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Refactor ghosts.cpp #3216

Merged
merged 40 commits into from
Oct 18, 2019
Merged

Refactor ghosts.cpp #3216

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85f235d
ghosts.cpp: Make predicates return bool
hirschsn Sep 26, 2019
b2444d6
ghosts.cpp: Remove unused MPI_Status variable
hirschsn Sep 26, 2019
3bb4449
ghosts.cpp: Use clear() instead of resize(0)
hirschsn Sep 26, 2019
aaab228
ghosts: Remove unused mpi_comm field
hirschsn Sep 26, 2019
ffe7113
Remove left-over typedefs from C days
hirschsn Sep 26, 2019
09f5140
ghosts: Make part_lists a std::vector
hirschsn Sep 26, 2019
eab1470
ghosts: Make s_buffer and r_buffer std::vectors
hirschsn Sep 26, 2019
03708a2
ghosts: Factor out memory handling
hirschsn Sep 26, 2019
5d77262
ghosts: Use boost::mpi for recv, send and bcst
hirschsn Sep 26, 2019
a5b811d
Explicitly cast length to int
hirschsn Sep 26, 2019
56e4572
ghost_rdce: Use boost::mpi
hirschsn Sep 26, 2019
2b910e8
ghosts: Remove n_bonds from payload
hirschsn Sep 26, 2019
c507697
ghosts: Use range-based for loops
hirschsn Sep 26, 2019
646d468
ghosts: Reformat
hirschsn Sep 26, 2019
a847b1c
More reformats
hirschsn Sep 27, 2019
8e8c581
Update comment
hirschsn Sep 27, 2019
b20fe3d
ghosts: Change two more instances of n_X_buffer
hirschsn Sep 27, 2019
b872b68
ghosts: Remove else. Check must always hold.
hirschsn Sep 27, 2019
0408706
ghosts: Early exit on GHOST_LOCL
hirschsn Sep 27, 2019
70f5a60
ghosts: Remove prefetch loop
hirschsn Sep 27, 2019
8097ec3
ghosts: else+if -> else if
hirschsn Sep 27, 2019
8a6ca56
ghosts: More else if
hirschsn Sep 27, 2019
f60d634
ghosts: Change friend decl to struct
hirschsn Sep 27, 2019
71de951
ghosts: Remove poststore loop
hirschsn Sep 27, 2019
551699d
ghosts: Make helper functions take references
hirschsn Sep 27, 2019
0d7aa14
ghosts: Make helper functions static
hirschsn Sep 27, 2019
84bea92
add_forces: range based for loop
hirschsn Sep 27, 2019
16ae7a9
mpi::reduce: Correct size of data
hirschsn Sep 27, 2019
50f789a
Merge branch 'python' of https://github.com/espressomd/espresso into …
fweik Oct 1, 2019
b5bd6e8
Merge branch 'python' of https://github.com/espressomd/espresso into …
fweik Oct 1, 2019
f060558
ghosts: cleanup
fweik Oct 1, 2019
d021d80
utils: make_span overload from container
fweik Oct 1, 2019
1ab35ff
ghosts: Decouple Archiver and BondArchiver
fweik Oct 1, 2019
513a8d5
Make CommBuf a class and add documentation
hirschsn Oct 2, 2019
8df0132
cell_cell_transfer: Remove pointers
hirschsn Oct 2, 2019
23007cb
ghosts: Rename variables
hirschsn Oct 2, 2019
0b50cb2
Make GhostCommunicator variables always "gcr".
hirschsn Oct 2, 2019
aef12a5
ghosts: Convert "additional checks" into asserts
hirschsn Oct 2, 2019
c62e278
ghosts: Another pointer->reference conversion
hirschsn Oct 2, 2019
f21d717
Merge branch 'python' into ghost-cleanup
hirschsn Oct 15, 2019
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22 changes: 9 additions & 13 deletions src/core/domain_decomposition.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -280,9 +280,7 @@ void dd_prepare_comm(GhostCommunicator *comm, int data_parts,
comm->comm[cnt].node = this_node;

/* Buffer has to contain Send and Recv cells -> factor 2 */
comm->comm[cnt].part_lists =
(Cell **)Utils::malloc(2 * n_comm_cells[dir] * sizeof(Cell *));
comm->comm[cnt].n_part_lists = 2 * n_comm_cells[dir];
comm->comm[cnt].part_lists.resize(2 * n_comm_cells[dir]);
/* prepare folding of ghost positions */
if ((data_parts & GHOSTTRANS_POSSHFTD) &&
local_geo.boundary()[2 * dir + lr] != 0) {
Expand All @@ -293,7 +291,7 @@ void dd_prepare_comm(GhostCommunicator *comm, int data_parts,
/* fill send comm cells */
lc[dir] = hc[dir] = 1 + lr * (dd.cell_grid[dir] - 1);

dd_fill_comm_cell_lists(comm->comm[cnt].part_lists, lc, hc);
dd_fill_comm_cell_lists(comm->comm[cnt].part_lists.data(), lc, hc);

/* fill recv comm cells */
lc[dir] = hc[dir] = 0 + (1 - lr) * (dd.cell_grid[dir] + 1);
Expand All @@ -312,9 +310,7 @@ void dd_prepare_comm(GhostCommunicator *comm, int data_parts,
if ((node_pos[dir] + i) % 2 == 0) {
comm->comm[cnt].type = GHOST_SEND;
comm->comm[cnt].node = node_neighbors[2 * dir + lr];
comm->comm[cnt].part_lists =
(Cell **)Utils::malloc(n_comm_cells[dir] * sizeof(Cell *));
comm->comm[cnt].n_part_lists = n_comm_cells[dir];
comm->comm[cnt].part_lists.resize(n_comm_cells[dir]);
/* prepare folding of ghost positions */
if ((data_parts & GHOSTTRANS_POSSHFTD) &&
local_geo.boundary()[2 * dir + lr] != 0) {
Expand All @@ -324,21 +320,21 @@ void dd_prepare_comm(GhostCommunicator *comm, int data_parts,

lc[dir] = hc[dir] = 1 + lr * (dd.cell_grid[dir] - 1);

dd_fill_comm_cell_lists(comm->comm[cnt].part_lists, lc, hc);
dd_fill_comm_cell_lists(comm->comm[cnt].part_lists.data(), lc,
hc);
cnt++;
}
if (box_geo.periodic(dir) ||
(local_geo.boundary()[2 * dir + (1 - lr)] == 0))
if ((node_pos[dir] + (1 - i)) % 2 == 0) {
comm->comm[cnt].type = GHOST_RECV;
comm->comm[cnt].node = node_neighbors[2 * dir + (1 - lr)];
comm->comm[cnt].part_lists =
(Cell **)Utils::malloc(n_comm_cells[dir] * sizeof(Cell *));
comm->comm[cnt].n_part_lists = n_comm_cells[dir];
comm->comm[cnt].part_lists.resize(n_comm_cells[dir]);

lc[dir] = hc[dir] = (1 - lr) * (dd.cell_grid[dir] + 1);

dd_fill_comm_cell_lists(comm->comm[cnt].part_lists, lc, hc);
dd_fill_comm_cell_lists(comm->comm[cnt].part_lists.data(), lc,
hc);
cnt++;
}
}
Expand Down Expand Up @@ -369,7 +365,7 @@ void dd_revert_comm_order(GhostCommunicator *comm) {
else if (comm->comm[i].type == GHOST_RECV)
comm->comm[i].type = GHOST_SEND;
else if (comm->comm[i].type == GHOST_LOCL) {
nlist2 = comm->comm[i].n_part_lists / 2;
nlist2 = comm->comm[i].part_lists.size() / 2;
for (j = 0; j < nlist2; j++) {
auto tmplist = comm->comm[i].part_lists[j];
comm->comm[i].part_lists[j] = comm->comm[i].part_lists[j + nlist2];
Expand Down
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