1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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34 * GROningen Mixture of Alchemy and Childrens' Stories
46 #ifdef HAVE_SYS_TIME_H
51 #include "gmx_fatal.h"
55 #include "gromacs/fileio/futil.h"
56 #include "gromacs/fileio/filenm.h"
57 #include "gromacs/fileio/gmxfio.h"
61 #include "gromacs/utility/exceptions.h"
62 #include "gromacs/utility/gmxmpi.h"
63 #include "gromacs/utility/programinfo.h"
65 /* The source code in this file should be thread-safe.
66 Please keep it that way. */
73 #ifdef GMX_NATIVE_WINDOWS
80 static void par_fn(char *base, int ftp, const t_commrec *cr,
81 gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
82 char buf[], int bufsize)
84 if ((size_t)bufsize < (strlen(base)+10))
86 gmx_mem("Character buffer too small!");
89 /* Copy to buf, and strip extension */
91 buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
95 sprintf(buf+strlen(buf), "%d", cr->ms->sim);
100 sprintf(buf+strlen(buf), "%d", cr->nodeid);
104 /* Add extension again */
105 strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
108 fprintf(debug, "node %d par_fn '%s'\n", cr->nodeid, buf);
109 if (fn2ftp(buf) == efLOG)
111 fprintf(debug, "log\n");
116 void check_multi_int(FILE *log, const gmx_multisim_t *ms, int val,
121 gmx_bool bCompatible;
123 if (NULL != log && !bQuiet)
125 fprintf(log, "Multi-checking %s ... ", name);
131 "check_multi_int called with a NULL communication pointer");
134 snew(ibuf, ms->nsim);
136 gmx_sumi_sim(ms->nsim, ibuf, ms);
139 for (p = 1; p < ms->nsim; p++)
141 bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
146 if (NULL != log && !bQuiet)
148 fprintf(log, "OK\n");
155 fprintf(log, "\n%s is not equal for all subsystems\n", name);
156 for (p = 0; p < ms->nsim; p++)
158 fprintf(log, " subsystem %d: %d\n", p, ibuf[p]);
161 gmx_fatal(FARGS, "The %d subsystems are not compatible\n", ms->nsim);
167 void check_multi_int64(FILE *log, const gmx_multisim_t *ms,
168 gmx_int64_t val, const char *name,
173 gmx_bool bCompatible;
175 if (NULL != log && !bQuiet)
177 fprintf(log, "Multi-checking %s ... ", name);
183 "check_multi_int called with a NULL communication pointer");
186 snew(ibuf, ms->nsim);
188 gmx_sumli_sim(ms->nsim, ibuf, ms);
191 for (p = 1; p < ms->nsim; p++)
193 bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
198 if (NULL != log && !bQuiet)
200 fprintf(log, "OK\n");
207 fprintf(log, "\n%s is not equal for all subsystems\n", name);
208 for (p = 0; p < ms->nsim; p++)
211 /* first make the format string */
212 snprintf(strbuf, 255, " subsystem %%d: %s\n",
214 fprintf(log, strbuf, p, ibuf[p]);
217 gmx_fatal(FARGS, "The %d subsystems are not compatible\n", ms->nsim);
224 char *gmx_gethostname(char *name, size_t len)
228 gmx_incons("gmx_gethostname called with len<8");
231 if (gethostname(name, len-1) != 0)
233 strncpy(name, "unknown", 8);
236 strncpy(name, "unknown", 8);
243 void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
244 gmx_bool bAppendFiles, FILE** fplog)
247 char buf[256], host[256];
249 char timebuf[STRLEN];
255 /* Communicate the filename for logfile */
256 if (cr->nnodes > 1 && !bMasterOnly
257 #ifdef GMX_THREAD_MPI
258 /* With thread MPI the non-master log files are opened later
259 * when the files names are already known on all nodes.
267 len = strlen(lognm) + 1;
269 gmx_bcast(sizeof(len), &len, cr);
276 tmpnm = gmx_strdup(lognm);
278 gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
282 tmpnm = gmx_strdup(lognm);
287 if (!bMasterOnly && !MASTER(cr))
289 /* Since log always ends with '.log' let's use this info */
290 par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
291 fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
293 else if (!bAppendFiles)
295 fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
300 gmx_fatal_set_log_file(fp);
302 /* Get some machine parameters */
303 gmx_gethostname(host, 256);
308 # ifdef GMX_NATIVE_WINDOWS
322 "-----------------------------------------------------------\n"
323 "Restarting from checkpoint, appending to previous log file.\n"
328 gmx_ctime_r(&t, timebuf, STRLEN);
331 "Log file opened on %s"
332 "Host: %s pid: %d nodeid: %d nnodes: %d\n",
333 timebuf, host, pid, cr->nodeid, cr->nnodes);
336 gmx::BinaryInformationSettings settings;
337 settings.extendedInfo(true);
338 settings.copyright(!bAppendFiles);
339 gmx::printBinaryInformation(fp, gmx::ProgramInfo::getInstance(), settings);
341 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
350 void gmx_log_close(FILE *fp)
354 gmx_fatal_set_log_file(NULL);
359 void init_multisystem(t_commrec *cr, int nsim, char **multidirs,
360 int nfile, const t_filenm fnm[], gmx_bool bParFn)
363 int nnodes, nnodpersim, sim, i, ftp;
366 MPI_Group mpi_group_world;
373 gmx_fatal(FARGS, "This binary is compiled without MPI support, can not do multiple simulations.");
378 if (nnodes % nsim != 0)
380 gmx_fatal(FARGS, "The number of nodes (%d) is not a multiple of the number of simulations (%d)", nnodes, nsim);
383 nnodpersim = nnodes/nsim;
384 sim = cr->nodeid/nnodpersim;
388 fprintf(debug, "We have %d simulations, %d nodes per simulation, local simulation is %d\n", nsim, nnodpersim, sim);
396 /* Create a communicator for the master nodes */
397 snew(rank, ms->nsim);
398 for (i = 0; i < ms->nsim; i++)
400 rank[i] = i*nnodpersim;
402 MPI_Comm_group(MPI_COMM_WORLD, &mpi_group_world);
403 MPI_Group_incl(mpi_group_world, nsim, rank, &ms->mpi_group_masters);
405 MPI_Comm_create(MPI_COMM_WORLD, ms->mpi_group_masters,
406 &ms->mpi_comm_masters);
408 #if !defined(MPI_IN_PLACE_EXISTS)
409 /* initialize the MPI_IN_PLACE replacement buffers */
411 ms->mpb->ibuf = NULL;
412 ms->mpb->libuf = NULL;
413 ms->mpb->fbuf = NULL;
414 ms->mpb->dbuf = NULL;
415 ms->mpb->ibuf_alloc = 0;
416 ms->mpb->libuf_alloc = 0;
417 ms->mpb->fbuf_alloc = 0;
418 ms->mpb->dbuf_alloc = 0;
423 /* Reduce the intra-simulation communication */
424 cr->sim_nodeid = cr->nodeid % nnodpersim;
425 cr->nnodes = nnodpersim;
427 MPI_Comm_split(MPI_COMM_WORLD, sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
428 cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
429 cr->nodeid = cr->sim_nodeid;
434 fprintf(debug, "This is simulation %d", cr->ms->sim);
437 fprintf(debug, ", local number of nodes %d, local nodeid %d",
438 cr->nnodes, cr->sim_nodeid);
440 fprintf(debug, "\n\n");
447 fprintf(debug, "Changing to directory %s\n", multidirs[cr->ms->sim]);
449 gmx_chdir(multidirs[cr->ms->sim]);
453 /* Patch output and tpx, cpt and rerun input file names */
454 for (i = 0; (i < nfile); i++)
456 /* Because of possible multiple extensions per type we must look
457 * at the actual file name
459 if (is_output(&fnm[i]) ||
460 fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
461 strcmp(fnm[i].opt, "-rerun") == 0)
463 ftp = fn2ftp(fnm[i].fns[0]);
464 par_fn(fnm[i].fns[0], ftp, cr, TRUE, FALSE, buf, 255);
465 sfree(fnm[i].fns[0]);
466 fnm[i].fns[0] = gmx_strdup(buf);