d1279b0d1e109b0cf5c
Mark Abraham [Fri, 15 Sep 2017 08:39:52 +0000 (10:39 +0200)]
Update testing matrices to test with (latest) icc-18
Change-Id: Ia1da377b40fcaba4f364b77437dcddea702968a2
Aleksei Iupinov [Mon, 18 Sep 2017 13:37:44 +0000 (15:37 +0200)]
Skip GPU reallocation of an empty non-local pairlist
This makes the corresponding timing event's usage consistent.
The common early return condition is moved into a new header
nbnbn_gpu_common.h, shared by OpenCL/CUDA.
Change-Id: I5b9cc027676cccda69f5b844d07e94e5fda620e7
Szilárd Páll [Wed, 13 Sep 2017 18:37:39 +0000 (20:37 +0200)]
Minor refactoring of CUDA non-bonded kernels
Refactored the dynamic shared memory pointer assignment for improved
robustness. Also reverted some unnecessary leftover changes introduced
with the Volta-enabling and dynamic pruning that resulted in differences
between the legacy and normal CUDA kernels with the goal of improving
maintainability.
Change-Id: I4ce58f3e1f963935d7e3832ed0e537c94d81a632
Mark Abraham [Sun, 17 Sep 2017 21:43:42 +0000 (23:43 +0200)]
Merge branch release-2016
Kept a cmake variable description string from release-2016
Change-Id: I2077780afbbe3cc610d699ea498caa6959e4000c
Berk Hess [Wed, 14 Sep 2016 10:42:31 +0000 (12:42 +0200)]
Remove nb-parameters from t_forcerec
Removed all Coulomb and Van der Waals mdp parameters from t_forcerec.
The ones that are not used in the Verlet scheme (yet) have been added
to interaction_const_t. Now init_interaction_const() is called early
in init_forcerec().
Change-Id: I9ca14f2194742cc8b0aef09a42dbd75fa3f94517
Mark Abraham [Mon, 11 Sep 2017 16:55:00 +0000 (18:55 +0200)]
Express intent of matrix release build types explicitly
We intend to do primary testing in Jenkins with all assertions
enabled, so that we maxmize our opportunities for useful feedback. We
do so in both Debug and Release flavours, so that we have confidence
that those different builds will remain maximally useful.
Expressing that we are building the Release+assert type explicitly
will help developers understand when and why they get feedback from
Jenkins.
This also permits us to build without assertions in a convenient
way. This is useful for e.g. checking that such builds remain free of
warnings, which is a useful corner case to have changed, since a
variable or parameter might only be used in an assertion expression.
This now happens in one post-submit and all release matrix
configurations.
Updated the release-matrix contents and documentation to be more
consistent with that of the other matrices.
Noted TODO for adding icc 17 testing.
Change-Id: I774602e361163337e9602f497e2302148ccbf544
Mark Abraham [Wed, 6 Sep 2017 08:38:55 +0000 (10:38 +0200)]
Bumped patch version for next release
Change-Id: I2d5758148734f746f9f03afd1ce3a92a02ab3355
Mark Abraham [Wed, 6 Sep 2017 08:36:54 +0000 (10:36 +0200)]
Version 2016.4
Change-Id: I1b8141d667629f77025b186364090e861fa3a428
Aleksei Iupinov [Thu, 14 Sep 2017 13:12:31 +0000 (15:12 +0200)]
Fix non-SIMD build failing
gmx_detect_simd() now returns an uppercase string,
making GMX_SIMD_ACTIVE uniformly uppercase.
Refs #2246
Change-Id: Idb1c2373dc8955ef8bdb36eb0361505238a117ff
Berk Hess [Thu, 14 Sep 2017 14:34:35 +0000 (16:34 +0200)]
Fix nbnxn SIMD 2xNN PME tabulated kernel
This kernel produced completety incorrect forces and slightly
incorrect energies.
This kernel was not (yet) selected by default in a 2016 release.
Fixes #2247
Change-Id: I297ad257932eaabe6cf84b17f34ad555921f48b0
Szilárd Páll [Tue, 29 Aug 2017 16:39:03 +0000 (18:39 +0200)]
CUDA 9/Volta support for the pruning kernel
Added syncwarp to prevent WAR hazard and changes any to any_sync.
Change-Id: I3d370e7c272dd0c2f0eaf8ee97f8797dd74a405d
Mark Abraham [Fri, 8 Sep 2017 16:21:12 +0000 (18:21 +0200)]
Form taskassignment module
Move existing code into new module, in preparation for an increase
in complexity of that new module.
Removed hyphenation of filename to move to more consistent style
overall.
Change-Id: I04e76048483b287485ac6872ed48ccba52df1e45
Mark Abraham [Mon, 11 Sep 2017 15:59:24 +0000 (17:59 +0200)]
Fix compat module definition
There needs to be a defgroup module_compat and whatever name it has
should match the name of the subdirectory. This needs to work
correctly before code in other modules can include a header from
compat module, else check-source will complain that a compat header
isn't documented as being used outside its module.
Change-Id: Ie6e17d92ecf7ede51e0e32af27bef732a52491f1
Erik Lindahl [Fri, 8 Sep 2017 19:03:58 +0000 (21:03 +0200)]
Improve accuracy of SIMD exp for small args
Introduce a separate check for small arguments and
set the result to zero below this cutoff. This change
also moves the exponential tests to ldexp(), which
as a side-effect also makes that function safer by
default, with an optional template parameter to avoid
the checks.
Fixes #2243.
Change-Id: I41bccaeec9921c3aead2cd2caf41cbe2206e0687
Mark Abraham [Tue, 12 Sep 2017 10:01:48 +0000 (12:01 +0200)]
Merge branch release-2016
No conflicts
Change-Id: Iababf3d2439f1b465ebdf8bcb3d29815cb7830e1
Aleksei Iupinov [Wed, 6 Sep 2017 15:18:44 +0000 (17:18 +0200)]
Prevent reference XML reader segfault on nullptr error strings
It is possible for TinyXML2 to return null pointers to the error strings.
This could cause XML reference data reader to segfault.
Refs #2241
Change-Id: I8b72917785080023f75388281dd2cbb4f30da925
Berk Hess [Fri, 8 Sep 2017 13:35:23 +0000 (15:35 +0200)]
Fix exception in SIMD LJ PME solve
Clear SIMD padding elements in solve helper arrays to avoid,
otherwise harmles, fp overflow exceptions.
Fixes #2242
Change-Id: I97e67c4fcc2ef361f54d1627fd0dab4621f4bd33
Berk Hess [Thu, 7 Sep 2017 17:52:29 +0000 (19:52 +0200)]
Do not pass state to init_replica_exchange
init_replica_exchange only used the state to check natoms,
so now we pass only that.
Change-Id: Ie75ca26b9899006f9ca4584c42391a50758c7ed5
Szilárd Páll [Mon, 11 Sep 2017 17:33:09 +0000 (19:33 +0200)]
Merge branch 'release-2016'
Note that changes to the simd_math module/tests from the 2016 branch
were omitted in favor of the current code in master.
Conflicts:
src/gromacs/fileio/oenv.cpp
src/gromacs/fileio/oenv.h
src/gromacs/gmxlib/nonbonded/CMakeLists.txt
src/gromacs/hardware/cpuinfo.cpp
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
src/gromacs/simd/simd_math.h
src/gromacs/simd/tests/simd_math.cpp
src/gromacs/swap/swapcoords.cpp
Change-Id: I357e40f97fd53a34ff900f40bb3fdeb20d864c13
Szilárd Páll [Mon, 4 Sep 2017 15:26:59 +0000 (17:26 +0200)]
NVIDIA Volta performance tweaks
Removed ballot syncs and replaced all computed masks with full warp
mask (as all branches in question are warp-synchronous).
This improves performance by 7-12%.
Change-Id: I769d6d8f0d171eb528d30868d567624d5e246dbf
Berk Hess [Fri, 8 Sep 2017 12:49:40 +0000 (14:49 +0200)]
Fix PBC bugs in the swap code
Fixes #2245
Change-Id: I90e2bed71a2499c63794e420dca383d91e6fc86c
Berk Hess [Sat, 22 Apr 2017 09:41:54 +0000 (11:41 +0200)]
Avoid inf in SIMD double sqrt()
Arguments >0 and <float_min to double precision SIMD sqrt()
would produce inf on many SIMD architectures. Now sqrt() will
return 0 for arguments in this range, which is not fully correct,
but should be unproblematic.
Updated the tests to check for this range and to produce output
that checks all double precision mantissa bits.
Fixes #2164.
Refs #2163.
Change-Id: Ic6d2c6d4102d602703b40e7e8bcc1974a7283f7c
Roland Schulz [Thu, 7 Sep 2017 00:40:06 +0000 (17:40 -0700)]
Fix compiler warning
Change-Id: Ic665baecec83f89bebb0fddea5385ae88c075adb
Mark Abraham [Mon, 4 Sep 2017 07:49:59 +0000 (09:49 +0200)]
Introduce type-safe GPU emulation variables
It's less clearly correct to pass around many variables of bool type,
as often happens in the high-level code.
Change-Id: I9ddb35fa8789e3eb5726fc0143a580493737bc29
Roland Schulz [Mon, 31 Jul 2017 23:56:00 +0000 (16:56 -0700)]
Add isIntegralConstant type trait
Add static assert to pme-gather to make overload safer
Change-Id: I71c67f3ee40185e31796752d090d2aa9f0918ec8
Mark Abraham [Wed, 6 Sep 2017 10:31:52 +0000 (12:31 +0200)]
Enable group-scheme SIMD kernels on recent AVX extensions
The group-scheme code only runs using the feature set of AVX_256, but
that is supported on the more recent hardware, so we should have the
group scheme run with the maximum suitable SIMD. Otherwise people will
need AVX_256 binaries for the group scheme, and other binaries for the
other support.
Change-Id: I7728e1d97998509368dfc456dc9c33489b6dfee5
Berk Hess [Thu, 7 Sep 2017 08:05:33 +0000 (10:05 +0200)]
Fix FEP state with rerun
When using FEP states with rerun, the FEP state was always 0.
Fixes #2244
Change-Id: I457bf444f6c7f8fd357212416311625981b833e6
Mark Abraham [Mon, 4 Sep 2017 21:53:49 +0000 (23:53 +0200)]
Prepare Verlet scheme later in runner
As noted in the TODO, preparing the Verlet scheme can wait until we
need rlist chosen so that we can set up the domain
decomposition. Moving it later in mdrun helps clarify the unrelated
process of setting up thread-MPI, and also means that the state used
when preparing the Verlet scheme is the one from the checkpoint file,
where applicable.
Moved a warning for the group scheme on BG/Q to a more appropriate
place.
Noted some TODOs for managing kinds of state better in future.
Change-Id: I99a014d9465b46b32038cfdcee99dc3896d2f265
Roland Schulz [Thu, 20 Jul 2017 22:07:49 +0000 (15:07 -0700)]
PME-gather: Use templated functor instead of preprocessor
Added restrict in several places, but this does not affect performance
with gcc and icc.
Change-Id: Id366621fa3ad02ca182b8a4da48cae940059cf46
Christoph Junghans [Sun, 13 Aug 2017 15:52:18 +0000 (09:52 -0600)]
Supported quiet trajectory-handling I/O
Permits GMX_TRAJECTORY_IO_VERBOSITY=0 to be set to keep frame-reading
code quiet, which is convenient for tools using libgromacs.
Change-Id: I873dcf229d9c20c8dd3b5097784236c2c2c478c1
Mark Abraham [Sun, 3 Sep 2017 13:59:12 +0000 (15:59 +0200)]
Fixes for Solaris
Suggested by Maureen Chew, of Oracle.
Change-Id: I5c3f868721944e7586b7001f3ffdf6ab17953526
Mark Abraham [Mon, 4 Sep 2017 21:27:04 +0000 (23:27 +0200)]
Fix use of GPU information for thread-MPI setup
Tweaked the logic for initially setting tryUsePhysicalGpu, since it
and forceUsePhysicalGpu are intended to be mutually exclusive. Note
that -gpu_id still works with both -nb auto and -nb gpu; what we
also need are some checks that -nb, -gpu_id and GMX_EMULATE_GPU
are mutually consistent, which is now true. We also don't need
to set tryUsePhysicalGpu based on GMX_GPU_NONE, since that will
take care of itself when no GPUs are detected.
Introduced nonbondedOnGpu to allow the logic that is aware of when
GPUs are supported / useful to set a variable that controls the
defaults for thread-MPI rank split, and npme choice. This restores
some of the approach removed in
e27440a4923e, and fixes a bug that was
introduced there.
Change-Id: I42aa9e6c36fef584437ece9ef4d3a8a249cd58db
Erik Lindahl [Thu, 25 May 2017 13:05:36 +0000 (15:05 +0200)]
More SIMD math argument checking, added unsafe options
This change adds more argument checking and safeguards
for sqrt, exp2, and exp-related SIMD math functions, and
properly documents allowed values. These functions now
have an (optional) template parameter that makes it possible
to avoid the checks where it is important to save every cycle,
and the developer is certain that this usage is fine. For
now we only use the unsafe versions in the nonbonded kernels.
The SIMD function test code has also been extended with options
to allow denormals to be considered zero.
Fixes #2164.
Refs #2163.
Change-Id: I93ddadf74dd0fa013f61cf27fd1993f11cde28bc
Berk Hess [Wed, 9 Aug 2017 15:07:11 +0000 (17:07 +0200)]
Fix two nbnxn search indexing bugs
The conversion for nbnxn i-cluster indexing to j-cluster indexing
in the SIMD cluster list generation code was incorrect for the
(common) case where the j-cluster size is 8 (i is always 4).
This bug was compensated by a bug that caused the input j-cluster
range, in terms of i-cluster size, to be to wide by 1 at both ends.
This change fixes both bugs, which leads to slightly fewer distance
checks.
Note that because of the compensating bugs, the pair-lists have
always been fully correct.
Change-Id: I79ff95d71880dc53305dbbf9282487895be71ed9
Roland Schulz [Tue, 29 Aug 2017 21:11:01 +0000 (14:11 -0700)]
Fix accuracy for cvtDouble2Float/cprod
After commit
b905792 gave incorrect results with ICC17u4
Change-Id: Ib945e979e9e3144342eed7a5cb4fc56d7f9a4b88
Berk Hess [Fri, 25 Aug 2017 20:25:18 +0000 (22:25 +0200)]
Consolidate architecture booleans
The booleans used in the hardware module for identifying architecures
are replaced by a single enum in archtecture.h. The duplicate
preprocessor code in cpuinfo.cpp now also uses this enum instead.
Note that hardwareinfo.cpp did not check for __i386, x86, __amd64__
and _M_AMD64, I don't know if this caused issues.
Also moved gpu_detec_res_str to new file gpu_hw_info.cpp.
Change-Id: I812482854d346c9290b0a428dada88072dc5a707
Aleksei Iupinov [Mon, 4 Sep 2017 11:13:40 +0000 (13:13 +0200)]
Merge "Merge branch release-5-1 into release-2016" into release-2016
Bernhard M. Wiedemann [Mon, 4 Sep 2017 09:32:31 +0000 (11:32 +0200)]
Use cmake's timestamp function
also use ISO date format and UTC timezone
to make it nicer to work with.
requires cmake-2.8.11+
Change-Id: I00fbf89c727624ad6ba89833ef146c2e16e2fee8
Teemu Murtola [Tue, 22 Aug 2017 19:12:04 +0000 (22:12 +0300)]
Introduce self-pairs search in nbsearch
Make it possible to search for all pairs within a single set of
positions using AnalysisNeighborhood. This effectively excludes half of
the pairs from the search, speeding things up.
Not used yet anywhere, but this makes the code a better reference for
performance comparisons, and for places where this is applicable it has
potential for speeding things up quite a bit.
Change-Id: Ib0e6f36460b8dbda97704447222c864c149d8e56
Teemu Murtola [Tue, 22 Aug 2017 19:09:49 +0000 (22:09 +0300)]
Refactor analysis nbsearch tests
Remove assumptions from the tests about the order in which pairs are
returned. Prepares the tests for an all-pairs search from a single set
of positions, where the order is not as predictable. And the test code
is actually easier to understand this way.
Change-Id: Id33eaff1c4c7f94a26099c6d4e34e7e008c1afa4
Mark Abraham [Sun, 3 Sep 2017 13:48:10 +0000 (15:48 +0200)]
Fix compiler flags for using MKL
Change-Id: I860e43da8de3b563167ecee1f52e2017a0f27f7f
Mark Abraham [Sun, 3 Sep 2017 14:51:20 +0000 (16:51 +0200)]
Merge branch release-5-1 into release-2016
Change-Id: I047ad1ab813b69582bdf5f4681549171724323f6
Berk Hess [Wed, 30 Aug 2017 21:14:01 +0000 (23:14 +0200)]
Put mdrun options in structs
Collects all mdrun options contained in flags, plus a few more,
into a new struct MdrunOptions with sub-structs.
All boolean options still use gmx_bool, and not bool, because
the command line parsing does not support bool yet.
Moved function declarations for expanded.cpp to expanded.h.
More options can be collected, but that would increase the size
of this change even more.
Change-Id: I21ea07b443e89cbfa21986bb8bd58a5657cbfbfa
M. Eric Irrgang [Wed, 30 Aug 2017 01:50:25 +0000 (21:50 -0400)]
Remove macro that confuses some debuggers
Replace FF macro with a lambda capturing a copy of Flags
to test for PCA flag bits set.
Change-Id: I9e87dc883d30c9c54115f2e47aa60d643f6061eb
Berk Hess [Wed, 30 Aug 2017 19:52:49 +0000 (21:52 +0200)]
Put all domdec options in a struct
Change-Id: I40c3cb979ea26188c4484138b1041f44ff9d5ad6
Berk Hess [Fri, 1 Sep 2017 21:10:34 +0000 (23:10 +0200)]
Fix mdrun -nb option pointer
Change-Id: I576a68161df6ebd071d58b8afef2268caac5524c
M. Eric Irrgang [Sun, 27 Aug 2017 01:34:09 +0000 (21:34 -0400)]
make a box parameter const
Change-Id: I6d9f472ac73f8d9fdde5b4dbd7ffdfc18544f634
Berk Hess [Fri, 1 Sep 2017 21:10:34 +0000 (23:10 +0200)]
Fix mdrun -nb option pointer
Change-Id: I576a68161df6ebd071d58b8afef2268caac5524c
Aleksei Iupinov [Thu, 31 Aug 2017 13:56:51 +0000 (15:56 +0200)]
Bring back space lost in commit
e43e83bf
Change-Id: Ie1c644fd372954d16d8bb9a098191e3ac072a226
M. Eric Irrgang [Wed, 30 Aug 2017 01:41:56 +0000 (21:41 -0400)]
Add more git ignores
Make it easier to work with some editors and packagers.
Change-Id: I582f76d4e160c02c3614219805c7ccd12af4de55
M. Eric Irrgang [Wed, 30 Aug 2017 01:35:38 +0000 (21:35 -0400)]
normalize some C header includes
Change-Id: I26f10375d7021c01718c2b0d26251963509880e2
M. Eric Irrgang [Wed, 30 Aug 2017 01:46:52 +0000 (21:46 -0400)]
small precaution in case *argc == 0
Change-Id: Ia33ee57ea9143348a3ad4b7c3266ee9452dd32ee
M. Eric Irrgang [Wed, 30 Aug 2017 01:44:45 +0000 (21:44 -0400)]
Declare an input parameter const
Change-Id: I9fcb156256fa58853bc01f9b0c9fe2d08cf10057
Aleksei Iupinov [Tue, 29 Aug 2017 15:57:00 +0000 (17:57 +0200)]
Remove leftover function declaration
Commit
a51b6feb removed gmx_check_hw_runconf_consistency(),
but not its declaration.
Change-Id: I82da91f735014ac131f8147950a2cb1114f73757
Aleksei Iupinov [Tue, 29 Aug 2017 15:15:35 +0000 (17:15 +0200)]
Fix typo
Change-Id: I94a630cd45f634f9e31478a330e28599b7a74100
Roland Schulz [Fri, 25 Aug 2017 01:26:34 +0000 (18:26 -0700)]
Enable missing declarations warning
Change-Id: I055e12554e40fea43d37590ea3989d0a8fbe732d