* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "config.h"
#include <stdlib.h>
#include <time.h>
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/readinp.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 "gmx_ana.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
-
-#include "gromacs/commandline/pargs.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"
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");
}
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);
}
{
/* To prevent confusion, do not again issue a gmx_fatal here since we already
* get the error message from mdrun itself */
- sprintf(msg, "Cannot run the benchmark simulations! Please check the error message of\n"
+ sprintf(msg,
+ "Cannot run the first benchmark simulation! Please check the error message of\n"
"mdrun for the source of the problem. Did you provide a command line\n"
- "argument that neither g_tune_pme nor mdrun understands? Offending command:\n"
+ "argument that neither gmx tune_pme nor mdrun understands? If you're\n"
+ "sure your command line should work, you can bypass this check with \n"
+ "gmx tune_pme -nocheck. The failing command was:\n"
"\n%s\n\n", command);
fprintf(stderr, "%s", msg);
int npme_fixed, /* If >= -1, test fixed number of PME
* nodes only */
const char *npmevalues_opt, /* Which -npme values should be tested */
- t_perf **perfdata, /* Here the performace data is stored */
+ t_perf **perfdata, /* Here the performance data is stored */
int *pmeentries, /* Entries in the nPMEnodes list */
int repeats, /* Repeat each test this often */
int nnodes, /* Total number of nodes = nPP + nPME */
const t_filenm *fnm, /* List of filenames from command line */
int nfile, /* Number of files specified on the cmdl. */
int presteps, /* DLB equilibration steps, is checked */
- gmx_int64_t cpt_steps) /* Time step counter in the checkpoint */
+ gmx_int64_t cpt_steps, /* Time step counter in the checkpoint */
+ gmx_bool bCheck) /* Check whether benchmark mdrun works */
{
int i, nr, k, ret, count = 0, totaltests;
int *nPMEnodes = NULL;
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 first */
- if (bFirst)
+ * on the mdrun command line, we make a quick check first.
+ * This check can be turned off in cases where the automatically chosen
+ * number of PME-only ranks leads to a number of PP ranks for which no
+ * decomposition can be found (e.g. for large prime numbers) */
+ if (bFirst && bCheck)
{
make_sure_it_runs(pd->mdrun_cmd_line, cmdline_length, fp, fnm, nfile);
}
"need to provide a machine- or hostfile. This can also be passed",
"via the MPIRUN variable, e.g.[PAR]",
"[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
+ "Before doing the actual benchmark runs, [THISMODULE] will do a quick",
+ "check whether mdrun works as expected with the provided parallel settings",
+ "if the [TT]-check[tt] option is activated (the default).",
"Please call [THISMODULE] with the normal options you would pass to",
"[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]",
"written with enlarged cutoffs and smaller Fourier grids respectively.",
"Typically, the first test (number 0) will be with the settings from the input",
"[TT].tpr[tt] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
- "specified by [TT]-rmax[tt] with a somwhat smaller PME grid at the same time. ",
+ "specified by [TT]-rmax[tt] with a somewhat smaller PME grid at the same time. ",
"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",
"MD systems. The dynamic load balancing needs about 100 time steps",
"to adapt to local load imbalances, therefore the time step counters",
"are by default reset after 100 steps. For large systems (>1M atoms), as well as ",
- "for a higher accuarcy of the measurements, you should set [TT]-resetstep[tt] to a higher value.",
+ "for a higher accuracy of the measurements, you should set [TT]-resetstep[tt] to a higher value.",
"From the 'DD' load imbalance entries in the md.log output file you",
"can tell after how many steps the load is sufficiently balanced. Example call:[PAR]"
"[TT]gmx tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
/* 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 },
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
gmx_bool bBenchmark = TRUE;
+ gmx_bool bCheck = TRUE;
output_env_t oenv = NULL;
"Launch the real simulation after optimization" },
{ "-bench", FALSE, etBOOL, {&bBenchmark},
"Run the benchmarks or just create the input [TT].tpr[tt] files?" },
+ { "-check", FALSE, etBOOL, {&bCheck},
+ "Before the benchmark runs, check whether mdrun works in parallel" },
/******************/
/* mdrun options: */
/******************/
{
do_the_tests(fp, tpr_names, maxPMEnodes, minPMEnodes, npme_fixed, npmevalues_opt[0], perfdata, &pmeentries,
repeats, nnodes, ntprs, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
- cmd_args_bench, fnm, NFILE, presteps, cpt_steps);
+ cmd_args_bench, fnm, NFILE, presteps, cpt_steps, bCheck);
fprintf(fp, "\nTuning took%8.1f minutes.\n", (gmx_gettime()-seconds)/60.0);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff