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5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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48 #include "gromacs/commandline/filenm.h"
49 #include "gromacs/mdtypes/commrec.h"
50 #include "gromacs/utility/basenetwork.h"
51 #include "gromacs/utility/cstringutil.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/futil.h"
54 #include "gromacs/utility/gmxmpi.h"
55 #include "gromacs/utility/smalloc.h"
57 /* The source code in this file should be thread-safe.
58 Please keep it that way. */
60 void gmx_fill_commrec_from_mpi(t_commrec gmx_unused
*cr
)
63 gmx_call("gmx_fill_commrec_from_mpi");
65 if (!gmx_mpi_initialized())
67 gmx_comm("MPI has not been initialized properly");
70 cr
->nnodes
= gmx_node_num();
71 cr
->nodeid
= gmx_node_rank();
72 cr
->sim_nodeid
= cr
->nodeid
;
73 cr
->mpi_comm_mysim
= MPI_COMM_WORLD
;
74 cr
->mpi_comm_mygroup
= MPI_COMM_WORLD
;
79 t_commrec
*init_commrec()
86 gmx_fill_commrec_from_mpi(cr
);
88 cr
->mpi_comm_mysim
= NULL
;
89 cr
->mpi_comm_mygroup
= NULL
;
92 cr
->nodeid
= cr
->sim_nodeid
;
95 // TODO cr->duty should not be initialized here
96 cr
->duty
= (DUTY_PP
| DUTY_PME
);
98 #if defined GMX_MPI && !MPI_IN_PLACE_EXISTS
99 /* initialize the MPI_IN_PLACE replacement buffers */
101 cr
->mpb
->ibuf
= NULL
;
102 cr
->mpb
->libuf
= NULL
;
103 cr
->mpb
->fbuf
= NULL
;
104 cr
->mpb
->dbuf
= NULL
;
105 cr
->mpb
->ibuf_alloc
= 0;
106 cr
->mpb
->libuf_alloc
= 0;
107 cr
->mpb
->fbuf_alloc
= 0;
108 cr
->mpb
->dbuf_alloc
= 0;
114 t_commrec
*reinitialize_commrec_for_this_thread(const t_commrec gmx_unused
*cro
)
116 #ifdef GMX_THREAD_MPI
119 /* make a thread-specific commrec */
121 /* now copy the whole thing, so settings like the number of PME nodes
125 /* and we start setting our own thread-specific values for things */
126 gmx_fill_commrec_from_mpi(cr
);
128 // TODO cr->duty should not be initialized here
129 cr
->duty
= (DUTY_PP
| DUTY_PME
);
137 void gmx_setup_nodecomm(FILE gmx_unused
*fplog
, t_commrec
*cr
)
141 /* Many MPI implementations do not optimize MPI_Allreduce
142 * (and probably also other global communication calls)
143 * for multi-core nodes connected by a network.
144 * We can optimize such communication by using one MPI call
145 * within each node and one between the nodes.
146 * For MVAPICH2 and Intel MPI this reduces the time for
147 * the global_stat communication by 25%
148 * for 2x2-core 3 GHz Woodcrest connected by mixed DDR/SDR Infiniband.
149 * B. Hess, November 2007
155 #ifndef GMX_THREAD_MPI
159 MPI_Comm_size(cr
->mpi_comm_mygroup
, &n
);
160 MPI_Comm_rank(cr
->mpi_comm_mygroup
, &rank
);
162 int nodehash
= gmx_physicalnode_id_hash();
166 fprintf(debug
, "In gmx_setup_nodecomm: splitting communicator of size %d\n", n
);
170 /* The intra-node communicator, split on node number */
171 MPI_Comm_split(cr
->mpi_comm_mygroup
, nodehash
, rank
, &nc
->comm_intra
);
172 MPI_Comm_rank(nc
->comm_intra
, &nc
->rank_intra
);
175 fprintf(debug
, "In gmx_setup_nodecomm: node ID %d rank within node %d\n",
176 rank
, nc
->rank_intra
);
178 /* The inter-node communicator, split on rank_intra.
179 * We actually only need the one for rank=0,
180 * but it is easier to create them all.
182 MPI_Comm_split(cr
->mpi_comm_mygroup
, nc
->rank_intra
, rank
, &nc
->comm_inter
);
183 /* Check if this really created two step communication */
186 MPI_Comm_size(nc
->comm_inter
, &ng
);
187 MPI_Comm_size(nc
->comm_intra
, &ni
);
190 fprintf(debug
, "In gmx_setup_nodecomm: groups %d, my group size %d\n",
194 if (getenv("GMX_NO_NODECOMM") == NULL
&&
195 ((ng
> 1 && ng
< n
) || (ni
> 1 && ni
< n
)))
200 fprintf(fplog
, "Using two step summing over %d groups of on average %.1f ranks\n\n",
201 ng
, (real
)n
/(real
)ng
);
203 if (nc
->rank_intra
> 0)
205 MPI_Comm_free(&nc
->comm_inter
);
210 /* One group or all processes in a separate group, use normal summing */
211 MPI_Comm_free(&nc
->comm_inter
);
212 MPI_Comm_free(&nc
->comm_intra
);
215 fprintf(debug
, "In gmx_setup_nodecomm: not unsing separate inter- and intra-node communicators.\n");
220 /* tMPI runs only on a single node so just use the nodeid */
221 nc
->rank_intra
= cr
->nodeid
;
225 void gmx_init_intranode_counters(t_commrec
*cr
)
227 /* counters for PP+PME and PP-only processes on my physical node */
228 int nrank_intranode
, rank_intranode
;
229 int nrank_pp_intranode
, rank_pp_intranode
;
230 /* thread-MPI is not initialized when not running in parallel */
231 #if defined GMX_MPI && !defined GMX_THREAD_MPI
232 int nrank_world
, rank_world
;
233 int i
, myhash
, *hash
, *hash_s
, *hash_pp
, *hash_pp_s
;
235 MPI_Comm_size(MPI_COMM_WORLD
, &nrank_world
);
236 MPI_Comm_rank(MPI_COMM_WORLD
, &rank_world
);
238 /* Get a (hopefully unique) hash that identifies our physical node */
239 myhash
= gmx_physicalnode_id_hash();
241 /* We can't rely on MPI_IN_PLACE, so we need send and receive buffers */
242 snew(hash
, nrank_world
);
243 snew(hash_s
, nrank_world
);
244 snew(hash_pp
, nrank_world
);
245 snew(hash_pp_s
, nrank_world
);
247 hash_s
[rank_world
] = myhash
;
248 hash_pp_s
[rank_world
] = (cr
->duty
& DUTY_PP
) ? myhash
: -1;
250 MPI_Allreduce(hash_s
, hash
, nrank_world
, MPI_INT
, MPI_SUM
, MPI_COMM_WORLD
);
251 MPI_Allreduce(hash_pp_s
, hash_pp
, nrank_world
, MPI_INT
, MPI_SUM
, MPI_COMM_WORLD
);
255 nrank_pp_intranode
= 0;
256 rank_pp_intranode
= 0;
257 for (i
= 0; i
< nrank_world
; i
++)
259 if (hash
[i
] == myhash
)
267 if (hash_pp
[i
] == myhash
)
269 nrank_pp_intranode
++;
270 if ((cr
->duty
& DUTY_PP
) && i
< rank_world
)
281 /* Serial or thread-MPI code: we run within a single physical node */
282 nrank_intranode
= cr
->nnodes
;
283 rank_intranode
= cr
->sim_nodeid
;
284 nrank_pp_intranode
= cr
->nnodes
- cr
->npmenodes
;
285 rank_pp_intranode
= cr
->nodeid
;
291 if (cr
->duty
& DUTY_PP
&& cr
->duty
& DUTY_PME
)
293 sprintf(sbuf
, "PP+PME");
297 sprintf(sbuf
, "%s", cr
->duty
& DUTY_PP
? "PP" : "PME");
299 fprintf(debug
, "On %3s rank %d: nrank_intranode=%d, rank_intranode=%d, "
300 "nrank_pp_intranode=%d, rank_pp_intranode=%d\n",
301 sbuf
, cr
->sim_nodeid
,
302 nrank_intranode
, rank_intranode
,
303 nrank_pp_intranode
, rank_pp_intranode
);
306 cr
->nrank_intranode
= nrank_intranode
;
307 cr
->rank_intranode
= rank_intranode
;
308 cr
->nrank_pp_intranode
= nrank_pp_intranode
;
309 cr
->rank_pp_intranode
= rank_pp_intranode
;
313 void gmx_barrier(const t_commrec gmx_unused
*cr
)
316 gmx_call("gmx_barrier");
318 MPI_Barrier(cr
->mpi_comm_mygroup
);
322 void gmx_bcast(int gmx_unused nbytes
, void gmx_unused
*b
, const t_commrec gmx_unused
*cr
)
325 gmx_call("gmx_bast");
327 MPI_Bcast(b
, nbytes
, MPI_BYTE
, MASTERRANK(cr
), cr
->mpi_comm_mygroup
);
331 void gmx_bcast_sim(int gmx_unused nbytes
, void gmx_unused
*b
, const t_commrec gmx_unused
*cr
)
334 gmx_call("gmx_bast");
336 MPI_Bcast(b
, nbytes
, MPI_BYTE
, MASTERRANK(cr
), cr
->mpi_comm_mysim
);
340 void gmx_sumd(int gmx_unused nr
, double gmx_unused r
[], const t_commrec gmx_unused
*cr
)
343 gmx_call("gmx_sumd");
345 #if MPI_IN_PLACE_EXISTS
348 if (cr
->nc
.rank_intra
== 0)
350 /* Use two step summing. */
351 MPI_Reduce(MPI_IN_PLACE
, r
, nr
, MPI_DOUBLE
, MPI_SUM
, 0,
353 /* Sum the roots of the internal (intra) buffers. */
354 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_DOUBLE
, MPI_SUM
,
359 /* This is here because of the silly MPI specification
360 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
361 MPI_Reduce(r
, NULL
, nr
, MPI_DOUBLE
, MPI_SUM
, 0, cr
->nc
.comm_intra
);
363 MPI_Bcast(r
, nr
, MPI_DOUBLE
, 0, cr
->nc
.comm_intra
);
367 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_DOUBLE
, MPI_SUM
,
368 cr
->mpi_comm_mygroup
);
373 if (nr
> cr
->mpb
->dbuf_alloc
)
375 cr
->mpb
->dbuf_alloc
= nr
;
376 srenew(cr
->mpb
->dbuf
, cr
->mpb
->dbuf_alloc
);
380 /* Use two step summing */
381 MPI_Allreduce(r
, cr
->mpb
->dbuf
, nr
, MPI_DOUBLE
, MPI_SUM
, cr
->nc
.comm_intra
);
382 if (cr
->nc
.rank_intra
== 0)
384 /* Sum with the buffers reversed */
385 MPI_Allreduce(cr
->mpb
->dbuf
, r
, nr
, MPI_DOUBLE
, MPI_SUM
,
388 MPI_Bcast(r
, nr
, MPI_DOUBLE
, 0, cr
->nc
.comm_intra
);
392 MPI_Allreduce(r
, cr
->mpb
->dbuf
, nr
, MPI_DOUBLE
, MPI_SUM
,
393 cr
->mpi_comm_mygroup
);
394 for (i
= 0; i
< nr
; i
++)
396 r
[i
] = cr
->mpb
->dbuf
[i
];
403 void gmx_sumf(int gmx_unused nr
, float gmx_unused r
[], const t_commrec gmx_unused
*cr
)
406 gmx_call("gmx_sumf");
408 #if MPI_IN_PLACE_EXISTS
411 /* Use two step summing. */
412 if (cr
->nc
.rank_intra
== 0)
414 MPI_Reduce(MPI_IN_PLACE
, r
, nr
, MPI_FLOAT
, MPI_SUM
, 0,
416 /* Sum the roots of the internal (intra) buffers */
417 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_FLOAT
, MPI_SUM
,
422 /* This is here because of the silly MPI specification
423 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
424 MPI_Reduce(r
, NULL
, nr
, MPI_FLOAT
, MPI_SUM
, 0, cr
->nc
.comm_intra
);
426 MPI_Bcast(r
, nr
, MPI_FLOAT
, 0, cr
->nc
.comm_intra
);
430 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_FLOAT
, MPI_SUM
, cr
->mpi_comm_mygroup
);
435 if (nr
> cr
->mpb
->fbuf_alloc
)
437 cr
->mpb
->fbuf_alloc
= nr
;
438 srenew(cr
->mpb
->fbuf
, cr
->mpb
->fbuf_alloc
);
442 /* Use two step summing */
443 MPI_Allreduce(r
, cr
->mpb
->fbuf
, nr
, MPI_FLOAT
, MPI_SUM
, cr
->nc
.comm_intra
);
444 if (cr
->nc
.rank_intra
== 0)
446 /* Sum with the buffers reversed */
447 MPI_Allreduce(cr
->mpb
->fbuf
, r
, nr
, MPI_FLOAT
, MPI_SUM
,
450 MPI_Bcast(r
, nr
, MPI_FLOAT
, 0, cr
->nc
.comm_intra
);
454 MPI_Allreduce(r
, cr
->mpb
->fbuf
, nr
, MPI_FLOAT
, MPI_SUM
,
455 cr
->mpi_comm_mygroup
);
456 for (i
= 0; i
< nr
; i
++)
458 r
[i
] = cr
->mpb
->fbuf
[i
];
465 void gmx_sumi(int gmx_unused nr
, int gmx_unused r
[], const t_commrec gmx_unused
*cr
)
468 gmx_call("gmx_sumi");
470 #if MPI_IN_PLACE_EXISTS
473 /* Use two step summing */
474 if (cr
->nc
.rank_intra
== 0)
476 MPI_Reduce(MPI_IN_PLACE
, r
, nr
, MPI_INT
, MPI_SUM
, 0, cr
->nc
.comm_intra
);
477 /* Sum with the buffers reversed */
478 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_INT
, MPI_SUM
, cr
->nc
.comm_inter
);
482 /* This is here because of the silly MPI specification
483 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
484 MPI_Reduce(r
, NULL
, nr
, MPI_INT
, MPI_SUM
, 0, cr
->nc
.comm_intra
);
486 MPI_Bcast(r
, nr
, MPI_INT
, 0, cr
->nc
.comm_intra
);
490 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_INT
, MPI_SUM
, cr
->mpi_comm_mygroup
);
495 if (nr
> cr
->mpb
->ibuf_alloc
)
497 cr
->mpb
->ibuf_alloc
= nr
;
498 srenew(cr
->mpb
->ibuf
, cr
->mpb
->ibuf_alloc
);
502 /* Use two step summing */
503 MPI_Allreduce(r
, cr
->mpb
->ibuf
, nr
, MPI_INT
, MPI_SUM
, cr
->nc
.comm_intra
);
504 if (cr
->nc
.rank_intra
== 0)
506 /* Sum with the buffers reversed */
507 MPI_Allreduce(cr
->mpb
->ibuf
, r
, nr
, MPI_INT
, MPI_SUM
, cr
->nc
.comm_inter
);
509 MPI_Bcast(r
, nr
, MPI_INT
, 0, cr
->nc
.comm_intra
);
513 MPI_Allreduce(r
, cr
->mpb
->ibuf
, nr
, MPI_INT
, MPI_SUM
, cr
->mpi_comm_mygroup
);
514 for (i
= 0; i
< nr
; i
++)
516 r
[i
] = cr
->mpb
->ibuf
[i
];
523 void gmx_sumli(int gmx_unused nr
, gmx_int64_t gmx_unused r
[], const t_commrec gmx_unused
*cr
)
526 gmx_call("gmx_sumli");
528 #if MPI_IN_PLACE_EXISTS
531 /* Use two step summing */
532 if (cr
->nc
.rank_intra
== 0)
534 MPI_Reduce(MPI_IN_PLACE
, r
, nr
, MPI_INT64_T
, MPI_SUM
, 0,
536 /* Sum with the buffers reversed */
537 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_INT64_T
, MPI_SUM
,
542 /* This is here because of the silly MPI specification
543 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
544 MPI_Reduce(r
, NULL
, nr
, MPI_INT64_T
, MPI_SUM
, 0, cr
->nc
.comm_intra
);
546 MPI_Bcast(r
, nr
, MPI_INT64_T
, 0, cr
->nc
.comm_intra
);
550 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_INT64_T
, MPI_SUM
, cr
->mpi_comm_mygroup
);
555 if (nr
> cr
->mpb
->libuf_alloc
)
557 cr
->mpb
->libuf_alloc
= nr
;
558 srenew(cr
->mpb
->libuf
, cr
->mpb
->libuf_alloc
);
562 /* Use two step summing */
563 MPI_Allreduce(r
, cr
->mpb
->libuf
, nr
, MPI_INT64_T
, MPI_SUM
,
565 if (cr
->nc
.rank_intra
== 0)
567 /* Sum with the buffers reversed */
568 MPI_Allreduce(cr
->mpb
->libuf
, r
, nr
, MPI_INT64_T
, MPI_SUM
,
571 MPI_Bcast(r
, nr
, MPI_INT64_T
, 0, cr
->nc
.comm_intra
);
575 MPI_Allreduce(r
, cr
->mpb
->libuf
, nr
, MPI_INT64_T
, MPI_SUM
,
576 cr
->mpi_comm_mygroup
);
577 for (i
= 0; i
< nr
; i
++)
579 r
[i
] = cr
->mpb
->libuf
[i
];
589 static void gmx_sumd_comm(int nr
, double r
[], MPI_Comm mpi_comm
)
591 #if MPI_IN_PLACE_EXISTS
592 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_DOUBLE
, MPI_SUM
, mpi_comm
);
594 /* this function is only used in code that is not performance critical,
595 (during setup, when comm_rec is not the appropriate communication
596 structure), so this isn't as bad as it looks. */
601 MPI_Allreduce(r
, buf
, nr
, MPI_DOUBLE
, MPI_SUM
, mpi_comm
);
602 for (i
= 0; i
< nr
; i
++)
612 static void gmx_sumf_comm(int nr
, float r
[], MPI_Comm mpi_comm
)
614 #if MPI_IN_PLACE_EXISTS
615 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_FLOAT
, MPI_SUM
, mpi_comm
);
617 /* this function is only used in code that is not performance critical,
618 (during setup, when comm_rec is not the appropriate communication
619 structure), so this isn't as bad as it looks. */
624 MPI_Allreduce(r
, buf
, nr
, MPI_FLOAT
, MPI_SUM
, mpi_comm
);
625 for (i
= 0; i
< nr
; i
++)
634 void gmx_sumd_sim(int gmx_unused nr
, double gmx_unused r
[], const gmx_multisim_t gmx_unused
*ms
)
637 gmx_call("gmx_sumd_sim");
639 gmx_sumd_comm(nr
, r
, ms
->mpi_comm_masters
);
643 void gmx_sumf_sim(int gmx_unused nr
, float gmx_unused r
[], const gmx_multisim_t gmx_unused
*ms
)
646 gmx_call("gmx_sumf_sim");
648 gmx_sumf_comm(nr
, r
, ms
->mpi_comm_masters
);
652 void gmx_sumi_sim(int gmx_unused nr
, int gmx_unused r
[], const gmx_multisim_t gmx_unused
*ms
)
655 gmx_call("gmx_sumi_sim");
657 #if MPI_IN_PLACE_EXISTS
658 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_INT
, MPI_SUM
, ms
->mpi_comm_masters
);
660 /* this is thread-unsafe, but it will do for now: */
663 if (nr
> ms
->mpb
->ibuf_alloc
)
665 ms
->mpb
->ibuf_alloc
= nr
;
666 srenew(ms
->mpb
->ibuf
, ms
->mpb
->ibuf_alloc
);
668 MPI_Allreduce(r
, ms
->mpb
->ibuf
, nr
, MPI_INT
, MPI_SUM
, ms
->mpi_comm_masters
);
669 for (i
= 0; i
< nr
; i
++)
671 r
[i
] = ms
->mpb
->ibuf
[i
];
677 void gmx_sumli_sim(int gmx_unused nr
, gmx_int64_t gmx_unused r
[], const gmx_multisim_t gmx_unused
*ms
)
680 gmx_call("gmx_sumli_sim");
682 #if MPI_IN_PLACE_EXISTS
683 MPI_Allreduce(MPI_IN_PLACE
, r
, nr
, MPI_INT64_T
, MPI_SUM
,
684 ms
->mpi_comm_masters
);
686 /* this is thread-unsafe, but it will do for now: */
689 if (nr
> ms
->mpb
->libuf_alloc
)
691 ms
->mpb
->libuf_alloc
= nr
;
692 srenew(ms
->mpb
->libuf
, ms
->mpb
->libuf_alloc
);
694 MPI_Allreduce(r
, ms
->mpb
->libuf
, nr
, MPI_INT64_T
, MPI_SUM
,
695 ms
->mpi_comm_masters
);
696 for (i
= 0; i
< nr
; i
++)
698 r
[i
] = ms
->mpb
->libuf
[i
];
704 const char *opt2fn_master(const char *opt
, int nfile
, const t_filenm fnm
[],
707 return SIMMASTER(cr
) ? opt2fn(opt
, nfile
, fnm
) : NULL
;
710 void gmx_fatal_collective(int f_errno
, const char *file
, int line
,
711 MPI_Comm comm
, gmx_bool bMaster
,
712 const char *fmt
, ...)
718 /* Check if we are calling on all processes in MPI_COMM_WORLD */
719 MPI_Comm_compare(comm
, MPI_COMM_WORLD
, &result
);
720 /* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
721 bFinalize
= (result
!= MPI_UNEQUAL
);
727 gmx_fatal_mpi_va(f_errno
, file
, line
, bMaster
, bFinalize
, fmt
, ap
);