-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
- *
- * If you want to redistribute modifications, 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 www.gromacs.org.
- *
+ *
+ * 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
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+ * 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 papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
-#include "gmx_fatal.h"
-#include "main.h"
-#include "smalloc.h"
-#include "network.h"
-#include "copyrite.h"
-#include "statutil.h"
-#include <ctype.h>
-#include "macros.h"
+#include "gromacs/legacyheaders/network.h"
-#ifdef GMX_LIB_MPI
-#include <mpi.h>
-#endif
-
-#ifdef GMX_THREAD_MPI
-#include "tmpi.h"
-#endif
+#include "config.h"
+#include <ctype.h>
+#include <stdarg.h>
+#include <stdlib.h>
+#include <string.h>
-/* The source code in this file should be thread-safe.
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/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/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+/* The source code in this file should be thread-safe.
Please keep it that way. */
-gmx_bool gmx_mpi_initialized(void)
+void gmx_fill_commrec_from_mpi(t_commrec gmx_unused *cr)
{
- int n;
#ifndef GMX_MPI
- return 0;
+ gmx_call("gmx_fill_commrec_from_mpi");
#else
- MPI_Initialized(&n);
-
- return n;
+ if (!gmx_mpi_initialized())
+ {
+ gmx_comm("MPI has not been initialized properly");
+ }
+
+ cr->nnodes = gmx_node_num();
+ cr->nodeid = gmx_node_rank();
+ cr->sim_nodeid = cr->nodeid;
+ cr->mpi_comm_mysim = MPI_COMM_WORLD;
+ cr->mpi_comm_mygroup = MPI_COMM_WORLD;
+
#endif
}
-int gmx_setup(int *argc,char **argv,int *nnodes)
+t_commrec *init_commrec()
{
-#ifndef GMX_MPI
- gmx_call("gmx_setup");
- return 0;
-#else
- char buf[256];
- int resultlen; /* actual length of node name */
- int i,flag;
- int mpi_num_nodes;
- int mpi_my_rank;
- char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
-
- /* Call the MPI routines */
+ t_commrec *cr;
+
+ snew(cr, 1);
+
#ifdef GMX_LIB_MPI
-#ifdef GMX_FAHCORE
- (void) fah_MPI_Init(argc,&argv);
+ gmx_fill_commrec_from_mpi(cr);
#else
- (void) MPI_Init(argc,&argv);
-#endif
-#endif
- (void) MPI_Comm_size( MPI_COMM_WORLD, &mpi_num_nodes );
- (void) MPI_Comm_rank( MPI_COMM_WORLD, &mpi_my_rank );
- (void) MPI_Get_processor_name( mpi_hostname, &resultlen );
-
-#ifdef GMX_LIB_MPI
- fprintf(stderr,"NNODES=%d, MYRANK=%d, HOSTNAME=%s\n",
- mpi_num_nodes,mpi_my_rank,mpi_hostname);
-#endif
-
- *nnodes=mpi_num_nodes;
-
- return mpi_my_rank;
-#endif
+ cr->mpi_comm_mysim = NULL;
+ cr->mpi_comm_mygroup = NULL;
+ cr->nnodes = 1;
+ cr->sim_nodeid = 0;
+ cr->nodeid = cr->sim_nodeid;
+#endif
+
+ // TODO cr->duty should not be initialized here
+ cr->duty = (DUTY_PP | DUTY_PME);
+
+#if defined GMX_MPI && !defined MPI_IN_PLACE_EXISTS
+ /* initialize the MPI_IN_PLACE replacement buffers */
+ snew(cr->mpb, 1);
+ cr->mpb->ibuf = NULL;
+ cr->mpb->libuf = NULL;
+ cr->mpb->fbuf = NULL;
+ cr->mpb->dbuf = NULL;
+ cr->mpb->ibuf_alloc = 0;
+ cr->mpb->libuf_alloc = 0;
+ cr->mpb->fbuf_alloc = 0;
+ cr->mpb->dbuf_alloc = 0;
+#endif
+
+ return cr;
}
-int gmx_node_num(void)
+t_commrec *reinitialize_commrec_for_this_thread(const t_commrec gmx_unused *cro)
{
-#ifndef GMX_MPI
- return 1;
-#else
- int i;
- (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
- return i;
-#endif
-}
+#ifdef GMX_THREAD_MPI
+ t_commrec *cr;
-int gmx_node_rank(void)
-{
-#ifndef GMX_MPI
- return 0;
-#else
- int i;
- (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
- return i;
-#endif
-}
+ /* make a thread-specific commrec */
+ snew(cr, 1);
+ /* now copy the whole thing, so settings like the number of PME nodes
+ get propagated. */
+ *cr = *cro;
+ /* and we start setting our own thread-specific values for things */
+ gmx_fill_commrec_from_mpi(cr);
-int gmx_hostname_num()
-{
-#ifndef GMX_MPI
- return 0;
-#else
-#ifdef GMX_THREAD_MPI
- /* thread-MPI currently puts the thread number in the process name,
- * we might want to change this, as this is inconsistent with what
- * most MPI implementations would do when running on a single node.
- */
- return 0;
+ // TODO cr->duty should not be initialized here
+ cr->duty = (DUTY_PP | DUTY_PME);
+
+ return cr;
#else
- int resultlen,hostnum,i,j;
- char mpi_hostname[MPI_MAX_PROCESSOR_NAME],hostnum_str[MPI_MAX_PROCESSOR_NAME];
-
- MPI_Get_processor_name(mpi_hostname,&resultlen);
- /* This procedure can only differentiate nodes with host names
- * that end on unique numbers.
- */
- i = 0;
- j = 0;
- /* Only parse the host name up to the first dot */
- while(i < resultlen && mpi_hostname[i] != '.') {
- if (isdigit(mpi_hostname[i])) {
- hostnum_str[j++] = mpi_hostname[i];
- }
- i++;
- }
- hostnum_str[j] = '\0';
- if (j == 0) {
- hostnum = 0;
- } else {
- /* Use only the last 9 decimals, so we don't overflow an int */
- hostnum = strtol(hostnum_str + max(0,j-9), NULL, 10);
- }
-
- if (debug) {
- fprintf(debug,"In gmx_setup_nodecomm: hostname '%s', hostnum %d\n",
- mpi_hostname,hostnum);
- }
- return hostnum;
-#endif
+ return NULL;
#endif
}
-void gmx_setup_nodecomm(FILE *fplog,t_commrec *cr)
+void gmx_setup_nodecomm(FILE gmx_unused *fplog, t_commrec *cr)
{
gmx_nodecomm_t *nc;
- int n,rank,hostnum,ng,ni;
+ int n, rank, nodehash, ng, ni;
/* Many MPI implementations do not optimize MPI_Allreduce
* (and probably also other global communication calls)
nc->bUse = FALSE;
#ifndef GMX_THREAD_MPI
#ifdef GMX_MPI
- MPI_Comm_size(cr->mpi_comm_mygroup,&n);
- MPI_Comm_rank(cr->mpi_comm_mygroup,&rank);
+ MPI_Comm_size(cr->mpi_comm_mygroup, &n);
+ MPI_Comm_rank(cr->mpi_comm_mygroup, &rank);
- hostnum = gmx_hostname_num();
+ nodehash = gmx_physicalnode_id_hash();
if (debug)
{
- fprintf(debug,"In gmx_setup_nodecomm: splitting communicator of size %d\n",n);
+ fprintf(debug, "In gmx_setup_nodecomm: splitting communicator of size %d\n", n);
}
/* The intra-node communicator, split on node number */
- MPI_Comm_split(cr->mpi_comm_mygroup,hostnum,rank,&nc->comm_intra);
- MPI_Comm_rank(nc->comm_intra,&nc->rank_intra);
+ MPI_Comm_split(cr->mpi_comm_mygroup, nodehash, rank, &nc->comm_intra);
+ MPI_Comm_rank(nc->comm_intra, &nc->rank_intra);
if (debug)
{
- fprintf(debug,"In gmx_setup_nodecomm: node rank %d rank_intra %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,
* but it is easier to create them all.
*/
- MPI_Comm_split(cr->mpi_comm_mygroup,nc->rank_intra,rank,&nc->comm_inter);
+ MPI_Comm_split(cr->mpi_comm_mygroup, nc->rank_intra, rank, &nc->comm_inter);
/* Check if this really created two step communication */
- MPI_Comm_size(nc->comm_inter,&ng);
- MPI_Comm_size(nc->comm_intra,&ni);
+ MPI_Comm_size(nc->comm_inter, &ng);
+ 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") == NULL &&
nc->bUse = TRUE;
if (fplog)
{
- fprintf(fplog,"Using two step summing over %d groups of on average %.1f processes\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
}
-void gmx_init_intra_counters(t_commrec *cr)
+void gmx_init_intranode_counters(t_commrec *cr)
{
- /* counters for PP+PME and PP-only processes on my node */
- int nnodes, nnodes_pp, id_mynode=-1, id_mynode_group=-1, nproc_mynode, nproc_mynode_pp;
+ /* counters for PP+PME and PP-only processes on my physical node */
+ int nrank_intranode, rank_intranode;
+ int nrank_pp_intranode, rank_pp_intranode;
+ /* thread-MPI is not initialized when not running in parallel */
#if defined GMX_MPI && !defined GMX_THREAD_MPI
- int i, mynum, *num, *num_s, *num_pp, *num_pp_s;
-#endif
+ int nrank_world, rank_world;
+ int i, myhash, *hash, *hash_s, *hash_pp, *hash_pp_s;
- nnodes = cr->nnodes;
- nnodes_pp = nnodes - cr->npmenodes;
+ MPI_Comm_size(MPI_COMM_WORLD, &nrank_world);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank_world);
-#if defined GMX_MPI && !defined GMX_THREAD_MPI
- /* We have MPI and can expect to have different compute nodes */
- mynum = gmx_hostname_num();
+ /* Get a (hopefully unique) hash that identifies our physical node */
+ myhash = gmx_physicalnode_id_hash();
/* We can't rely on MPI_IN_PLACE, so we need send and receive buffers */
- snew(num, nnodes);
- snew(num_s, nnodes);
- snew(num_pp, nnodes_pp);
- snew(num_pp_s, nnodes_pp);
-
- num_s[cr->sim_nodeid] = mynum;
- if (cr->duty & DUTY_PP)
- {
- num_pp_s[cr->nodeid] = mynum;
- }
-
- MPI_Allreduce(num_s, num, nnodes, MPI_INT, MPI_SUM, cr->mpi_comm_mysim);
- MPI_Allreduce(num_pp_s, num_pp, nnodes_pp, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
-
- id_mynode = 0;
- id_mynode_group = 0;
- nproc_mynode = 0;
- nproc_mynode_pp = 0;
- for(i=0; i<nnodes; i++)
+ snew(hash, nrank_world);
+ snew(hash_s, nrank_world);
+ snew(hash_pp, nrank_world);
+ snew(hash_pp_s, nrank_world);
+
+ hash_s[rank_world] = myhash;
+ hash_pp_s[rank_world] = (cr->duty & DUTY_PP) ? myhash : -1;
+
+ MPI_Allreduce(hash_s, hash, nrank_world, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(hash_pp_s, hash_pp, nrank_world, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+
+ nrank_intranode = 0;
+ rank_intranode = 0;
+ nrank_pp_intranode = 0;
+ rank_pp_intranode = 0;
+ for (i = 0; i < nrank_world; i++)
{
- if (num[i] == mynum)
+ if (hash[i] == myhash)
{
- nproc_mynode++;
- if (i < cr->sim_nodeid)
+ nrank_intranode++;
+ if (i < rank_world)
{
- id_mynode++;
- }
- if (i < cr->nodeid)
- {
- id_mynode_group++;
+ rank_intranode++;
}
}
- }
- for(i=0; i<nnodes_pp; i++)
- {
- if (num_pp[i] == mynum)
+ if (hash_pp[i] == myhash)
{
- nproc_mynode_pp++;
+ nrank_pp_intranode++;
+ if ((cr->duty & DUTY_PP) && i < rank_world)
+ {
+ rank_pp_intranode++;
+ }
}
}
- sfree(num);
- sfree(num_s);
- sfree(num_pp);
- sfree(num_pp_s);
+ sfree(hash);
+ sfree(hash_s);
+ sfree(hash_pp);
+ sfree(hash_pp_s);
#else
- /* Serial or thread-MPI code, we are running within a node */
- id_mynode = cr->sim_nodeid;
- id_mynode_group = cr->nodeid;
- nproc_mynode = cr->nnodes;
- nproc_mynode_pp = cr->nnodes - cr->npmenodes;
+ /* Serial or thread-MPI code: we run within a single physical node */
+ nrank_intranode = cr->nnodes;
+ rank_intranode = cr->sim_nodeid;
+ nrank_pp_intranode = cr->nnodes - cr->npmenodes;
+ rank_pp_intranode = cr->nodeid;
#endif
if (debug)
{
sprintf(sbuf, "%s", cr->duty & DUTY_PP ? "PP" : "PME");
}
- fprintf(debug, "On %3s node %d: nodeid_intra=%d, nodeid_group_intra=%d, "
- "nnodes_intra=%d, nnodes_pp_intra=%d\n", sbuf, cr->sim_nodeid,
- id_mynode, id_mynode_group, nproc_mynode, nproc_mynode_pp);
+ fprintf(debug, "On %3s rank %d: nrank_intranode=%d, rank_intranode=%d, "
+ "nrank_pp_intranode=%d, rank_pp_intranode=%d\n",
+ sbuf, cr->sim_nodeid,
+ nrank_intranode, rank_intranode,
+ nrank_pp_intranode, rank_pp_intranode);
}
- cr->nodeid_intra = id_mynode;
- cr->nodeid_group_intra = id_mynode_group;
- cr->nnodes_intra = nproc_mynode;
- cr->nnodes_pp_intra = nproc_mynode_pp;
+ cr->nrank_intranode = nrank_intranode;
+ cr->rank_intranode = rank_intranode;
+ cr->nrank_pp_intranode = nrank_pp_intranode;
+ cr->rank_pp_intranode = rank_pp_intranode;
}
-void gmx_barrier(const t_commrec *cr)
+void gmx_barrier(const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
- gmx_call("gmx_barrier");
+ gmx_call("gmx_barrier");
#else
- MPI_Barrier(cr->mpi_comm_mygroup);
+ MPI_Barrier(cr->mpi_comm_mygroup);
#endif
}
-void gmx_abort(int noderank,int nnodes,int errorno)
+void gmx_bcast(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
- gmx_call("gmx_abort");
+ gmx_call("gmx_bast");
#else
-#ifdef GMX_THREAD_MPI
- fprintf(stderr,"Halting program %s\n",ShortProgram());
- thanx(stderr);
- exit(1);
-#else
- if (nnodes > 1)
- {
- fprintf(stderr,"Halting parallel program %s on CPU %d out of %d\n",
- ShortProgram(),noderank,nnodes);
- }
- else
- {
- fprintf(stderr,"Halting program %s\n",ShortProgram());
- }
-
- thanx(stderr);
- MPI_Abort(MPI_COMM_WORLD,errorno);
- exit(1);
-#endif
+ MPI_Bcast(b, nbytes, MPI_BYTE, MASTERRANK(cr), cr->mpi_comm_mygroup);
#endif
}
-void gmx_bcast(int nbytes,void *b,const t_commrec *cr)
+void gmx_bcast_sim(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
- gmx_call("gmx_bast");
+ gmx_call("gmx_bast");
#else
- MPI_Bcast(b,nbytes,MPI_BYTE,MASTERRANK(cr),cr->mpi_comm_mygroup);
+ MPI_Bcast(b, nbytes, MPI_BYTE, MASTERRANK(cr), cr->mpi_comm_mysim);
#endif
}
-void gmx_bcast_sim(int nbytes,void *b,const t_commrec *cr)
-{
-#ifndef GMX_MPI
- gmx_call("gmx_bast");
-#else
- MPI_Bcast(b,nbytes,MPI_BYTE,MASTERRANK(cr),cr->mpi_comm_mysim);
-#endif
-}
-
-void gmx_sumd(int nr,double r[],const t_commrec *cr)
+void gmx_sumd(int gmx_unused nr, double gmx_unused r[], const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_sumd");
#else
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- if (cr->nc.bUse) {
+#if defined(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,
+ 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,
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, 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,NULL,nr,MPI_DOUBLE,MPI_SUM,0,cr->nc.comm_intra);
+ MPI_Reduce(r, NULL, nr, MPI_DOUBLE, MPI_SUM, 0, cr->nc.comm_intra);
}
- MPI_Bcast(r,nr,MPI_DOUBLE,0,cr->nc.comm_intra);
- }
- else
+ MPI_Bcast(r, nr, MPI_DOUBLE, 0, cr->nc.comm_intra);
+ }
+ else
{
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM,
cr->mpi_comm_mygroup);
}
#else
int i;
- if (nr > cr->mpb->dbuf_alloc) {
+ if (nr > cr->mpb->dbuf_alloc)
+ {
cr->mpb->dbuf_alloc = nr;
- srenew(cr->mpb->dbuf,cr->mpb->dbuf_alloc);
+ srenew(cr->mpb->dbuf, cr->mpb->dbuf_alloc);
}
- if (cr->nc.bUse) {
+ 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) {
+ 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,
+ 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,
+ 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++)
+ for (i = 0; i < nr; i++)
+ {
r[i] = cr->mpb->dbuf[i];
+ }
}
#endif
#endif
}
-void gmx_sumf(int nr,float r[],const t_commrec *cr)
+void gmx_sumf(int gmx_unused nr, float gmx_unused r[], const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_sumf");
#else
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- if (cr->nc.bUse) {
+#if defined(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_FLOAT,MPI_SUM,0,
+ 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,
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, 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,NULL,nr,MPI_FLOAT,MPI_SUM,0,cr->nc.comm_intra);
+ MPI_Reduce(r, NULL, nr, MPI_FLOAT, MPI_SUM, 0, cr->nc.comm_intra);
}
- MPI_Bcast(r,nr,MPI_FLOAT,0,cr->nc.comm_intra);
- }
- else
+ MPI_Bcast(r, nr, MPI_FLOAT, 0, cr->nc.comm_intra);
+ }
+ else
{
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,cr->mpi_comm_mygroup);
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, cr->mpi_comm_mygroup);
}
#else
int i;
- if (nr > cr->mpb->fbuf_alloc) {
+ if (nr > cr->mpb->fbuf_alloc)
+ {
cr->mpb->fbuf_alloc = nr;
- srenew(cr->mpb->fbuf,cr->mpb->fbuf_alloc);
+ srenew(cr->mpb->fbuf, cr->mpb->fbuf_alloc);
}
- if (cr->nc.bUse) {
+ 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) {
+ 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,
+ 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,
+ 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++)
+ for (i = 0; i < nr; i++)
+ {
r[i] = cr->mpb->fbuf[i];
+ }
}
#endif
#endif
}
-void gmx_sumi(int nr,int r[],const t_commrec *cr)
+void gmx_sumi(int gmx_unused nr, int gmx_unused r[], const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_sumi");
#else
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- if (cr->nc.bUse) {
+#if defined(MPI_IN_PLACE_EXISTS)
+ if (cr->nc.bUse)
+ {
/* Use two step summing */
- if (cr->nc.rank_intra == 0)
+ if (cr->nc.rank_intra == 0)
{
- MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,0,cr->nc.comm_intra);
+ MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, 0, cr->nc.comm_intra);
/* Sum with the buffers reversed */
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,cr->nc.comm_inter);
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, 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,NULL,nr,MPI_INT,MPI_SUM,0,cr->nc.comm_intra);
+ MPI_Reduce(r, NULL, nr, MPI_INT, MPI_SUM, 0, cr->nc.comm_intra);
}
- MPI_Bcast(r,nr,MPI_INT,0,cr->nc.comm_intra);
- }
- else
+ MPI_Bcast(r, nr, MPI_INT, 0, cr->nc.comm_intra);
+ }
+ else
{
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,cr->mpi_comm_mygroup);
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
}
#else
int i;
- if (nr > cr->mpb->ibuf_alloc) {
+ if (nr > cr->mpb->ibuf_alloc)
+ {
cr->mpb->ibuf_alloc = nr;
- srenew(cr->mpb->ibuf,cr->mpb->ibuf_alloc);
+ srenew(cr->mpb->ibuf, cr->mpb->ibuf_alloc);
}
- if (cr->nc.bUse) {
+ 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) {
+ 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_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++)
+ 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 nr,gmx_large_int_t r[],const t_commrec *cr)
+void gmx_sumli(int gmx_unused nr, gmx_int64_t gmx_unused r[], const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_sumli");
#else
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- if (cr->nc.bUse) {
+#if defined(MPI_IN_PLACE_EXISTS)
+ if (cr->nc.bUse)
+ {
/* Use two step summing */
- if (cr->nc.rank_intra == 0)
+ if (cr->nc.rank_intra == 0)
{
- MPI_Reduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,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,GMX_MPI_LARGE_INT,MPI_SUM,
+ 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,NULL,nr,GMX_MPI_LARGE_INT,MPI_SUM,0,cr->nc.comm_intra);
+ MPI_Reduce(r, NULL, nr, MPI_INT64_T, MPI_SUM, 0, cr->nc.comm_intra);
}
- MPI_Bcast(r,nr,GMX_MPI_LARGE_INT,0,cr->nc.comm_intra);
- }
- else
+ MPI_Bcast(r, nr, MPI_INT64_T, 0, cr->nc.comm_intra);
+ }
+ else
{
- MPI_Allreduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,cr->mpi_comm_mygroup);
+ 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) {
+ if (nr > cr->mpb->libuf_alloc)
+ {
cr->mpb->libuf_alloc = nr;
- srenew(cr->mpb->libuf,cr->mpb->libuf_alloc);
+ srenew(cr->mpb->libuf, cr->mpb->libuf_alloc);
}
- if (cr->nc.bUse) {
+ if (cr->nc.bUse)
+ {
/* Use two step summing */
- MPI_Allreduce(r,cr->mpb->libuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ MPI_Allreduce(r, cr->mpb->libuf, nr, MPI_INT64_T, MPI_SUM,
cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0) {
+ if (cr->nc.rank_intra == 0)
+ {
/* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->libuf,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ MPI_Allreduce(cr->mpb->libuf, r, nr, MPI_INT64_T, MPI_SUM,
cr->nc.comm_inter);
}
- MPI_Bcast(r,nr,GMX_MPI_LARGE_INT,0,cr->nc.comm_intra);
- } else {
- MPI_Allreduce(r,cr->mpb->libuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ 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++)
+ for (i = 0; i < nr; i++)
+ {
r[i] = cr->mpb->libuf[i];
+ }
}
#endif
#endif
#ifdef GMX_MPI
-void gmx_sumd_comm(int nr,double r[],MPI_Comm mpi_comm)
+static void gmx_sumd_comm(int nr, double r[], MPI_Comm mpi_comm)
{
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,mpi_comm);
+#if defined(MPI_IN_PLACE_EXISTS)
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, mpi_comm);
#else
/* this function is only used in code that is not performance critical,
- (during setup, when comm_rec is not the appropriate communication
+ (during setup, when comm_rec is not the appropriate communication
structure), so this isn't as bad as it looks. */
double *buf;
- int i;
+ int i;
snew(buf, nr);
- MPI_Allreduce(r,buf,nr,MPI_DOUBLE,MPI_SUM,mpi_comm);
- for(i=0; i<nr; i++)
+ MPI_Allreduce(r, buf, nr, MPI_DOUBLE, MPI_SUM, mpi_comm);
+ for (i = 0; i < nr; i++)
+ {
r[i] = buf[i];
+ }
sfree(buf);
#endif
}
#endif
#ifdef GMX_MPI
-void gmx_sumf_comm(int nr,float r[],MPI_Comm mpi_comm)
+static void gmx_sumf_comm(int nr, float r[], MPI_Comm mpi_comm)
{
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,mpi_comm);
+#if defined(MPI_IN_PLACE_EXISTS)
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, mpi_comm);
#else
/* this function is only used in code that is not performance critical,
- (during setup, when comm_rec is not the appropriate communication
+ (during setup, when comm_rec is not the appropriate communication
structure), so this isn't as bad as it looks. */
float *buf;
- int i;
+ int i;
snew(buf, nr);
- MPI_Allreduce(r,buf,nr,MPI_FLOAT,MPI_SUM,mpi_comm);
- for(i=0; i<nr; i++)
+ MPI_Allreduce(r, buf, nr, MPI_FLOAT, MPI_SUM, mpi_comm);
+ for (i = 0; i < nr; i++)
+ {
r[i] = buf[i];
+ }
sfree(buf);
#endif
}
#endif
-void gmx_sumd_sim(int nr,double r[],const gmx_multisim_t *ms)
+void gmx_sumd_sim(int gmx_unused nr, double gmx_unused r[], const gmx_multisim_t gmx_unused *ms)
{
#ifndef GMX_MPI
- gmx_call("gmx_sumd_sim");
+ gmx_call("gmx_sumd_sim");
#else
- gmx_sumd_comm(nr,r,ms->mpi_comm_masters);
+ gmx_sumd_comm(nr, r, ms->mpi_comm_masters);
#endif
}
-void gmx_sumf_sim(int nr,float r[],const gmx_multisim_t *ms)
+void gmx_sumf_sim(int gmx_unused nr, float gmx_unused r[], const gmx_multisim_t gmx_unused *ms)
{
#ifndef GMX_MPI
- gmx_call("gmx_sumf_sim");
+ gmx_call("gmx_sumf_sim");
#else
- gmx_sumf_comm(nr,r,ms->mpi_comm_masters);
+ gmx_sumf_comm(nr, r, ms->mpi_comm_masters);
#endif
}
-void gmx_sumi_sim(int nr,int r[], const gmx_multisim_t *ms)
+void gmx_sumi_sim(int gmx_unused nr, int gmx_unused r[], const gmx_multisim_t gmx_unused *ms)
{
#ifndef GMX_MPI
gmx_call("gmx_sumi_sim");
#else
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
+#if defined(MPI_IN_PLACE_EXISTS)
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, ms->mpi_comm_masters);
#else
/* this is thread-unsafe, but it will do for now: */
int i;
- if (nr > ms->mpb->ibuf_alloc) {
+ if (nr > ms->mpb->ibuf_alloc)
+ {
ms->mpb->ibuf_alloc = nr;
- srenew(ms->mpb->ibuf,ms->mpb->ibuf_alloc);
+ srenew(ms->mpb->ibuf, ms->mpb->ibuf_alloc);
}
- MPI_Allreduce(r,ms->mpb->ibuf,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
- for(i=0; i<nr; i++)
+ MPI_Allreduce(r, ms->mpb->ibuf, nr, MPI_INT, MPI_SUM, ms->mpi_comm_masters);
+ for (i = 0; i < nr; i++)
+ {
r[i] = ms->mpb->ibuf[i];
+ }
#endif
#endif
}
-void gmx_sumli_sim(int nr,gmx_large_int_t r[], const gmx_multisim_t *ms)
+void gmx_sumli_sim(int gmx_unused nr, gmx_int64_t gmx_unused r[], const gmx_multisim_t gmx_unused *ms)
{
#ifndef GMX_MPI
gmx_call("gmx_sumli_sim");
#else
-#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
- MPI_Allreduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+#if defined(MPI_IN_PLACE_EXISTS)
+ MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT64_T, MPI_SUM,
ms->mpi_comm_masters);
#else
/* this is thread-unsafe, but it will do for now: */
int i;
- if (nr > ms->mpb->libuf_alloc) {
+ if (nr > ms->mpb->libuf_alloc)
+ {
ms->mpb->libuf_alloc = nr;
- srenew(ms->mpb->libuf,ms->mpb->libuf_alloc);
+ srenew(ms->mpb->libuf, ms->mpb->libuf_alloc);
}
- MPI_Allreduce(r,ms->mpb->libuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ MPI_Allreduce(r, ms->mpb->libuf, nr, MPI_INT64_T, MPI_SUM,
ms->mpi_comm_masters);
- for(i=0; i<nr; i++)
+ for (i = 0; i < nr; i++)
+ {
r[i] = ms->mpb->libuf[i];
+ }
#endif
#endif
}
-
-void gmx_finalize_par(void)
+gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
{
-#ifndef GMX_MPI
- /* Compiled without MPI, no MPI finalizing needed */
- return;
-#else
- int initialized,finalized;
- int ret;
+ gmx_bool bExist;
- MPI_Initialized(&initialized);
- if (!initialized)
+ if (SIMMASTER(cr))
{
- return;
+ bExist = gmx_fexist(fname);
}
- /* just as a check; we don't want to finalize twice */
- MPI_Finalized(&finalized);
- if (finalized)
+ if (PAR(cr))
{
- return;
+ gmx_bcast(sizeof(bExist), &bExist, cr);
}
+ return bExist;
+}
- /* We sync the processes here to try to avoid problems
- * with buggy MPI implementations that could cause
- * unfinished processes to terminate.
- */
- MPI_Barrier(MPI_COMM_WORLD);
-
- /*
- if (DOMAINDECOMP(cr)) {
- if (cr->npmenodes > 0 || cr->dd->bCartesian)
- MPI_Comm_free(&cr->mpi_comm_mygroup);
- if (cr->dd->bCartesian)
- MPI_Comm_free(&cr->mpi_comm_mysim);
- }
- */
-
- /* Apparently certain mpich implementations cause problems
- * with MPI_Finalize. In that case comment out MPI_Finalize.
- */
- if (debug)
- fprintf(debug,"Will call MPI_Finalize now\n");
-
- ret = MPI_Finalize();
- if (debug)
- fprintf(debug,"Return code from MPI_Finalize = %d\n",ret);
+void gmx_fatal_collective(int f_errno, const char *file, int line,
+ const t_commrec *cr, gmx_domdec_t *dd,
+ const char *fmt, ...)
+{
+ va_list ap;
+ gmx_bool bMaster, bFinalize;
+#ifdef GMX_MPI
+ int result;
+ /* Check if we are calling on all processes in MPI_COMM_WORLD */
+ if (cr != NULL)
+ {
+ MPI_Comm_compare(cr->mpi_comm_mysim, MPI_COMM_WORLD, &result);
+ }
+ else
+ {
+ MPI_Comm_compare(dd->mpi_comm_all, MPI_COMM_WORLD, &result);
+ }
+ /* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
+ bFinalize = (result != MPI_UNEQUAL);
+#else
+ bFinalize = TRUE;
#endif
-}
+ bMaster = (cr != NULL && MASTER(cr)) || (dd != NULL && DDMASTER(dd));
+ va_start(ap, fmt);
+ gmx_fatal_mpi_va(f_errno, file, line, bMaster, bFinalize, fmt, ap);
+ va_end(ap);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff