* Paul Bauer <paul.bauer.q@gmail.com>
* Eric Irrgang <ericirrgang@gmail.com>
* Joe Jordan <e.jjordan12@gmail.com>
+ * Mark Abraham <mark.j.abraham@gmail.com>
Usage::
return []
-def get_compiler(args, tsan_stage: hpccm.Stage = None) -> bb_base:
+def get_compiler(args, compiler_build_stage: hpccm.Stage = None) -> bb_base:
# Compiler
if args.icc is not None:
raise RuntimeError('Intel compiler toolchain recipe not implemented yet')
if args.llvm is not None:
# Build our own version instead to get TSAN + OMP
if args.tsan is not None:
- if tsan_stage is not None:
- compiler = tsan_stage.runtime(_from='tsan')
+ if compiler_build_stage is not None:
+ compiler = compiler_build_stage.runtime(_from='tsan')
else:
- raise RuntimeError('No TSAN stage!')
+ raise RuntimeError('No TSAN compiler build stage!')
# Build the default compiler if we don't need special support
else:
compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
- elif (args.gcc is not None):
+ elif args.gcc is not None:
compiler = hpccm.building_blocks.gnu(extra_repository=True,
version=args.gcc,
fortran=False)
raise RuntimeError('compiler is not an HPCCM compiler building block!')
elif args.mpi == 'impi':
+ # TODO also consider hpccm's intel_mpi package if that doesn't need
+ # a license to run.
raise RuntimeError('Intel MPI recipe not implemented yet.')
else:
raise RuntimeError('Requested unknown MPI implementation.')
return None
-def add_tsan_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
+def add_tsan_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
"""Isolate the expensive TSAN preparation stage.
This is a very expensive stage, but has few and disjoint dependencies, and
'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-' + str(input_args.llvm),
'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-' + str(input_args.llvm),
'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
- output_stages['tsan'] = tsan_stage
-
+ output_stages['compiler_build'] = tsan_stage
def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
"""Get shell commands to set up the venv for the requested Python version."""
# object early in this function.
stages = collections.OrderedDict()
- # If we need the TSAN compilers, the early build is more involved.
+ # If we need TSAN or oneAPI support the early build is more complex,
+ # so that our compiler images don't have all the cruft needed to get those things
+ # installed.
if args.llvm is not None and args.tsan is not None:
- add_tsan_stage(input_args=args, output_stages=stages)
+ add_tsan_compiler_build_stage(input_args=args, output_stages=stages)
# Building blocks are chunks of container-builder instructions that can be
# copied to any build stage with the addition operator.
building_blocks = collections.OrderedDict()
# These are the most expensive and most reusable layers, so we put them first.
- building_blocks['compiler'] = get_compiler(args, tsan_stage=stages.get('tsan'))
+ building_blocks['compiler'] = get_compiler(args, compiler_build_stage=stages.get('compiler_build'))
building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
# Install additional packages early in the build to optimize Docker build layer cache.
* Paul Bauer <paul.bauer.q@gmail.com>
* Eric Irrgang <ericirrgang@gmail.com>
* Joe Jordan <e.jjordan12@gmail.com>
+ * Mark Abraham <mark.j.abraham@gmail.com>
"""
While it is our best belief that |Gromacs| will build and run pretty
much everywhere, it is important that we tell you where we really know
-it works because we have tested it. We do test on Linux, Windows, and
-Mac with a range of compilers and libraries for a range of our
-configuration options. Every commit in our git source code repository
-is currently tested on x86 with a number of gcc versions ranging from 5.1
-through 9.1, version 19 of the Intel compiler, and Clang
-versions 3.6 through 8. For this, we use a variety of GNU/Linux
-flavors and versions as well as Windows (where we test only MSVC 2017).
+it works because we have tested it.
+Every commit in our git source code repository
+is currently tested with a range of configuration options on x86 with
+gcc versions 6 and 7,
+clang versions 3.6 and 8,
+and
+For this testing, we use Ubuntu 16.04 or 18.04 operating system.
Other compiler, library, and OS versions are tested less frequently.
For details, you can
have a look at the `continuous integration server used by GROMACS`_,
-which runs Jenkins_.
+which uses GitLab runner on a local k8s x86 cluster with NVIDIA and
+AMD GPU support.
We test irregularly on ARM v7, ARM v8, Cray, Fujitsu
PRIMEHPC, Power8, Power9,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformintdistribution.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
int nthreads;
gmx::DefaultRandomEngine* trng = nullptr;
#endif
- int64_t mc = 0, mc_max;
+ int64_t mc_max;
gmx::DefaultRandomEngine rng(seed);
/* allocate memory for pr */
snew(tgr[i], pr->grn);
trng[i].seed(rng());
}
-# pragma omp parallel shared(tgr, trng, mc) private(tid, i, j)
+# pragma omp parallel shared(tgr, trng) private(tid, i, j)
{
gmx::UniformIntDistribution<int> tdist(0, isize - 1);
tid = gmx_omp_get_thread_num();
-/* now starting parallel threads */
+ /* now starting parallel threads */
+ INTEL_DIAGNOSTIC_IGNORE(593)
# pragma omp for
- for (mc = 0; mc < mc_max; mc++)
+ for (int64_t mc = 0; mc < mc_max; mc++)
{
try
{
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
}
+ INTEL_DIAGNOSTIC_RESET
/* collecting data from threads */
for (i = 0; i < pr->grn; i++)
{
delete[] trng;
#else
gmx::UniformIntDistribution<int> dist(0, isize - 1);
- for (mc = 0; mc < mc_max; mc++)
+ for (int64_t mc = 0; mc < mc_max; mc++)
{
i = dist(rng); // [0,isize-1]
j = dist(rng); // [0,isize-1]
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* 2 seconds, or until all cores have come online. This can be used prior to
* hardware detection for platforms that take unused processors offline.
*
- * This routine will not throw exceptions.
+ * This routine will not throw exceptions. In principle it should be
+ * declared noexcept, but at least icc 19.1 and 21-beta08 with the
+ * libstdc++-7.5 has difficulty implementing a std::vector of
+ * std::thread started with this function when declared noexcept. It
+ * is a known compiler bug that should be fixed after 19.1.
+ * Fortunately, this function is not performance sensitive,
+ * and only runs on platforms other than x86 and POWER (ie ARM),
+ * so the possible overhead introduced by omitting noexcept is not
+ * important.
*/
-static void spinUpCore() noexcept
+static void spinUpCore()
{
#if defined(HAVE_SYSCONF) && defined(_SC_NPROCESSORS_CONF) && defined(_SC_NPROCESSORS_ONLN)
float dummy = 0.1;
int64_t step, step_rel;
double t, t0 = ir->init_t, lam0[efptNR];
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
- gmx_bool bNS, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
+ gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose;
gmx_bool bMasterState;
bExchanged = FALSE;
bNeedRepartition = FALSE;
+ step = ir->init_step;
+ step_rel = 0;
+
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
- step = ir->init_step;
- step_rel = 0;
-
// TODO extract this to new multi-simulation module
if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
{
"MiMiC does not report kinetic energy, total energy, temperature, virial and "
"pressure.");
+ step = ir->init_step;
+ step_rel = 0;
+
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
- step = ir->init_step;
- step_rel = 0;
-
/* and stop now if we should */
isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
while (!isLastStep)
calc_shifts(rerun_fr.box, fr->shift_vec);
}
+ step = ir->init_step;
+ step_rel = 0;
+
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
- step = ir->init_step;
- step_rel = 0;
-
/* and stop now if we should */
isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
while (!isLastStep)
gmx_target_warning_suppression(scanner -Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
gmx_target_warning_suppression(scanner -Wno-missing-declarations HAS_NO_MISSING_DECLARATIONS)
gmx_target_warning_suppression(scanner -Wno-null-conversion HAS_NO_NULL_CONVERSIONS)
- gmx_target_warning_suppression(scanner -wd1419 HAS_DECL_IN_SOURCE)
endif()
list(APPEND libgromacs_object_library_dependencies scanner)
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
# define MSVC_DIAGNOSTIC_RESET
#endif
+#ifdef __INTEL_COMPILER
+// Ignore unused loop variable warning - it was used until the compiler removes the use!
+# define DO_PRAGMA(x) _Pragma(# x)
+# define INTEL_DIAGNOSTIC_IGNORE(id) DO_PRAGMA(warning push) DO_PRAGMA(warning(disable : id))
+# define INTEL_DIAGNOSTIC_RESET DO_PRAGMA(warning pop)
+#else
+# define INTEL_DIAGNOSTIC_IGNORE(id)
+# define INTEL_DIAGNOSTIC_RESET
+#endif
+
namespace gmx
{
namespace internal
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff