* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "config.h"
+#include <stdlib.h>
#include <time.h>
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-
-
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
#include "gromacs/fileio/tpxio.h"
-#include "string2.h"
-#include "readinp.h"
-#include "calcgrid.h"
-#include "checkpoint.h"
-#include "macros.h"
-#include "gmx_ana.h"
-#include "names.h"
-#include "perf_est.h"
-#include "inputrec.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
#include "gromacs/timing/walltime_accounting.h"
-
+#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* Enum for situations that can occur during log file parsing, the
* corresponding string entries can be found in do_the_tests() in
}
-static gmx_bool is_equal(real a, real b)
+static void remove_if_exists(const char *fn)
{
- real diff, eps = 1.0e-7;
-
-
- diff = a - b;
-
- if (diff < 0.0)
+ if (gmx_fexist(fn))
{
- diff = -diff;
- }
-
- if (diff < eps)
- {
- return TRUE;
- }
- else
- {
- return FALSE;
+ fprintf(stdout, "Deleting %s\n", fn);
+ remove(fn);
}
}
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";
const char errSIG[] = "signal, stopping at the next";
int iFound;
- int procs;
float dum1, dum2, dum3, dum4;
int ndum;
int npme;
/* Look for domain decomp grid and separate PME nodes: */
if (str_starts(line, matchstrdd))
{
- sscanf(line, "Domain decomposition grid %d x %d x %d, separate PME nodes %d",
+ sscanf(line, "Domain decomposition grid %d x %d x %d, separate PME ranks %d",
&(perfdata->nx), &(perfdata->ny), &(perfdata->nz), &npme);
if (perfdata->nPMEnodes == -1)
{
}
else if (perfdata->nPMEnodes != npme)
{
- gmx_fatal(FARGS, "PME nodes from command line and output file are not identical");
+ gmx_fatal(FARGS, "PME ranks from command line and output file are not identical");
}
iFound = eFoundDDStr;
}
fclose(fp);
return eParselogNoDDGrid;
}
- else if (str_starts(line, "The number of nodes you selected"))
+ else if (str_starts(line, "The number of ranks you selected"))
{
fclose(fp);
return eParselogLargePrimeFactor;
/* Already found matchstring - look for cycle data */
if (str_starts(line, "Total "))
{
- sscanf(line, "Total %d %lf", &procs, &(perfdata->Gcycles[test_nr]));
+ sscanf(line, "Total %*f %lf", &(perfdata->Gcycles[test_nr]));
iFound = eFoundCycleStr;
}
break;
{
sep_line(fp);
fprintf(fp, "Summary of successful runs:\n");
- fprintf(fp, "Line tpr PME nodes Gcycles Av. Std.dev. ns/day PME/f");
+ fprintf(fp, "Line tpr PME ranks Gcycles Av. Std.dev. ns/day PME/f");
if (nnodes > 1)
{
fprintf(fp, " DD grid");
/* We have optimized the number of PME-only nodes */
if (winPME == -1)
{
- sprintf(strbuf, "%s", "the automatic number of PME nodes");
+ sprintf(strbuf, "%s", "the automatic number of PME ranks");
}
else
{
- sprintf(strbuf, "%d PME nodes", winPME);
+ sprintf(strbuf, "%d PME ranks", winPME);
}
}
fprintf(fp, "Best performance was achieved with %s", strbuf);
fprintf(fp, "\n");
/* Only mention settings if they were modified: */
- bRefinedCoul = !is_equal(info->rcoulomb[k_win], info->rcoulomb[0]);
- bRefinedVdW = !is_equal(info->rvdw[k_win], info->rvdw[0] );
+ bRefinedCoul = !gmx_within_tol(info->rcoulomb[k_win], info->rcoulomb[0], GMX_REAL_EPS);
+ bRefinedVdW = !gmx_within_tol(info->rvdw[k_win], info->rvdw[0], GMX_REAL_EPS);
bRefinedGrid = !(info->nkx[k_win] == info->nkx[0] &&
info->nky[k_win] == info->nky[0] &&
info->nkz[k_win] == info->nkz[0]);
{
if ( (cp = getenv("MPIRUN")) != NULL)
{
- *cmd_mpirun = strdup(cp);
+ *cmd_mpirun = gmx_strdup(cp);
}
else
{
- *cmd_mpirun = strdup(def_mpirun);
+ *cmd_mpirun = gmx_strdup(def_mpirun);
}
}
else
{
- *cmd_mpirun = strdup(empty_mpirun);
+ *cmd_mpirun = gmx_strdup(empty_mpirun);
}
if ( (cp = getenv("MDRUN" )) != NULL)
{
- *cmd_mdrun = strdup(cp);
+ *cmd_mdrun = gmx_strdup(cp);
}
else
{
- *cmd_mdrun = strdup(def_mdrun);
+ *cmd_mdrun = gmx_strdup(def_mdrun);
}
}
/* This string should always be identical to the one in copyrite.c,
* gmx_print_version_info() in the defined(GMX_MPI) section */
const char match_mpi[] = "MPI library: MPI";
- const char match_mdrun[] = "Program: ";
+ const char match_mdrun[] = "Executable: ";
gmx_bool bMdrun = FALSE;
gmx_bool bMPI = FALSE;
gmx_fatal(FARGS, "Need a threaded version of mdrun. This one\n"
"(%s)\n"
"seems to have been compiled with MPI instead.",
- *cmd_mdrun);
+ cmd_mdrun);
}
}
else
gmx_fatal(FARGS, "Need an MPI-enabled version of mdrun. This one\n"
"(%s)\n"
"seems to have been compiled without MPI support.",
- *cmd_mdrun);
+ cmd_mdrun);
}
}
sfree(ir);
}
+static gmx_bool can_scale_rvdw(int vdwtype)
+{
+ return (evdwCUT == vdwtype ||
+ evdwPME == vdwtype);
+}
#define EPME_SWITCHED(e) ((e) == eelPMESWITCH || (e) == eelPMEUSERSWITCH)
fprintf(fp, " No. scaling rcoulomb");
fprintf(fp, " nkx nky nkz");
fprintf(fp, " spacing");
- if (evdwCUT == ir->vdwtype)
+ if (can_scale_rvdw(ir->vdwtype))
{
fprintf(fp, " rvdw");
}
{
/* Determine which Coulomb radii rc to use in the benchmarks */
add = (rmax-rmin)/(*ntprs-1);
- if (is_equal(rmin, info->rcoulomb[0]))
+ if (gmx_within_tol(rmin, info->rcoulomb[0], GMX_REAL_EPS))
{
ir->rcoulomb = rmin + j*add;
}
- else if (is_equal(rmax, info->rcoulomb[0]))
+ else if (gmx_within_tol(rmax, info->rcoulomb[0], GMX_REAL_EPS))
{
ir->rcoulomb = rmin + (j-1)*add;
}
ir->rlist = ir->rcoulomb + nlist_buffer;
}
- if (bScaleRvdw && evdwCUT == ir->vdwtype)
+ if (bScaleRvdw && can_scale_rvdw(ir->vdwtype))
{
- if (ecutsVERLET == ir->cutoff_scheme)
+ if (ecutsVERLET == ir->cutoff_scheme ||
+ evdwPME == ir->vdwtype)
{
- /* With Verlet, the van der Waals radius must always equal the Coulomb radius */
+ /* With either the Verlet cutoff-scheme or LJ-PME,
+ the van der Waals radius must always equal the
+ Coulomb radius */
ir->rvdw = ir->rcoulomb;
}
else
fprintf(fp, "%4d%10f%10f", j, fac, ir->rcoulomb);
fprintf(fp, "%5d%5d%5d", ir->nkx, ir->nky, ir->nkz);
fprintf(fp, " %9f ", info->fsx[j]);
- if (evdwCUT == ir->vdwtype)
+ if (can_scale_rvdw(ir->vdwtype))
{
fprintf(fp, "%10f", ir->rvdw);
}
fprintf(fp, " %-14s\n", fn_bench_tprs[j]);
/* Make it clear to the user that some additional settings were modified */
- if (!is_equal(ir->rvdw, info->rvdw[0])
- || !is_equal(ir->rlistlong, info->rlistlong[0]) )
+ if (!gmx_within_tol(ir->rvdw, info->rvdw[0], GMX_REAL_EPS)
+ || !gmx_within_tol(ir->rlistlong, info->rlistlong[0], GMX_REAL_EPS) )
{
bNote = TRUE;
}
/* Delete the files which are created for each benchmark run: (options -b*) */
else if ( (0 == strncmp(opt, "-b", 2)) && (opt2bSet(opt, nfile, fnm) || !is_optional(&fnm[i])) )
{
- fn = opt2fn(opt, nfile, fnm);
- if (gmx_fexist(fn))
- {
- fprintf(stdout, "Deleting %s\n", fn);
- remove(fn);
- }
+ remove_if_exists(opt2fn(opt, nfile, fnm));
}
}
}
-/* Returns the largest common factor of n1 and n2 */
-static int largest_common_factor(int n1, int n2)
-{
- int factor, nmax;
-
- nmax = min(n1, n2);
- for (factor = nmax; factor > 0; factor--)
- {
- if (0 == (n1 % factor) && 0 == (n2 % factor) )
- {
- return(factor);
- }
- }
- return 0; /* one for the compiler */
-}
-
enum {
eNpmeAuto, eNpmeAll, eNpmeReduced, eNpmeSubset, eNpmeNr
};
gmx_fatal(FARGS, "Unknown option for eNPME in make_npme_list");
break;
}
- if (largest_common_factor(npp, npme) >= min_factor)
+ if (gmx_greatest_common_divisor(npp, npme) >= min_factor)
{
(*nPMEnodes)[nlist] = npme;
nlist++;
/* Check for errors on mdrun -h */
-static void make_sure_it_runs(char *mdrun_cmd_line, int length, FILE *fp)
+static void make_sure_it_runs(char *mdrun_cmd_line, int length, FILE *fp,
+ const t_filenm *fnm, int nfile)
{
- char *command, *msg;
- int ret;
+ const char *fn = NULL;
+ char *command, *msg;
+ int ret;
snew(command, length + 15);
snew(msg, length + 500);
- fprintf(stdout, "Making sure the benchmarks can be executed ...\n");
- /* FIXME: mdrun -h no longer actually does anything useful.
- * It unconditionally prints the help, ignoring all other options. */
- sprintf(command, "%s-h -quiet", mdrun_cmd_line);
+ fprintf(stdout, "Making sure the benchmarks can be executed by running just 1 step...\n");
+ sprintf(command, "%s -nsteps 1 -quiet", mdrun_cmd_line);
+ fprintf(stdout, "Executing '%s' ...\n", command);
ret = gmx_system_call(command);
if (0 != ret)
exit(ret);
}
+ fprintf(stdout, "Benchmarks can be executed!\n");
+
+ /* Clean up the benchmark output files we just created */
+ fprintf(stdout, "Cleaning up ...\n");
+ remove_if_exists(opt2fn("-bc", nfile, fnm));
+ remove_if_exists(opt2fn("-be", nfile, fnm));
+ remove_if_exists(opt2fn("-bcpo", nfile, fnm));
+ remove_if_exists(opt2fn("-bg", nfile, fnm));
sfree(command);
sfree(msg );
"No DD grid found for these settings.",
"TPX version conflict!",
"mdrun was not started in parallel!",
- "Number of PP nodes has a prime factor that is too large.",
+ "Number of PP ranks has a prime factor that is too large.",
"An error occured."
};
char str_PME_f_load[13];
*pmeentries = 1;
snew(nPMEnodes, 1);
nPMEnodes[0] = npme_fixed;
- fprintf(stderr, "Will use a fixed number of %d PME-only nodes.\n", nPMEnodes[0]);
+ fprintf(stderr, "Will use a fixed number of %d PME-only ranks.\n", nPMEnodes[0]);
}
if (0 == repeats)
for (k = 0; k < nr_tprs; k++)
{
fprintf(fp, "\nIndividual timings for input file %d (%s):\n", k, tpr_names[k]);
- fprintf(fp, "PME nodes Gcycles ns/day PME/f Remark\n");
+ fprintf(fp, "PME ranks Gcycles ns/day PME/f Remark\n");
/* Loop over various numbers of PME nodes: */
for (i = 0; i < *pmeentries; i++)
{
cmd_stub, pd->nPMEnodes, tpr_names[k], cmd_args_bench);
/* To prevent that all benchmarks fail due to a show-stopper argument
- * on the mdrun command line, we make a quick check with mdrun -h first */
+ * on the mdrun command line, we make a quick check first */
if (bFirst)
{
- make_sure_it_runs(pd->mdrun_cmd_line, cmdline_length, fp);
+ make_sure_it_runs(pd->mdrun_cmd_line, cmdline_length, fp, fnm, nfile);
}
bFirst = FALSE;
/* Check number of nodes */
if (nnodes < 1)
{
- gmx_fatal(FARGS, "Number of nodes/threads must be a positive integer.");
+ gmx_fatal(FARGS, "Number of ranks/threads must be a positive integer.");
}
/* Automatically choose -ntpr if not set */
/* Add test scenarios if rmin or rmax were set */
if (*ntprs <= 2)
{
- if (!is_equal(*rmin, rcoulomb) && (*ntprs == 1) )
+ if (!gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) && (*ntprs == 1) )
{
(*ntprs)++;
fprintf(stderr, "NOTE: Setting -rmin to %g changed -ntpr to %d\n",
*rmin, *ntprs);
}
- if (!is_equal(*rmax, rcoulomb) && (*ntprs == 1) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) && (*ntprs == 1) )
{
(*ntprs)++;
fprintf(stderr, "NOTE: Setting -rmax to %g changed -ntpr to %d\n",
}
old = *ntprs;
/* If one of rmin, rmax is set, we need 2 tpr files at minimum */
- if (!is_equal(*rmax, rcoulomb) || !is_equal(*rmin, rcoulomb) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) || !gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) )
{
*ntprs = max(*ntprs, 2);
}
/* If both rmin, rmax are set, we need 3 tpr files at minimum */
- if (!is_equal(*rmax, rcoulomb) && !is_equal(*rmin, rcoulomb) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) && !gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) )
{
*ntprs = max(*ntprs, 3);
}
if (*ntprs > 1)
{
- if (is_equal(*rmin, rcoulomb) && is_equal(rcoulomb, *rmax)) /* We have just a single rc */
+ if (gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) && gmx_within_tol(rcoulomb, *rmax, GMX_REAL_EPS)) /* We have just a single rc */
{
fprintf(stderr, "WARNING: Resetting -ntpr to 1 since no Coulomb radius scaling is requested.\n"
"Please set rmin < rmax to test Coulomb radii in the [rmin, rmax] interval\n"
/* No more than 50% of all nodes can be assigned as PME-only nodes. */
if (2*npme_fixed > nnodes)
{
- gmx_fatal(FARGS, "Cannot have more than %d PME-only nodes for a total of %d nodes (you chose %d).\n",
+ gmx_fatal(FARGS, "Cannot have more than %d PME-only ranks for a total of %d ranks (you chose %d).\n",
nnodes/2, nnodes, npme_fixed);
}
if ((npme_fixed > 0) && (5*npme_fixed < nnodes))
{
- fprintf(stderr, "WARNING: Only %g percent of the nodes are assigned as PME-only nodes.\n",
+ fprintf(stderr, "WARNING: Only %g percent of the ranks are assigned as PME-only ranks.\n",
100.0*((real)npme_fixed / (real)nnodes));
}
if (opt2parg_bSet("-min", npargs, pa) || opt2parg_bSet("-max", npargs, pa))
{
fprintf(stderr, "NOTE: The -min, -max, and -npme options have no effect when a\n"
- " fixed number of PME-only nodes is requested with -fix.\n");
+ " fixed number of PME-only ranks is requested with -fix.\n");
}
}
}
int gmx_tune_pme(int argc, char *argv[])
{
const char *desc[] = {
- "For a given number [TT]-np[tt] or [TT]-ntmpi[tt] of processors/threads, [THISMODULE] systematically",
- "times [gmx-mdrun] with various numbers of PME-only nodes and determines",
+ "For a given number [TT]-np[tt] or [TT]-ntmpi[tt] of ranks, [THISMODULE] systematically",
+ "times [gmx-mdrun] with various numbers of PME-only ranks and determines",
"which setting is fastest. It will also test whether performance can",
"be enhanced by shifting load from the reciprocal to the real space",
"part of the Ewald sum. ",
"via the MPIRUN variable, e.g.[PAR]",
"[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
"Please call [THISMODULE] with the normal options you would pass to",
- "[gmx-mdrun] and add [TT]-np[tt] for the number of processors to perform the",
+ "[gmx-mdrun] and add [TT]-np[tt] for the number of ranks to perform the",
"tests on, or [TT]-ntmpi[tt] for the number of threads. You can also add [TT]-r[tt]",
"to repeat each test several times to get better statistics. [PAR]",
"[THISMODULE] can test various real space / reciprocal space workloads",
"In this last test, the Fourier spacing is multiplied with [TT]rmax[tt]/rcoulomb. ",
"The remaining [TT].tpr[tt] files will have equally-spaced Coulomb radii (and Fourier "
"spacings) between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
- "if you just seek the optimal number of PME-only nodes; in that case",
+ "if you just seek the optimal number of PME-only ranks; in that case",
"your input [TT].tpr[tt] file will remain unchanged.[PAR]",
"For the benchmark runs, the default of 1000 time steps should suffice for most",
"MD systems. The dynamic load balancing needs about 100 time steps",
/* g_tune_pme */
{ efOUT, "-p", "perf", ffWRITE },
{ efLOG, "-err", "bencherr", ffWRITE },
- { efTPX, "-so", "tuned", ffWRITE },
+ { efTPR, "-so", "tuned", ffWRITE },
/* mdrun: */
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
/* g_tune_pme options: */
/***********************/
{ "-np", FALSE, etINT, {&nnodes},
- "Number of nodes to run the tests on (must be > 2 for separate PME nodes)" },
+ "Number of ranks to run the tests on (must be > 2 for separate PME ranks)" },
{ "-npstring", FALSE, etENUM, {procstring},
- "Specify the number of processors to [TT]$MPIRUN[tt] using this string"},
+ "Specify the number of ranks to [TT]$MPIRUN[tt] using this string"},
{ "-ntmpi", FALSE, etINT, {&nthreads},
"Number of MPI-threads to run the tests on (turns MPI & mpirun off)"},
{ "-r", FALSE, etINT, {&repeats},
"Repeat each test this often" },
{ "-max", FALSE, etREAL, {&maxPMEfraction},
- "Max fraction of PME nodes to test with" },
+ "Max fraction of PME ranks to test with" },
{ "-min", FALSE, etREAL, {&minPMEfraction},
- "Min fraction of PME nodes to test with" },
+ "Min fraction of PME ranks to test with" },
{ "-npme", FALSE, etENUM, {npmevalues_opt},
"Within -min and -max, benchmark all possible values for [TT]-npme[tt], or just a reasonable subset. "
"Auto neglects -min and -max and chooses reasonable values around a guess for npme derived from the .tpr"},
{ "-fix", FALSE, etINT, {&npme_fixed},
- "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."},
+ "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."},
{ "-rmax", FALSE, etREAL, {&rmax},
"If >0, maximal rcoulomb for -ntpr>1 (rcoulomb upscaling results in fourier grid downscaling)" },
{ "-rmin", FALSE, etREAL, {&rmin},
{
fprintf(stdout, "- %d ", maxPMEnodes);
}
- fprintf(stdout, "PME-only nodes.\n Note that the automatic number of PME-only nodes and no separate PME nodes are always tested.\n");
+ fprintf(stdout, "PME-only ranks.\n Note that the automatic number of PME-only ranks and no separate PME ranks are always tested.\n");
}
}
else
sep_line(fp);
fprintf(fp, "\n P E R F O R M A N C E R E S U L T S\n");
sep_line(fp);
- fprintf(fp, "%s for Gromacs %s\n", ShortProgram(), GromacsVersion());
+ fprintf(fp, "%s for Gromacs %s\n", output_env_get_program_display_name(oenv),
+ gmx_version());
if (!bThreads)
{
- fprintf(fp, "Number of nodes : %d\n", nnodes);
+ fprintf(fp, "Number of ranks : %d\n", nnodes);
fprintf(fp, "The mpirun command is : %s\n", cmd_mpirun);
if (strcmp(procstring[0], "none") != 0)
{
- fprintf(fp, "Passing # of nodes via : %s\n", procstring[0]);
+ fprintf(fp, "Passing # of ranks via : %s\n", procstring[0]);
}
else
{
- fprintf(fp, "Not setting number of nodes in system call\n");
+ fprintf(fp, "Not setting number of ranks in system call\n");
}
}
else
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff