*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2012, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019, 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.
* The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override.
*/
#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
-#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
+# define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
#endif
/*! \brief Default for the prune kernel's j4 processing concurrency.
*
/*! \brief number of clusters per supercluster. */
static const int c_numClPerSupercl = c_nbnxnGpuNumClusterPerSupercluster;
/*! \brief cluster size = number of atoms per cluster. */
-static const int c_clSize = c_nbnxnGpuClusterSize;
+static const int c_clSize = c_nbnxnGpuClusterSize;
/*! \brief Electrostatic CUDA kernel flavors.
*
* nbnxn_cuda.cu by the nb_*_kfunc_ptr function pointer table
* should match the order of enumerated types below.
*/
-enum eelCu {
- eelCuCUT, eelCuRF, eelCuEWALD_TAB, eelCuEWALD_TAB_TWIN, eelCuEWALD_ANA, eelCuEWALD_ANA_TWIN, eelCuNR
+enum eelCu
+{
+ eelCuCUT,
+ eelCuRF,
+ eelCuEWALD_TAB,
+ eelCuEWALD_TAB_TWIN,
+ eelCuEWALD_ANA,
+ eelCuEWALD_ANA_TWIN,
+ eelCuNR
};
/*! \brief VdW CUDA kernel flavors.
* nbnxn_cuda.cu by the nb_*_kfunc_ptr function pointer table
* should match the order of enumerated types below.
*/
-enum evdwCu {
- evdwCuCUT, evdwCuCUTCOMBGEOM, evdwCuCUTCOMBLB, evdwCuFSWITCH, evdwCuPSWITCH, evdwCuEWALDGEOM, evdwCuEWALDLB, evdwCuNR
+enum evdwCu
+{
+ evdwCuCUT,
+ evdwCuCUTCOMBGEOM,
+ evdwCuCUTCOMBLB,
+ evdwCuFSWITCH,
+ evdwCuPSWITCH,
+ evdwCuEWALDGEOM,
+ evdwCuEWALDLB,
+ evdwCuNR
};
/* All structs prefixed with "cu_" hold data used in GPU calculations and
* are passed to the kernels, except cu_timers_t. */
/*! \cond */
-typedef struct cu_atomdata cu_atomdata_t;
-typedef struct cu_nbparam cu_nbparam_t;
-typedef struct nb_staging nb_staging_t;
+typedef struct cu_atomdata cu_atomdata_t;
+typedef struct cu_nbparam cu_nbparam_t;
+typedef struct nb_staging nb_staging_t;
/*! \endcond */
*/
struct nb_staging
{
- float *e_lj; /**< LJ energy */
- float *e_el; /**< electrostatic energy */
- float3 *fshift; /**< shift forces */
+ float* e_lj; /**< LJ energy */
+ float* e_el; /**< electrostatic energy */
+ float3* fshift; /**< shift forces */
};
/** \internal
*/
struct cu_atomdata
{
- int natoms; /**< number of atoms */
- int natoms_local; /**< number of local atoms */
- int nalloc; /**< allocation size for the atom data (xq, f) */
+ int natoms; /**< number of atoms */
+ int natoms_local; /**< number of local atoms */
+ int nalloc; /**< allocation size for the atom data (xq, f) */
- float4 *xq; /**< atom coordinates + charges, size natoms */
- float3 *f; /**< force output array, size natoms */
+ float4* xq; /**< atom coordinates + charges, size natoms */
+ float3* f; /**< force output array, size natoms */
- float *e_lj; /**< LJ energy output, size 1 */
- float *e_el; /**< Electrostatics energy input, size 1 */
+ float* e_lj; /**< LJ energy output, size 1 */
+ float* e_el; /**< Electrostatics energy input, size 1 */
- float3 *fshift; /**< shift forces */
+ float3* fshift; /**< shift forces */
- int ntypes; /**< number of atom types */
- int *atom_types; /**< atom type indices, size natoms */
- float2 *lj_comb; /**< sqrt(c6),sqrt(c12) size natoms */
+ int ntypes; /**< number of atom types */
+ int* atom_types; /**< atom type indices, size natoms */
+ float2* lj_comb; /**< sqrt(c6),sqrt(c12) size natoms */
- float3 *shift_vec; /**< shifts */
- bool bShiftVecUploaded; /**< true if the shift vector has been uploaded */
+ float3* shift_vec; /**< shifts */
+ bool bShiftVecUploaded; /**< true if the shift vector has been uploaded */
};
/** \internal
struct cu_nbparam
{
- int eeltype; /**< type of electrostatics, takes values from #eelCu */
- int vdwtype; /**< type of VdW impl., takes values from #evdwCu */
+ int eeltype; /**< type of electrostatics, takes values from #eelCu */
+ int vdwtype; /**< type of VdW impl., takes values from #evdwCu */
- float epsfac; /**< charge multiplication factor */
- float c_rf; /**< Reaction-field/plain cutoff electrostatics const. */
- float two_k_rf; /**< Reaction-field electrostatics constant */
- float ewald_beta; /**< Ewald/PME parameter */
- float sh_ewald; /**< Ewald/PME correction term substracted from the direct-space potential */
- float sh_lj_ewald; /**< LJ-Ewald/PME correction term added to the correction potential */
- float ewaldcoeff_lj; /**< LJ-Ewald/PME coefficient */
+ float epsfac; /**< charge multiplication factor */
+ float c_rf; /**< Reaction-field/plain cutoff electrostatics const. */
+ float two_k_rf; /**< Reaction-field electrostatics constant */
+ float ewald_beta; /**< Ewald/PME parameter */
+ float sh_ewald; /**< Ewald/PME correction term substracted from the direct-space potential */
+ float sh_lj_ewald; /**< LJ-Ewald/PME correction term added to the correction potential */
+ float ewaldcoeff_lj; /**< LJ-Ewald/PME coefficient */
- float rcoulomb_sq; /**< Coulomb cut-off squared */
+ float rcoulomb_sq; /**< Coulomb cut-off squared */
- float rvdw_sq; /**< VdW cut-off squared */
- float rvdw_switch; /**< VdW switched cut-off */
- float rlistOuter_sq; /**< Full, outer pair-list cut-off squared */
- float rlistInner_sq; /**< Inner, dynamic pruned pair-list cut-off squared */
- bool useDynamicPruning; /**< True if we use dynamic pair-list pruning */
+ float rvdw_sq; /**< VdW cut-off squared */
+ float rvdw_switch; /**< VdW switched cut-off */
+ float rlistOuter_sq; /**< Full, outer pair-list cut-off squared */
+ float rlistInner_sq; /**< Inner, dynamic pruned pair-list cut-off squared */
+ bool useDynamicPruning; /**< True if we use dynamic pair-list pruning */
- shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
- shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
- switch_consts_t vdw_switch; /**< VdW switch constants */
+ shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
+ shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
+ switch_consts_t vdw_switch; /**< VdW switch constants */
/* LJ non-bonded parameters - accessed through texture memory */
- float *nbfp; /**< nonbonded parameter table with C6/C12 pairs per atom type-pair, 2*ntype^2 elements */
- cudaTextureObject_t nbfp_texobj; /**< texture object bound to nbfp */
- float *nbfp_comb; /**< nonbonded parameter table per atom type, 2*ntype elements */
- cudaTextureObject_t nbfp_comb_texobj; /**< texture object bound to nbfp_texobj */
+ float* nbfp; /**< nonbonded parameter table with C6/C12 pairs per atom type-pair, 2*ntype^2 elements */
+ cudaTextureObject_t nbfp_texobj; /**< texture object bound to nbfp */
+ float* nbfp_comb; /**< nonbonded parameter table per atom type, 2*ntype elements */
+ cudaTextureObject_t nbfp_comb_texobj; /**< texture object bound to nbfp_texobj */
/* Ewald Coulomb force table data - accessed through texture memory */
- float coulomb_tab_scale; /**< table scale/spacing */
- float *coulomb_tab; /**< pointer to the table in the device memory */
- cudaTextureObject_t coulomb_tab_texobj; /**< texture object bound to coulomb_tab */
+ float coulomb_tab_scale; /**< table scale/spacing */
+ float* coulomb_tab; /**< pointer to the table in the device memory */
+ cudaTextureObject_t coulomb_tab_texobj; /**< texture object bound to coulomb_tab */
};
/** \internal
struct gmx_nbnxn_cuda_t
{
//! CUDA device information
- const gmx_device_info_t *dev_info;
+ const gmx_device_info_t* dev_info;
//! true if doing both local/non-local NB work on GPU
- bool bUseTwoStreams;
+ bool bUseTwoStreams;
//! atom data
- cu_atomdata_t *atdat;
+ cu_atomdata_t* atdat;
//! f buf ops cell index mapping
- int *cell;
+ int* cell;
//! number of indices in cell buffer
- int ncell;
+ int ncell;
//! number of indices allocated in cell buffer
- int ncell_alloc;
+ int ncell_alloc;
//! array of atom indices
- int *atomIndices;
+ int* atomIndices;
//! size of atom indices
- int atomIndicesSize;
+ int atomIndicesSize;
//! size of atom indices allocated in device buffer
- int atomIndicesSize_alloc;
+ int atomIndicesSize_alloc;
//! x buf ops num of atoms
- int *cxy_na;
+ int* cxy_na;
//! number of elements in cxy_na
- int ncxy_na;
+ int ncxy_na;
//! number of elements allocated allocated in device buffer
- int ncxy_na_alloc;
+ int ncxy_na_alloc;
//! x buf ops cell index mapping
- int *cxy_ind;
+ int* cxy_ind;
//! number of elements in cxy_ind
- int ncxy_ind;
+ int ncxy_ind;
//! number of elements allocated allocated in device buffer
- int ncxy_ind_alloc;
+ int ncxy_ind_alloc;
//! parameters required for the non-bonded calc.
- cu_nbparam_t *nbparam;
+ cu_nbparam_t* nbparam;
//! pair-list data structures (local and non-local)
- gmx::EnumerationArray<Nbnxm::InteractionLocality, cu_plist_t *> plist;
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, cu_plist_t*> plist;
//! staging area where fshift/energies get downloaded
- nb_staging_t nbst;
+ nb_staging_t nbst;
//! local and non-local GPU streams
gmx::EnumerationArray<Nbnxm::InteractionLocality, cudaStream_t> stream;
/** events used for synchronization */
- cudaEvent_t nonlocal_done; /**< event triggered when the non-local non-bonded kernel
- is done (and the local transfer can proceed) */
- cudaEvent_t misc_ops_and_local_H2D_done; /**< event triggered when the tasks issued in
- the local stream that need to precede the
- non-local force or buffer operation calculations are done
- (e.g. f buffer 0-ing, local x/q H2D, buffer op
- initialization in local stream that is required also
- by nonlocal stream ) */
+ cudaEvent_t nonlocal_done; /**< event triggered when the non-local non-bonded kernel
+ is done (and the local transfer can proceed) */
+ cudaEvent_t misc_ops_and_local_H2D_done; /**< event triggered when the tasks issued in
+ the local stream that need to precede the
+ non-local force or buffer operation calculations are
+ done (e.g. f buffer 0-ing, local x/q H2D, buffer op
+ initialization in local stream that is required also
+ by nonlocal stream ) */
//! True if there has been local/nonlocal GPU work, either bonded or nonbonded, scheduled
// to be executed in the current domain. As long as bonded work is not split up into
*
* \note That the synchronizer is managed outside of this module in StatePropagatorDataGpu.
*/
- GpuEventSynchronizer *localFReductionDone;
+ GpuEventSynchronizer* localFReductionDone;
- GpuEventSynchronizer *xNonLocalCopyD2HDone; /**< event triggered when
+ GpuEventSynchronizer* xNonLocalCopyD2HDone; /**< event triggered when
non-local coordinate buffer has been
copied from device to host*/
* Timer init/uninit is still done even with timing off so only the condition
* setting bDoTime needs to be change if this CUDA "feature" gets fixed. */
//! True if event-based timing is enabled.
- bool bDoTime;
+ bool bDoTime;
//! CUDA event-based timers.
- cu_timers_t *timers;
+ cu_timers_t* timers;
//! Timing data. TODO: deprecate this and query timers for accumulated data instead
- gmx_wallclock_gpu_nbnxn_t *timings;
+ gmx_wallclock_gpu_nbnxn_t* timings;
};
-#endif /* NBNXN_CUDA_TYPES_H */
+#endif /* NBNXN_CUDA_TYPES_H */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff