Mark Abraham [Wed, 25 Oct 2017 09:45:32 +0000 (11:45 +0200)]
Update treatment of GPU compatibility data structure
Now we only construct the vector of compatible GPUs once per mdrun,
and are less coupled to hw_info and gpu_info structs.
Change-Id: I181f0486d0ea1670de7a85046c94c1fef83dce17
David van der Spoel [Mon, 30 Oct 2017 08:03:13 +0000 (09:03 +0100)]
Fixed mdp output from electric field code.
Added two new tests for MDP output.
Fixes #2258
Change-Id: I495454bd2349be836c1a3ef5985288a996abf20e
Aleksei Iupinov [Mon, 30 Oct 2017 10:56:17 +0000 (11:56 +0100)]
Fix reference mode build unused function warnings
Change-Id: Ibd1ad83c5dbeffe86e47156d456d78ab1ab8aeeb
Berk Hess [Sun, 29 Oct 2017 21:20:54 +0000 (22:20 +0100)]
Remove unused sign parameter from dih_angle()
Change-Id: I88a73ca49b6acfc59b4baf0d847aa81542a870ca
Roland Schulz [Fri, 13 Oct 2017 18:49:46 +0000 (11:49 -0700)]
ArrayRef: Replace fromVector with subArray
Creating ArrayRef from iterators is potentially dangerous,
because it is incorrect for non-contiguous containers.
arrayRefFromVector(v.begin()+start, v.begin()+start+length)
is replaced with
ArrayRef<T>(v).subArray(start, length)
Also:
- Combine all conversion constructors
Removes code duplication and makes conversion more powerful
(e.g. base pointer or containers with allocators).
- remove fromPointers and arrayRefFromPointers
Wasn't used by any code
- remove fromArray and replace wih arrayRefFromArray
Change-Id: I05ad6b285ece58739d9f5bce48f9ecf4ade3454e
David van der Spoel [Fri, 13 Oct 2017 16:36:27 +0000 (18:36 +0200)]
Added option -water tips3p to pdb2gmx.
Fixes #2272
Change-Id: Ibfc63009767fd667df51ff10041791268351e1ca
Aleksei Iupinov [Fri, 27 Oct 2017 11:01:19 +0000 (13:01 +0200)]
Bring PME GPU/CUDA internal structure names to CamelCase
This only does mechanical renaming (e.g. pme_gpu_settings_t to
PmeGpuSettings). Any meaningful renames will be done separately.
Change-Id: I7ea2af94fd0212ff6edcf433ff21842c5bbb67b0
Mark Abraham [Tue, 24 Oct 2017 19:59:45 +0000 (21:59 +0200)]
Fix and update hw_info
Stopped using typedef struct (so later we can put a vector into the
struct).
Managed the memory using a unique_ptr, and made the interface reflect
that it is a file static, rather than something that is owned by
e.g. the runner.
Amended docs to clarify the sense of "global."
Change-Id: I1ce9bc42e03668498051b59aaeeb9e50a9f6f762
Aleksei Iupinov [Fri, 27 Oct 2017 13:09:04 +0000 (15:09 +0200)]
Use new/delete for gmx_pme_t
Change-Id: I176b1d26d484514c65cae412c474b65410191d38
Aleksei Iupinov [Thu, 26 Oct 2017 15:04:34 +0000 (17:04 +0200)]
Simplify PME data handling in runner
Differing ownership of the PME data for PME-only and other ranks
is now hidden behind a reference. gmx_pme_init() now returns
a pointer to the allocated structure.
Change-Id: Ia9c5117a0db43a6564298dd621cf9254f0423acf
Aleksei Iupinov [Thu, 26 Oct 2017 14:48:06 +0000 (16:48 +0200)]
Make PME tuning logic more readable
Change-Id: Ie53693a84264ed33c17894aa551cf476a3ced26b
Aleksei Iupinov [Thu, 26 Oct 2017 11:25:23 +0000 (13:25 +0200)]
Remove unused PME grid dump debug functions
Change-Id: Iac748080fdf29e6f35ecf37de2b968e70c72605e
Mark Abraham [Thu, 26 Oct 2017 08:36:13 +0000 (10:36 +0200)]
Fix hw detection more
gmx_hardware_detect was called in response to GoogleTest environment
SetUp function, so the cleanup for its global should occur in response
to the corresponding TearDown function. Both those should be virtual.
Thus the hardwareInfo should not be in a smart pointer called by a
destructor that might be called at a different point from TearDown.
The new getter function and the callback that handles making the first
call to it conform better to GoogleTest's recommendation to arrange to
call AddGlobalTestEnvironment from main() rather than rely on static
initialization.
Made hardwareInit a non-member function because that improves
encapsulation.
Change-Id: I2f8e14ecc1707bf31d023a4eb4fea0a20543910b
Aleksei Iupinov [Thu, 26 Oct 2017 08:36:48 +0000 (10:36 +0200)]
Replace a few asserts with GMX_ASSERT's
Change-Id: I18e614de57fc06f3faabc687140821223bd7c4f4
Aleksei Iupinov [Thu, 26 Oct 2017 11:49:22 +0000 (13:49 +0200)]
Remove defunct PME initialization error code return
The error was never actually returned, and invalid inputs
are already treated with exceptions anyway.
Change-Id: I6063612c3a2e760fb56b7bdf5b1624ab2fc031bd
Mark Abraham [Mon, 9 Oct 2017 11:50:25 +0000 (13:50 +0200)]
Make release matrix work again
Seems we didn't test this matrix when we updated infrastructure some
time.
Change-Id: Ib19672db6144bb40f08d2fcace4d43dbd52e6823
Szilárd Páll [Mon, 16 Oct 2017 18:15:25 +0000 (20:15 +0200)]
Reorganize PME GPU launch
Wrapped the first (prep/spread) and second stage (fft/gather) of PME GPU
in functions. Moved the second stage of the regular PME GPU mode to after
the nonbonded x transform to ensure that the transform can overlap with
spread even when the launch overhead of the FFT kernels is high.
Also removed TPI-related PME-GPU launch conditions as this should be
checked much earlier. Noted in the force flags docs that the current
code assumes GMX_FORCE_STATECHANGED is used only with TPI.
Change-Id: I7f765d66c6c4e7e54812b81b2dd23751af0b06b5
Mark Abraham [Wed, 18 Oct 2017 21:02:44 +0000 (23:02 +0200)]
New quote
Change-Id: Id1625b1c836c64a5bd1e24fbf5b3ef2b104f102d
Mark Abraham [Tue, 24 Oct 2017 16:03:24 +0000 (18:03 +0200)]
Teach the copyright checker about template.cpp
Now it won't warn about having to ignore it when calling
uncrustify via the scripts.
Change-Id: I2d5675a1a16dc01f6f9a45440f6807319c766944
Aleksei Iupinov [Tue, 24 Oct 2017 14:24:11 +0000 (16:24 +0200)]
Remove duplicate/outdated function declaration
Change-Id: Ie54afcc501e0658c8a29a80831ff87765e5e7786
Aleksei Iupinov [Tue, 17 Oct 2017 11:15:24 +0000 (13:15 +0200)]
Move commrec duty checking into simple getters
This isolates all reads of cr->duty, and asserts on cr->duty being valid,
allowing to refactor its assignment in later changes.
Change-Id: I9b48be06b8d2db18105619ea1acfe38aa541b622
Aleksei Iupinov [Mon, 23 Oct 2017 09:14:19 +0000 (11:14 +0200)]
Correct the page allocator description
Change-Id: Iea0190978b483ed01fc8279f34ef2a304a11b612
Szilárd Páll [Fri, 20 Oct 2017 14:37:49 +0000 (16:37 +0200)]
Eliminate some OCL/CUDA code code duplication
Atom to interaction locality conversion and atom range calculation has
been duplicated across the OpenCL and CUDA modules. As an intermediate
step this functionality is now gathered in the common header.
Change-Id: I55b1b34992621ecebed6dad0978a47553511fc87
David van der Spoel [Tue, 23 May 2017 11:20:30 +0000 (13:20 +0200)]
Split off the NMR related analyses from gmx energy.
A new tool gmx nmr is created by straight copying code from
gmx energy to a new tool. The reason is to reduce complexity.
A few cleanups are introduced to pass the valgrind memory
test.
Added references the gmx nmr in the manual.
Change-Id: I8e4d1dec8806a0518c571d7a01c4f70de5bbbd35
Aleksei Iupinov [Fri, 20 Oct 2017 12:53:01 +0000 (14:53 +0200)]
Change PME GPU gather reduction argument from boolean to enum class
Change-Id: Idacbdfb79313ebf16cf1a7dc19435436d6366d27
Berk Hess [Sat, 21 Oct 2017 19:33:39 +0000 (21:33 +0200)]
Merge "Merge branch release-2016"
Aleksei Iupinov [Tue, 30 May 2017 14:00:35 +0000 (16:00 +0200)]
Add calls to the PME GPU stages
This adds the inactive calls to PME GPU stages both for PP+PME
and PME-only ranks.
Ref #2054
Change-Id: I5af2ab95cedff422c39592255f01205d42fc7eb7
Mark Abraham [Fri, 20 Oct 2017 10:05:05 +0000 (12:05 +0200)]
Merge branch release-2016
Dropped the post-submit change because where we test
with older clang we now always specify a suitable
status for openmp.
Change-Id: I993da20856861c0b8a0888f7fa0deed8853349a8
Berk Hess [Wed, 18 Oct 2017 18:18:31 +0000 (20:18 +0200)]
Fix warning for confout with periodic molecules
With periodic molecules, mdrun would, incorrectly, attempt to make
molecules whole for writing the final state to confout.
Fixes #2275
Change-Id: Ib19ca5c2ae6fcca6126773bcdd8a05c8e141c3ce
Szilárd Páll [Thu, 19 Oct 2017 16:53:04 +0000 (18:53 +0200)]
Disable OpenMP with clang 3.4 post-submit config
This avoid a CMake warning which we now parse and catch in jenkins.
Fixes #2277
Change-Id: Id129f9907af32bdecfe07c4ca37d4cb7376d79e2
Szilárd Páll [Tue, 17 Oct 2017 18:29:58 +0000 (20:29 +0200)]
Remove unised OpenCL debugging helpers
This also helps avoid -Wmissing-declarations in OpenCL utils module.
Change-Id: I16584fca485790e98fd3865ac65c06ac78d58194
Berk Hess [Mon, 16 Oct 2017 07:24:05 +0000 (09:24 +0200)]
Made CUDA PME texture reference conditional
Without texture support we should not reference textures.
Also added const struct to textures.
Change-Id: I1ca4e534da7b9130d12fd6831c119d2139eb16eb
David van der Spoel [Tue, 17 Oct 2017 20:26:21 +0000 (22:26 +0200)]
Fixed missing entries in nrnb arrays.
Some nrnb index entries were missing in the interaction_function
array, others were zero leading to that the wrong megaflops
accounting was printed.
Fixes #2274
Change-Id: Ic0b05d30eb5fdfeb7f3e822b42ec7ca4cda58bc5
Mark Abraham [Mon, 16 Oct 2017 06:10:34 +0000 (08:10 +0200)]
Merge branch release-2016
Change-Id: Ia56e987f52e4dee425b12b02940ad9ca18d0c13a
Berk Hess [Sun, 24 Sep 2017 20:27:02 +0000 (22:27 +0200)]
Improve vsite parallel checking
The vsite struct now stores internally whether it has been configured
with domain decomposition. This allows for internal checks on valid
commrec, which have now been added.
The vsite constructor now initializes to atom range to invalid values,
so we can check that the thread splitting has been called before
constructing. This would have caught bug #2257.
Removed the vsite struct from the global construct function argument
list, which simplifies the vsite code in several places and
fixes #2257.
Also some general clean-up: removed some snews, added some camelCasing
and doxygen documentation.
More renaming would be beneficial, but should be a separate commit.
Change-Id: I467ec8b8ebfa0da090d4ac0a1d096ad9fab87eb5
Aleksei Iupinov [Fri, 13 Oct 2017 09:50:19 +0000 (11:50 +0200)]
Relax PME spline computation tolerance in double precision tests
Change-Id: I8c3502dd84e21d20be057d47d4afa589d779eb90
Mark Abraham [Thu, 9 Feb 2017 10:49:38 +0000 (11:49 +0100)]
Update tests for C++11 compiler and standard library
We've started using some more features, so broaden the
range of things for which we check at cmake time.
Also made an explicit error message for older icc that can't handle
newer gcc standard libraries, since this might come up a few times.
Fixes #2116
Change-Id: I3656edb3f7e6f81bbf6ed3ed764bcac56802f87f
Roland Schulz [Wed, 4 Oct 2017 06:48:49 +0000 (23:48 -0700)]
Replace all ConstArrayRef with ArrayRef<const T>
1) Remove the alias itself in arrayref.h.
2) All replacements done automatically using sed:
s#ConstArrayRef<const char \*>#ArrayRef<const char *const>#
s#ConstArrayRef<\(.*\)>#ArrayRef<const \1>#
This worked because "const char*" was the only pointer type used as
template argument.
Change-Id: I5eba895a5dc235b95d77670b4f258e423f64f3b8
Roland Schulz [Fri, 22 Sep 2017 20:43:50 +0000 (13:43 -0700)]
Specialize ArrayRef for SimdReal
ArrayRef<SimdReal> maps to a range of aligned memory and returns a
Simd type from operator[] (more precisely a reference to a Simd type).
This allows to iterate over memory and not have to explicitly call
load/store while also avoiding undefined behavior (strict aliasing rule)
caused by casting between reals and SimdReals.
Change-Id: I3d00df088669dacc810052cbcaebe15e62e1d530
Magnus Lundborg [Tue, 10 Oct 2017 12:13:45 +0000 (14:13 +0200)]
Do not include headers related to ObservablesHistory
Define destructor for ObservablesHistory to avoid having to include
many extra headers.
Change-Id: I2681b519ace728dc494f967d17db5478af09f5df
Mark Abraham [Tue, 10 Oct 2017 09:22:02 +0000 (09:22 +0000)]
Fix cpuinfo on clang + non-x86
Compilers that pretend to be GCC often define such symbols, and the
support for inline assembly does not compile e.g. on ARM. This broke
CPU detection at cmake time, and subsequent compilation. Probably
introduced by commit
863768a4dad. The latest ARM compiler is based on
clang, so we should fix this.
Also de-duplicated some use of compiler target defines
Change-Id: Ia21363b9c0fe112762750d93b9feea267a34319f
Szilárd Páll [Thu, 12 Oct 2017 15:52:15 +0000 (17:52 +0200)]
Remove the size_t from the PME gather CUDA kenels
Change-Id: If53b9eabc1ac081b33933cc773b5ea932c9e8392
Aleksei Iupinov [Thu, 12 Oct 2017 11:00:59 +0000 (13:00 +0200)]
Remove useless extern CUDA texture reference declarations from PME
These are only accessed from the same compilation unit (pme-spread.cu)
on the device side, and the host side is only using nearby getters.
Change-Id: Ie846193c71142ff5e519e990ef1155b534546a9b
Aleksei Iupinov [Thu, 12 Oct 2017 10:31:45 +0000 (12:31 +0200)]
Revert "Drop NB_ from GMX_CUDA_NB_SINGLE_COMPILATION_UNIT cmake define"
This reverts commit
3880255b0, which was made in confusion
stemming from combination of multiple CUDA compilation units,
disabling CUDA textures, and NB CUDA module structure.
The define in question is actually NB-exclusive,
and PME with CUDA does not need to check it to declare
extern texture references. As PME textures are not accessed
from different PME kernels, those extern declarations are removed
in the child change Ie846193c71142ff5e519e990ef1155b534546a9b.
Change-Id: I75a0e62bc92c7161ba0fbf00d8db2f35cef80bc7
Berk Hess [Sat, 30 Sep 2017 21:10:06 +0000 (23:10 +0200)]
Simplify virial handling
The force and virial are tightly connected. This is now expressed
through the new ForceWithVirial object, which is used for algorithms
that compute a separate virial contribution. This clarifies and
simplifies the core mdrun code in several places.
Change-Id: If0f65f1a6f67fb3efc5e4637a183faf4abd5f969
Roland Schulz [Fri, 6 Oct 2017 23:36:50 +0000 (16:36 -0700)]
Require template parameter for load function
The implicit conversion from load(float*) to both float
and SimdFloat caused multiple issues. The primary ones:
- Extra complexity in the implementation of traits, ArrayRef, SimdReference
- required compiler tests for ambiguity
- SimdReal x = f(load(m)) //confusing broadcast if f is scalar function
- x = s*load(m) //error-prone scalar multiply if s is scalar
New syntax in templated function is load<T>(m) and in non-templated function
load<SimdReal>(m). While this is slightly longer by itself, it is clearer
and doesn't require to store values in tempories (no ambigious overload errors).
Also avoids the need for the load proxies.
Change-Id: I8109e9365e956aaea428ec338b6a810444e03d77
Roland Schulz [Sat, 7 Oct 2017 00:34:02 +0000 (17:34 -0700)]
Use tag for simdLoad
Use same simdLoad name for all types. In preparation
for removing the need for SimdLoadProxyInternal.
C++ doesn't support template specialization for
function thus making simdLoad have a template argument
and specialize on it doesn't work. By passing a tag as
a 2nd argument std overloading can be used.
Change-Id: Iaf42ebb74a3347787bcac3bdfd0ef11db1e333bf
Mark Abraham [Thu, 13 Apr 2017 23:31:46 +0000 (01:31 +0200)]
Introduced header for communication to/from PME ranks
No functionality changes. This cleans up some structure, and will be
useful for some modernization, use of std::vector, and then new
allocation strategies to suit PME on GPUs.
Eliminated some things in pme-internal.h by moving some declarations
to a header that can be included by the only two source files that are
interested in PP-PME communication. Now gmx_pmeonly() doesn't have to
pass around a large pile of arguments.
Removed a use of typedef struct, and some function parameter types
that no longer need to specify struct in C++.
Removed some unused PP_PME_* constants.
Change-Id: I51629fb6d91b3a486ef24d1f60065e65261d0376
Aleksei Iupinov [Wed, 11 Oct 2017 16:16:07 +0000 (18:16 +0200)]
Fix clang warnings for PME CUDA kernels
Change-Id: I28f67c70b1ff4611f2456a5935a727c49e10e691
Aleksei Iupinov [Wed, 11 Oct 2017 16:28:24 +0000 (18:28 +0200)]
Relax PME solving test complex grid tolerance
PME CUDA solving change (Ic610e7f) tightened the output grid
tolerance from 50 down to 16 ULPs, making one of the LJPME tests
fail in post-submit. This change relaxes the tolerance to 40 ULPs.
Change-Id: Icd0c1aff868e2d1ecb76522a1a2174b3156fc356
Mark Abraham [Fri, 14 Apr 2017 02:23:44 +0000 (04:23 +0200)]
Cleaned up ewaldcoeff for PME-only ranks
Earlier, runner initializes all kinds of PME ranks with the initial
values of Ewald coefficients. The values passed to gmx_pmeonly were
never read - the variables are used only to store new values, which
happens when the PP rank directs the PME grid to switch grids during
load balancing.
Change-Id: Ibe581a7111239f28f874b43dc13dcc6abd025b60
Aleksei Iupinov [Fri, 25 Aug 2017 17:16:13 +0000 (19:16 +0200)]
CUDA 9/Volta support for PME
Change-Id: Icd5cdf16f9118347179dfcbdd162f0cb39cbdd69
Aleksei Iupinov [Tue, 7 Feb 2017 14:01:54 +0000 (15:01 +0100)]
PME solving - CUDA kernel + unit tests
The CUDA implementation of PME solving is added in pme-solve.cu.
The unit tests for PME CPU solving are extended to work with the CUDA kernel,
using the same reference data.
The CUDA solver supports 2 grid dimension orders: YZX and XYZ
(unlike the CPU one which only supports YZX). This is also tested.
Lennard-Jones solving is not implemented.
The tests iterate over all Gromacs-compatible CUDA GPUs.
Refs #2054
Change-Id: Ic610e7f077f39a64089dd9b80df9905094b10459
Paul Bauer [Mon, 9 Oct 2017 07:48:51 +0000 (09:48 +0200)]
Change to modules for build of web documentation
The modules loaded to build the web documentation with Sphinx have been
incorrect for the minimum version specified by the configuration file.
In particular, the imgmath extension had not been available for
version 1.3 that was indicated as being the minimum version. As
there are no references that I found to any math macros in the files
used to build the docs, I removed the extension to make sure it will
build again. It might be better to have a conditional there, building the
docs without imgmath when using lower versions of sphinx, and having it
active for higher versions.
Changed to require 1.4.1 for now, and added variables that set it
automatically from the information passed to cmake.
Change-Id: Ia329575288e5d622b8e679d76b63759bae54a3b0
Aleksei Iupinov [Fri, 27 Jan 2017 14:49:55 +0000 (15:49 +0100)]
PME force gathering - CUDA kernel + unit tests
The CUDA implementation of PME force gathering for PME order 4 is added
in pme-gather.cu. The unit tests for PME CPU force gathering
(
d20a5d36) are extended to work with the CUDA kernel, using
the same reference data. The tests iterate over all Gromacs-compatible
CUDA GPUs.
Ref #2054
Change-Id: I162e3a14cb9aa8ddeac17c5ad1ca709df72b8986
Aleksei Iupinov [Fri, 6 Oct 2017 14:47:42 +0000 (16:47 +0200)]
Drop NB_ from GMX_CUDA_NB_SINGLE_COMPILATION_UNIT cmake define
Update the messages as well; the build setting should not be NB-exclusive.
Change-Id: I6b730ed7471253d50ce3294de86a1e3ce2733210
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
Berk Hess [Sat, 23 Sep 2017 10:15:57 +0000 (12:15 +0200)]
Fix grompp with Andersen massive and no COM removal
Fixed a floating point exception leading to a segv.
Also fixed possible different rounding for the interval for
Andersen massive in grompp in mdrun for the common case where tau_t
is a multiple of delta_t.
Fixes #2256
Change-Id: I161e8a9db2c31fde8a6e8c2fd32551b21423fd9b
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
Vedran Miletić [Tue, 19 Sep 2017 17:32:41 +0000 (19:32 +0200)]
Document t_commrec struct
Describe the mysim and mygroup MPI communicators and add a note about
the communicator subsetting.
Change-Id: I2d39bd6827da59db5b3c38bd33de6903e17d0d06