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41 #ifdef HAVE_SYS_TIME_H
45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/legacyheaders/types/commrec.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/fileio/tpxio.h"
49 #include "gromacs/utility/cstringutil.h"
50 #include "gromacs/legacyheaders/readinp.h"
51 #include "gromacs/legacyheaders/calcgrid.h"
52 #include "gromacs/legacyheaders/checkpoint.h"
53 #include "gromacs/legacyheaders/macros.h"
55 #include "gromacs/legacyheaders/names.h"
56 #include "gromacs/legacyheaders/perf_est.h"
57 #include "gromacs/legacyheaders/inputrec.h"
58 #include "gromacs/timing/walltime_accounting.h"
59 #include "gromacs/math/utilities.h"
61 #include "gromacs/commandline/pargs.h"
62 #include "gromacs/utility/baseversion.h"
63 #include "gromacs/utility/fatalerror.h"
64 #include "gromacs/utility/smalloc.h"
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
,
78 eParselogLargePrimeFactor
,
86 int nPMEnodes
; /* number of PME-only nodes used in this test */
87 int nx
, ny
, nz
; /* DD grid */
88 int guessPME
; /* if nPMEnodes == -1, this is the guessed number of PME nodes */
89 double *Gcycles
; /* This can contain more than one value if doing multiple tests */
93 float *PME_f_load
; /* PME mesh/force load average*/
94 float PME_f_load_Av
; /* Average average ;) ... */
95 char *mdrun_cmd_line
; /* Mdrun command line used for this test */
101 int nr_inputfiles
; /* The number of tpr and mdp input files */
102 gmx_int64_t orig_sim_steps
; /* Number of steps to be done in the real simulation */
103 gmx_int64_t orig_init_step
; /* Init step for the real simulation */
104 real
*rcoulomb
; /* The coulomb radii [0...nr_inputfiles] */
105 real
*rvdw
; /* The vdW radii */
106 real
*rlist
; /* Neighbourlist cutoff radius */
108 int *nkx
, *nky
, *nkz
;
109 real
*fsx
, *fsy
, *fsz
; /* Fourierspacing in x,y,z dimension */
113 static void sep_line(FILE *fp
)
115 fprintf(fp
, "\n------------------------------------------------------------\n");
119 /* Wrapper for system calls */
120 static int gmx_system_call(char *command
)
123 gmx_fatal(FARGS
, "No calls to system(3) supported on this platform. Attempted to call:\n'%s'\n", command
);
125 return ( system(command
) );
130 /* Check if string starts with substring */
131 static gmx_bool
str_starts(const char *string
, const char *substring
)
133 return ( strncmp(string
, substring
, strlen(substring
)) == 0);
137 static void cleandata(t_perf
*perfdata
, int test_nr
)
139 perfdata
->Gcycles
[test_nr
] = 0.0;
140 perfdata
->ns_per_day
[test_nr
] = 0.0;
141 perfdata
->PME_f_load
[test_nr
] = 0.0;
147 static void remove_if_exists(const char *fn
)
151 fprintf(stdout
, "Deleting %s\n", fn
);
157 static void finalize(const char *fn_out
)
163 fp
= fopen(fn_out
, "r");
164 fprintf(stdout
, "\n\n");
166 while (fgets(buf
, STRLEN
-1, fp
) != NULL
)
168 fprintf(stdout
, "%s", buf
);
171 fprintf(stdout
, "\n\n");
176 eFoundNothing
, eFoundDDStr
, eFoundAccountingStr
, eFoundCycleStr
179 static int parse_logfile(const char *logfile
, const char *errfile
,
180 t_perf
*perfdata
, int test_nr
, int presteps
, gmx_int64_t cpt_steps
,
184 char line
[STRLEN
], dumstring
[STRLEN
], dumstring2
[STRLEN
];
185 const char matchstrdd
[] = "Domain decomposition grid";
186 const char matchstrcr
[] = "resetting all time and cycle counters";
187 const char matchstrbal
[] = "Average PME mesh/force load:";
188 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";
189 const char errSIG
[] = "signal, stopping at the next";
191 float dum1
, dum2
, dum3
, dum4
;
194 gmx_int64_t resetsteps
= -1;
195 gmx_bool bFoundResetStr
= FALSE
;
196 gmx_bool bResetChecked
= FALSE
;
199 if (!gmx_fexist(logfile
))
201 fprintf(stderr
, "WARNING: Could not find logfile %s.\n", logfile
);
202 cleandata(perfdata
, test_nr
);
203 return eParselogNotFound
;
206 fp
= fopen(logfile
, "r");
207 perfdata
->PME_f_load
[test_nr
] = -1.0;
208 perfdata
->guessPME
= -1;
210 iFound
= eFoundNothing
;
213 iFound
= eFoundDDStr
; /* Skip some case statements */
216 while (fgets(line
, STRLEN
, fp
) != NULL
)
218 /* Remove leading spaces */
221 /* Check for TERM and INT signals from user: */
222 if (strstr(line
, errSIG
) != NULL
)
225 cleandata(perfdata
, test_nr
);
226 return eParselogTerm
;
229 /* Check whether cycle resetting worked */
230 if (presteps
> 0 && !bFoundResetStr
)
232 if (strstr(line
, matchstrcr
) != NULL
)
234 sprintf(dumstring
, "step %s", "%"GMX_SCNd64
);
235 sscanf(line
, dumstring
, &resetsteps
);
236 bFoundResetStr
= TRUE
;
237 if (resetsteps
== presteps
+cpt_steps
)
239 bResetChecked
= TRUE
;
243 sprintf(dumstring
, "%"GMX_PRId64
, resetsteps
);
244 sprintf(dumstring2
, "%"GMX_PRId64
, presteps
+cpt_steps
);
245 fprintf(stderr
, "WARNING: Time step counters were reset at step %s,\n"
246 " though they were supposed to be reset at step %s!\n",
247 dumstring
, dumstring2
);
252 /* Look for strings that appear in a certain order in the log file: */
256 /* Look for domain decomp grid and separate PME nodes: */
257 if (str_starts(line
, matchstrdd
))
259 sscanf(line
, "Domain decomposition grid %d x %d x %d, separate PME ranks %d",
260 &(perfdata
->nx
), &(perfdata
->ny
), &(perfdata
->nz
), &npme
);
261 if (perfdata
->nPMEnodes
== -1)
263 perfdata
->guessPME
= npme
;
265 else if (perfdata
->nPMEnodes
!= npme
)
267 gmx_fatal(FARGS
, "PME ranks from command line and output file are not identical");
269 iFound
= eFoundDDStr
;
271 /* Catch a few errors that might have occured: */
272 else if (str_starts(line
, "There is no domain decomposition for"))
275 return eParselogNoDDGrid
;
277 else if (str_starts(line
, "The number of ranks you selected"))
280 return eParselogLargePrimeFactor
;
282 else if (str_starts(line
, "reading tpx file"))
285 return eParselogTPXVersion
;
287 else if (str_starts(line
, "The -dd or -npme option request a parallel simulation"))
290 return eParselogNotParallel
;
294 /* Look for PME mesh/force balance (not necessarily present, though) */
295 if (str_starts(line
, matchstrbal
))
297 sscanf(&line
[strlen(matchstrbal
)], "%f", &(perfdata
->PME_f_load
[test_nr
]));
299 /* Look for matchstring */
300 if (str_starts(line
, matchstring
))
302 iFound
= eFoundAccountingStr
;
305 case eFoundAccountingStr
:
306 /* Already found matchstring - look for cycle data */
307 if (str_starts(line
, "Total "))
309 sscanf(line
, "Total %*f %lf", &(perfdata
->Gcycles
[test_nr
]));
310 iFound
= eFoundCycleStr
;
314 /* Already found cycle data - look for remaining performance info and return */
315 if (str_starts(line
, "Performance:"))
317 ndum
= sscanf(line
, "%s %f %f %f %f", dumstring
, &dum1
, &dum2
, &dum3
, &dum4
);
318 /* (ns/day) is the second last entry, depending on whether GMX_DETAILED_PERF_STATS was set in print_perf(), nrnb.c */
319 perfdata
->ns_per_day
[test_nr
] = (ndum
== 5) ? dum3
: dum1
;
321 if (bResetChecked
|| presteps
== 0)
327 return eParselogResetProblem
;
334 /* Close the log file */
337 /* Check why there is no performance data in the log file.
338 * Did a fatal errors occur? */
339 if (gmx_fexist(errfile
))
341 fp
= fopen(errfile
, "r");
342 while (fgets(line
, STRLEN
, fp
) != NULL
)
344 if (str_starts(line
, "Fatal error:") )
346 if (fgets(line
, STRLEN
, fp
) != NULL
)
348 fprintf(stderr
, "\nWARNING: An error occured during this benchmark:\n"
352 cleandata(perfdata
, test_nr
);
353 return eParselogFatal
;
360 fprintf(stderr
, "WARNING: Could not find stderr file %s.\n", errfile
);
363 /* Giving up ... we could not find out why there is no performance data in
365 fprintf(stdout
, "No performance data in log file.\n");
366 cleandata(perfdata
, test_nr
);
368 return eParselogNoPerfData
;
372 static gmx_bool
analyze_data(
381 int *index_tpr
, /* OUT: Nr of mdp file with best settings */
382 int *npme_optimal
) /* OUT: Optimal number of PME nodes */
385 int line
= 0, line_win
= -1;
386 int k_win
= -1, i_win
= -1, winPME
;
387 double s
= 0.0; /* standard deviation */
390 char str_PME_f_load
[13];
391 gmx_bool bCanUseOrigTPR
;
392 gmx_bool bRefinedCoul
, bRefinedVdW
, bRefinedGrid
;
398 fprintf(fp
, "Summary of successful runs:\n");
399 fprintf(fp
, "Line tpr PME ranks Gcycles Av. Std.dev. ns/day PME/f");
402 fprintf(fp
, " DD grid");
408 for (k
= 0; k
< ntprs
; k
++)
410 for (i
= 0; i
< ntests
; i
++)
412 /* Select the right dataset: */
413 pd
= &(perfdata
[k
][i
]);
415 pd
->Gcycles_Av
= 0.0;
416 pd
->PME_f_load_Av
= 0.0;
417 pd
->ns_per_day_Av
= 0.0;
419 if (pd
->nPMEnodes
== -1)
421 sprintf(strbuf
, "(%3d)", pd
->guessPME
);
425 sprintf(strbuf
, " ");
428 /* Get the average run time of a setting */
429 for (j
= 0; j
< nrepeats
; j
++)
431 pd
->Gcycles_Av
+= pd
->Gcycles
[j
];
432 pd
->PME_f_load_Av
+= pd
->PME_f_load
[j
];
434 pd
->Gcycles_Av
/= nrepeats
;
435 pd
->PME_f_load_Av
/= nrepeats
;
437 for (j
= 0; j
< nrepeats
; j
++)
439 if (pd
->ns_per_day
[j
] > 0.0)
441 pd
->ns_per_day_Av
+= pd
->ns_per_day
[j
];
445 /* Somehow the performance number was not aquired for this run,
446 * therefor set the average to some negative value: */
447 pd
->ns_per_day_Av
= -1.0f
*nrepeats
;
451 pd
->ns_per_day_Av
/= nrepeats
;
454 if (pd
->PME_f_load_Av
> 0.0)
456 sprintf(str_PME_f_load
, "%12.3f", pd
->PME_f_load_Av
);
460 sprintf(str_PME_f_load
, "%s", " - ");
464 /* We assume we had a successful run if both averages are positive */
465 if (pd
->Gcycles_Av
> 0.0 && pd
->ns_per_day_Av
> 0.0)
467 /* Output statistics if repeats were done */
470 /* Calculate the standard deviation */
472 for (j
= 0; j
< nrepeats
; j
++)
474 s
+= pow( pd
->Gcycles
[j
] - pd
->Gcycles_Av
, 2 );
479 fprintf(fp
, "%4d %3d %4d%s %12.3f %12.3f %12.3f %s",
480 line
, k
, pd
->nPMEnodes
, strbuf
, pd
->Gcycles_Av
, s
,
481 pd
->ns_per_day_Av
, str_PME_f_load
);
484 fprintf(fp
, " %3d %3d %3d", pd
->nx
, pd
->ny
, pd
->nz
);
488 /* Store the index of the best run found so far in 'winner': */
489 if ( (k_win
== -1) || (pd
->Gcycles_Av
< perfdata
[k_win
][i_win
].Gcycles_Av
) )
502 gmx_fatal(FARGS
, "None of the runs was successful! Check %s for problems.", fn
);
507 winPME
= perfdata
[k_win
][i_win
].nPMEnodes
;
511 /* We stuck to a fixed number of PME-only nodes */
512 sprintf(strbuf
, "settings No. %d", k_win
);
516 /* We have optimized the number of PME-only nodes */
519 sprintf(strbuf
, "%s", "the automatic number of PME ranks");
523 sprintf(strbuf
, "%d PME ranks", winPME
);
526 fprintf(fp
, "Best performance was achieved with %s", strbuf
);
527 if ((nrepeats
> 1) && (ntests
> 1))
529 fprintf(fp
, " (see line %d)", line_win
);
533 /* Only mention settings if they were modified: */
534 bRefinedCoul
= !gmx_within_tol(info
->rcoulomb
[k_win
], info
->rcoulomb
[0], GMX_REAL_EPS
);
535 bRefinedVdW
= !gmx_within_tol(info
->rvdw
[k_win
], info
->rvdw
[0], GMX_REAL_EPS
);
536 bRefinedGrid
= !(info
->nkx
[k_win
] == info
->nkx
[0] &&
537 info
->nky
[k_win
] == info
->nky
[0] &&
538 info
->nkz
[k_win
] == info
->nkz
[0]);
540 if (bRefinedCoul
|| bRefinedVdW
|| bRefinedGrid
)
542 fprintf(fp
, "Optimized PME settings:\n");
543 bCanUseOrigTPR
= FALSE
;
547 bCanUseOrigTPR
= TRUE
;
552 fprintf(fp
, " New Coulomb radius: %f nm (was %f nm)\n", info
->rcoulomb
[k_win
], info
->rcoulomb
[0]);
557 fprintf(fp
, " New Van der Waals radius: %f nm (was %f nm)\n", info
->rvdw
[k_win
], info
->rvdw
[0]);
562 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
],
563 info
->nkx
[0], info
->nky
[0], info
->nkz
[0]);
566 if (bCanUseOrigTPR
&& ntprs
> 1)
568 fprintf(fp
, "and original PME settings.\n");
573 /* Return the index of the mdp file that showed the highest performance
574 * and the optimal number of PME nodes */
576 *npme_optimal
= winPME
;
578 return bCanUseOrigTPR
;
582 /* Get the commands we need to set up the runs from environment variables */
583 static void get_program_paths(gmx_bool bThreads
, char *cmd_mpirun
[], char *cmd_mdrun
[])
587 const char def_mpirun
[] = "mpirun";
588 const char def_mdrun
[] = "mdrun";
590 const char empty_mpirun
[] = "";
592 /* Get the commands we need to set up the runs from environment variables */
595 if ( (cp
= getenv("MPIRUN")) != NULL
)
597 *cmd_mpirun
= gmx_strdup(cp
);
601 *cmd_mpirun
= gmx_strdup(def_mpirun
);
606 *cmd_mpirun
= gmx_strdup(empty_mpirun
);
609 if ( (cp
= getenv("MDRUN" )) != NULL
)
611 *cmd_mdrun
= gmx_strdup(cp
);
615 *cmd_mdrun
= gmx_strdup(def_mdrun
);
619 /* Check that the commands will run mdrun (perhaps via mpirun) by
620 * running a very quick test simulation. Requires MPI environment to
621 * be available if applicable. */
622 static void check_mdrun_works(gmx_bool bThreads
,
623 const char *cmd_mpirun
,
625 const char *cmd_mdrun
)
627 char *command
= NULL
;
631 const char filename
[] = "benchtest.log";
633 /* This string should always be identical to the one in copyrite.c,
634 * gmx_print_version_info() in the defined(GMX_MPI) section */
635 const char match_mpi
[] = "MPI library: MPI";
636 const char match_mdrun
[] = "Executable: ";
637 gmx_bool bMdrun
= FALSE
;
638 gmx_bool bMPI
= FALSE
;
640 /* Run a small test to see whether mpirun + mdrun work */
641 fprintf(stdout
, "Making sure that mdrun can be executed. ");
644 snew(command
, strlen(cmd_mdrun
) + strlen(cmd_np
) + strlen(filename
) + 50);
645 sprintf(command
, "%s%s-version -maxh 0.001 1> %s 2>&1", cmd_mdrun
, cmd_np
, filename
);
649 snew(command
, strlen(cmd_mpirun
) + strlen(cmd_np
) + strlen(cmd_mdrun
) + strlen(filename
) + 50);
650 sprintf(command
, "%s%s%s -version -maxh 0.001 1> %s 2>&1", cmd_mpirun
, cmd_np
, cmd_mdrun
, filename
);
652 fprintf(stdout
, "Trying '%s' ... ", command
);
653 make_backup(filename
);
654 gmx_system_call(command
);
656 /* Check if we find the characteristic string in the output: */
657 if (!gmx_fexist(filename
))
659 gmx_fatal(FARGS
, "Output from test run could not be found.");
662 fp
= fopen(filename
, "r");
663 /* We need to scan the whole output file, since sometimes the queuing system
664 * also writes stuff to stdout/err */
667 cp
= fgets(line
, STRLEN
, fp
);
670 if (str_starts(line
, match_mdrun
) )
674 if (str_starts(line
, match_mpi
) )
686 gmx_fatal(FARGS
, "Need a threaded version of mdrun. This one\n"
688 "seems to have been compiled with MPI instead.",
696 gmx_fatal(FARGS
, "Need an MPI-enabled version of mdrun. This one\n"
698 "seems to have been compiled without MPI support.",
705 gmx_fatal(FARGS
, "Cannot execute mdrun. Please check %s for problems!",
709 fprintf(stdout
, "passed.\n");
717 static void launch_simulation(
718 gmx_bool bLaunch
, /* Should the simulation be launched? */
719 FILE *fp
, /* General log file */
720 gmx_bool bThreads
, /* whether to use threads */
721 char *cmd_mpirun
, /* Command for mpirun */
722 char *cmd_np
, /* Switch for -np or -ntmpi or empty */
723 char *cmd_mdrun
, /* Command for mdrun */
724 char *args_for_mdrun
, /* Arguments for mdrun */
725 const char *simulation_tpr
, /* This tpr will be simulated */
726 int nPMEnodes
) /* Number of PME nodes to use */
731 /* Make enough space for the system call command,
732 * (100 extra chars for -npme ... etc. options should suffice): */
733 snew(command
, strlen(cmd_mpirun
)+strlen(cmd_mdrun
)+strlen(cmd_np
)+strlen(args_for_mdrun
)+strlen(simulation_tpr
)+100);
735 /* Note that the -passall options requires args_for_mdrun to be at the end
736 * of the command line string */
739 sprintf(command
, "%s%s-npme %d -s %s %s",
740 cmd_mdrun
, cmd_np
, nPMEnodes
, simulation_tpr
, args_for_mdrun
);
744 sprintf(command
, "%s%s%s -npme %d -s %s %s",
745 cmd_mpirun
, cmd_np
, cmd_mdrun
, nPMEnodes
, simulation_tpr
, args_for_mdrun
);
748 fprintf(fp
, "%s this command line to launch the simulation:\n\n%s", bLaunch
? "Using" : "Please use", command
);
752 /* Now the real thing! */
755 fprintf(stdout
, "\nLaunching simulation with best parameters now.\nExecuting '%s'", command
);
758 gmx_system_call(command
);
763 static void modify_PMEsettings(
764 gmx_int64_t simsteps
, /* Set this value as number of time steps */
765 gmx_int64_t init_step
, /* Set this value as init_step */
766 const char *fn_best_tpr
, /* tpr file with the best performance */
767 const char *fn_sim_tpr
) /* name of tpr file to be launched */
775 read_tpx_state(fn_best_tpr
, ir
, &state
, NULL
, &mtop
);
777 /* Reset nsteps and init_step to the value of the input .tpr file */
778 ir
->nsteps
= simsteps
;
779 ir
->init_step
= init_step
;
781 /* Write the tpr file which will be launched */
782 sprintf(buf
, "Writing optimized simulation file %s with nsteps=%s.\n", fn_sim_tpr
, "%"GMX_PRId64
);
783 fprintf(stdout
, buf
, ir
->nsteps
);
785 write_tpx_state(fn_sim_tpr
, ir
, &state
, &mtop
);
790 static gmx_bool
can_scale_rvdw(int vdwtype
)
792 return (evdwCUT
== vdwtype
||
796 #define EPME_SWITCHED(e) ((e) == eelPMESWITCH || (e) == eelPMEUSERSWITCH)
798 /* Make additional TPR files with more computational load for the
799 * direct space processors: */
800 static void make_benchmark_tprs(
801 const char *fn_sim_tpr
, /* READ : User-provided tpr file */
802 char *fn_bench_tprs
[], /* WRITE: Names of benchmark tpr files */
803 gmx_int64_t benchsteps
, /* Number of time steps for benchmark runs */
804 gmx_int64_t statesteps
, /* Step counter in checkpoint file */
805 real rmin
, /* Minimal Coulomb radius */
806 real rmax
, /* Maximal Coulomb radius */
807 real bScaleRvdw
, /* Scale rvdw along with rcoulomb */
808 int *ntprs
, /* No. of TPRs to write, each with a different
809 rcoulomb and fourierspacing */
810 t_inputinfo
*info
, /* Contains information about mdp file options */
811 FILE *fp
) /* Write the output here */
817 real nlist_buffer
; /* Thickness of the buffer regions for PME-switch potentials */
820 gmx_bool bNote
= FALSE
;
821 real add
; /* Add this to rcoul for the next test */
822 real fac
= 1.0; /* Scaling factor for Coulomb radius */
823 real fourierspacing
; /* Basic fourierspacing from tpr */
826 sprintf(buf
, "Making benchmark tpr file%s with %s time step%s",
827 *ntprs
> 1 ? "s" : "", "%"GMX_PRId64
, benchsteps
> 1 ? "s" : "");
828 fprintf(stdout
, buf
, benchsteps
);
831 sprintf(buf
, " (adding %s steps from checkpoint file)", "%"GMX_PRId64
);
832 fprintf(stdout
, buf
, statesteps
);
833 benchsteps
+= statesteps
;
835 fprintf(stdout
, ".\n");
839 read_tpx_state(fn_sim_tpr
, ir
, &state
, NULL
, &mtop
);
841 /* Check if some kind of PME was chosen */
842 if (EEL_PME(ir
->coulombtype
) == FALSE
)
844 gmx_fatal(FARGS
, "Can only do optimizations for simulations with %s electrostatics.",
848 /* Check if rcoulomb == rlist, which is necessary for plain PME. */
849 if ( (ir
->cutoff_scheme
!= ecutsVERLET
) &&
850 (eelPME
== ir
->coulombtype
) && !(ir
->rcoulomb
== ir
->rlist
))
852 gmx_fatal(FARGS
, "%s requires rcoulomb (%f) to be equal to rlist (%f).",
853 EELTYPE(eelPME
), ir
->rcoulomb
, ir
->rlist
);
855 /* For other PME types, rcoulomb is allowed to be smaller than rlist */
856 else if (ir
->rcoulomb
> ir
->rlist
)
858 gmx_fatal(FARGS
, "%s requires rcoulomb (%f) to be equal to or smaller than rlist (%f)",
859 EELTYPE(ir
->coulombtype
), ir
->rcoulomb
, ir
->rlist
);
862 if (bScaleRvdw
&& ir
->rvdw
!= ir
->rcoulomb
)
864 fprintf(stdout
, "NOTE: input rvdw != rcoulomb, will not scale rvdw\n");
868 /* Reduce the number of steps for the benchmarks */
869 info
->orig_sim_steps
= ir
->nsteps
;
870 ir
->nsteps
= benchsteps
;
871 /* We must not use init_step from the input tpr file for the benchmarks */
872 info
->orig_init_step
= ir
->init_step
;
875 /* For PME-switch potentials, keep the radial distance of the buffer region */
876 nlist_buffer
= ir
->rlist
- ir
->rcoulomb
;
878 /* Determine length of triclinic box vectors */
879 for (d
= 0; d
< DIM
; d
++)
882 for (i
= 0; i
< DIM
; i
++)
884 box_size
[d
] += state
.box
[d
][i
]*state
.box
[d
][i
];
886 box_size
[d
] = sqrt(box_size
[d
]);
889 if (ir
->fourier_spacing
> 0)
891 info
->fsx
[0] = ir
->fourier_spacing
;
892 info
->fsy
[0] = ir
->fourier_spacing
;
893 info
->fsz
[0] = ir
->fourier_spacing
;
897 /* Reconstruct fourierspacing per dimension from the number of grid points and box size */
898 info
->fsx
[0] = box_size
[XX
]/ir
->nkx
;
899 info
->fsy
[0] = box_size
[YY
]/ir
->nky
;
900 info
->fsz
[0] = box_size
[ZZ
]/ir
->nkz
;
903 /* If no value for the fourierspacing was provided on the command line, we
904 * use the reconstruction from the tpr file */
905 if (ir
->fourier_spacing
> 0)
907 /* Use the spacing from the tpr */
908 fourierspacing
= ir
->fourier_spacing
;
912 /* Use the maximum observed spacing */
913 fourierspacing
= max(max(info
->fsx
[0], info
->fsy
[0]), info
->fsz
[0]);
916 fprintf(stdout
, "Calculating PME grid points on the basis of a fourierspacing of %f nm\n", fourierspacing
);
918 /* For performance comparisons the number of particles is useful to have */
919 fprintf(fp
, " Number of particles : %d\n", mtop
.natoms
);
921 /* Print information about settings of which some are potentially modified: */
922 fprintf(fp
, " Coulomb type : %s\n", EELTYPE(ir
->coulombtype
));
923 fprintf(fp
, " Grid spacing x y z : %f %f %f\n",
924 box_size
[XX
]/ir
->nkx
, box_size
[YY
]/ir
->nky
, box_size
[ZZ
]/ir
->nkz
);
925 fprintf(fp
, " Van der Waals type : %s\n", EVDWTYPE(ir
->vdwtype
));
926 if (ir_vdw_switched(ir
))
928 fprintf(fp
, " rvdw_switch : %f nm\n", ir
->rvdw_switch
);
930 if (EPME_SWITCHED(ir
->coulombtype
))
932 fprintf(fp
, " rlist : %f nm\n", ir
->rlist
);
934 if (ir
->rlistlong
!= max_cutoff(ir
->rvdw
, ir
->rcoulomb
))
936 fprintf(fp
, " rlistlong : %f nm\n", ir
->rlistlong
);
939 /* Print a descriptive line about the tpr settings tested */
940 fprintf(fp
, "\nWill try these real/reciprocal workload settings:\n");
941 fprintf(fp
, " No. scaling rcoulomb");
942 fprintf(fp
, " nkx nky nkz");
943 fprintf(fp
, " spacing");
944 if (can_scale_rvdw(ir
->vdwtype
))
946 fprintf(fp
, " rvdw");
948 if (EPME_SWITCHED(ir
->coulombtype
))
950 fprintf(fp
, " rlist");
952 if (ir
->rlistlong
!= max_cutoff(ir
->rlist
, max_cutoff(ir
->rvdw
, ir
->rcoulomb
)) )
954 fprintf(fp
, " rlistlong");
956 fprintf(fp
, " tpr file\n");
958 /* Loop to create the requested number of tpr input files */
959 for (j
= 0; j
< *ntprs
; j
++)
961 /* The first .tpr is the provided one, just need to modify nsteps,
962 * so skip the following block */
965 /* Determine which Coulomb radii rc to use in the benchmarks */
966 add
= (rmax
-rmin
)/(*ntprs
-1);
967 if (gmx_within_tol(rmin
, info
->rcoulomb
[0], GMX_REAL_EPS
))
969 ir
->rcoulomb
= rmin
+ j
*add
;
971 else if (gmx_within_tol(rmax
, info
->rcoulomb
[0], GMX_REAL_EPS
))
973 ir
->rcoulomb
= rmin
+ (j
-1)*add
;
977 /* rmin != rcoul != rmax, ergo test between rmin and rmax */
978 add
= (rmax
-rmin
)/(*ntprs
-2);
979 ir
->rcoulomb
= rmin
+ (j
-1)*add
;
982 /* Determine the scaling factor fac */
983 fac
= ir
->rcoulomb
/info
->rcoulomb
[0];
985 /* Scale the Fourier grid spacing */
986 ir
->nkx
= ir
->nky
= ir
->nkz
= 0;
987 calc_grid(NULL
, state
.box
, fourierspacing
*fac
, &ir
->nkx
, &ir
->nky
, &ir
->nkz
);
989 /* Adjust other radii since various conditions need to be fulfilled */
990 if (eelPME
== ir
->coulombtype
)
992 /* plain PME, rcoulomb must be equal to rlist */
993 ir
->rlist
= ir
->rcoulomb
;
997 /* rlist must be >= rcoulomb, we keep the size of the buffer region */
998 ir
->rlist
= ir
->rcoulomb
+ nlist_buffer
;
1001 if (bScaleRvdw
&& can_scale_rvdw(ir
->vdwtype
))
1003 if (ecutsVERLET
== ir
->cutoff_scheme
||
1004 evdwPME
== ir
->vdwtype
)
1006 /* With either the Verlet cutoff-scheme or LJ-PME,
1007 the van der Waals radius must always equal the
1009 ir
->rvdw
= ir
->rcoulomb
;
1013 /* For vdw cutoff, rvdw >= rlist */
1014 ir
->rvdw
= max(info
->rvdw
[0], ir
->rlist
);
1018 ir
->rlistlong
= max_cutoff(ir
->rlist
, max_cutoff(ir
->rvdw
, ir
->rcoulomb
));
1020 } /* end of "if (j != 0)" */
1022 /* for j==0: Save the original settings
1023 * for j >0: Save modified radii and Fourier grids */
1024 info
->rcoulomb
[j
] = ir
->rcoulomb
;
1025 info
->rvdw
[j
] = ir
->rvdw
;
1026 info
->nkx
[j
] = ir
->nkx
;
1027 info
->nky
[j
] = ir
->nky
;
1028 info
->nkz
[j
] = ir
->nkz
;
1029 info
->rlist
[j
] = ir
->rlist
;
1030 info
->rlistlong
[j
] = ir
->rlistlong
;
1031 info
->fsx
[j
] = fac
*fourierspacing
;
1032 info
->fsy
[j
] = fac
*fourierspacing
;
1033 info
->fsz
[j
] = fac
*fourierspacing
;
1035 /* Write the benchmark tpr file */
1036 strncpy(fn_bench_tprs
[j
], fn_sim_tpr
, strlen(fn_sim_tpr
)-strlen(".tpr"));
1037 sprintf(buf
, "_bench%.2d.tpr", j
);
1038 strcat(fn_bench_tprs
[j
], buf
);
1039 fprintf(stdout
, "Writing benchmark tpr %s with nsteps=", fn_bench_tprs
[j
]);
1040 fprintf(stdout
, "%"GMX_PRId64
, ir
->nsteps
);
1043 fprintf(stdout
, ", scaling factor %f\n", fac
);
1047 fprintf(stdout
, ", unmodified settings\n");
1050 write_tpx_state(fn_bench_tprs
[j
], ir
, &state
, &mtop
);
1052 /* Write information about modified tpr settings to log file */
1053 fprintf(fp
, "%4d%10f%10f", j
, fac
, ir
->rcoulomb
);
1054 fprintf(fp
, "%5d%5d%5d", ir
->nkx
, ir
->nky
, ir
->nkz
);
1055 fprintf(fp
, " %9f ", info
->fsx
[j
]);
1056 if (can_scale_rvdw(ir
->vdwtype
))
1058 fprintf(fp
, "%10f", ir
->rvdw
);
1060 if (EPME_SWITCHED(ir
->coulombtype
))
1062 fprintf(fp
, "%10f", ir
->rlist
);
1064 if (info
->rlistlong
[0] != max_cutoff(info
->rlist
[0], max_cutoff(info
->rvdw
[0], info
->rcoulomb
[0])) )
1066 fprintf(fp
, "%10f", ir
->rlistlong
);
1068 fprintf(fp
, " %-14s\n", fn_bench_tprs
[j
]);
1070 /* Make it clear to the user that some additional settings were modified */
1071 if (!gmx_within_tol(ir
->rvdw
, info
->rvdw
[0], GMX_REAL_EPS
)
1072 || !gmx_within_tol(ir
->rlistlong
, info
->rlistlong
[0], GMX_REAL_EPS
) )
1079 fprintf(fp
, "\nNote that in addition to the Coulomb radius and the Fourier grid\n"
1080 "other input settings were also changed (see table above).\n"
1081 "Please check if the modified settings are appropriate.\n");
1089 /* Rename the files we want to keep to some meaningful filename and
1090 * delete the rest */
1091 static void cleanup(const t_filenm
*fnm
, int nfile
, int k
, int nnodes
,
1092 int nPMEnodes
, int nr
, gmx_bool bKeepStderr
)
1094 char numstring
[STRLEN
];
1095 char newfilename
[STRLEN
];
1096 const char *fn
= NULL
;
1101 fprintf(stdout
, "Cleaning up, deleting benchmark temp files ...\n");
1103 for (i
= 0; i
< nfile
; i
++)
1105 opt
= (char *)fnm
[i
].opt
;
1106 if (strcmp(opt
, "-p") == 0)
1108 /* do nothing; keep this file */
1111 else if (strcmp(opt
, "-bg") == 0)
1113 /* Give the log file a nice name so one can later see which parameters were used */
1114 numstring
[0] = '\0';
1117 sprintf(numstring
, "_%d", nr
);
1119 sprintf(newfilename
, "%s_no%d_np%d_npme%d%s", opt2fn("-bg", nfile
, fnm
), k
, nnodes
, nPMEnodes
, numstring
);
1120 if (gmx_fexist(opt2fn("-bg", nfile
, fnm
)))
1122 fprintf(stdout
, "renaming log file to %s\n", newfilename
);
1123 make_backup(newfilename
);
1124 rename(opt2fn("-bg", nfile
, fnm
), newfilename
);
1127 else if (strcmp(opt
, "-err") == 0)
1129 /* This file contains the output of stderr. We want to keep it in
1130 * cases where there have been problems. */
1131 fn
= opt2fn(opt
, nfile
, fnm
);
1132 numstring
[0] = '\0';
1135 sprintf(numstring
, "_%d", nr
);
1137 sprintf(newfilename
, "%s_no%d_np%d_npme%d%s", fn
, k
, nnodes
, nPMEnodes
, numstring
);
1142 fprintf(stdout
, "Saving stderr output in %s\n", newfilename
);
1143 make_backup(newfilename
);
1144 rename(fn
, newfilename
);
1148 fprintf(stdout
, "Deleting %s\n", fn
);
1153 /* Delete the files which are created for each benchmark run: (options -b*) */
1154 else if ( (0 == strncmp(opt
, "-b", 2)) && (opt2bSet(opt
, nfile
, fnm
) || !is_optional(&fnm
[i
])) )
1156 remove_if_exists(opt2fn(opt
, nfile
, fnm
));
1163 eNpmeAuto
, eNpmeAll
, eNpmeReduced
, eNpmeSubset
, eNpmeNr
1166 /* Create a list of numbers of PME nodes to test */
1167 static void make_npme_list(
1168 const char *npmevalues_opt
, /* Make a complete list with all
1169 * possibilities or a short list that keeps only
1170 * reasonable numbers of PME nodes */
1171 int *nentries
, /* Number of entries we put in the nPMEnodes list */
1172 int *nPMEnodes
[], /* Each entry contains the value for -npme */
1173 int nnodes
, /* Total number of nodes to do the tests on */
1174 int minPMEnodes
, /* Minimum number of PME nodes */
1175 int maxPMEnodes
) /* Maximum number of PME nodes */
1178 int min_factor
= 1; /* We request that npp and npme have this minimal
1179 * largest common factor (depends on npp) */
1180 int nlistmax
; /* Max. list size */
1181 int nlist
; /* Actual number of entries in list */
1185 /* Do we need to check all possible values for -npme or is a reduced list enough? */
1186 if (0 == strcmp(npmevalues_opt
, "all") )
1190 else if (0 == strcmp(npmevalues_opt
, "subset") )
1192 eNPME
= eNpmeSubset
;
1194 else /* "auto" or "range" */
1200 else if (nnodes
< 128)
1202 eNPME
= eNpmeReduced
;
1206 eNPME
= eNpmeSubset
;
1210 /* Calculate how many entries we could possibly have (in case of -npme all) */
1213 nlistmax
= maxPMEnodes
- minPMEnodes
+ 3;
1214 if (0 == minPMEnodes
)
1224 /* Now make the actual list which is at most of size nlist */
1225 snew(*nPMEnodes
, nlistmax
);
1226 nlist
= 0; /* start counting again, now the real entries in the list */
1227 for (i
= 0; i
< nlistmax
- 2; i
++)
1229 npme
= maxPMEnodes
- i
;
1240 /* For 2d PME we want a common largest factor of at least the cube
1241 * root of the number of PP nodes */
1242 min_factor
= (int) pow(npp
, 1.0/3.0);
1245 gmx_fatal(FARGS
, "Unknown option for eNPME in make_npme_list");
1248 if (gmx_greatest_common_divisor(npp
, npme
) >= min_factor
)
1250 (*nPMEnodes
)[nlist
] = npme
;
1254 /* We always test 0 PME nodes and the automatic number */
1255 *nentries
= nlist
+ 2;
1256 (*nPMEnodes
)[nlist
] = 0;
1257 (*nPMEnodes
)[nlist
+1] = -1;
1259 fprintf(stderr
, "Will try the following %d different values for -npme:\n", *nentries
);
1260 for (i
= 0; i
< *nentries
-1; i
++)
1262 fprintf(stderr
, "%d, ", (*nPMEnodes
)[i
]);
1264 fprintf(stderr
, "and %d (auto).\n", (*nPMEnodes
)[*nentries
-1]);
1268 /* Allocate memory to store the performance data */
1269 static void init_perfdata(t_perf
*perfdata
[], int ntprs
, int datasets
, int repeats
)
1274 for (k
= 0; k
< ntprs
; k
++)
1276 snew(perfdata
[k
], datasets
);
1277 for (i
= 0; i
< datasets
; i
++)
1279 for (j
= 0; j
< repeats
; j
++)
1281 snew(perfdata
[k
][i
].Gcycles
, repeats
);
1282 snew(perfdata
[k
][i
].ns_per_day
, repeats
);
1283 snew(perfdata
[k
][i
].PME_f_load
, repeats
);
1290 /* Check for errors on mdrun -h */
1291 static void make_sure_it_runs(char *mdrun_cmd_line
, int length
, FILE *fp
,
1292 const t_filenm
*fnm
, int nfile
)
1294 const char *fn
= NULL
;
1295 char *command
, *msg
;
1299 snew(command
, length
+ 15);
1300 snew(msg
, length
+ 500);
1302 fprintf(stdout
, "Making sure the benchmarks can be executed by running just 1 step...\n");
1303 sprintf(command
, "%s -nsteps 1 -quiet", mdrun_cmd_line
);
1304 fprintf(stdout
, "Executing '%s' ...\n", command
);
1305 ret
= gmx_system_call(command
);
1309 /* To prevent confusion, do not again issue a gmx_fatal here since we already
1310 * get the error message from mdrun itself */
1311 sprintf(msg
, "Cannot run the benchmark simulations! Please check the error message of\n"
1312 "mdrun for the source of the problem. Did you provide a command line\n"
1313 "argument that neither g_tune_pme nor mdrun understands? Offending command:\n"
1314 "\n%s\n\n", command
);
1316 fprintf(stderr
, "%s", msg
);
1318 fprintf(fp
, "%s", msg
);
1322 fprintf(stdout
, "Benchmarks can be executed!\n");
1324 /* Clean up the benchmark output files we just created */
1325 fprintf(stdout
, "Cleaning up ...\n");
1326 remove_if_exists(opt2fn("-bc", nfile
, fnm
));
1327 remove_if_exists(opt2fn("-be", nfile
, fnm
));
1328 remove_if_exists(opt2fn("-bcpo", nfile
, fnm
));
1329 remove_if_exists(opt2fn("-bg", nfile
, fnm
));
1336 static void do_the_tests(
1337 FILE *fp
, /* General g_tune_pme output file */
1338 char **tpr_names
, /* Filenames of the input files to test */
1339 int maxPMEnodes
, /* Max fraction of nodes to use for PME */
1340 int minPMEnodes
, /* Min fraction of nodes to use for PME */
1341 int npme_fixed
, /* If >= -1, test fixed number of PME
1343 const char *npmevalues_opt
, /* Which -npme values should be tested */
1344 t_perf
**perfdata
, /* Here the performace data is stored */
1345 int *pmeentries
, /* Entries in the nPMEnodes list */
1346 int repeats
, /* Repeat each test this often */
1347 int nnodes
, /* Total number of nodes = nPP + nPME */
1348 int nr_tprs
, /* Total number of tpr files to test */
1349 gmx_bool bThreads
, /* Threads or MPI? */
1350 char *cmd_mpirun
, /* mpirun command string */
1351 char *cmd_np
, /* "-np", "-n", whatever mpirun needs */
1352 char *cmd_mdrun
, /* mdrun command string */
1353 char *cmd_args_bench
, /* arguments for mdrun in a string */
1354 const t_filenm
*fnm
, /* List of filenames from command line */
1355 int nfile
, /* Number of files specified on the cmdl. */
1356 int presteps
, /* DLB equilibration steps, is checked */
1357 gmx_int64_t cpt_steps
) /* Time step counter in the checkpoint */
1359 int i
, nr
, k
, ret
, count
= 0, totaltests
;
1360 int *nPMEnodes
= NULL
;
1363 char *command
, *cmd_stub
;
1365 gmx_bool bResetProblem
= FALSE
;
1366 gmx_bool bFirst
= TRUE
;
1369 /* This string array corresponds to the eParselog enum type at the start
1371 const char* ParseLog
[] = {
1373 "Logfile not found!",
1374 "No timings, logfile truncated?",
1375 "Run was terminated.",
1376 "Counters were not reset properly.",
1377 "No DD grid found for these settings.",
1378 "TPX version conflict!",
1379 "mdrun was not started in parallel!",
1380 "Number of PP ranks has a prime factor that is too large.",
1383 char str_PME_f_load
[13];
1386 /* Allocate space for the mdrun command line. 100 extra characters should
1387 be more than enough for the -npme etcetera arguments */
1388 cmdline_length
= strlen(cmd_mpirun
)
1391 + strlen(cmd_args_bench
)
1392 + strlen(tpr_names
[0]) + 100;
1393 snew(command
, cmdline_length
);
1394 snew(cmd_stub
, cmdline_length
);
1396 /* Construct the part of the command line that stays the same for all tests: */
1399 sprintf(cmd_stub
, "%s%s", cmd_mdrun
, cmd_np
);
1403 sprintf(cmd_stub
, "%s%s%s ", cmd_mpirun
, cmd_np
, cmd_mdrun
);
1406 /* Create a list of numbers of PME nodes to test */
1407 if (npme_fixed
< -1)
1409 make_npme_list(npmevalues_opt
, pmeentries
, &nPMEnodes
,
1410 nnodes
, minPMEnodes
, maxPMEnodes
);
1416 nPMEnodes
[0] = npme_fixed
;
1417 fprintf(stderr
, "Will use a fixed number of %d PME-only ranks.\n", nPMEnodes
[0]);
1422 fprintf(fp
, "\nNo benchmarks done since number of repeats (-r) is 0.\n");
1424 finalize(opt2fn("-p", nfile
, fnm
));
1428 /* Allocate one dataset for each tpr input file: */
1429 init_perfdata(perfdata
, nr_tprs
, *pmeentries
, repeats
);
1431 /*****************************************/
1432 /* Main loop over all tpr files to test: */
1433 /*****************************************/
1434 totaltests
= nr_tprs
*(*pmeentries
)*repeats
;
1435 for (k
= 0; k
< nr_tprs
; k
++)
1437 fprintf(fp
, "\nIndividual timings for input file %d (%s):\n", k
, tpr_names
[k
]);
1438 fprintf(fp
, "PME ranks Gcycles ns/day PME/f Remark\n");
1439 /* Loop over various numbers of PME nodes: */
1440 for (i
= 0; i
< *pmeentries
; i
++)
1442 pd
= &perfdata
[k
][i
];
1444 /* Loop over the repeats for each scenario: */
1445 for (nr
= 0; nr
< repeats
; nr
++)
1447 pd
->nPMEnodes
= nPMEnodes
[i
];
1449 /* Add -npme and -s to the command line and save it. Note that
1450 * the -passall (if set) options requires cmd_args_bench to be
1451 * at the end of the command line string */
1452 snew(pd
->mdrun_cmd_line
, cmdline_length
);
1453 sprintf(pd
->mdrun_cmd_line
, "%s-npme %d -s %s %s",
1454 cmd_stub
, pd
->nPMEnodes
, tpr_names
[k
], cmd_args_bench
);
1456 /* To prevent that all benchmarks fail due to a show-stopper argument
1457 * on the mdrun command line, we make a quick check first */
1460 make_sure_it_runs(pd
->mdrun_cmd_line
, cmdline_length
, fp
, fnm
, nfile
);
1464 /* Do a benchmark simulation: */
1467 sprintf(buf
, ", pass %d/%d", nr
+1, repeats
);
1473 fprintf(stdout
, "\n=== Progress %2.0f%%, tpr %d/%d, run %d/%d%s:\n",
1474 (100.0*count
)/totaltests
,
1475 k
+1, nr_tprs
, i
+1, *pmeentries
, buf
);
1476 make_backup(opt2fn("-err", nfile
, fnm
));
1477 sprintf(command
, "%s 1> /dev/null 2>%s", pd
->mdrun_cmd_line
, opt2fn("-err", nfile
, fnm
));
1478 fprintf(stdout
, "%s\n", pd
->mdrun_cmd_line
);
1479 gmx_system_call(command
);
1481 /* Collect the performance data from the log file; also check stderr
1482 * for fatal errors */
1483 ret
= parse_logfile(opt2fn("-bg", nfile
, fnm
), opt2fn("-err", nfile
, fnm
),
1484 pd
, nr
, presteps
, cpt_steps
, nnodes
);
1485 if ((presteps
> 0) && (ret
== eParselogResetProblem
))
1487 bResetProblem
= TRUE
;
1490 if (-1 == pd
->nPMEnodes
)
1492 sprintf(buf
, "(%3d)", pd
->guessPME
);
1500 if (pd
->PME_f_load
[nr
] > 0.0)
1502 sprintf(str_PME_f_load
, "%12.3f", pd
->PME_f_load
[nr
]);
1506 sprintf(str_PME_f_load
, "%s", " - ");
1509 /* Write the data we got to disk */
1510 fprintf(fp
, "%4d%s %12.3f %12.3f %s %s", pd
->nPMEnodes
,
1511 buf
, pd
->Gcycles
[nr
], pd
->ns_per_day
[nr
], str_PME_f_load
, ParseLog
[ret
]);
1512 if (!(ret
== eParselogOK
|| ret
== eParselogNoDDGrid
|| ret
== eParselogNotFound
) )
1514 fprintf(fp
, " Check %s file for problems.", ret
== eParselogFatal
? "err" : "log");
1520 /* Do some cleaning up and delete the files we do not need any more */
1521 cleanup(fnm
, nfile
, k
, nnodes
, pd
->nPMEnodes
, nr
, ret
== eParselogFatal
);
1523 /* If the first run with this number of processors already failed, do not try again: */
1524 if (pd
->Gcycles
[0] <= 0.0 && repeats
> 1)
1526 fprintf(stdout
, "Skipping remaining passes of unsuccessful setting, see log file for details.\n");
1527 count
+= repeats
-(nr
+1);
1530 } /* end of repeats loop */
1531 } /* end of -npme loop */
1532 } /* end of tpr file loop */
1537 fprintf(fp
, "WARNING: The cycle and time step counters could not be reset properly. ");
1545 static void check_input(
1552 real maxPMEfraction
,
1553 real minPMEfraction
,
1555 gmx_int64_t bench_nsteps
,
1556 const t_filenm
*fnm
,
1566 /* Make sure the input file exists */
1567 if (!gmx_fexist(opt2fn("-s", nfile
, fnm
)))
1569 gmx_fatal(FARGS
, "File %s not found.", opt2fn("-s", nfile
, fnm
));
1572 /* Make sure that the checkpoint file is not overwritten during benchmarking */
1573 if ( (0 == strcmp(opt2fn("-cpi", nfile
, fnm
), opt2fn("-bcpo", nfile
, fnm
)) ) && (sim_part
> 1) )
1575 gmx_fatal(FARGS
, "Checkpoint input (-cpi) and benchmark checkpoint output (-bcpo) files must not be identical.\n"
1576 "The checkpoint input file must not be overwritten during the benchmarks.\n");
1579 /* Make sure that repeats is >= 0 (if == 0, only write tpr files) */
1582 gmx_fatal(FARGS
, "Number of repeats < 0!");
1585 /* Check number of nodes */
1588 gmx_fatal(FARGS
, "Number of ranks/threads must be a positive integer.");
1591 /* Automatically choose -ntpr if not set */
1601 /* Set a reasonable scaling factor for rcoulomb */
1604 *rmax
= rcoulomb
* 1.2;
1607 fprintf(stderr
, "Will test %d tpr file%s.\n", *ntprs
, *ntprs
== 1 ? "" : "s");
1613 fprintf(stderr
, "Note: Choose ntpr>1 to shift PME load between real and reciprocal space.\n");
1617 /* Make shure that rmin <= rcoulomb <= rmax */
1626 if (!(*rmin
<= *rmax
) )
1628 gmx_fatal(FARGS
, "Please choose the Coulomb radii such that rmin <= rmax.\n"
1629 "rmin = %g, rmax = %g, actual rcoul from .tpr file = %g\n", *rmin
, *rmax
, rcoulomb
);
1631 /* Add test scenarios if rmin or rmax were set */
1634 if (!gmx_within_tol(*rmin
, rcoulomb
, GMX_REAL_EPS
) && (*ntprs
== 1) )
1637 fprintf(stderr
, "NOTE: Setting -rmin to %g changed -ntpr to %d\n",
1640 if (!gmx_within_tol(*rmax
, rcoulomb
, GMX_REAL_EPS
) && (*ntprs
== 1) )
1643 fprintf(stderr
, "NOTE: Setting -rmax to %g changed -ntpr to %d\n",
1648 /* If one of rmin, rmax is set, we need 2 tpr files at minimum */
1649 if (!gmx_within_tol(*rmax
, rcoulomb
, GMX_REAL_EPS
) || !gmx_within_tol(*rmin
, rcoulomb
, GMX_REAL_EPS
) )
1651 *ntprs
= max(*ntprs
, 2);
1654 /* If both rmin, rmax are set, we need 3 tpr files at minimum */
1655 if (!gmx_within_tol(*rmax
, rcoulomb
, GMX_REAL_EPS
) && !gmx_within_tol(*rmin
, rcoulomb
, GMX_REAL_EPS
) )
1657 *ntprs
= max(*ntprs
, 3);
1662 fprintf(stderr
, "NOTE: Your rmin, rmax setting changed -ntpr to %d\n", *ntprs
);
1667 if (gmx_within_tol(*rmin
, rcoulomb
, GMX_REAL_EPS
) && gmx_within_tol(rcoulomb
, *rmax
, GMX_REAL_EPS
)) /* We have just a single rc */
1669 fprintf(stderr
, "WARNING: Resetting -ntpr to 1 since no Coulomb radius scaling is requested.\n"
1670 "Please set rmin < rmax to test Coulomb radii in the [rmin, rmax] interval\n"
1671 "with correspondingly adjusted PME grid settings\n");
1676 /* Check whether max and min fraction are within required values */
1677 if (maxPMEfraction
> 0.5 || maxPMEfraction
< 0)
1679 gmx_fatal(FARGS
, "-max must be between 0 and 0.5");
1681 if (minPMEfraction
> 0.5 || minPMEfraction
< 0)
1683 gmx_fatal(FARGS
, "-min must be between 0 and 0.5");
1685 if (maxPMEfraction
< minPMEfraction
)
1687 gmx_fatal(FARGS
, "-max must be larger or equal to -min");
1690 /* Check whether the number of steps - if it was set - has a reasonable value */
1691 if (bench_nsteps
< 0)
1693 gmx_fatal(FARGS
, "Number of steps must be positive.");
1696 if (bench_nsteps
> 10000 || bench_nsteps
< 100)
1698 fprintf(stderr
, "WARNING: steps=");
1699 fprintf(stderr
, "%"GMX_PRId64
, bench_nsteps
);
1700 fprintf(stderr
, ". Are you sure you want to perform so %s steps for each benchmark?\n", (bench_nsteps
< 100) ? "few" : "many");
1705 gmx_fatal(FARGS
, "Cannot have a negative number of presteps.\n");
1708 /* Check for rcoulomb scaling if more than one .tpr file is tested */
1711 if (*rmin
/rcoulomb
< 0.75 || *rmax
/rcoulomb
> 1.25)
1713 fprintf(stderr
, "WARNING: Applying extreme scaling factor. I hope you know what you are doing.\n");
1717 /* If a fixed number of PME nodes is set we do rcoulomb and PME gird tuning
1718 * only. We need to check whether the requested number of PME-only nodes
1720 if (npme_fixed
> -1)
1722 /* No more than 50% of all nodes can be assigned as PME-only nodes. */
1723 if (2*npme_fixed
> nnodes
)
1725 gmx_fatal(FARGS
, "Cannot have more than %d PME-only ranks for a total of %d ranks (you chose %d).\n",
1726 nnodes
/2, nnodes
, npme_fixed
);
1728 if ((npme_fixed
> 0) && (5*npme_fixed
< nnodes
))
1730 fprintf(stderr
, "WARNING: Only %g percent of the ranks are assigned as PME-only ranks.\n",
1731 100.0*((real
)npme_fixed
/ (real
)nnodes
));
1733 if (opt2parg_bSet("-min", npargs
, pa
) || opt2parg_bSet("-max", npargs
, pa
))
1735 fprintf(stderr
, "NOTE: The -min, -max, and -npme options have no effect when a\n"
1736 " fixed number of PME-only ranks is requested with -fix.\n");
1742 /* Returns TRUE when "opt" is needed at launch time */
1743 static gmx_bool
is_launch_file(char *opt
, gmx_bool bSet
)
1745 if (0 == strncmp(opt
, "-swap", 5))
1750 /* Apart from the input .tpr and the output log files we need all options that
1751 * were set on the command line and that do not start with -b */
1752 if (0 == strncmp(opt
, "-b", 2) || 0 == strncmp(opt
, "-s", 2)
1753 || 0 == strncmp(opt
, "-err", 4) || 0 == strncmp(opt
, "-p", 2) )
1762 /* Returns TRUE when "opt" defines a file which is needed for the benchmarks runs */
1763 static gmx_bool
is_bench_file(char *opt
, gmx_bool bSet
, gmx_bool bOptional
, gmx_bool bIsOutput
)
1765 /* Apart from the input .tpr, all files starting with "-b" are for
1766 * _b_enchmark files exclusively */
1767 if (0 == strncmp(opt
, "-s", 2))
1772 if (0 == strncmp(opt
, "-b", 2) || 0 == strncmp(opt
, "-s", 2))
1774 if (!bOptional
|| bSet
)
1791 if (bSet
) /* These are additional input files like -cpi -ei */
1804 /* Adds 'buf' to 'str' */
1805 static void add_to_string(char **str
, char *buf
)
1810 len
= strlen(*str
) + strlen(buf
) + 1;
1816 /* Create the command line for the benchmark as well as for the real run */
1817 static void create_command_line_snippets(
1818 gmx_bool bAppendFiles
,
1819 gmx_bool bKeepAndNumCPT
,
1820 gmx_bool bResetHWay
,
1824 char *cmd_args_bench
[], /* command line arguments for benchmark runs */
1825 char *cmd_args_launch
[], /* command line arguments for simulation run */
1826 char extra_args
[]) /* Add this to the end of the command line */
1831 char strbuf
[STRLEN
];
1834 /* strlen needs at least '\0' as a string: */
1835 snew(*cmd_args_bench
, 1);
1836 snew(*cmd_args_launch
, 1);
1837 *cmd_args_launch
[0] = '\0';
1838 *cmd_args_bench
[0] = '\0';
1841 /*******************************************/
1842 /* 1. Process other command line arguments */
1843 /*******************************************/
1846 /* Add equilibration steps to benchmark options */
1847 sprintf(strbuf
, "-resetstep %d ", presteps
);
1848 add_to_string(cmd_args_bench
, strbuf
);
1850 /* These switches take effect only at launch time */
1851 if (FALSE
== bAppendFiles
)
1853 add_to_string(cmd_args_launch
, "-noappend ");
1857 add_to_string(cmd_args_launch
, "-cpnum ");
1861 add_to_string(cmd_args_launch
, "-resethway ");
1864 /********************/
1865 /* 2. Process files */
1866 /********************/
1867 for (i
= 0; i
< nfile
; i
++)
1869 opt
= (char *)fnm
[i
].opt
;
1870 name
= opt2fn(opt
, nfile
, fnm
);
1872 /* Strbuf contains the options, now let's sort out where we need that */
1873 sprintf(strbuf
, "%s %s ", opt
, name
);
1875 if (is_bench_file(opt
, opt2bSet(opt
, nfile
, fnm
), is_optional(&fnm
[i
]), is_output(&fnm
[i
])) )
1877 /* All options starting with -b* need the 'b' removed,
1878 * therefore overwrite strbuf */
1879 if (0 == strncmp(opt
, "-b", 2))
1881 sprintf(strbuf
, "-%s %s ", &opt
[2], name
);
1884 add_to_string(cmd_args_bench
, strbuf
);
1887 if (is_launch_file(opt
, opt2bSet(opt
, nfile
, fnm
)) )
1889 add_to_string(cmd_args_launch
, strbuf
);
1893 add_to_string(cmd_args_bench
, extra_args
);
1894 add_to_string(cmd_args_launch
, extra_args
);
1898 /* Set option opt */
1899 static void setopt(const char *opt
, int nfile
, t_filenm fnm
[])
1903 for (i
= 0; (i
< nfile
); i
++)
1905 if (strcmp(opt
, fnm
[i
].opt
) == 0)
1907 fnm
[i
].flag
|= ffSET
;
1913 /* This routine inspects the tpr file and ...
1914 * 1. checks for output files that get triggered by a tpr option. These output
1915 * files are marked as 'set' to allow for a proper cleanup after each
1917 * 2. returns the PME:PP load ratio
1918 * 3. returns rcoulomb from the tpr */
1919 static float inspect_tpr(int nfile
, t_filenm fnm
[], real
*rcoulomb
)
1921 gmx_bool bPull
; /* Is pulling requested in .tpr file? */
1922 gmx_bool bTpi
; /* Is test particle insertion requested? */
1923 gmx_bool bFree
; /* Is a free energy simulation requested? */
1924 gmx_bool bNM
; /* Is a normal mode analysis requested? */
1925 gmx_bool bSwap
; /* Is water/ion position swapping requested? */
1931 /* Check tpr file for options that trigger extra output files */
1932 read_tpx_state(opt2fn("-s", nfile
, fnm
), &ir
, &state
, NULL
, &mtop
);
1933 bPull
= (epullNO
!= ir
.ePull
);
1934 bFree
= (efepNO
!= ir
.efep
);
1935 bNM
= (eiNM
== ir
.eI
);
1936 bSwap
= (eswapNO
!= ir
.eSwapCoords
);
1937 bTpi
= EI_TPI(ir
.eI
);
1939 /* Set these output files on the tuning command-line */
1942 setopt("-pf", nfile
, fnm
);
1943 setopt("-px", nfile
, fnm
);
1947 setopt("-dhdl", nfile
, fnm
);
1951 setopt("-tpi", nfile
, fnm
);
1952 setopt("-tpid", nfile
, fnm
);
1956 setopt("-mtx", nfile
, fnm
);
1960 setopt("-swap", nfile
, fnm
);
1963 *rcoulomb
= ir
.rcoulomb
;
1965 /* Return the estimate for the number of PME nodes */
1966 return pme_load_estimate(&mtop
, &ir
, state
.box
);
1970 static void couple_files_options(int nfile
, t_filenm fnm
[])
1973 gmx_bool bSet
, bBench
;
1978 for (i
= 0; i
< nfile
; i
++)
1980 opt
= (char *)fnm
[i
].opt
;
1981 bSet
= ((fnm
[i
].flag
& ffSET
) != 0);
1982 bBench
= (0 == strncmp(opt
, "-b", 2));
1984 /* Check optional files */
1985 /* If e.g. -eo is set, then -beo also needs to be set */
1986 if (is_optional(&fnm
[i
]) && bSet
&& !bBench
)
1988 sprintf(buf
, "-b%s", &opt
[1]);
1989 setopt(buf
, nfile
, fnm
);
1991 /* If -beo is set, then -eo also needs to be! */
1992 if (is_optional(&fnm
[i
]) && bSet
&& bBench
)
1994 sprintf(buf
, "-%s", &opt
[2]);
1995 setopt(buf
, nfile
, fnm
);
2001 #define BENCHSTEPS (1000)
2003 int gmx_tune_pme(int argc
, char *argv
[])
2005 const char *desc
[] = {
2006 "For a given number [TT]-np[tt] or [TT]-ntmpi[tt] of ranks, [THISMODULE] systematically",
2007 "times [gmx-mdrun] with various numbers of PME-only ranks and determines",
2008 "which setting is fastest. It will also test whether performance can",
2009 "be enhanced by shifting load from the reciprocal to the real space",
2010 "part of the Ewald sum. ",
2011 "Simply pass your [TT].tpr[tt] file to [THISMODULE] together with other options",
2012 "for [gmx-mdrun] as needed.[PAR]",
2013 "Which executables are used can be set in the environment variables",
2014 "MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
2015 "will be used as defaults. Note that for certain MPI frameworks you",
2016 "need to provide a machine- or hostfile. This can also be passed",
2017 "via the MPIRUN variable, e.g.[PAR]",
2018 "[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
2019 "Please call [THISMODULE] with the normal options you would pass to",
2020 "[gmx-mdrun] and add [TT]-np[tt] for the number of ranks to perform the",
2021 "tests on, or [TT]-ntmpi[tt] for the number of threads. You can also add [TT]-r[tt]",
2022 "to repeat each test several times to get better statistics. [PAR]",
2023 "[THISMODULE] can test various real space / reciprocal space workloads",
2024 "for you. With [TT]-ntpr[tt] you control how many extra [TT].tpr[tt] files will be",
2025 "written with enlarged cutoffs and smaller Fourier grids respectively.",
2026 "Typically, the first test (number 0) will be with the settings from the input",
2027 "[TT].tpr[tt] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
2028 "specified by [TT]-rmax[tt] with a somwhat smaller PME grid at the same time. ",
2029 "In this last test, the Fourier spacing is multiplied with [TT]rmax[tt]/rcoulomb. ",
2030 "The remaining [TT].tpr[tt] files will have equally-spaced Coulomb radii (and Fourier "
2031 "spacings) between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
2032 "if you just seek the optimal number of PME-only ranks; in that case",
2033 "your input [TT].tpr[tt] file will remain unchanged.[PAR]",
2034 "For the benchmark runs, the default of 1000 time steps should suffice for most",
2035 "MD systems. The dynamic load balancing needs about 100 time steps",
2036 "to adapt to local load imbalances, therefore the time step counters",
2037 "are by default reset after 100 steps. For large systems (>1M atoms), as well as ",
2038 "for a higher accuarcy of the measurements, you should set [TT]-resetstep[tt] to a higher value.",
2039 "From the 'DD' load imbalance entries in the md.log output file you",
2040 "can tell after how many steps the load is sufficiently balanced. Example call:[PAR]"
2041 "[TT]gmx tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
2042 "After calling [gmx-mdrun] several times, detailed performance information",
2043 "is available in the output file [TT]perf.out[tt].",
2044 "[BB]Note[bb] that during the benchmarks, a couple of temporary files are written",
2045 "(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
2046 "If you want the simulation to be started automatically with the",
2047 "optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
2052 int pmeentries
= 0; /* How many values for -npme do we actually test for each tpr file */
2053 real maxPMEfraction
= 0.50;
2054 real minPMEfraction
= 0.25;
2055 int maxPMEnodes
, minPMEnodes
;
2056 float guessPMEratio
; /* guessed PME:PP ratio based on the tpr file */
2057 float guessPMEnodes
;
2058 int npme_fixed
= -2; /* If >= -1, use only this number
2059 * of PME-only nodes */
2061 real rmin
= 0.0, rmax
= 0.0; /* min and max value for rcoulomb if scaling is requested */
2062 real rcoulomb
= -1.0; /* Coulomb radius as set in .tpr file */
2063 gmx_bool bScaleRvdw
= TRUE
;
2064 gmx_int64_t bench_nsteps
= BENCHSTEPS
;
2065 gmx_int64_t new_sim_nsteps
= -1; /* -1 indicates: not set by the user */
2066 gmx_int64_t cpt_steps
= 0; /* Step counter in .cpt input file */
2067 int presteps
= 100; /* Do a full cycle reset after presteps steps */
2068 gmx_bool bOverwrite
= FALSE
, bKeepTPR
;
2069 gmx_bool bLaunch
= FALSE
;
2070 char *ExtraArgs
= NULL
;
2071 char **tpr_names
= NULL
;
2072 const char *simulation_tpr
= NULL
;
2073 int best_npme
, best_tpr
;
2074 int sim_part
= 1; /* For benchmarks with checkpoint files */
2077 /* Default program names if nothing else is found */
2078 char *cmd_mpirun
= NULL
, *cmd_mdrun
= NULL
;
2079 char *cmd_args_bench
, *cmd_args_launch
;
2080 char *cmd_np
= NULL
;
2082 t_perf
**perfdata
= NULL
;
2088 /* Print out how long the tuning took */
2091 static t_filenm fnm
[] = {
2093 { efOUT
, "-p", "perf", ffWRITE
},
2094 { efLOG
, "-err", "bencherr", ffWRITE
},
2095 { efTPX
, "-so", "tuned", ffWRITE
},
2097 { efTPX
, NULL
, NULL
, ffREAD
},
2098 { efTRN
, "-o", NULL
, ffWRITE
},
2099 { efCOMPRESSED
, "-x", NULL
, ffOPTWR
},
2100 { efCPT
, "-cpi", NULL
, ffOPTRD
},
2101 { efCPT
, "-cpo", NULL
, ffOPTWR
},
2102 { efSTO
, "-c", "confout", ffWRITE
},
2103 { efEDR
, "-e", "ener", ffWRITE
},
2104 { efLOG
, "-g", "md", ffWRITE
},
2105 { efXVG
, "-dhdl", "dhdl", ffOPTWR
},
2106 { efXVG
, "-field", "field", ffOPTWR
},
2107 { efXVG
, "-table", "table", ffOPTRD
},
2108 { efXVG
, "-tabletf", "tabletf", ffOPTRD
},
2109 { efXVG
, "-tablep", "tablep", ffOPTRD
},
2110 { efXVG
, "-tableb", "table", ffOPTRD
},
2111 { efTRX
, "-rerun", "rerun", ffOPTRD
},
2112 { efXVG
, "-tpi", "tpi", ffOPTWR
},
2113 { efXVG
, "-tpid", "tpidist", ffOPTWR
},
2114 { efEDI
, "-ei", "sam", ffOPTRD
},
2115 { efXVG
, "-eo", "edsam", ffOPTWR
},
2116 { efXVG
, "-devout", "deviatie", ffOPTWR
},
2117 { efXVG
, "-runav", "runaver", ffOPTWR
},
2118 { efXVG
, "-px", "pullx", ffOPTWR
},
2119 { efXVG
, "-pf", "pullf", ffOPTWR
},
2120 { efXVG
, "-ro", "rotation", ffOPTWR
},
2121 { efLOG
, "-ra", "rotangles", ffOPTWR
},
2122 { efLOG
, "-rs", "rotslabs", ffOPTWR
},
2123 { efLOG
, "-rt", "rottorque", ffOPTWR
},
2124 { efMTX
, "-mtx", "nm", ffOPTWR
},
2125 { efNDX
, "-dn", "dipole", ffOPTWR
},
2126 { efXVG
, "-swap", "swapions", ffOPTWR
},
2127 /* Output files that are deleted after each benchmark run */
2128 { efTRN
, "-bo", "bench", ffWRITE
},
2129 { efXTC
, "-bx", "bench", ffWRITE
},
2130 { efCPT
, "-bcpo", "bench", ffWRITE
},
2131 { efSTO
, "-bc", "bench", ffWRITE
},
2132 { efEDR
, "-be", "bench", ffWRITE
},
2133 { efLOG
, "-bg", "bench", ffWRITE
},
2134 { efXVG
, "-beo", "benchedo", ffOPTWR
},
2135 { efXVG
, "-bdhdl", "benchdhdl", ffOPTWR
},
2136 { efXVG
, "-bfield", "benchfld", ffOPTWR
},
2137 { efXVG
, "-btpi", "benchtpi", ffOPTWR
},
2138 { efXVG
, "-btpid", "benchtpid", ffOPTWR
},
2139 { efXVG
, "-bdevout", "benchdev", ffOPTWR
},
2140 { efXVG
, "-brunav", "benchrnav", ffOPTWR
},
2141 { efXVG
, "-bpx", "benchpx", ffOPTWR
},
2142 { efXVG
, "-bpf", "benchpf", ffOPTWR
},
2143 { efXVG
, "-bro", "benchrot", ffOPTWR
},
2144 { efLOG
, "-bra", "benchrota", ffOPTWR
},
2145 { efLOG
, "-brs", "benchrots", ffOPTWR
},
2146 { efLOG
, "-brt", "benchrott", ffOPTWR
},
2147 { efMTX
, "-bmtx", "benchn", ffOPTWR
},
2148 { efNDX
, "-bdn", "bench", ffOPTWR
},
2149 { efXVG
, "-bswap", "benchswp", ffOPTWR
}
2152 gmx_bool bThreads
= FALSE
;
2156 const char *procstring
[] =
2157 { NULL
, "-np", "-n", "none", NULL
};
2158 const char *npmevalues_opt
[] =
2159 { NULL
, "auto", "all", "subset", NULL
};
2161 gmx_bool bAppendFiles
= TRUE
;
2162 gmx_bool bKeepAndNumCPT
= FALSE
;
2163 gmx_bool bResetCountersHalfWay
= FALSE
;
2164 gmx_bool bBenchmark
= TRUE
;
2166 output_env_t oenv
= NULL
;
2169 /***********************/
2170 /* g_tune_pme options: */
2171 /***********************/
2172 { "-np", FALSE
, etINT
, {&nnodes
},
2173 "Number of ranks to run the tests on (must be > 2 for separate PME ranks)" },
2174 { "-npstring", FALSE
, etENUM
, {procstring
},
2175 "Specify the number of ranks to [TT]$MPIRUN[tt] using this string"},
2176 { "-ntmpi", FALSE
, etINT
, {&nthreads
},
2177 "Number of MPI-threads to run the tests on (turns MPI & mpirun off)"},
2178 { "-r", FALSE
, etINT
, {&repeats
},
2179 "Repeat each test this often" },
2180 { "-max", FALSE
, etREAL
, {&maxPMEfraction
},
2181 "Max fraction of PME ranks to test with" },
2182 { "-min", FALSE
, etREAL
, {&minPMEfraction
},
2183 "Min fraction of PME ranks to test with" },
2184 { "-npme", FALSE
, etENUM
, {npmevalues_opt
},
2185 "Within -min and -max, benchmark all possible values for [TT]-npme[tt], or just a reasonable subset. "
2186 "Auto neglects -min and -max and chooses reasonable values around a guess for npme derived from the .tpr"},
2187 { "-fix", FALSE
, etINT
, {&npme_fixed
},
2188 "If >= -1, do not vary the number of PME-only ranks, instead use this fixed value and only vary rcoulomb and the PME grid spacing."},
2189 { "-rmax", FALSE
, etREAL
, {&rmax
},
2190 "If >0, maximal rcoulomb for -ntpr>1 (rcoulomb upscaling results in fourier grid downscaling)" },
2191 { "-rmin", FALSE
, etREAL
, {&rmin
},
2192 "If >0, minimal rcoulomb for -ntpr>1" },
2193 { "-scalevdw", FALSE
, etBOOL
, {&bScaleRvdw
},
2194 "Scale rvdw along with rcoulomb"},
2195 { "-ntpr", FALSE
, etINT
, {&ntprs
},
2196 "Number of [TT].tpr[tt] files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. "
2197 "If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
2198 { "-steps", FALSE
, etINT64
, {&bench_nsteps
},
2199 "Take timings for this many steps in the benchmark runs" },
2200 { "-resetstep", FALSE
, etINT
, {&presteps
},
2201 "Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
2202 { "-simsteps", FALSE
, etINT64
, {&new_sim_nsteps
},
2203 "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
2204 { "-launch", FALSE
, etBOOL
, {&bLaunch
},
2205 "Launch the real simulation after optimization" },
2206 { "-bench", FALSE
, etBOOL
, {&bBenchmark
},
2207 "Run the benchmarks or just create the input [TT].tpr[tt] files?" },
2208 /******************/
2209 /* mdrun options: */
2210 /******************/
2211 /* We let g_tune_pme parse and understand these options, because we need to
2212 * prevent that they appear on the mdrun command line for the benchmarks */
2213 { "-append", FALSE
, etBOOL
, {&bAppendFiles
},
2214 "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only)" },
2215 { "-cpnum", FALSE
, etBOOL
, {&bKeepAndNumCPT
},
2216 "Keep and number checkpoint files (launch only)" },
2217 { "-resethway", FALSE
, etBOOL
, {&bResetCountersHalfWay
},
2218 "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt] (launch only)" }
2221 #define NFILE asize(fnm)
2223 seconds
= gmx_gettime();
2225 if (!parse_common_args(&argc
, argv
, PCA_NOEXIT_ON_ARGS
,
2226 NFILE
, fnm
, asize(pa
), pa
, asize(desc
), desc
,
2232 /* Store the remaining unparsed command line entries in a string which
2233 * is then attached to the mdrun command line */
2235 ExtraArgs
[0] = '\0';
2236 for (i
= 1; i
< argc
; i
++) /* argc will now be 1 if everything was understood */
2238 add_to_string(&ExtraArgs
, argv
[i
]);
2239 add_to_string(&ExtraArgs
, " ");
2242 if (opt2parg_bSet("-ntmpi", asize(pa
), pa
))
2245 if (opt2parg_bSet("-npstring", asize(pa
), pa
))
2247 fprintf(stderr
, "WARNING: -npstring has no effect when using threads.\n");
2252 gmx_fatal(FARGS
, "Can't run multi-threaded MPI simulation yet!");
2254 /* and now we just set this; a bit of an ugly hack*/
2257 /* Check for PME:PP ratio and whether tpr triggers additional output files */
2258 guessPMEratio
= inspect_tpr(NFILE
, fnm
, &rcoulomb
);
2260 /* Automatically set -beo options if -eo is set etc. */
2261 couple_files_options(NFILE
, fnm
);
2263 /* Construct the command line arguments for benchmark runs
2264 * as well as for the simulation run */
2267 sprintf(bbuf
, " -ntmpi %d ", nthreads
);
2271 /* This string will be used for MPI runs and will appear after the
2272 * mpirun command. */
2273 if (strcmp(procstring
[0], "none") != 0)
2275 sprintf(bbuf
, " %s %d ", procstring
[0], nnodes
);
2285 create_command_line_snippets(bAppendFiles
, bKeepAndNumCPT
, bResetCountersHalfWay
, presteps
,
2286 NFILE
, fnm
, &cmd_args_bench
, &cmd_args_launch
, ExtraArgs
);
2288 /* Read in checkpoint file if requested */
2290 if (opt2bSet("-cpi", NFILE
, fnm
))
2293 cr
->duty
= DUTY_PP
; /* makes the following routine happy */
2294 read_checkpoint_simulation_part(opt2fn("-cpi", NFILE
, fnm
),
2295 &sim_part
, &cpt_steps
, cr
,
2296 FALSE
, NFILE
, fnm
, NULL
, NULL
);
2299 /* sim_part will now be 1 if no checkpoint file was found */
2302 gmx_fatal(FARGS
, "Checkpoint file %s not found!", opt2fn("-cpi", NFILE
, fnm
));
2306 /* Open performance output file and write header info */
2307 fp
= gmx_ffopen(opt2fn("-p", NFILE
, fnm
), "w");
2309 /* Make a quick consistency check of command line parameters */
2310 check_input(nnodes
, repeats
, &ntprs
, &rmin
, rcoulomb
, &rmax
,
2311 maxPMEfraction
, minPMEfraction
, npme_fixed
,
2312 bench_nsteps
, fnm
, NFILE
, sim_part
, presteps
,
2315 /* Determine the maximum and minimum number of PME nodes to test,
2316 * the actual list of settings is build in do_the_tests(). */
2317 if ((nnodes
> 2) && (npme_fixed
< -1))
2319 if (0 == strcmp(npmevalues_opt
[0], "auto"))
2321 /* Determine the npme range automatically based on the PME:PP load guess */
2322 if (guessPMEratio
> 1.0)
2324 /* More PME than PP work, probably we do not need separate PME nodes at all! */
2325 maxPMEnodes
= nnodes
/2;
2326 minPMEnodes
= nnodes
/2;
2330 /* PME : PP load is in the range 0..1, let's test around the guess */
2331 guessPMEnodes
= nnodes
/(1.0 + 1.0/guessPMEratio
);
2332 minPMEnodes
= floor(0.7*guessPMEnodes
);
2333 maxPMEnodes
= ceil(1.6*guessPMEnodes
);
2334 maxPMEnodes
= min(maxPMEnodes
, nnodes
/2);
2339 /* Determine the npme range based on user input */
2340 maxPMEnodes
= floor(maxPMEfraction
*nnodes
);
2341 minPMEnodes
= max(floor(minPMEfraction
*nnodes
), 0);
2342 fprintf(stdout
, "Will try runs with %d ", minPMEnodes
);
2343 if (maxPMEnodes
!= minPMEnodes
)
2345 fprintf(stdout
, "- %d ", maxPMEnodes
);
2347 fprintf(stdout
, "PME-only ranks.\n Note that the automatic number of PME-only ranks and no separate PME ranks are always tested.\n");
2356 /* Get the commands we need to set up the runs from environment variables */
2357 get_program_paths(bThreads
, &cmd_mpirun
, &cmd_mdrun
);
2358 if (bBenchmark
&& repeats
> 0)
2360 check_mdrun_works(bThreads
, cmd_mpirun
, cmd_np
, cmd_mdrun
);
2363 /* Print some header info to file */
2365 fprintf(fp
, "\n P E R F O R M A N C E R E S U L T S\n");
2367 fprintf(fp
, "%s for Gromacs %s\n", output_env_get_program_display_name(oenv
),
2371 fprintf(fp
, "Number of ranks : %d\n", nnodes
);
2372 fprintf(fp
, "The mpirun command is : %s\n", cmd_mpirun
);
2373 if (strcmp(procstring
[0], "none") != 0)
2375 fprintf(fp
, "Passing # of ranks via : %s\n", procstring
[0]);
2379 fprintf(fp
, "Not setting number of ranks in system call\n");
2384 fprintf(fp
, "Number of threads : %d\n", nnodes
);
2387 fprintf(fp
, "The mdrun command is : %s\n", cmd_mdrun
);
2388 fprintf(fp
, "mdrun args benchmarks : %s\n", cmd_args_bench
);
2389 fprintf(fp
, "Benchmark steps : ");
2390 fprintf(fp
, "%"GMX_PRId64
, bench_nsteps
);
2392 fprintf(fp
, "dlb equilibration steps : %d\n", presteps
);
2395 fprintf(fp
, "Checkpoint time step : ");
2396 fprintf(fp
, "%"GMX_PRId64
, cpt_steps
);
2399 fprintf(fp
, "mdrun args at launchtime: %s\n", cmd_args_launch
);
2401 if (new_sim_nsteps
>= 0)
2404 fprintf(stderr
, "Note: Simulation input file %s will have ", opt2fn("-so", NFILE
, fnm
));
2405 fprintf(stderr
, "%"GMX_PRId64
, new_sim_nsteps
+cpt_steps
);
2406 fprintf(stderr
, " steps.\n");
2407 fprintf(fp
, "Simulation steps : ");
2408 fprintf(fp
, "%"GMX_PRId64
, new_sim_nsteps
);
2413 fprintf(fp
, "Repeats for each test : %d\n", repeats
);
2416 if (npme_fixed
>= -1)
2418 fprintf(fp
, "Fixing -npme at : %d\n", npme_fixed
);
2421 fprintf(fp
, "Input file : %s\n", opt2fn("-s", NFILE
, fnm
));
2422 fprintf(fp
, " PME/PP load estimate : %g\n", guessPMEratio
);
2424 /* Allocate memory for the inputinfo struct: */
2426 info
->nr_inputfiles
= ntprs
;
2427 for (i
= 0; i
< ntprs
; i
++)
2429 snew(info
->rcoulomb
, ntprs
);
2430 snew(info
->rvdw
, ntprs
);
2431 snew(info
->rlist
, ntprs
);
2432 snew(info
->rlistlong
, ntprs
);
2433 snew(info
->nkx
, ntprs
);
2434 snew(info
->nky
, ntprs
);
2435 snew(info
->nkz
, ntprs
);
2436 snew(info
->fsx
, ntprs
);
2437 snew(info
->fsy
, ntprs
);
2438 snew(info
->fsz
, ntprs
);
2440 /* Make alternative tpr files to test: */
2441 snew(tpr_names
, ntprs
);
2442 for (i
= 0; i
< ntprs
; i
++)
2444 snew(tpr_names
[i
], STRLEN
);
2447 /* It can be that ntprs is reduced by make_benchmark_tprs if not enough
2448 * different grids could be found. */
2449 make_benchmark_tprs(opt2fn("-s", NFILE
, fnm
), tpr_names
, bench_nsteps
+presteps
,
2450 cpt_steps
, rmin
, rmax
, bScaleRvdw
, &ntprs
, info
, fp
);
2452 /********************************************************************************/
2453 /* Main loop over all scenarios we need to test: tpr files, PME nodes, repeats */
2454 /********************************************************************************/
2455 snew(perfdata
, ntprs
);
2458 do_the_tests(fp
, tpr_names
, maxPMEnodes
, minPMEnodes
, npme_fixed
, npmevalues_opt
[0], perfdata
, &pmeentries
,
2459 repeats
, nnodes
, ntprs
, bThreads
, cmd_mpirun
, cmd_np
, cmd_mdrun
,
2460 cmd_args_bench
, fnm
, NFILE
, presteps
, cpt_steps
);
2462 fprintf(fp
, "\nTuning took%8.1f minutes.\n", (gmx_gettime()-seconds
)/60.0);
2464 /* Analyse the results and give a suggestion for optimal settings: */
2465 bKeepTPR
= analyze_data(fp
, opt2fn("-p", NFILE
, fnm
), perfdata
, nnodes
, ntprs
, pmeentries
,
2466 repeats
, info
, &best_tpr
, &best_npme
);
2468 /* Take the best-performing tpr file and enlarge nsteps to original value */
2469 if (bKeepTPR
&& !bOverwrite
)
2471 simulation_tpr
= opt2fn("-s", NFILE
, fnm
);
2475 simulation_tpr
= opt2fn("-so", NFILE
, fnm
);
2476 modify_PMEsettings(bOverwrite
? (new_sim_nsteps
+cpt_steps
) : info
->orig_sim_steps
,
2477 info
->orig_init_step
, tpr_names
[best_tpr
], simulation_tpr
);
2480 /* Let's get rid of the temporary benchmark input files */
2481 for (i
= 0; i
< ntprs
; i
++)
2483 fprintf(stdout
, "Deleting temporary benchmark input file %s\n", tpr_names
[i
]);
2484 remove(tpr_names
[i
]);
2487 /* Now start the real simulation if the user requested it ... */
2488 launch_simulation(bLaunch
, fp
, bThreads
, cmd_mpirun
, cmd_np
, cmd_mdrun
,
2489 cmd_args_launch
, simulation_tpr
, best_npme
);
2493 /* ... or simply print the performance results to screen: */
2496 finalize(opt2fn("-p", NFILE
, fnm
));