#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/ga2la.h"
+#include "gromacs/domdec/options.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "redistribute.h"
#include "utility.h"
+// TODO remove this when moving domdec into gmx namespace
+using gmx::DdRankOrder;
+using gmx::DlbOption;
+using gmx::DomdecOptions;
+
static const char *edlbs_names[int(DlbState::nr)] = { "off", "auto", "locked", "on", "on" };
/* The size per atom group of the cggl_flag buffer in gmx_domdec_comm_t */
namespace gmx
{
class MDLogger;
-struct MdrunOptions;
class LocalAtomSetManager;
+struct DomdecOptions;
+struct MdrunOptions;
} // namespace
/*! \brief Returns the global topology atom number belonging to local atom index i.
/*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
int dd_pme_maxshift_y(const gmx_domdec_t *dd);
-/*! \brief The options for the domain decomposition MPI task ordering. */
-enum class DdRankOrder
-{
- select, //!< First value (needed to cope with command-line parsing)
- interleave, //!< Interleave the PP and PME ranks
- pp_pme, //!< First all PP ranks, all PME rank at the end
- cartesian, //!< Use Cartesian communicators for PP, PME and PP-PME
- nr //!< The number of options
-};
-
-/*! \brief The options for the dynamic load balancing. */
-enum class DlbOption
-{
- select, //!< First value (needed to cope with command-line parsing)
- turnOnWhenUseful, //!< Turn on DLB when we think it would improve performance
- no, //!< Never turn on DLB
- yes, //!< Turn on DLB from the start and keep it on
- nr //!< The number of options
-};
-
-/*! \libinternal \brief Structure containing all (command line) options for the domain decomposition */
-struct DomdecOptions
-{
- //! If true, check that all bonded interactions have been assigned to exactly one domain/rank.
- gmx_bool checkBondedInteractions = TRUE;
- //! If true, don't communicate all atoms between the non-bonded cut-off and the larger bonded cut-off, but only those that have non-local bonded interactions. This significantly reduces the communication volume.
- gmx_bool useBondedCommunication = TRUE;
- //! The domain decomposition grid cell count, 0 means let domdec choose based on the number of ranks.
- ivec numCells = {0};
- //! The number of separate PME ranks requested, -1 = auto.
- int numPmeRanks = -1;
- //! Ordering of the PP and PME ranks, values from enum above.
- DdRankOrder rankOrder = DdRankOrder::interleave;
- //! The minimum communication range, used for extended the communication range for bonded interactions (nm).
- real minimumCommunicationRange = 0;
- //! Communication range for atom involved in constraints (P-LINCS) (nm).
- real constraintCommunicationRange = 0;
- //! Dynamic load balancing option, values from enum above.
- DlbOption dlbOption = DlbOption::turnOnWhenUseful;
- /*! \brief Fraction in (0,1) by whose reciprocal the initial
- * DD cell size will be increased in order to provide a margin
- * in which dynamic load balancing can act, while preserving
- * the minimum cell size. */
- real dlbScaling = 0.8;
- //! String containing a vector of the relative sizes in the x direction of the corresponding DD cells.
- const char *cellSizeX = nullptr;
- //! String containing a vector of the relative sizes in the y direction of the corresponding DD cells.
- const char *cellSizeY = nullptr;
- //! String containing a vector of the relative sizes in the z direction of the corresponding DD cells.
- const char *cellSizeZ = nullptr;
-};
-
/*! \brief Initialized the domain decomposition, chooses the DD grid and PME ranks, return the DD struct */
gmx_domdec_t *
init_domain_decomposition(const gmx::MDLogger &mdlog,
t_commrec *cr,
- const DomdecOptions &options,
+ const gmx::DomdecOptions &options,
const gmx::MdrunOptions &mdrunOptions,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file declares command-line options for mdrun related to
+ * domain decomposition.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ * \ingroup module_domdec
+ */
+
+#ifndef GMX_DOMDEC_OPTIONS_H
+#define GMX_DOMDEC_OPTIONS_H
+
+#include <vector>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
+
+namespace gmx
+{
+
+/*! \brief The options for the domain decomposition MPI task ordering. */
+enum class DdRankOrder
+{
+ select, //!< First value (needed to cope with command-line parsing)
+ interleave, //!< Interleave the PP and PME ranks
+ pp_pme, //!< First all PP ranks, all PME rank at the end
+ cartesian, //!< Use Cartesian communicators for PP, PME and PP-PME
+ Count //!< The number of options
+};
+
+/*! \brief The options for the dynamic load balancing. */
+enum class DlbOption
+{
+ select, //!< First value (needed to cope with command-line parsing)
+ turnOnWhenUseful, //!< Turn on DLB when we think it would improve performance
+ no, //!< Never turn on DLB
+ yes, //!< Turn on DLB from the start and keep it on
+ Count //!< The number of options
+};
+
+/*! \libinternal \brief Structure containing all (command line) options for the domain decomposition */
+struct DomdecOptions
+{
+ //! If true, check that all bonded interactions have been assigned to exactly one domain/rank.
+ bool checkBondedInteractions = true;
+ //! If true, don't communicate all atoms between the non-bonded cut-off and the larger bonded cut-off, but only those that have non-local bonded interactions. This significantly reduces the communication volume.
+ bool useBondedCommunication = true;
+ //! The domain decomposition grid cell count, 0 means let domdec choose based on the number of ranks.
+ ivec numCells = {0};
+ //! The number of separate PME ranks requested, -1 = auto.
+ int numPmeRanks = -1;
+ //! Ordering of the PP and PME ranks, values from enum above.
+ DdRankOrder rankOrder = DdRankOrder::interleave;
+ //! The minimum communication range, used for extended the communication range for bonded interactions (nm).
+ real minimumCommunicationRange = 0;
+ //! Communication range for atom involved in constraints (P-LINCS) (nm).
+ real constraintCommunicationRange = 0;
+ //! Dynamic load balancing option, values from enum above.
+ DlbOption dlbOption = DlbOption::turnOnWhenUseful;
+ /*! \brief Fraction in (0,1) by whose reciprocal the initial
+ * DD cell size will be increased in order to provide a margin
+ * in which dynamic load balancing can act, while preserving
+ * the minimum cell size. */
+ real dlbScaling = 0.8;
+ //! String containing a vector of the relative sizes in the x direction of the corresponding DD cells.
+ const char *cellSizeX = nullptr;
+ //! String containing a vector of the relative sizes in the y direction of the corresponding DD cells.
+ const char *cellSizeY = nullptr;
+ //! String containing a vector of the relative sizes in the z direction of the corresponding DD cells.
+ const char *cellSizeZ = nullptr;
+};
+
+} // namespace gmx
+
+#endif
#include "gromacs/commandline/filenm.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/options.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/mdrun/logging.h"
#include "gromacs/mdtypes/mdrunoptions.h"
/*! \brief Command line options, defaults, docs and storage for them to fill. */
/*! \{ */
- rvec realddxyz = {0, 0, 0};
- const char *ddrank_opt_choices[static_cast<int>(DdRankOrder::nr)+1] =
+ rvec realddxyz = {0, 0, 0};
+ const char *ddrank_opt_choices[static_cast<int>(DdRankOrder::Count)+1] =
{ nullptr, "interleave", "pp_pme", "cartesian", nullptr };
- const char *dddlb_opt_choices[static_cast<int>(DlbOption::nr)+1] =
+ const char *dddlb_opt_choices[static_cast<int>(DlbOption::Count)+1] =
{ nullptr, "auto", "no", "yes", nullptr };
const char *thread_aff_opt_choices[threadaffNR+1] =
{ nullptr, "auto", "on", "off", nullptr };
#include "gromacs/commandline/filenm.h"
#include "gromacs/compat/pointers.h"
-#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/options.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/mdrunoptions.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/compat/pointers.h"
-#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/options.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdrun/legacymdrunoptions.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff