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32 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
40 #ifdef HAVE_SYS_TIME_H
56 #include "checkpoint.h"
63 ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
66 /* Enum for situations that can occur during log file parsing, the
67 * corresponding string entries can be found in do_the_tests() in
68 * const char* ParseLog[] */
74 eParselogResetProblem,
85 int nPMEnodes; /* number of PME-only nodes used in this test */
86 int nx, ny, nz; /* DD grid */
87 int guessPME; /* if nPMEnodes == -1, this is the guessed number of PME nodes */
88 double *Gcycles; /* This can contain more than one value if doing multiple tests */
92 float *PME_f_load; /* PME mesh/force load average*/
93 float PME_f_load_Av; /* Average average ;) ... */
94 char *mdrun_cmd_line; /* Mdrun command line used for this test */
100 int nr_inputfiles; /* The number of tpr and mdp input files */
101 gmx_large_int_t orig_sim_steps; /* Number of steps to be done in the real simulation */
102 real *rcoulomb; /* The coulomb radii [0...nr_inputfiles] */
103 real *rvdw; /* The vdW radii */
104 real *rlist; /* Neighbourlist cutoff radius */
106 int *nkx, *nky, *nkz;
107 real *fsx, *fsy, *fsz; /* Fourierspacing in x,y,z dimension */
111 static void sep_line(FILE *fp)
113 fprintf(fp, "\n------------------------------------------------------------\n");
117 /* Wrapper for system calls */
118 static int gmx_system_call(char *command)
121 gmx_fatal(FARGS,"No calls to system(3) supported on this platform. Attempted to call:\n'%s'\n",command);
123 return ( system(command) );
128 /* Check if string starts with substring */
129 static gmx_bool str_starts(const char *string, const char *substring)
131 return ( strncmp(string, substring, strlen(substring)) == 0);
135 static void cleandata(t_perf *perfdata, int test_nr)
137 perfdata->Gcycles[test_nr] = 0.0;
138 perfdata->ns_per_day[test_nr] = 0.0;
139 perfdata->PME_f_load[test_nr] = 0.0;
145 static gmx_bool is_equal(real a, real b)
147 real diff, eps=1.0e-7;
152 if (diff < 0.0) diff = -diff;
161 static void finalize(const char *fn_out)
167 fp = fopen(fn_out,"r");
168 fprintf(stdout,"\n\n");
170 while( fgets(buf,STRLEN-1,fp) != NULL )
172 fprintf(stdout,"%s",buf);
175 fprintf(stdout,"\n\n");
180 enum {eFoundNothing, eFoundDDStr, eFoundAccountingStr, eFoundCycleStr};
182 static int parse_logfile(const char *logfile, const char *errfile,
183 t_perf *perfdata, int test_nr, int presteps, gmx_large_int_t cpt_steps,
187 char line[STRLEN], dumstring[STRLEN], dumstring2[STRLEN];
188 const char matchstrdd[]="Domain decomposition grid";
189 const char matchstrcr[]="resetting all time and cycle counters";
190 const char matchstrbal[]="Average PME mesh/force load:";
191 const char matchstring[]="R E A L C Y C L E A N D T I M E A C C O U N T I N G";
192 const char errSIG[]="signal, stopping at the next";
195 float dum1,dum2,dum3;
197 gmx_large_int_t resetsteps=-1;
198 gmx_bool bFoundResetStr = FALSE;
199 gmx_bool bResetChecked = FALSE;
202 if (!gmx_fexist(logfile))
204 fprintf(stderr, "WARNING: Could not find logfile %s.\n", logfile);
205 cleandata(perfdata, test_nr);
206 return eParselogNotFound;
209 fp = fopen(logfile, "r");
210 perfdata->PME_f_load[test_nr] = -1.0;
211 perfdata->guessPME = -1;
213 iFound = eFoundNothing;
215 iFound = eFoundDDStr; /* Skip some case statements */
217 while (fgets(line, STRLEN, fp) != NULL)
219 /* Remove leading spaces */
222 /* Check for TERM and INT signals from user: */
223 if ( strstr(line, errSIG) != NULL )
226 cleandata(perfdata, test_nr);
227 return eParselogTerm;
230 /* Check whether cycle resetting worked */
231 if (presteps > 0 && !bFoundResetStr)
233 if (strstr(line, matchstrcr) != NULL)
235 sprintf(dumstring, "Step %s", gmx_large_int_pfmt);
236 sscanf(line, dumstring, &resetsteps);
237 bFoundResetStr = TRUE;
238 if (resetsteps == presteps+cpt_steps)
240 bResetChecked = TRUE;
244 sprintf(dumstring , gmx_large_int_pfmt, resetsteps);
245 sprintf(dumstring2, gmx_large_int_pfmt, presteps+cpt_steps);
246 fprintf(stderr, "WARNING: Time step counters were reset at step %s,\n"
247 " though they were supposed to be reset at step %s!\n",
248 dumstring, dumstring2);
253 /* Look for strings that appear in a certain order in the log file: */
257 /* Look for domain decomp grid and separate PME nodes: */
258 if (str_starts(line, matchstrdd))
260 sscanf(line, "Domain decomposition grid %d x %d x %d, separate PME nodes %d",
261 &(perfdata->nx), &(perfdata->ny), &(perfdata->nz), &npme);
262 if (perfdata->nPMEnodes == -1)
263 perfdata->guessPME = npme;
264 else if (perfdata->nPMEnodes != npme)
265 gmx_fatal(FARGS, "PME nodes from command line and output file are not identical");
266 iFound = eFoundDDStr;
268 /* Catch a few errors that might have occured: */
269 else if (str_starts(line, "There is no domain decomposition for"))
272 return eParselogNoDDGrid;
274 else if (str_starts(line, "reading tpx file"))
277 return eParselogTPXVersion;
279 else if (str_starts(line, "The -dd or -npme option request a parallel simulation"))
282 return eParselogNotParallel;
286 /* Look for PME mesh/force balance (not necessarily present, though) */
287 if (str_starts(line, matchstrbal))
288 sscanf(&line[strlen(matchstrbal)], "%f", &(perfdata->PME_f_load[test_nr]));
289 /* Look for matchstring */
290 if (str_starts(line, matchstring))
291 iFound = eFoundAccountingStr;
293 case eFoundAccountingStr:
294 /* Already found matchstring - look for cycle data */
295 if (str_starts(line, "Total "))
297 sscanf(line,"Total %d %lf",&procs,&(perfdata->Gcycles[test_nr]));
298 iFound = eFoundCycleStr;
302 /* Already found cycle data - look for remaining performance info and return */
303 if (str_starts(line, "Performance:"))
305 sscanf(line,"%s %f %f %f %f", dumstring, &dum1, &dum2, &(perfdata->ns_per_day[test_nr]), &dum3);
307 if (bResetChecked || presteps == 0)
310 return eParselogResetProblem;
316 /* Close the log file */
319 /* Check why there is no performance data in the log file.
320 * Did a fatal errors occur? */
321 if (gmx_fexist(errfile))
323 fp = fopen(errfile, "r");
324 while (fgets(line, STRLEN, fp) != NULL)
326 if ( str_starts(line, "Fatal error:") )
328 if (fgets(line, STRLEN, fp) != NULL)
329 fprintf(stderr, "\nWARNING: A fatal error has occured during this benchmark:\n"
332 cleandata(perfdata, test_nr);
333 return eParselogFatal;
340 fprintf(stderr, "WARNING: Could not find stderr file %s.\n", errfile);
343 /* Giving up ... we could not find out why there is no performance data in
345 fprintf(stdout, "No performance data in log file.\n");
346 cleandata(perfdata, test_nr);
348 return eParselogNoPerfData;
352 static gmx_bool analyze_data(
361 int *index_tpr, /* OUT: Nr of mdp file with best settings */
362 int *npme_optimal) /* OUT: Optimal number of PME nodes */
365 int line=0, line_win=-1;
366 int k_win=-1, i_win=-1, winPME;
367 double s=0.0; /* standard deviation */
370 char str_PME_f_load[13];
371 gmx_bool bCanUseOrigTPR;
372 gmx_bool bRefinedCoul, bRefinedVdW, bRefinedGrid;
378 fprintf(fp, "Summary of successful runs:\n");
379 fprintf(fp, "Line tpr PME nodes Gcycles Av. Std.dev. ns/day PME/f");
381 fprintf(fp, " DD grid");
386 for (k=0; k<ntprs; k++)
388 for (i=0; i<ntests; i++)
390 /* Select the right dataset: */
391 pd = &(perfdata[k][i]);
393 pd->Gcycles_Av = 0.0;
394 pd->PME_f_load_Av = 0.0;
395 pd->ns_per_day_Av = 0.0;
397 if (pd->nPMEnodes == -1)
398 sprintf(strbuf, "(%3d)", pd->guessPME);
400 sprintf(strbuf, " ");
402 /* Get the average run time of a setting */
403 for (j=0; j<nrepeats; j++)
405 pd->Gcycles_Av += pd->Gcycles[j];
406 pd->PME_f_load_Av += pd->PME_f_load[j];
408 pd->Gcycles_Av /= nrepeats;
409 pd->PME_f_load_Av /= nrepeats;
411 for (j=0; j<nrepeats; j++)
413 if (pd->ns_per_day[j] > 0.0)
414 pd->ns_per_day_Av += pd->ns_per_day[j];
417 /* Somehow the performance number was not aquired for this run,
418 * therefor set the average to some negative value: */
419 pd->ns_per_day_Av = -1.0f*nrepeats;
423 pd->ns_per_day_Av /= nrepeats;
426 if (pd->PME_f_load_Av > 0.0)
427 sprintf(str_PME_f_load, "%12.3f", pd->PME_f_load_Av);
429 sprintf(str_PME_f_load, "%s", " - ");
432 /* We assume we had a successful run if both averages are positive */
433 if (pd->Gcycles_Av > 0.0 && pd->ns_per_day_Av > 0.0)
435 /* Output statistics if repeats were done */
438 /* Calculate the standard deviation */
440 for (j=0; j<nrepeats; j++)
441 s += pow( pd->Gcycles[j] - pd->Gcycles_Av, 2 );
445 fprintf(fp, "%4d %3d %4d%s %12.3f %12.3f %12.3f %s",
446 line, k, pd->nPMEnodes, strbuf, pd->Gcycles_Av, s,
447 pd->ns_per_day_Av, str_PME_f_load);
449 fprintf(fp, " %3d %3d %3d", pd->nx, pd->ny, pd->nz);
452 /* Store the index of the best run found so far in 'winner': */
453 if ( (k_win == -1) || (pd->Gcycles_Av < perfdata[k_win][i_win].Gcycles_Av) )
465 gmx_fatal(FARGS, "None of the runs was successful! Check %s for problems.", fn);
469 winPME = perfdata[k_win][i_win].nPMEnodes;
473 /* We stuck to a fixed number of PME-only nodes */
474 sprintf(strbuf, "settings No. %d", k_win);
478 /* We have optimized the number of PME-only nodes */
480 sprintf(strbuf, "%s", "the automatic number of PME nodes");
482 sprintf(strbuf, "%d PME nodes", winPME);
484 fprintf(fp, "Best performance was achieved with %s", strbuf);
485 if ((nrepeats > 1) && (ntests > 1))
486 fprintf(fp, " (see line %d)", line_win);
489 /* Only mention settings if they were modified: */
490 bRefinedCoul = !is_equal(info->rcoulomb[k_win], info->rcoulomb[0]);
491 bRefinedVdW = !is_equal(info->rvdw[k_win] , info->rvdw[0] );
492 bRefinedGrid = !(info->nkx[k_win] == info->nkx[0] &&
493 info->nky[k_win] == info->nky[0] &&
494 info->nkz[k_win] == info->nkz[0]);
496 if (bRefinedCoul || bRefinedVdW || bRefinedGrid)
498 fprintf(fp, "Optimized PME settings:\n");
499 bCanUseOrigTPR = FALSE;
503 bCanUseOrigTPR = TRUE;
507 fprintf(fp, " New Coulomb radius: %f nm (was %f nm)\n", info->rcoulomb[k_win], info->rcoulomb[0]);
510 fprintf(fp, " New Van der Waals radius: %f nm (was %f nm)\n", info->rvdw[k_win], info->rvdw[0]);
513 fprintf(fp, " New Fourier grid xyz: %d %d %d (was %d %d %d)\n", info->nkx[k_win], info->nky[k_win], info->nkz[k_win],
514 info->nkx[0], info->nky[0], info->nkz[0]);
516 if (bCanUseOrigTPR && ntprs > 1)
517 fprintf(fp, "and original PME settings.\n");
521 /* Return the index of the mdp file that showed the highest performance
522 * and the optimal number of PME nodes */
524 *npme_optimal = winPME;
526 return bCanUseOrigTPR;
530 /* Get the commands we need to set up the runs from environment variables */
531 static void get_program_paths(gmx_bool bThreads, char *cmd_mpirun[], char cmd_np[],
532 char *cmd_mdrun[], int repeats)
539 const char def_mpirun[] = "mpirun";
540 const char def_mdrun[] = "mdrun";
541 const char filename[] = "benchtest.log";
542 const char match_mpi[] = "NNODES=";
543 const char match_mdrun[]= "Program: ";
544 const char empty_mpirun[] = "";
545 gmx_bool bMdrun = FALSE;
546 gmx_bool bMPI = FALSE;
549 /* Get the commands we need to set up the runs from environment variables */
552 if ( (cp = getenv("MPIRUN")) != NULL)
553 *cmd_mpirun = strdup(cp);
555 *cmd_mpirun = strdup(def_mpirun);
559 *cmd_mpirun = strdup(empty_mpirun);
562 if ( (cp = getenv("MDRUN" )) != NULL )
563 *cmd_mdrun = strdup(cp);
565 *cmd_mdrun = strdup(def_mdrun);
568 /* If no simulations have to be performed, we are done here */
572 /* Run a small test to see whether mpirun + mdrun work */
573 fprintf(stdout, "Making sure that mdrun can be executed. ");
576 snew(command, strlen(*cmd_mdrun) + strlen(cmd_np) + strlen(filename) + 50);
577 sprintf(command, "%s%s-version -maxh 0.001 1> %s 2>&1", *cmd_mdrun, cmd_np, filename);
581 snew(command, strlen(*cmd_mpirun) + strlen(cmd_np) + strlen(*cmd_mdrun) + strlen(filename) + 50);
582 sprintf(command, "%s%s%s -version -maxh 0.001 1> %s 2>&1", *cmd_mpirun, cmd_np, *cmd_mdrun, filename);
584 fprintf(stdout, "Trying '%s' ... ", command);
585 make_backup(filename);
586 gmx_system_call(command);
588 /* Check if we find the characteristic string in the output: */
589 if (!gmx_fexist(filename))
590 gmx_fatal(FARGS, "Output from test run could not be found.");
592 fp = fopen(filename, "r");
593 /* We need to scan the whole output file, since sometimes the queuing system
594 * also writes stuff to stdout/err */
597 cp2=fgets(line, STRLEN, fp);
600 if ( str_starts(line, match_mdrun) )
602 if ( str_starts(line, match_mpi) )
612 gmx_fatal(FARGS, "Need a threaded version of mdrun. This one\n"
614 "seems to have been compiled with MPI instead.",
622 gmx_fatal(FARGS, "Need an MPI-enabled version of mdrun. This one\n"
624 "seems to have been compiled without MPI support.",
631 gmx_fatal(FARGS, "Cannot execute mdrun. Please check %s for problems!",
635 fprintf(stdout, "passed.\n");
643 static void launch_simulation(
644 gmx_bool bLaunch, /* Should the simulation be launched? */
645 FILE *fp, /* General log file */
646 gmx_bool bThreads, /* whether to use threads */
647 char *cmd_mpirun, /* Command for mpirun */
648 char *cmd_np, /* Switch for -np or -nt or empty */
649 char *cmd_mdrun, /* Command for mdrun */
650 char *args_for_mdrun, /* Arguments for mdrun */
651 const char *simulation_tpr, /* This tpr will be simulated */
652 int nnodes, /* Number of nodes to run on */
653 int nPMEnodes) /* Number of PME nodes to use */
658 /* Make enough space for the system call command,
659 * (100 extra chars for -npme ... etc. options should suffice): */
660 snew(command, strlen(cmd_mpirun)+strlen(cmd_mdrun)+strlen(cmd_np)+strlen(args_for_mdrun)+strlen(simulation_tpr)+100);
662 /* Note that the -passall options requires args_for_mdrun to be at the end
663 * of the command line string */
666 sprintf(command, "%s%s-npme %d -s %s %s",
667 cmd_mdrun, cmd_np, nPMEnodes, simulation_tpr, args_for_mdrun);
671 sprintf(command, "%s%s%s -npme %d -s %s %s",
672 cmd_mpirun, cmd_np, cmd_mdrun, nPMEnodes, simulation_tpr, args_for_mdrun);
675 fprintf(fp, "%s this command line to launch the simulation:\n\n%s", bLaunch? "Using":"Please use", command);
679 /* Now the real thing! */
682 fprintf(stdout, "\nLaunching simulation with best parameters now.\nExecuting '%s'", command);
685 gmx_system_call(command);
691 static void modify_PMEsettings(
692 gmx_large_int_t simsteps, /* Set this value as number of time steps */
693 const char *fn_best_tpr, /* tpr file with the best performance */
694 const char *fn_sim_tpr) /* name of tpr file to be launched */
702 read_tpx_state(fn_best_tpr,ir,&state,NULL,&mtop);
704 /* Set nsteps to the right value */
705 ir->nsteps = simsteps;
707 /* Write the tpr file which will be launched */
708 sprintf(buf, "Writing optimized simulation file %s with nsteps=%s.\n", fn_sim_tpr, gmx_large_int_pfmt);
709 fprintf(stdout,buf,ir->nsteps);
711 write_tpx_state(fn_sim_tpr,ir,&state,&mtop);
719 int nkx, nky, nkz; /* Fourier grid */
720 real fac; /* actual scaling factor */
721 real fs; /* Fourierspacing */
725 static void copy_grid(t_pmegrid *ingrid, t_pmegrid *outgrid)
727 outgrid->nkx = ingrid->nkx;
728 outgrid->nky = ingrid->nky;
729 outgrid->nkz = ingrid->nkz;
730 outgrid->fac = ingrid->fac;
731 outgrid->fs = ingrid->fs;
734 /* Removes entry 'index' from the t_pmegrid list */
735 static void remove_from_list(
736 t_pmegrid gridlist[],
737 int *nlist, /* Length of the list */
738 int index) /* Index to remove from the list */
743 for (j = index; j < (*nlist - 1); j++)
745 copy_grid(&gridlist[j+1], &gridlist[j]);
751 /* Returns the index of the least necessary grid in the list.
753 * This is the one where the following conditions hold for the scaling factor:
754 * 1. this grid has the smallest distance to its neighboring grid (distance
755 * measured by fac) -> this condition is true for two grids at the same time
756 * 2. this grid (of the two) has the smaller distance to the other neighboring
759 * The extreme grids (the ones with the smallest and largest
760 * scaling factor) are never thrown away.
762 static int get_throwaway_index(
763 t_pmegrid gridlist[],
764 int nlist) /* Length of the list */
767 real dist,mindist,d_left,d_right;
770 /* Find the two factors with the smallest mutual distance */
771 mindist = GMX_FLOAT_MAX;
772 for (i = 1; i < nlist; i++)
774 dist = fabs(gridlist[i].fac - gridlist[i-1].fac);
781 /* index and index-1 have the smallest mutual distance */
784 /* Never return the first index, i.e. index == 0 */
789 d_left = fabs(gridlist[index-1].fac - gridlist[index-2].fac);
790 d_right = fabs(gridlist[index+1].fac - gridlist[index ].fac);
792 /* Return the left index if its distance to its left neighbor is shorter
793 * than the distance of the right index to its right neighbor */
794 if (d_left < d_right)
797 /* Never return the last index */
798 if (index == nlist-1)
805 static void make_grid_list(
806 real fmin, /* minimum scaling factor (downscaling fac) */
807 real fmax, /* maximum scaling factor (upscaling fac) */
808 int *ntprs, /* Number of tpr files to test */
809 matrix box, /* The box */
810 t_pmegrid *griduse[], /* List of grids that have to be tested */
811 real fs) /* Requested fourierspacing at a scaling factor
814 real req_fac,act_fac=0,act_fs,eps;
816 int i,jmin=0,d,ngridall=0;
817 int nkx=0,nky=0,nkz=0;
818 int nkx_old=0,nky_old=0,nkz_old=0;
820 int gridalloc,excess;
823 /* Determine length of triclinic box vectors */
828 box_size[d] += box[d][i]*box[d][i];
829 box_size[d] = sqrt(box_size[d]);
833 snew(gridall, gridalloc);
835 fprintf(stdout, "Possible PME grid settings (apart from input file settings):\n");
836 fprintf(stdout, " nkx nky nkz max spacing scaling factor\n");
838 /* eps should provide a fine enough spacing not to miss any grid */
840 eps = (fmax-fmin)/(100.0*(*ntprs - 1));
842 eps = 1.0/max( (*griduse)[0].nkz, max( (*griduse)[0].nkx, (*griduse)[0].nky ) );
844 for (req_fac = fmin; act_fac < fmax; req_fac += eps)
849 calc_grid(NULL,box,fs*req_fac,&nkx,&nky,&nkz);
850 act_fs = max(box_size[XX]/nkx,max(box_size[YY]/nky,box_size[ZZ]/nkz));
852 if ( ! ( nkx==nkx_old && nky==nky_old && nkz==nkz_old ) /* Exclude if grid is already in list */
853 && ! ( nkx==(*griduse)[0].nkx && nky==(*griduse)[0].nky && nkz==(*griduse)[0].nkz ) ) /* Exclude input file grid */
855 /* We found a new grid that will do */
859 gridall[ngridall].nkx = nkx;
860 gridall[ngridall].nky = nky;
861 gridall[ngridall].nkz = nkz;
862 gridall[ngridall].fac = act_fac;
863 gridall[ngridall].fs = act_fs;
864 fprintf(stdout, "%5d%5d%5d %12f %12f\n",nkx,nky,nkz,act_fs,act_fac);
866 if (ngridall >= gridalloc)
869 srenew(gridall, gridalloc);
874 /* excess is the number of grids we have to get rid of */
875 excess = ngridall+1 - *ntprs;
877 /* If we found less grids than tpr files were requested, simply test all
878 * the grid there are ... */
881 fprintf(stdout, "NOTE: You requested %d tpr files, but apart from the input file grid only the\n"
882 " above listed %d suitable PME grids were found. Will test all suitable settings.\n",
890 /* We can only keep the input tpr file plus one extra tpr file.
891 * We make that choice depending on the values of -upfac and -downfac */
894 /* Keep the one with the -downfac as scaling factor. This is already
895 * stored in gridall[0] */
900 /* Keep the one with -upfac as scaling factor */
901 copy_grid(&(gridall[ngridall-1]), &(gridall[0]));
907 /* From the grid list throw away the unnecessary ones (keep the extremes) */
908 for (i = 0; i < excess; i++)
910 /* Get the index of the least necessary grid from the list ... */
911 jmin = get_throwaway_index(gridall, ngridall);
912 /* ... and remove the grid from the list */
913 remove_from_list(gridall, &ngridall, jmin);
918 /* The remaining list contains the grids we want to test */
919 for (i=1; i < *ntprs; i++)
920 copy_grid(&(gridall[i-1]), &((*griduse)[i]));
926 #define EPME_SWITCHED(e) ((e) == eelPMESWITCH || (e) == eelPMEUSERSWITCH)
928 /* Make additional TPR files with more computational load for the
929 * direct space processors: */
930 static void make_benchmark_tprs(
931 const char *fn_sim_tpr, /* READ : User-provided tpr file */
932 char *fn_bench_tprs[], /* WRITE: Names of benchmark tpr files */
933 gmx_large_int_t benchsteps, /* Number of time steps for benchmark runs */
934 gmx_large_int_t statesteps, /* Step counter in checkpoint file */
935 real upfac, /* Scale rcoulomb inbetween downfac and upfac */
937 int *ntprs, /* No. of TPRs to write, each with a different
938 rcoulomb and fourierspacing. If not enough
939 grids are found, ntprs is reduced accordingly */
940 real fourierspacing, /* Basic fourierspacing from tpr input file */
941 t_inputinfo *info, /* Contains information about mdp file options */
942 FILE *fp) /* Write the output here */
948 real nlist_buffer; /* Thickness of the buffer regions for PME-switch potentials: */
951 gmx_bool bNote = FALSE;
952 t_pmegrid *pmegrid=NULL; /* Grid settings for the PME grids to test */
955 sprintf(buf, "Making benchmark tpr file%s with %s time step%s",
956 *ntprs > 1? "s":"", gmx_large_int_pfmt, benchsteps>1?"s":"");
957 fprintf(stdout, buf, benchsteps);
960 sprintf(buf, " (adding %s steps from checkpoint file)", gmx_large_int_pfmt);
961 fprintf(stdout, buf, statesteps);
962 benchsteps += statesteps;
964 fprintf(stdout, ".\n");
968 read_tpx_state(fn_sim_tpr,ir,&state,NULL,&mtop);
970 /* Check if some kind of PME was chosen */
971 if (EEL_PME(ir->coulombtype) == FALSE)
972 gmx_fatal(FARGS, "Can only do optimizations for simulations with %s electrostatics.",
975 /* Check if rcoulomb == rlist, which is necessary for plain PME. */
976 if ( (eelPME == ir->coulombtype) && !(ir->rcoulomb == ir->rlist) )
978 gmx_fatal(FARGS, "%s requires rcoulomb (%f) to be equal to rlist (%f).",
979 EELTYPE(eelPME), ir->rcoulomb, ir->rlist);
981 /* For other PME types, rcoulomb is allowed to be smaller than rlist */
982 else if (ir->rcoulomb > ir->rlist)
984 gmx_fatal(FARGS, "%s requires rcoulomb (%f) to be equal to or smaller than rlist (%f)",
985 EELTYPE(ir->coulombtype), ir->rcoulomb, ir->rlist);
988 /* Reduce the number of steps for the benchmarks */
989 info->orig_sim_steps = ir->nsteps;
990 ir->nsteps = benchsteps;
992 /* For PME-switch potentials, keep the radial distance of the buffer region */
993 nlist_buffer = ir->rlist - ir->rcoulomb;
995 /* Determine length of triclinic box vectors */
1000 box_size[d] += state.box[d][i]*state.box[d][i];
1001 box_size[d] = sqrt(box_size[d]);
1004 /* Reconstruct fourierspacing per dimension from the number of grid points and box size */
1005 info->fsx[0] = box_size[XX]/ir->nkx;
1006 info->fsy[0] = box_size[YY]/ir->nky;
1007 info->fsz[0] = box_size[ZZ]/ir->nkz;
1009 /* Put the input grid as first entry into the grid list */
1010 snew(pmegrid, *ntprs);
1011 pmegrid[0].fac = 1.00;
1012 pmegrid[0].nkx = ir->nkx;
1013 pmegrid[0].nky = ir->nky;
1014 pmegrid[0].nkz = ir->nkz;
1015 pmegrid[0].fs = max(box_size[ZZ]/ir->nkz, max(box_size[XX]/ir->nkx, box_size[YY]/ir->nky));
1017 /* If no value for the fourierspacing was provided on the command line, we
1018 * use the reconstruction from the tpr file */
1019 if (fourierspacing <= 0)
1021 fourierspacing = pmegrid[0].fs;
1024 fprintf(stdout, "Calculating PME grid points on the basis of a fourierspacing of %f nm\n", fourierspacing);
1026 /* Print information about settings of which some are potentially modified: */
1027 fprintf(fp, " Coulomb type : %s\n", EELTYPE(ir->coulombtype));
1028 fprintf(fp, " Grid spacing x y z : %f %f %f\n",
1029 box_size[XX]/ir->nkx, box_size[YY]/ir->nky, box_size[ZZ]/ir->nkz);
1030 fprintf(fp, " Van der Waals type : %s\n", EVDWTYPE(ir->vdwtype));
1031 if (EVDW_SWITCHED(ir->vdwtype))
1032 fprintf(fp, " rvdw_switch : %f nm\n", ir->rvdw_switch);
1033 if (EPME_SWITCHED(ir->coulombtype))
1034 fprintf(fp, " rlist : %f nm\n", ir->rlist);
1035 if (ir->rlistlong != max_cutoff(ir->rvdw,ir->rcoulomb))
1036 fprintf(fp, " rlistlong : %f nm\n", ir->rlistlong);
1038 /* Print a descriptive line about the tpr settings tested */
1039 fprintf(fp, "\nWill try these real/reciprocal workload settings:\n");
1040 fprintf(fp, " No. scaling rcoulomb");
1041 fprintf(fp, " nkx nky nkz");
1042 fprintf(fp, " spacing");
1043 if (evdwCUT == ir->vdwtype)
1044 fprintf(fp, " rvdw");
1045 if (EPME_SWITCHED(ir->coulombtype))
1046 fprintf(fp, " rlist");
1047 if ( ir->rlistlong != max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb)) )
1048 fprintf(fp, " rlistlong");
1049 fprintf(fp, " tpr file\n");
1052 /* Get useful PME grids if requested, the actual number of entries is
1053 * returned in npmegrid */
1055 make_grid_list(downfac, upfac, ntprs, state.box, &pmegrid, fourierspacing);
1057 /* Loop to create the requested number of tpr input files */
1058 for (j = 0; j < *ntprs; j++)
1060 /* The first one is the provided tpr file, just need to modify the number
1061 * of steps, so skip the following block */
1064 /* Scale the Coulomb radius */
1065 ir->rcoulomb = info->rcoulomb[0]*pmegrid[j].fac;
1067 /* Adjust other radii since various conditions neet to be fulfilled */
1068 if (eelPME == ir->coulombtype)
1070 /* plain PME, rcoulomb must be equal to rlist */
1071 ir->rlist = ir->rcoulomb;
1075 /* rlist must be >= rcoulomb, we keep the size of the buffer region */
1076 ir->rlist = ir->rcoulomb + nlist_buffer;
1079 if (evdwCUT == ir->vdwtype)
1081 /* For vdw cutoff, rvdw >= rlist */
1082 ir->rvdw = max(info->rvdw[0], ir->rlist);
1085 ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
1087 /* Copy the optimal grid dimensions to ir */
1088 ir->nkx = pmegrid[j].nkx;
1089 ir->nky = pmegrid[j].nky;
1090 ir->nkz = pmegrid[j].nkz;
1092 } /* end of "if (j != 0)" */
1094 /* for j==0: Save the original settings
1095 * for j >0: Save modified radii and fourier grids */
1096 info->rcoulomb[j] = ir->rcoulomb;
1097 info->rvdw[j] = ir->rvdw;
1098 info->nkx[j] = ir->nkx;
1099 info->nky[j] = ir->nky;
1100 info->nkz[j] = ir->nkz;
1101 info->rlist[j] = ir->rlist;
1102 info->rlistlong[j] = ir->rlistlong;
1103 info->fsx[j] = pmegrid[j].fs;
1104 info->fsy[j] = pmegrid[j].fs;
1105 info->fsz[j] = pmegrid[j].fs;
1107 /* Write the benchmark tpr file */
1108 strncpy(fn_bench_tprs[j],fn_sim_tpr,strlen(fn_sim_tpr)-strlen(".tpr"));
1109 sprintf(buf, "_bench%.2d.tpr", j);
1110 strcat(fn_bench_tprs[j], buf);
1111 fprintf(stdout,"Writing benchmark tpr %s with nsteps=", fn_bench_tprs[j]);
1112 fprintf(stdout, gmx_large_int_pfmt, ir->nsteps);
1114 fprintf(stdout,", scaling factor %f\n", pmegrid[j].fac);
1116 fprintf(stdout,", unmodified settings\n");
1118 write_tpx_state(fn_bench_tprs[j],ir,&state,&mtop);
1120 /* Write information about modified tpr settings to log file */
1122 fprintf(fp, "%4d%10s%10f", j, "-input-", ir->rcoulomb);
1124 fprintf(fp, "%4d%10f%10f", j, pmegrid[j].fac, ir->rcoulomb);
1125 fprintf(fp, "%5d%5d%5d", ir->nkx, ir->nky, ir->nkz);
1126 fprintf(fp, " %9f ", info->fsx[j]);
1127 if (evdwCUT == ir->vdwtype)
1128 fprintf(fp, "%10f", ir->rvdw);
1129 if (EPME_SWITCHED(ir->coulombtype))
1130 fprintf(fp, "%10f", ir->rlist);
1131 if ( info->rlistlong[0] != max_cutoff(info->rlist[0],max_cutoff(info->rvdw[0],info->rcoulomb[0])) )
1132 fprintf(fp, "%10f", ir->rlistlong);
1133 fprintf(fp, " %-14s\n",fn_bench_tprs[j]);
1135 /* Make it clear to the user that some additional settings were modified */
1136 if ( !is_equal(ir->rvdw , info->rvdw[0])
1137 || !is_equal(ir->rlistlong, info->rlistlong[0]) )
1143 fprintf(fp, "\nNote that in addition to rcoulomb and the fourier grid\n"
1144 "also other input settings were changed (see table above).\n"
1145 "Please check if the modified settings are appropriate.\n");
1152 /* Rename the files we want to keep to some meaningful filename and
1153 * delete the rest */
1154 static void cleanup(const t_filenm *fnm, int nfile, int k, int nnodes,
1155 int nPMEnodes, int nr, gmx_bool bKeepStderr)
1157 char numstring[STRLEN];
1158 char newfilename[STRLEN];
1159 const char *fn=NULL;
1164 fprintf(stdout, "Cleaning up, deleting benchmark temp files ...\n");
1166 for (i=0; i<nfile; i++)
1168 opt = (char *)fnm[i].opt;
1169 if ( strcmp(opt, "-p") == 0 )
1171 /* do nothing; keep this file */
1174 else if (strcmp(opt, "-bg") == 0)
1176 /* Give the log file a nice name so one can later see which parameters were used */
1177 numstring[0] = '\0';
1179 sprintf(numstring, "_%d", nr);
1180 sprintf(newfilename, "%s_no%d_np%d_npme%d%s", opt2fn("-bg",nfile,fnm), k, nnodes, nPMEnodes, numstring);
1181 if (gmx_fexist(opt2fn("-bg",nfile,fnm)))
1183 fprintf(stdout, "renaming log file to %s\n", newfilename);
1184 make_backup(newfilename);
1185 rename(opt2fn("-bg",nfile,fnm), newfilename);
1188 else if (strcmp(opt, "-err") == 0)
1190 /* This file contains the output of stderr. We want to keep it in
1191 * cases where there have been problems. */
1192 fn = opt2fn(opt, nfile, fnm);
1193 numstring[0] = '\0';
1195 sprintf(numstring, "_%d", nr);
1196 sprintf(newfilename, "%s_no%d_np%d_npme%d%s", fn, k, nnodes, nPMEnodes, numstring);
1201 fprintf(stdout, "Saving stderr output in %s\n", newfilename);
1202 make_backup(newfilename);
1203 rename(fn, newfilename);
1207 fprintf(stdout, "Deleting %s\n", fn);
1212 /* Delete the files which are created for each benchmark run: (options -b*) */
1213 else if ( (0 == strncmp(opt, "-b", 2)) && (opt2bSet(opt,nfile,fnm) || !is_optional(&fnm[i])) )
1215 fn = opt2fn(opt, nfile, fnm);
1218 fprintf(stdout, "Deleting %s\n", fn);
1226 /* Returns the largest common factor of n1 and n2 */
1227 static int largest_common_factor(int n1, int n2)
1232 for (factor=nmax; factor > 0; factor--)
1234 if ( 0==(n1 % factor) && 0==(n2 % factor) )
1239 return 0; /* one for the compiler */
1242 enum {eNpmeAuto, eNpmeAll, eNpmeReduced, eNpmeSubset, eNpmeNr};
1244 /* Create a list of numbers of PME nodes to test */
1245 static void make_npme_list(
1246 const char *npmevalues_opt, /* Make a complete list with all
1247 * possibilities or a short list that keeps only
1248 * reasonable numbers of PME nodes */
1249 int *nentries, /* Number of entries we put in the nPMEnodes list */
1250 int *nPMEnodes[], /* Each entry contains the value for -npme */
1251 int nnodes, /* Total number of nodes to do the tests on */
1252 int minPMEnodes, /* Minimum number of PME nodes */
1253 int maxPMEnodes) /* Maximum number of PME nodes */
1256 int min_factor=1; /* We request that npp and npme have this minimal
1257 * largest common factor (depends on npp) */
1258 int nlistmax; /* Max. list size */
1259 int nlist; /* Actual number of entries in list */
1263 /* Do we need to check all possible values for -npme or is a reduced list enough? */
1264 if ( 0 == strcmp(npmevalues_opt, "all") )
1268 else if ( 0 == strcmp(npmevalues_opt, "subset") )
1270 eNPME = eNpmeSubset;
1272 else if ( 0 == strcmp(npmevalues_opt, "auto") )
1276 else if (nnodes < 128)
1277 eNPME = eNpmeReduced;
1279 eNPME = eNpmeSubset;
1283 gmx_fatal(FARGS, "Unknown option for -npme in make_npme_list");
1286 /* Calculate how many entries we could possibly have (in case of -npme all) */
1289 nlistmax = maxPMEnodes - minPMEnodes + 3;
1290 if (0 == minPMEnodes)
1296 /* Now make the actual list which is at most of size nlist */
1297 snew(*nPMEnodes, nlistmax);
1298 nlist = 0; /* start counting again, now the real entries in the list */
1299 for (i = 0; i < nlistmax - 2; i++)
1301 npme = maxPMEnodes - i;
1312 /* For 2d PME we want a common largest factor of at least the cube
1313 * root of the number of PP nodes */
1314 min_factor = (int) pow(npp, 1.0/3.0);
1317 gmx_fatal(FARGS, "Unknown option for eNPME in make_npme_list");
1320 if (largest_common_factor(npp, npme) >= min_factor)
1322 (*nPMEnodes)[nlist] = npme;
1326 /* We always test 0 PME nodes and the automatic number */
1327 *nentries = nlist + 2;
1328 (*nPMEnodes)[nlist ] = 0;
1329 (*nPMEnodes)[nlist+1] = -1;
1331 fprintf(stderr, "Will try the following %d different values for -npme:\n", *nentries);
1332 for (i=0; i<*nentries-1; i++)
1333 fprintf(stderr, "%d, ", (*nPMEnodes)[i]);
1334 fprintf(stderr, "and %d (auto).\n", (*nPMEnodes)[*nentries-1]);
1338 /* Allocate memory to store the performance data */
1339 static void init_perfdata(t_perf *perfdata[], int ntprs, int datasets, int repeats)
1344 for (k=0; k<ntprs; k++)
1346 snew(perfdata[k], datasets);
1347 for (i=0; i<datasets; i++)
1349 for (j=0; j<repeats; j++)
1351 snew(perfdata[k][i].Gcycles , repeats);
1352 snew(perfdata[k][i].ns_per_day, repeats);
1353 snew(perfdata[k][i].PME_f_load, repeats);
1360 static void do_the_tests(
1361 FILE *fp, /* General g_tune_pme output file */
1362 char **tpr_names, /* Filenames of the input files to test */
1363 int maxPMEnodes, /* Max fraction of nodes to use for PME */
1364 int minPMEnodes, /* Min fraction of nodes to use for PME */
1365 int npme_fixed, /* If >= -1, test fixed number of PME
1367 const char *npmevalues_opt, /* Which -npme values should be tested */
1368 t_perf **perfdata, /* Here the performace data is stored */
1369 int *pmeentries, /* Entries in the nPMEnodes list */
1370 int repeats, /* Repeat each test this often */
1371 int nnodes, /* Total number of nodes = nPP + nPME */
1372 int nr_tprs, /* Total number of tpr files to test */
1373 gmx_bool bThreads, /* Threads or MPI? */
1374 char *cmd_mpirun, /* mpirun command string */
1375 char *cmd_np, /* "-np", "-n", whatever mpirun needs */
1376 char *cmd_mdrun, /* mdrun command string */
1377 char *cmd_args_bench, /* arguments for mdrun in a string */
1378 const t_filenm *fnm, /* List of filenames from command line */
1379 int nfile, /* Number of files specified on the cmdl. */
1380 int sim_part, /* For checkpointing */
1381 int presteps, /* DLB equilibration steps, is checked */
1382 gmx_large_int_t cpt_steps) /* Time step counter in the checkpoint */
1384 int i,nr,k,ret,count=0,totaltests;
1385 int *nPMEnodes=NULL;
1388 char *command, *cmd_stub;
1390 gmx_bool bResetProblem=FALSE;
1393 /* This string array corresponds to the eParselog enum type at the start
1395 const char* ParseLog[] = {"OK.",
1396 "Logfile not found!",
1397 "No timings, logfile truncated?",
1398 "Run was terminated.",
1399 "Counters were not reset properly.",
1400 "No DD grid found for these settings.",
1401 "TPX version conflict!",
1402 "mdrun was not started in parallel!",
1403 "A fatal error occured!" };
1404 char str_PME_f_load[13];
1407 /* Allocate space for the mdrun command line. 100 extra characters should
1408 be more than enough for the -npme etcetera arguments */
1409 cmdline_length = strlen(cmd_mpirun)
1412 + strlen(cmd_args_bench)
1413 + strlen(tpr_names[0]) + 100;
1414 snew(command , cmdline_length);
1415 snew(cmd_stub, cmdline_length);
1417 /* Construct the part of the command line that stays the same for all tests: */
1420 sprintf(cmd_stub, "%s%s", cmd_mdrun, cmd_np);
1424 sprintf(cmd_stub, "%s%s%s ", cmd_mpirun, cmd_np, cmd_mdrun);
1427 /* Create a list of numbers of PME nodes to test */
1428 if (npme_fixed < -1)
1430 make_npme_list(npmevalues_opt, pmeentries, &nPMEnodes,
1431 nnodes, minPMEnodes, maxPMEnodes);
1437 nPMEnodes[0] = npme_fixed;
1438 fprintf(stderr, "Will use a fixed number of %d PME-only nodes.\n", nPMEnodes[0]);
1443 fprintf(fp, "\nNo benchmarks done since number of repeats (-r) is 0.\n");
1445 finalize(opt2fn("-p", nfile, fnm));
1449 /* Allocate one dataset for each tpr input file: */
1450 init_perfdata(perfdata, nr_tprs, *pmeentries, repeats);
1452 /*****************************************/
1453 /* Main loop over all tpr files to test: */
1454 /*****************************************/
1455 totaltests = nr_tprs*(*pmeentries)*repeats;
1456 for (k=0; k<nr_tprs;k++)
1458 fprintf(fp, "\nIndividual timings for input file %d (%s):\n", k, tpr_names[k]);
1459 fprintf(fp, "PME nodes Gcycles ns/day PME/f Remark\n");
1460 /* Loop over various numbers of PME nodes: */
1461 for (i = 0; i < *pmeentries; i++)
1463 pd = &perfdata[k][i];
1465 /* Loop over the repeats for each scenario: */
1466 for (nr = 0; nr < repeats; nr++)
1468 pd->nPMEnodes = nPMEnodes[i];
1470 /* Add -npme and -s to the command line and save it. Note that
1471 * the -passall (if set) options requires cmd_args_bench to be
1472 * at the end of the command line string */
1473 snew(pd->mdrun_cmd_line, cmdline_length);
1474 sprintf(pd->mdrun_cmd_line, "%s-npme %d -s %s %s",
1475 cmd_stub, pd->nPMEnodes, tpr_names[k], cmd_args_bench);
1477 /* Do a benchmark simulation: */
1479 sprintf(buf, ", pass %d/%d", nr+1, repeats);
1482 fprintf(stdout, "\n=== Progress %2.0f%%, tpr %d/%d, run %d/%d%s:\n",
1483 (100.0*count)/totaltests,
1484 k+1, nr_tprs, i+1, *pmeentries, buf);
1485 make_backup(opt2fn("-err",nfile,fnm));
1486 sprintf(command, "%s 1> /dev/null 2>%s", pd->mdrun_cmd_line, opt2fn("-err",nfile,fnm));
1487 fprintf(stdout, "%s\n", pd->mdrun_cmd_line);
1488 gmx_system_call(command);
1490 /* Collect the performance data from the log file; also check stderr
1491 * for fatal errors */
1492 ret = parse_logfile(opt2fn("-bg",nfile,fnm), opt2fn("-err",nfile,fnm),
1493 pd, nr, presteps, cpt_steps, nnodes);
1494 if ((presteps > 0) && (ret == eParselogResetProblem))
1495 bResetProblem = TRUE;
1497 if (-1 == pd->nPMEnodes)
1498 sprintf(buf, "(%3d)", pd->guessPME);
1503 if (pd->PME_f_load[nr] > 0.0)
1504 sprintf(str_PME_f_load, "%12.3f", pd->PME_f_load[nr]);
1506 sprintf(str_PME_f_load, "%s", " - ");
1508 /* Write the data we got to disk */
1509 fprintf(fp, "%4d%s %12.3f %12.3f %s %s", pd->nPMEnodes,
1510 buf, pd->Gcycles[nr], pd->ns_per_day[nr], str_PME_f_load, ParseLog[ret]);
1511 if (! (ret==eParselogOK || ret==eParselogNoDDGrid || ret==eParselogNotFound) )
1512 fprintf(fp, " Check %s file for problems.", ret==eParselogFatal? "err":"log");
1517 /* Do some cleaning up and delete the files we do not need any more */
1518 cleanup(fnm, nfile, k, nnodes, pd->nPMEnodes, nr, ret==eParselogFatal);
1520 /* If the first run with this number of processors already failed, do not try again: */
1521 if (pd->Gcycles[0] <= 0.0 && repeats > 1)
1523 fprintf(stdout, "Skipping remaining passes of unsuccessful setting, see log file for details.\n");
1524 count += repeats-(nr+1);
1527 } /* end of repeats loop */
1528 } /* end of -npme loop */
1529 } /* end of tpr file loop */
1533 fprintf(fp, "WARNING: The cycle and time step counters could not be reset\n"
1534 "properly. The reason could be that mpirun did not manage to\n"
1535 "export the environment variable GMX_RESET_COUNTER. You might\n"
1536 "have to give a special switch to mpirun for that.\n"
1537 "Alternatively, you can manually set GMX_RESET_COUNTER to the\n"
1538 "value normally provided by -presteps.");
1546 static void check_input(
1552 real maxPMEfraction,
1553 real minPMEfraction,
1555 real fourierspacing,
1556 gmx_large_int_t bench_nsteps,
1557 const t_filenm *fnm,
1564 /* Make sure the input file exists */
1565 if (!gmx_fexist(opt2fn("-s",nfile,fnm)))
1566 gmx_fatal(FARGS, "File %s not found.", opt2fn("-s",nfile,fnm));
1568 /* Make sure that the checkpoint file is not overwritten during benchmarking */
1569 if ( (0 == strcmp(opt2fn("-cpi",nfile,fnm), opt2fn("-bcpo",nfile,fnm)) ) && (sim_part > 1) )
1570 gmx_fatal(FARGS, "Checkpoint input (-cpi) and benchmark checkpoint output (-bcpo) files must not be identical.\n"
1571 "The checkpoint input file must not be overwritten during the benchmarks.\n");
1573 /* Make sure that repeats is >= 0 (if == 0, only write tpr files) */
1575 gmx_fatal(FARGS, "Number of repeats < 0!");
1577 /* Check number of nodes */
1579 gmx_fatal(FARGS, "Number of nodes/threads must be a positive integer.");
1581 /* Automatically choose -ntpr if not set */
1588 fprintf(stderr, "Will test %d tpr file%s.\n", *ntprs, *ntprs==1?"":"s");
1593 fprintf(stderr, "Note: Choose ntpr>1 to shift PME load between real and reciprocal space.\n");
1596 if ( is_equal(*downfac,*upfac) && (*ntprs > 2) && !(fourierspacing > 0.0))
1598 fprintf(stderr, "WARNING: Resetting -ntpr to 2 since both scaling factors are the same.\n"
1599 "Please choose upfac unequal to downfac to test various PME grid settings\n");
1603 /* Check whether max and min fraction are within required values */
1604 if (maxPMEfraction > 0.5 || maxPMEfraction < 0)
1605 gmx_fatal(FARGS, "-max must be between 0 and 0.5");
1606 if (minPMEfraction > 0.5 || minPMEfraction < 0)
1607 gmx_fatal(FARGS, "-min must be between 0 and 0.5");
1608 if (maxPMEfraction < minPMEfraction)
1609 gmx_fatal(FARGS, "-max must be larger or equal to -min");
1611 /* Check whether the number of steps - if it was set - has a reasonable value */
1612 if (bench_nsteps < 0)
1613 gmx_fatal(FARGS, "Number of steps must be positive.");
1615 if (bench_nsteps > 10000 || bench_nsteps < 100)
1617 fprintf(stderr, "WARNING: steps=");
1618 fprintf(stderr, gmx_large_int_pfmt, bench_nsteps);
1619 fprintf(stderr, ". Are you sure you want to perform so %s steps for each benchmark?\n", (bench_nsteps < 100)? "few" : "many");
1624 gmx_fatal(FARGS, "Cannot have a negative number of presteps.\n");
1627 if (*upfac <= 0.0 || *downfac <= 0.0 || *downfac > *upfac)
1628 gmx_fatal(FARGS, "Both scaling factors must be larger than zero and upper\n"
1629 "scaling limit (%f) must be larger than lower limit (%f).",
1632 if (*downfac < 0.75 || *upfac > 1.25)
1633 fprintf(stderr, "WARNING: Applying extreme scaling factor. I hope you know what you are doing.\n");
1635 if (fourierspacing < 0)
1636 gmx_fatal(FARGS, "Please choose a positive value for fourierspacing.");
1638 /* Make shure that the scaling factor options are compatible with the number of tprs */
1639 if ( (*ntprs < 3) && ( opt2parg_bSet("-upfac",npargs,pa) || opt2parg_bSet("-downfac",npargs,pa) ) )
1641 if (opt2parg_bSet("-upfac",npargs,pa) && opt2parg_bSet("-downfac",npargs,pa) && !is_equal(*upfac,*downfac))
1643 fprintf(stderr, "NOTE: Specify -ntpr > 2 for both scaling factors to take effect.\n"
1644 "(upfac=%f, downfac=%f)\n", *upfac, *downfac);
1646 if (opt2parg_bSet("-upfac",npargs,pa))
1648 if (opt2parg_bSet("-downfac",npargs,pa))
1651 if ( (2 == *ntprs) && (opt2parg_bSet("-downfac",npargs,pa)) && !is_equal(*downfac, 1.0))
1656 /* If a fixed number of PME nodes is set we do rcoulomb and PME gird tuning
1657 * only. We need to check whether the requested number of PME-only nodes
1659 if (npme_fixed > -1)
1661 /* No more than 50% of all nodes can be assigned as PME-only nodes. */
1662 if (2*npme_fixed > nnodes)
1664 gmx_fatal(FARGS, "Cannot have more than %d PME-only nodes for a total of %d nodes (you chose %d).\n",
1665 nnodes/2, nnodes, npme_fixed);
1667 if ((npme_fixed > 0) && (5*npme_fixed < nnodes))
1669 fprintf(stderr, "WARNING: Only %g percent of the nodes are assigned as PME-only nodes.\n",
1670 100.0*((real)npme_fixed / (real)nnodes));
1672 if (opt2parg_bSet("-min",npargs,pa) || opt2parg_bSet("-max",npargs,pa))
1674 fprintf(stderr, "NOTE: The -min, -max, and -npme options have no effect when a\n"
1675 " fixed number of PME-only nodes is requested with -fix.\n");
1681 /* Returns TRUE when "opt" is a switch for g_tune_pme itself */
1682 static gmx_bool is_main_switch(char *opt)
1684 if ( (0 == strcmp(opt,"-s" ))
1685 || (0 == strcmp(opt,"-p" ))
1686 || (0 == strcmp(opt,"-launch" ))
1687 || (0 == strcmp(opt,"-r" ))
1688 || (0 == strcmp(opt,"-ntpr" ))
1689 || (0 == strcmp(opt,"-max" ))
1690 || (0 == strcmp(opt,"-min" ))
1691 || (0 == strcmp(opt,"-upfac" ))
1692 || (0 == strcmp(opt,"-downfac" ))
1693 || (0 == strcmp(opt,"-fix" ))
1694 || (0 == strcmp(opt,"-four" ))
1695 || (0 == strcmp(opt,"-steps" ))
1696 || (0 == strcmp(opt,"-simsteps" ))
1697 || (0 == strcmp(opt,"-resetstep"))
1698 || (0 == strcmp(opt,"-so" ))
1699 || (0 == strcmp(opt,"-npstring" ))
1700 || (0 == strcmp(opt,"-npme" ))
1701 || (0 == strcmp(opt,"-err" ))
1702 || (0 == strcmp(opt,"-passall" )) )
1709 /* Returns TRUE when "opt" is needed at launch time */
1710 static gmx_bool is_launch_option(char *opt, gmx_bool bSet)
1719 /* Returns TRUE when "opt" is needed at launch time */
1720 static gmx_bool is_launch_file(char *opt, gmx_bool bSet)
1722 /* We need all options that were set on the command line
1723 * and that do not start with -b */
1724 if (0 == strncmp(opt,"-b", 2))
1734 /* Returns TRUE when "opt" gives an option needed for the benchmarks runs */
1735 static gmx_bool is_bench_option(char *opt, gmx_bool bSet)
1737 /* If option is set, we might need it for the benchmarks.
1738 * This includes -cpi */
1741 if ( (0 == strcmp(opt, "-append" ))
1742 || (0 == strcmp(opt, "-maxh" ))
1743 || (0 == strcmp(opt, "-deffnm" ))
1744 || (0 == strcmp(opt, "-resethway"))
1745 || (0 == strcmp(opt, "-cpnum" )) )
1755 /* Returns TRUE when "opt" defines a file which is needed for the benchmarks runs */
1756 static gmx_bool is_bench_file(char *opt, gmx_bool bSet, gmx_bool bOptional, gmx_bool bIsOutput)
1758 /* All options starting with "-b" are for _b_enchmark files exclusively */
1759 if (0 == strncmp(opt,"-b", 2))
1761 if (!bOptional || bSet)
1771 if (bSet) /* These are additional input files like -cpi -ei */
1779 /* Adds 'buf' to 'str' */
1780 static void add_to_string(char **str, char *buf)
1785 len = strlen(*str) + strlen(buf) + 1;
1791 /* Create the command line for the benchmark as well as for the real run */
1792 static void create_command_line_snippets(
1799 const char *procstring, /* How to pass the number of processors to $MPIRUN */
1800 char *cmd_np[], /* Actual command line snippet, e.g. '-np <N>' */
1801 char *cmd_args_bench[], /* command line arguments for benchmark runs */
1802 char *cmd_args_launch[], /* command line arguments for simulation run */
1803 char extra_args[]) /* Add this to the end of the command line */
1809 #define BUFLENGTH 255
1810 char buf[BUFLENGTH];
1811 char strbuf[BUFLENGTH];
1812 char strbuf2[BUFLENGTH];
1816 np_or_nt=strdup("-nt");
1818 np_or_nt=strdup("-np");
1820 /* strlen needs at least '\0' as a string: */
1821 snew(*cmd_args_bench ,1);
1822 snew(*cmd_args_launch,1);
1823 *cmd_args_launch[0]='\0';
1824 *cmd_args_bench[0] ='\0';
1827 /*******************************************/
1828 /* 1. Process other command line arguments */
1829 /*******************************************/
1830 for (i=0; i<npargs; i++)
1832 /* What command line switch are we currently processing: */
1833 opt = (char *)pa[i].option;
1834 /* Skip options not meant for mdrun */
1835 if (!is_main_switch(opt))
1837 /* Boolean arguments need to be generated in the -[no]argname format */
1838 if (pa[i].type == etBOOL)
1840 sprintf(strbuf,"-%s%s ",*pa[i].u.b ? "" : "no",opt+1);
1844 /* Print it to a string buffer, strip away trailing whitespaces that pa_val also returns: */
1845 sprintf(strbuf2, "%s", pa_val(&pa[i],buf,BUFLENGTH));
1847 sprintf(strbuf, "%s %s ", opt, strbuf2);
1850 /* We need the -np (or -nt) switch in a separate buffer - whether or not it was set! */
1851 if (0 == strcmp(opt,np_or_nt))
1853 if (strcmp(procstring, "none")==0 && !bThreads)
1855 /* Omit -np <N> entirely */
1857 sprintf(*cmd_np, " ");
1861 /* This is the normal case with -np <N> */
1862 snew(*cmd_np, strlen(procstring)+strlen(strbuf2)+4);
1863 sprintf(*cmd_np, " %s %s ", bThreads? "-nt" : procstring, strbuf2);
1868 if (is_bench_option(opt,pa[i].bSet))
1869 add_to_string(cmd_args_bench, strbuf);
1871 if (is_launch_option(opt,pa[i].bSet))
1872 add_to_string(cmd_args_launch, strbuf);
1878 /* Add equilibration steps to benchmark options */
1879 sprintf(strbuf, "-resetstep %d ", presteps);
1880 add_to_string(cmd_args_bench, strbuf);
1883 /********************/
1884 /* 2. Process files */
1885 /********************/
1886 for (i=0; i<nfile; i++)
1888 opt = (char *)fnm[i].opt;
1889 name = opt2fn(opt,nfile,fnm);
1891 /* Strbuf contains the options, now let's sort out where we need that */
1892 sprintf(strbuf, "%s %s ", opt, name);
1894 /* Skip options not meant for mdrun */
1895 if (!is_main_switch(opt))
1898 if ( is_bench_file(opt, opt2bSet(opt,nfile,fnm), is_optional(&fnm[i]), is_output(&fnm[i])) )
1900 /* All options starting with -b* need the 'b' removed,
1901 * therefore overwrite strbuf */
1902 if (0 == strncmp(opt, "-b", 2))
1903 sprintf(strbuf, "-%s %s ", &opt[2], name);
1905 add_to_string(cmd_args_bench, strbuf);
1908 if ( is_launch_file(opt,opt2bSet(opt,nfile,fnm)) )
1909 add_to_string(cmd_args_launch, strbuf);
1913 add_to_string(cmd_args_bench , extra_args);
1914 add_to_string(cmd_args_launch, extra_args);
1919 /* Set option opt */
1920 static void setopt(const char *opt,int nfile,t_filenm fnm[])
1924 for(i=0; (i<nfile); i++)
1925 if (strcmp(opt,fnm[i].opt)==0)
1926 fnm[i].flag |= ffSET;
1930 /* This routine checks for output files that get triggered by a tpr option.
1931 * These output files are marked as set to allow for proper cleanup after
1932 * each tuning run. */
1933 static void get_tpr_outfiles(int nfile, t_filenm fnm[])
1935 gmx_bool bPull; /* Is pulling requested in .tpr file? */
1936 gmx_bool bTpi; /* Is test particle insertion requested? */
1937 gmx_bool bFree; /* Is a free energy simulation requested? */
1938 gmx_bool bNM; /* Is a normal mode analysis requested? */
1944 /* Check tpr file for options that trigger extra output files */
1945 read_tpx_state(opt2fn("-s",nfile,fnm),&ir,&state,NULL,&mtop);
1946 bPull = (epullNO != ir.ePull);
1947 bFree = (efepNO != ir.efep );
1948 bNM = (eiNM == ir.eI );
1949 bTpi = EI_TPI(ir.eI);
1951 /* Set these output files on the tuning command-line */
1954 setopt("-pf" , nfile, fnm);
1955 setopt("-px" , nfile, fnm);
1959 setopt("-dhdl", nfile, fnm);
1963 setopt("-tpi" , nfile, fnm);
1964 setopt("-tpid", nfile, fnm);
1968 setopt("-mtx" , nfile, fnm);
1973 static void couple_files_options(int nfile, t_filenm fnm[])
1976 gmx_bool bSet,bBench;
1981 for (i=0; i<nfile; i++)
1983 opt = (char *)fnm[i].opt;
1984 bSet = ((fnm[i].flag & ffSET) != 0);
1985 bBench = (0 == strncmp(opt,"-b", 2));
1987 /* Check optional files */
1988 /* If e.g. -eo is set, then -beo also needs to be set */
1989 if (is_optional(&fnm[i]) && bSet && !bBench)
1991 sprintf(buf, "-b%s", &opt[1]);
1992 setopt(buf,nfile,fnm);
1994 /* If -beo is set, then -eo also needs to be! */
1995 if (is_optional(&fnm[i]) && bSet && bBench)
1997 sprintf(buf, "-%s", &opt[2]);
1998 setopt(buf,nfile,fnm);
2004 static double gettime()
2006 #ifdef HAVE_GETTIMEOFDAY
2010 gettimeofday(&t,NULL);
2012 seconds = (double) t.tv_sec + 1e-6*(double)t.tv_usec;
2018 seconds = time(NULL);
2025 #define BENCHSTEPS (1000)
2027 int gmx_tune_pme(int argc,char *argv[])
2029 const char *desc[] = {
2030 "For a given number [TT]-np[tt] or [TT]-nt[tt] of processors/threads, this program systematically",
2031 "times [TT]mdrun[tt] with various numbers of PME-only nodes and determines",
2032 "which setting is fastest. It will also test whether performance can",
2033 "be enhanced by shifting load from the reciprocal to the real space",
2034 "part of the Ewald sum. ",
2035 "Simply pass your [TT].tpr[tt] file to [TT]g_tune_pme[tt] together with other options",
2036 "for [TT]mdrun[tt] as needed.[PAR]",
2037 "Which executables are used can be set in the environment variables",
2038 "MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
2039 "will be used as defaults. Note that for certain MPI frameworks you",
2040 "need to provide a machine- or hostfile. This can also be passed",
2041 "via the MPIRUN variable, e.g.[PAR]",
2042 "[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
2043 "Please call [TT]g_tune_pme[tt] with the normal options you would pass to",
2044 "[TT]mdrun[tt] and add [TT]-np[tt] for the number of processors to perform the",
2045 "tests on, or [TT]-nt[tt] for the number of threads. You can also add [TT]-r[tt]",
2046 "to repeat each test several times to get better statistics. [PAR]",
2047 "[TT]g_tune_pme[tt] can test various real space / reciprocal space workloads",
2048 "for you. With [TT]-ntpr[tt] you control how many extra [TT].tpr[tt] files will be",
2049 "written with enlarged cutoffs and smaller fourier grids respectively.",
2050 "Typically, the first test (number 0) will be with the settings from the input",
2051 "[TT].tpr[tt] file; the last test (number [TT]ntpr[tt]) will have cutoffs multiplied",
2052 "by (and at the same time fourier grid dimensions divided by) the scaling",
2053 "factor [TT]-fac[tt] (default 1.2). The remaining [TT].tpr[tt] files will have about ",
2054 "equally-spaced values in between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
2055 "if you just want to find the optimal number of PME-only nodes; in that case",
2056 "your input [TT].tpr[tt] file will remain unchanged.[PAR]",
2057 "For the benchmark runs, the default of 1000 time steps should suffice for most",
2058 "MD systems. The dynamic load balancing needs about 100 time steps",
2059 "to adapt to local load imbalances, therefore the time step counters",
2060 "are by default reset after 100 steps. For large systems",
2061 "(>1M atoms) you may have to set [TT]-resetstep[tt] to a higher value.",
2062 "From the 'DD' load imbalance entries in the md.log output file you",
2063 "can tell after how many steps the load is sufficiently balanced. Example call:[PAR]"
2064 "[TT]g_tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
2065 "After calling [TT]mdrun[tt] several times, detailed performance information",
2066 "is available in the output file [TT]perf.out.[tt] ",
2067 "[BB]Note[bb] that during the benchmarks, a couple of temporary files are written",
2068 "(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
2069 "If you want the simulation to be started automatically with the",
2070 "optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
2075 int pmeentries=0; /* How many values for -npme do we actually test for each tpr file */
2076 real maxPMEfraction=0.50;
2077 real minPMEfraction=0.25;
2078 int maxPMEnodes, minPMEnodes;
2079 int npme_fixed=-2; /* If >= -1, use only this number
2080 * of PME-only nodes */
2081 real downfac=1.0,upfac=1.2;
2083 real fs=0.0; /* 0 indicates: not set by the user */
2084 gmx_large_int_t bench_nsteps=BENCHSTEPS;
2085 gmx_large_int_t new_sim_nsteps=-1; /* -1 indicates: not set by the user */
2086 gmx_large_int_t cpt_steps=0; /* Step counter in .cpt input file */
2087 int presteps=100; /* Do a full cycle reset after presteps steps */
2088 gmx_bool bOverwrite=FALSE, bKeepTPR;
2089 gmx_bool bLaunch=FALSE;
2090 gmx_bool bPassAll=FALSE;
2091 char *ExtraArgs=NULL;
2092 char **tpr_names=NULL;
2093 const char *simulation_tpr=NULL;
2094 int best_npme, best_tpr;
2095 int sim_part = 1; /* For benchmarks with checkpoint files */
2097 /* Default program names if nothing else is found */
2098 char *cmd_mpirun=NULL, *cmd_mdrun=NULL;
2099 char *cmd_args_bench, *cmd_args_launch;
2102 t_perf **perfdata=NULL;
2108 /* Print out how long the tuning took */
2111 static t_filenm fnm[] = {
2113 { efOUT, "-p", "perf", ffWRITE },
2114 { efLOG, "-err", "errors", ffWRITE },
2115 { efTPX, "-so", "tuned", ffWRITE },
2117 { efTPX, NULL, NULL, ffREAD },
2118 { efTRN, "-o", NULL, ffWRITE },
2119 { efXTC, "-x", NULL, ffOPTWR },
2120 { efCPT, "-cpi", NULL, ffOPTRD },
2121 { efCPT, "-cpo", NULL, ffOPTWR },
2122 { efSTO, "-c", "confout", ffWRITE },
2123 { efEDR, "-e", "ener", ffWRITE },
2124 { efLOG, "-g", "md", ffWRITE },
2125 { efXVG, "-dhdl", "dhdl", ffOPTWR },
2126 { efXVG, "-field", "field", ffOPTWR },
2127 { efXVG, "-table", "table", ffOPTRD },
2128 { efXVG, "-tablep", "tablep", ffOPTRD },
2129 { efXVG, "-tableb", "table", ffOPTRD },
2130 { efTRX, "-rerun", "rerun", ffOPTRD },
2131 { efXVG, "-tpi", "tpi", ffOPTWR },
2132 { efXVG, "-tpid", "tpidist", ffOPTWR },
2133 { efEDI, "-ei", "sam", ffOPTRD },
2134 { efEDO, "-eo", "sam", ffOPTWR },
2135 { efGCT, "-j", "wham", ffOPTRD },
2136 { efGCT, "-jo", "bam", ffOPTWR },
2137 { efXVG, "-ffout", "gct", ffOPTWR },
2138 { efXVG, "-devout", "deviatie", ffOPTWR },
2139 { efXVG, "-runav", "runaver", ffOPTWR },
2140 { efXVG, "-px", "pullx", ffOPTWR },
2141 { efXVG, "-pf", "pullf", ffOPTWR },
2142 { efMTX, "-mtx", "nm", ffOPTWR },
2143 { efNDX, "-dn", "dipole", ffOPTWR },
2144 /* Output files that are deleted after each benchmark run */
2145 { efTRN, "-bo", "bench", ffWRITE },
2146 { efXTC, "-bx", "bench", ffWRITE },
2147 { efCPT, "-bcpo", "bench", ffWRITE },
2148 { efSTO, "-bc", "bench", ffWRITE },
2149 { efEDR, "-be", "bench", ffWRITE },
2150 { efLOG, "-bg", "bench", ffWRITE },
2151 { efEDO, "-beo", "bench", ffOPTWR },
2152 { efXVG, "-bdhdl", "benchdhdl",ffOPTWR },
2153 { efXVG, "-bfield", "benchfld" ,ffOPTWR },
2154 { efXVG, "-btpi", "benchtpi", ffOPTWR },
2155 { efXVG, "-btpid", "benchtpid",ffOPTWR },
2156 { efGCT, "-bjo", "bench", ffOPTWR },
2157 { efXVG, "-bffout", "benchgct", ffOPTWR },
2158 { efXVG, "-bdevout","benchdev", ffOPTWR },
2159 { efXVG, "-brunav", "benchrnav",ffOPTWR },
2160 { efXVG, "-bpx", "benchpx", ffOPTWR },
2161 { efXVG, "-bpf", "benchpf", ffOPTWR },
2162 { efMTX, "-bmtx", "benchn", ffOPTWR },
2163 { efNDX, "-bdn", "bench", ffOPTWR }
2166 /* Command line options of mdrun */
2167 gmx_bool bDDBondCheck = TRUE;
2168 gmx_bool bDDBondComm = TRUE;
2169 gmx_bool bVerbose = FALSE;
2170 gmx_bool bCompact = TRUE;
2171 gmx_bool bSepPot = FALSE;
2172 gmx_bool bRerunVSite = FALSE;
2173 gmx_bool bIonize = FALSE;
2174 gmx_bool bConfout = TRUE;
2175 gmx_bool bReproducible = FALSE;
2176 gmx_bool bThreads = FALSE;
2179 int nstglobalcomm=-1;
2181 int repl_ex_seed=-1;
2185 const char *ddno_opt[ddnoNR+1] =
2186 { NULL, "interleave", "pp_pme", "cartesian", NULL };
2187 const char *dddlb_opt[] =
2188 { NULL, "auto", "no", "yes", NULL };
2189 const char *procstring[] =
2190 { NULL, "-np", "-n", "none", NULL };
2191 const char *npmevalues_opt[] =
2192 { NULL, "auto", "all", "subset", NULL };
2193 real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
2194 char *ddcsx=NULL,*ddcsy=NULL,*ddcsz=NULL;
2196 #define STD_CPT_PERIOD (15.0)
2197 real cpt_period=STD_CPT_PERIOD,max_hours=-1;
2198 gmx_bool bAppendFiles=TRUE;
2199 gmx_bool bKeepAndNumCPT=FALSE;
2200 gmx_bool bResetCountersHalfWay=FALSE;
2201 output_env_t oenv=NULL;
2204 /***********************/
2205 /* g_tune_pme options: */
2206 /***********************/
2207 { "-np", FALSE, etINT, {&nnodes},
2208 "Number of nodes to run the tests on (must be > 2 for separate PME nodes)" },
2209 { "-npstring", FALSE, etENUM, {procstring},
2210 "Specify the number of processors to [TT]$MPIRUN[tt] using this string"},
2211 { "-passall", FALSE, etBOOL, {&bPassAll},
2212 "HIDDENPut arguments unknown to [TT]mdrun[tt] at the end of the command line. Can be used for debugging purposes. "},
2213 { "-nt", FALSE, etINT, {&nthreads},
2214 "Number of threads to run the tests on (turns MPI & mpirun off)"},
2215 { "-r", FALSE, etINT, {&repeats},
2216 "Repeat each test this often" },
2217 { "-max", FALSE, etREAL, {&maxPMEfraction},
2218 "Max fraction of PME nodes to test with" },
2219 { "-min", FALSE, etREAL, {&minPMEfraction},
2220 "Min fraction of PME nodes to test with" },
2221 { "-npme", FALSE, etENUM, {npmevalues_opt},
2222 "Benchmark all possible values for [TT]-npme[tt] or just the subset that is expected to perform well"},
2223 { "-fix", FALSE, etINT, {&npme_fixed},
2224 "If >= -1, do not vary the number of PME-only nodes, instead use this fixed value and only vary rcoulomb and the PME grid spacing."},
2225 { "-upfac", FALSE, etREAL, {&upfac},
2226 "Upper limit for rcoulomb scaling factor (Note that rcoulomb upscaling results in fourier grid downscaling)" },
2227 { "-downfac", FALSE, etREAL, {&downfac},
2228 "Lower limit for rcoulomb scaling factor" },
2229 { "-ntpr", FALSE, etINT, {&ntprs},
2230 "Number of [TT].tpr[tt] files to benchmark. Create this many files with scaling factors ranging from 1.0 to fac. If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
2231 { "-four", FALSE, etREAL, {&fs},
2232 "Use this fourierspacing value instead of the grid found in the [TT].tpr[tt] input file. (Spacing applies to a scaling factor of 1.0 if multiple [TT].tpr[tt] files are written)" },
2233 { "-steps", FALSE, etGMX_LARGE_INT, {&bench_nsteps},
2234 "Take timings for this many steps in the benchmark runs" },
2235 { "-resetstep",FALSE, etINT, {&presteps},
2236 "Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
2237 { "-simsteps", FALSE, etGMX_LARGE_INT, {&new_sim_nsteps},
2238 "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
2239 { "-launch", FALSE, etBOOL, {&bLaunch},
2240 "Launch the real simulation after optimization" },
2241 /******************/
2242 /* mdrun options: */
2243 /******************/
2244 { "-deffnm", FALSE, etSTR, {&deffnm},
2245 "Set the default filename for all file options at launch time" },
2246 { "-ddorder", FALSE, etENUM, {ddno_opt},
2248 { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
2249 "Check for all bonded interactions with DD" },
2250 { "-ddbondcomm",FALSE, etBOOL, {&bDDBondComm},
2251 "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
2252 { "-rdd", FALSE, etREAL, {&rdd},
2253 "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
2254 { "-rcon", FALSE, etREAL, {&rconstr},
2255 "Maximum distance for P-LINCS (nm), 0 is estimate" },
2256 { "-dlb", FALSE, etENUM, {dddlb_opt},
2257 "Dynamic load balancing (with DD)" },
2258 { "-dds", FALSE, etREAL, {&dlb_scale},
2259 "Minimum allowed dlb scaling of the DD cell size" },
2260 { "-ddcsx", FALSE, etSTR, {&ddcsx},
2261 "HIDDENThe DD cell sizes in x" },
2262 { "-ddcsy", FALSE, etSTR, {&ddcsy},
2263 "HIDDENThe DD cell sizes in y" },
2264 { "-ddcsz", FALSE, etSTR, {&ddcsz},
2265 "HIDDENThe DD cell sizes in z" },
2266 { "-gcom", FALSE, etINT, {&nstglobalcomm},
2267 "Global communication frequency" },
2268 { "-v", FALSE, etBOOL, {&bVerbose},
2269 "Be loud and noisy" },
2270 { "-compact", FALSE, etBOOL, {&bCompact},
2271 "Write a compact log file" },
2272 { "-seppot", FALSE, etBOOL, {&bSepPot},
2273 "Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
2274 { "-pforce", FALSE, etREAL, {&pforce},
2275 "Print all forces larger than this (kJ/mol nm)" },
2276 { "-reprod", FALSE, etBOOL, {&bReproducible},
2277 "Try to avoid optimizations that affect binary reproducibility" },
2278 { "-cpt", FALSE, etREAL, {&cpt_period},
2279 "Checkpoint interval (minutes)" },
2280 { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
2281 "Keep and number checkpoint files" },
2282 { "-append", FALSE, etBOOL, {&bAppendFiles},
2283 "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only)" },
2284 { "-maxh", FALSE, etREAL, {&max_hours},
2285 "Terminate after 0.99 times this time (hours)" },
2286 { "-multi", FALSE, etINT, {&nmultisim},
2287 "Do multiple simulations in parallel" },
2288 { "-replex", FALSE, etINT, {&repl_ex_nst},
2289 "Attempt replica exchange periodically with this period (steps)" },
2290 { "-reseed", FALSE, etINT, {&repl_ex_seed},
2291 "Seed for replica exchange, -1 is generate a seed" },
2292 { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
2293 "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
2294 { "-ionize", FALSE, etBOOL, {&bIonize},
2295 "Do a simulation including the effect of an X-ray bombardment on your system" },
2296 { "-confout", FALSE, etBOOL, {&bConfout},
2297 "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
2298 { "-stepout", FALSE, etINT, {&nstepout},
2299 "HIDDENFrequency of writing the remaining runtime" },
2300 { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
2301 "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt] (launch only)" }
2305 #define NFILE asize(fnm)
2307 CopyRight(stderr,argv[0]);
2309 seconds = gettime();
2311 parse_common_args(&argc,argv,PCA_NOEXIT_ON_ARGS,
2312 NFILE,fnm,asize(pa),pa,asize(desc),desc,
2315 /* Store the remaining unparsed command line entries in a string */
2317 ExtraArgs[0] = '\0';
2318 for (i=1; i<argc; i++) /* argc will now be 1 if everything was understood */
2320 add_to_string(&ExtraArgs, argv[i]);
2321 add_to_string(&ExtraArgs, " ");
2323 if ( !bPassAll && (ExtraArgs[0] != '\0') )
2325 fprintf(stderr, "\nWARNING: The following arguments you provided have no effect:\n"
2327 "Use the -passall option to force them to appear on the command lines\n"
2328 "for the benchmark simulations%s.\n\n",
2329 ExtraArgs, bLaunch? " and at launch time" : "");
2332 if (opt2parg_bSet("-nt",asize(pa),pa))
2335 if (opt2parg_bSet("-npstring",asize(pa),pa))
2336 fprintf(stderr, "WARNING: -npstring has no effect when using threads.\n");
2339 gmx_fatal(FARGS, "Can't run multi-threaded MPI simulation yet!");
2340 /* and now we just set this; a bit of an ugly hack*/
2343 /* tpr-triggered output files */
2344 get_tpr_outfiles(NFILE,fnm);
2346 /* Automatically set -beo options if -eo is set etc. */
2347 couple_files_options(NFILE,fnm);
2349 /* Construct the command line arguments for benchmark runs
2350 * as well as for the simulation run
2352 create_command_line_snippets(bThreads,presteps,NFILE,fnm,asize(pa),pa,procstring[0],
2353 &cmd_np, &cmd_args_bench, &cmd_args_launch,
2354 bPassAll? ExtraArgs : (char *)"");
2356 /* Read in checkpoint file if requested */
2358 if(opt2bSet("-cpi",NFILE,fnm))
2361 cr->duty=DUTY_PP; /* makes the following routine happy */
2362 read_checkpoint_simulation_part(opt2fn("-cpi",NFILE,fnm),
2363 &sim_part,&cpt_steps,cr,
2364 FALSE,NFILE,fnm,NULL,NULL);
2367 /* sim_part will now be 1 if no checkpoint file was found */
2369 gmx_fatal(FARGS, "Checkpoint file %s not found!", opt2fn("-cpi",
2374 /* Open performance output file and write header info */
2375 fp = ffopen(opt2fn("-p",NFILE,fnm),"w");
2377 /* Make a quick consistency check of command line parameters */
2378 check_input(nnodes, repeats, &ntprs, &upfac, &downfac,
2379 maxPMEfraction, minPMEfraction, npme_fixed,
2380 fs, bench_nsteps, fnm, NFILE, sim_part, presteps,
2383 /* Determine the maximum and minimum number of PME nodes to test,
2384 * the actual list of settings is build in do_the_tests(). */
2385 if ((nnodes > 2) && (npme_fixed < -1))
2387 maxPMEnodes = floor(maxPMEfraction*nnodes);
2388 minPMEnodes = max(floor(minPMEfraction*nnodes), 0);
2389 fprintf(stdout, "Will try runs with %d ", minPMEnodes);
2390 if (maxPMEnodes != minPMEnodes)
2391 fprintf(stdout, "- %d ", maxPMEnodes);
2392 fprintf(stdout, "PME-only nodes.\n Note that the automatic number of PME-only nodes and no separate PME nodes are always tested.\n");
2400 /* Get the commands we need to set up the runs from environment variables */
2401 get_program_paths(bThreads, &cmd_mpirun, cmd_np, &cmd_mdrun, repeats);
2403 /* Print some header info to file */
2405 fprintf(fp, "\n P E R F O R M A N C E R E S U L T S\n");
2407 fprintf(fp, "%s for Gromacs %s\n", ShortProgram(),GromacsVersion());
2410 fprintf(fp, "Number of nodes : %d\n", nnodes);
2411 fprintf(fp, "The mpirun command is : %s\n", cmd_mpirun);
2412 if ( strcmp(procstring[0], "none") != 0)
2413 fprintf(fp, "Passing # of nodes via : %s\n", procstring[0]);
2415 fprintf(fp, "Not setting number of nodes in system call\n");
2418 fprintf(fp, "Number of threads : %d\n", nnodes);
2420 fprintf(fp, "The mdrun command is : %s\n", cmd_mdrun);
2421 fprintf(fp, "mdrun args benchmarks : %s\n", cmd_args_bench);
2422 fprintf(fp, "Benchmark steps : ");
2423 fprintf(fp, gmx_large_int_pfmt, bench_nsteps);
2425 fprintf(fp, "dlb equilibration steps : %d\n", presteps);
2428 fprintf(fp, "Checkpoint time step : ");
2429 fprintf(fp, gmx_large_int_pfmt, cpt_steps);
2433 fprintf(fp, "mdrun args at launchtime: %s\n", cmd_args_launch);
2434 if (!bPassAll && ExtraArgs[0] != '\0')
2435 fprintf(fp, "Unused arguments : %s\n", ExtraArgs);
2436 if (new_sim_nsteps >= 0)
2439 fprintf(stderr, "Note: Simulation input file %s will have ", opt2fn("-so",NFILE,fnm));
2440 fprintf(stderr, gmx_large_int_pfmt, new_sim_nsteps+cpt_steps);
2441 fprintf(stderr, " steps.\n");
2442 fprintf(fp, "Simulation steps : ");
2443 fprintf(fp, gmx_large_int_pfmt, new_sim_nsteps);
2447 fprintf(fp, "Repeats for each test : %d\n", repeats);
2451 fprintf(fp, "Requested grid spacing : %f (This will be the grid spacing at a scaling factor of 1.0)\n", fs);
2454 if (npme_fixed >= -1)
2456 fprintf(fp, "Fixing -npme at : %d\n", npme_fixed);
2459 fprintf(fp, "Input file : %s\n", opt2fn("-s",NFILE,fnm));
2461 /* Allocate memory for the inputinfo struct: */
2463 info->nr_inputfiles = ntprs;
2464 for (i=0; i<ntprs; i++)
2466 snew(info->rcoulomb , ntprs);
2467 snew(info->rvdw , ntprs);
2468 snew(info->rlist , ntprs);
2469 snew(info->rlistlong, ntprs);
2470 snew(info->nkx , ntprs);
2471 snew(info->nky , ntprs);
2472 snew(info->nkz , ntprs);
2473 snew(info->fsx , ntprs);
2474 snew(info->fsy , ntprs);
2475 snew(info->fsz , ntprs);
2477 /* Make alternative tpr files to test: */
2478 snew(tpr_names, ntprs);
2479 for (i=0; i<ntprs; i++)
2480 snew(tpr_names[i], STRLEN);
2482 /* It can be that ntprs is reduced by make_benchmark_tprs if not enough
2483 * different grids could be found. */
2484 make_benchmark_tprs(opt2fn("-s",NFILE,fnm), tpr_names, bench_nsteps+presteps,
2485 cpt_steps, upfac, downfac, &ntprs, fs, info, fp);
2488 /********************************************************************************/
2489 /* Main loop over all scenarios we need to test: tpr files, PME nodes, repeats */
2490 /********************************************************************************/
2491 snew(perfdata, ntprs);
2492 do_the_tests(fp, tpr_names, maxPMEnodes, minPMEnodes, npme_fixed, npmevalues_opt[0], perfdata, &pmeentries,
2493 repeats, nnodes, ntprs, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
2494 cmd_args_bench, fnm, NFILE, sim_part, presteps, cpt_steps);
2496 fprintf(fp, "\nTuning took%8.1f minutes.\n", (gettime()-seconds)/60.0);
2498 /* Analyse the results and give a suggestion for optimal settings: */
2499 bKeepTPR = analyze_data(fp, opt2fn("-p", NFILE, fnm), perfdata, nnodes, ntprs, pmeentries,
2500 repeats, info, &best_tpr, &best_npme);
2502 /* Take the best-performing tpr file and enlarge nsteps to original value */
2503 if ( bKeepTPR && !bOverwrite && !(fs > 0.0) )
2505 simulation_tpr = opt2fn("-s",NFILE,fnm);
2509 simulation_tpr = opt2fn("-so",NFILE,fnm);
2510 modify_PMEsettings(bOverwrite? (new_sim_nsteps+cpt_steps) :
2511 info->orig_sim_steps, tpr_names[best_tpr],
2515 /* Now start the real simulation if the user requested it ... */
2516 launch_simulation(bLaunch, fp, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
2517 cmd_args_launch, simulation_tpr, nnodes, best_npme);
2520 /* ... or simply print the performance results to screen: */
2522 finalize(opt2fn("-p", NFILE, fnm));