*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, 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 <cstring>
#include "gromacs/commandline/filenm.h"
-#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/mpiinplacebuffers.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-CommrecHandle init_commrec(MPI_Comm communicator,
- const gmx_multisim_t *ms)
+CommrecHandle init_commrec(MPI_Comm communicator)
{
CommrecHandle handle;
- t_commrec *cr;
+ t_commrec* cr;
snew(cr, 1);
handle.reset(cr);
int rankInCommunicator, sizeOfCommunicator;
#if GMX_MPI
-# if GMX_LIB_MPI
+# if GMX_LIB_MPI
GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "Must have initialized MPI before building commrec");
-# endif
+# endif
MPI_Comm_rank(communicator, &rankInCommunicator);
MPI_Comm_size(communicator, &sizeOfCommunicator);
#else
sizeOfCommunicator = 1;
#endif
- if (ms != nullptr)
- {
-#if GMX_MPI
- cr->nnodes = sizeOfCommunicator / ms->nsim;
- MPI_Comm_split(communicator, ms->sim, rankInCommunicator, &cr->mpi_comm_mysim);
- cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
- MPI_Comm_rank(cr->mpi_comm_mysim, &cr->sim_nodeid);
- MPI_Comm_rank(cr->mpi_comm_mygroup, &cr->nodeid);
-#endif
- }
- else
- {
- cr->nnodes = sizeOfCommunicator;
- cr->nodeid = rankInCommunicator;
- cr->sim_nodeid = cr->nodeid;
- cr->mpi_comm_mysim = communicator;
- cr->mpi_comm_mygroup = communicator;
- }
+ cr->mpiDefaultCommunicator = communicator;
+ cr->sizeOfDefaultCommunicator = sizeOfCommunicator;
+ cr->rankInDefaultCommunicator = rankInCommunicator;
+
+ // For now, we want things to go horribly wrong if this is used too early...
+ // TODO: Remove when communicators are removed from commrec (#2395)
+ cr->nnodes = -1;
+ cr->sizeOfMyGroupCommunicator = -1;
+ cr->nodeid = -1;
+ cr->sim_nodeid = -1;
+ cr->mpi_comm_mysim = MPI_COMM_NULL;
+ cr->mpi_comm_mygroup = MPI_COMM_NULL;
// TODO cr->duty should not be initialized here
cr->duty = (DUTY_PP | DUTY_PME);
-#if GMX_MPI && !MPI_IN_PLACE_EXISTS
- /* initialize the MPI_IN_PLACE replacement buffers */
- snew(cr->mpb, 1);
- cr->mpb->ibuf = nullptr;
- cr->mpb->libuf = nullptr;
- cr->mpb->fbuf = nullptr;
- cr->mpb->dbuf = nullptr;
- cr->mpb->ibuf_alloc = 0;
- cr->mpb->libuf_alloc = 0;
- cr->mpb->fbuf_alloc = 0;
- cr->mpb->dbuf_alloc = 0;
-#endif
-
return handle;
}
-void done_commrec(t_commrec *cr)
+void done_commrec(t_commrec* cr)
{
if (MASTER(cr))
{
// TODO: implement
// done_domdec(cr->dd);
}
- done_mpi_in_place_buf(cr->mpb);
}
#if GMX_MPI
// TODO We need to be able to free communicators, but the
// structure of the commrec and domdec initialization code makes
// it hard to avoid both leaks and double frees.
bool mySimIsMyGroup = (cr->mpi_comm_mysim == cr->mpi_comm_mygroup);
- if (cr->mpi_comm_mysim != MPI_COMM_NULL &&
- cr->mpi_comm_mysim != MPI_COMM_WORLD)
+ if (cr->mpi_comm_mysim != MPI_COMM_NULL && cr->mpi_comm_mysim != MPI_COMM_WORLD)
{
// TODO see above
// MPI_Comm_free(&cr->mpi_comm_mysim);
}
- if (!mySimIsMyGroup &&
- cr->mpi_comm_mygroup != MPI_COMM_NULL &&
- cr->mpi_comm_mygroup != MPI_COMM_WORLD)
+ if (!mySimIsMyGroup && cr->mpi_comm_mygroup != MPI_COMM_NULL && cr->mpi_comm_mygroup != MPI_COMM_WORLD)
{
// TODO see above
// MPI_Comm_free(&cr->mpi_comm_mygroup);
sfree(cr);
}
-void gmx_setup_nodecomm(FILE gmx_unused *fplog, t_commrec *cr)
+void gmx_setup_nodecomm(FILE gmx_unused* fplog, t_commrec* cr)
{
- gmx_nodecomm_t *nc;
+ gmx_nodecomm_t* nc;
/* Many MPI implementations do not optimize MPI_Allreduce
* (and probably also other global communication calls)
nc->bUse = FALSE;
#if !GMX_THREAD_MPI
-#if GMX_MPI
+# if GMX_MPI
int n, rank;
// TODO PhysicalNodeCommunicator could be extended/used to handle
MPI_Comm_rank(nc->comm_intra, &nc->rank_intra);
if (debug)
{
- fprintf(debug, "In gmx_setup_nodecomm: node ID %d rank within node %d\n",
- rank, nc->rank_intra);
+ fprintf(debug, "In gmx_setup_nodecomm: node ID %d rank within node %d\n", rank, nc->rank_intra);
}
/* The inter-node communicator, split on rank_intra.
* We actually only need the one for rank=0,
MPI_Comm_size(nc->comm_intra, &ni);
if (debug)
{
- fprintf(debug, "In gmx_setup_nodecomm: groups %d, my group size %d\n",
- ng, ni);
+ fprintf(debug, "In gmx_setup_nodecomm: groups %d, my group size %d\n", ng, ni);
}
- if (getenv("GMX_NO_NODECOMM") == nullptr &&
- ((ng > 1 && ng < n) || (ni > 1 && ni < n)))
+ if (getenv("GMX_NO_NODECOMM") == nullptr && ((ng > 1 && ng < n) || (ni > 1 && ni < n)))
{
nc->bUse = TRUE;
if (fplog)
{
- fprintf(fplog, "Using two step summing over %d groups of on average %.1f ranks\n\n",
- ng, (real)n/(real)ng);
+ fprintf(fplog,
+ "Using two step summing over %d groups of on average %.1f ranks\n\n",
+ ng,
+ real(n) / real(ng));
}
if (nc->rank_intra > 0)
{
MPI_Comm_free(&nc->comm_intra);
if (debug)
{
- fprintf(debug, "In gmx_setup_nodecomm: not unsing separate inter- and intra-node communicators.\n");
+ fprintf(debug,
+ "In gmx_setup_nodecomm: not unsing separate inter- and intra-node "
+ "communicators.\n");
}
}
-#endif
+# endif
#else
/* tMPI runs only on a single node so just use the nodeid */
nc->rank_intra = cr->nodeid;
#endif
}
-void gmx_barrier(const t_commrec gmx_unused *cr)
+void gmx_barrier(MPI_Comm gmx_unused communicator)
{
+ if (communicator == MPI_COMM_NULL)
+ {
+ return;
+ }
#if !GMX_MPI
- gmx_call("gmx_barrier");
+ GMX_RELEASE_ASSERT(false, "Invalid call to gmx_barrier");
#else
- MPI_Barrier(cr->mpi_comm_mygroup);
+ MPI_Barrier(communicator);
#endif
}
-void gmx_bcast(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
+void gmx_bcast(int gmx_unused nbytes, void gmx_unused* b, MPI_Comm gmx_unused communicator)
{
-#if !GMX_MPI
- gmx_call("gmx_bast");
-#else
- MPI_Bcast(b, nbytes, MPI_BYTE, MASTERRANK(cr), cr->mpi_comm_mygroup);
+ // Without MPI we have a single rank, so bcast is a no-op
+#if GMX_MPI
+ MPI_Bcast(b, nbytes, MPI_BYTE, 0, communicator);
#endif
}
-void gmx_bcast_sim(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
+void gmx_sumd(int gmx_unused nr, double gmx_unused r[], const t_commrec gmx_unused* cr)
{
-#if !GMX_MPI
- gmx_call("gmx_bast");
-#else
- MPI_Bcast(b, nbytes, MPI_BYTE, MASTERRANK(cr), cr->mpi_comm_mysim);
-#endif
-}
+ // Without MPI we have a single rank, so sum is a no-op
+#if GMX_MPI
+ if (cr->sizeOfMyGroupCommunicator == 1)
+ {
+ return;
+ }
-void gmx_sumd(int gmx_unused nr, double gmx_unused r[], const t_commrec gmx_unused *cr)
-{
-#if !GMX_MPI
- gmx_call("gmx_sumd");
-#else
-#if MPI_IN_PLACE_EXISTS
if (cr->nc.bUse)
{
if (cr->nc.rank_intra == 0)
{
/* Use two step summing. */
- MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, 0,
- cr->nc.comm_intra);
+ MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, 0, cr->nc.comm_intra);
/* Sum the roots of the internal (intra) buffers. */
- MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM,
- cr->nc.comm_inter);
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, cr->nc.comm_inter);
}
else
{
}
else
{
- MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM,
- cr->mpi_comm_mygroup);
- }
-#else
- int i;
-
- if (nr > cr->mpb->dbuf_alloc)
- {
- cr->mpb->dbuf_alloc = nr;
- srenew(cr->mpb->dbuf, cr->mpb->dbuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->dbuf, nr, MPI_DOUBLE, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->dbuf, r, nr, MPI_DOUBLE, MPI_SUM,
- cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_DOUBLE, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->dbuf, nr, MPI_DOUBLE, MPI_SUM,
- cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->dbuf[i];
- }
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mygroup);
}
#endif
-#endif
}
-void gmx_sumf(int gmx_unused nr, float gmx_unused r[], const t_commrec gmx_unused *cr)
+void gmx_sumf(int gmx_unused nr, float gmx_unused r[], const t_commrec gmx_unused* cr)
{
-#if !GMX_MPI
- gmx_call("gmx_sumf");
-#else
-#if MPI_IN_PLACE_EXISTS
+ // Without MPI we have a single rank, so sum is a no-op
+#if GMX_MPI
+ if (cr->sizeOfMyGroupCommunicator == 1)
+ {
+ return;
+ }
+
if (cr->nc.bUse)
{
/* Use two step summing. */
if (cr->nc.rank_intra == 0)
{
- MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, 0,
- cr->nc.comm_intra);
+ MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, 0, cr->nc.comm_intra);
/* Sum the roots of the internal (intra) buffers */
- MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM,
- cr->nc.comm_inter);
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, cr->nc.comm_inter);
}
else
{
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, cr->mpi_comm_mygroup);
}
-#else
- int i;
-
- if (nr > cr->mpb->fbuf_alloc)
- {
- cr->mpb->fbuf_alloc = nr;
- srenew(cr->mpb->fbuf, cr->mpb->fbuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->fbuf, nr, MPI_FLOAT, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->fbuf, r, nr, MPI_FLOAT, MPI_SUM,
- cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_FLOAT, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->fbuf, nr, MPI_FLOAT, MPI_SUM,
- cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->fbuf[i];
- }
- }
-#endif
#endif
}
-void gmx_sumi(int gmx_unused nr, int gmx_unused r[], const t_commrec gmx_unused *cr)
+void gmx_sumi(int gmx_unused nr, int gmx_unused r[], const t_commrec gmx_unused* cr)
{
-#if !GMX_MPI
- gmx_call("gmx_sumi");
-#else
-#if MPI_IN_PLACE_EXISTS
+ // Without MPI we have a single rank, so sum is a no-op
+#if GMX_MPI
+ if (cr->sizeOfMyGroupCommunicator == 1)
+ {
+ return;
+ }
+
if (cr->nc.bUse)
{
/* Use two step summing */
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
}
-#else
- int i;
-
- if (nr > cr->mpb->ibuf_alloc)
- {
- cr->mpb->ibuf_alloc = nr;
- srenew(cr->mpb->ibuf, cr->mpb->ibuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->ibuf, nr, MPI_INT, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->ibuf, r, nr, MPI_INT, MPI_SUM, cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_INT, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->ibuf, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->ibuf[i];
- }
- }
-#endif
#endif
}
-void gmx_sumli(int gmx_unused nr, int64_t gmx_unused r[], const t_commrec gmx_unused *cr)
-{
-#if !GMX_MPI
- gmx_call("gmx_sumli");
-#else
-#if MPI_IN_PLACE_EXISTS
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- if (cr->nc.rank_intra == 0)
- {
- MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_INT64_T, MPI_SUM, 0,
- cr->nc.comm_intra);
- /* Sum with the buffers reversed */
- MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT64_T, MPI_SUM,
- cr->nc.comm_inter);
- }
- else
- {
- /* This is here because of the silly MPI specification
- that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
- MPI_Reduce(r, nullptr, nr, MPI_INT64_T, MPI_SUM, 0, cr->nc.comm_intra);
- }
- MPI_Bcast(r, nr, MPI_INT64_T, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT64_T, MPI_SUM, cr->mpi_comm_mygroup);
- }
-#else
- int i;
-
- if (nr > cr->mpb->libuf_alloc)
- {
- cr->mpb->libuf_alloc = nr;
- srenew(cr->mpb->libuf, cr->mpb->libuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->libuf, nr, MPI_INT64_T, MPI_SUM,
- cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->libuf, r, nr, MPI_INT64_T, MPI_SUM,
- cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_INT64_T, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->libuf, nr, MPI_INT64_T, MPI_SUM,
- cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->libuf[i];
- }
- }
-#endif
-#endif
-}
-
-const char *opt2fn_master(const char *opt, int nfile, const t_filenm fnm[],
- t_commrec *cr)
+const char* opt2fn_master(const char* opt, int nfile, const t_filenm fnm[], t_commrec* cr)
{
return SIMMASTER(cr) ? opt2fn(opt, nfile, fnm) : nullptr;
}
-void gmx_fatal_collective(int f_errno, const char *file, int line,
- MPI_Comm comm, gmx_bool bMaster,
- gmx_fmtstr const char *fmt, ...)
+void gmx_fatal_collective(int f_errno,
+ const char* file,
+ int line,
+ MPI_Comm comm,
+ gmx_bool bMaster,
+ gmx_fmtstr const char* fmt,
+ ...)
{
va_list ap;
gmx_bool bFinalize;
#if GMX_MPI
- int result;
+ int result;
/* Check if we are calling on all processes in MPI_COMM_WORLD */
MPI_Comm_compare(comm, MPI_COMM_WORLD, &result);
/* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
gmx_fatal_mpi_va(f_errno, file, line, bMaster, bFinalize, fmt, ap);
va_end(ap);
}
-
-void simulationBarrier(const t_commrec *cr)
-{
- if (PAR(cr))
- {
-#if GMX_MPI
- MPI_Barrier(cr->mpi_comm_mysim);
-#endif
- }
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff