added Verlet scheme and NxN non-bonded functionality

[gromacs.git] / src / tools / gmx_tune_pme.c

/*
 * 
 *                This source code is part of
 *
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2008, The GROMACS development team,
 * check out http://www.gromacs.org for more information.
 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * For more info, check our website at http://www.gromacs.org
 * 
 * And Hey:
 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif


#include <time.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif



#include "statutil.h"
#include "typedefs.h"
#include "smalloc.h"
#include "vec.h"
#include "copyrite.h"
#include "statutil.h"
#include "tpxio.h"
#include "string2.h"
#include "readinp.h"
#include "calcgrid.h"
#include "checkpoint.h"
#include "gmx_ana.h"
#include "names.h"
#include "perf_est.h"



/* Enum for situations that can occur during log file parsing, the
 * corresponding string entries can be found in do_the_tests() in
 * const char* ParseLog[] */
enum {
    eParselogOK,
    eParselogNotFound,
    eParselogNoPerfData,
    eParselogTerm,
    eParselogResetProblem,
    eParselogNoDDGrid,
    eParselogTPXVersion,
    eParselogNotParallel,
    eParselogFatal,
    eParselogNr
};


typedef struct
{
    int  nPMEnodes;       /* number of PME-only nodes used in this test */
    int  nx, ny, nz;      /* DD grid */
    int  guessPME;        /* if nPMEnodes == -1, this is the guessed number of PME nodes */
    double *Gcycles;      /* This can contain more than one value if doing multiple tests */
    double Gcycles_Av;
    float *ns_per_day;
    float ns_per_day_Av;
    float *PME_f_load;    /* PME mesh/force load average*/
    float PME_f_load_Av;  /* Average average ;) ... */
    char *mdrun_cmd_line; /* Mdrun command line used for this test */
} t_perf;


typedef struct
{
    int  nr_inputfiles;         /* The number of tpr and mdp input files */
    gmx_large_int_t orig_sim_steps;  /* Number of steps to be done in the real simulation */
    real *rcoulomb;             /* The coulomb radii [0...nr_inputfiles] */
    real *rvdw;                 /* The vdW radii */
    real *rlist;                /* Neighbourlist cutoff radius */
    real *rlistlong;
    int  *nkx, *nky, *nkz;
    real *fsx, *fsy, *fsz;      /* Fourierspacing in x,y,z dimension */
} t_inputinfo;


static void sep_line(FILE *fp)
{
    fprintf(fp, "\n------------------------------------------------------------\n");
}


/* Wrapper for system calls */
static int gmx_system_call(char *command)
{
#ifdef GMX_NO_SYSTEM
    gmx_fatal(FARGS,"No calls to system(3) supported on this platform. Attempted to call:\n'%s'\n",command);
#else
    return ( system(command) );
#endif
}


/* Check if string starts with substring */
static gmx_bool str_starts(const char *string, const char *substring)
{
    return ( strncmp(string, substring, strlen(substring)) == 0);
}


static void cleandata(t_perf *perfdata, int test_nr)
{
    perfdata->Gcycles[test_nr]    = 0.0;
    perfdata->ns_per_day[test_nr] = 0.0;
    perfdata->PME_f_load[test_nr] = 0.0;

    return;
}


static gmx_bool is_equal(real a, real b)
{
    real diff, eps=1.0e-7;


    diff = a - b;

    if (diff < 0.0) diff = -diff;

    if (diff < eps)
        return TRUE;
    else
        return FALSE;
}


static void finalize(const char *fn_out)
{
    char buf[STRLEN];
    FILE *fp;


    fp = fopen(fn_out,"r");
    fprintf(stdout,"\n\n");

    while( fgets(buf,STRLEN-1,fp) != NULL )
    {
        fprintf(stdout,"%s",buf);
    }
    fclose(fp);
    fprintf(stdout,"\n\n");
}


enum {eFoundNothing, eFoundDDStr, eFoundAccountingStr, eFoundCycleStr};

static int parse_logfile(const char *logfile, const char *errfile,
        t_perf *perfdata, int test_nr, int presteps, gmx_large_int_t cpt_steps,
        int nnodes)
{
    FILE  *fp;
    char  line[STRLEN], dumstring[STRLEN], dumstring2[STRLEN];
    const char matchstrdd[]="Domain decomposition grid";
    const char matchstrcr[]="resetting all time and cycle counters";
    const char matchstrbal[]="Average PME mesh/force load:";
    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;
    int   npme;
    gmx_large_int_t resetsteps=-1;
    gmx_bool  bFoundResetStr = FALSE;
    gmx_bool  bResetChecked  = FALSE;


    if (!gmx_fexist(logfile))
    {
        fprintf(stderr, "WARNING: Could not find logfile %s.\n", logfile);
        cleandata(perfdata, test_nr);
        return eParselogNotFound;
    }

    fp = fopen(logfile, "r");
    perfdata->PME_f_load[test_nr] = -1.0;
    perfdata->guessPME            = -1;

    iFound = eFoundNothing;
    if (1 == nnodes)
        iFound = eFoundDDStr; /* Skip some case statements */

    while (fgets(line, STRLEN, fp) != NULL)
    {
        /* Remove leading spaces */
        ltrim(line);

        /* Check for TERM and INT signals from user: */
        if ( strstr(line, errSIG) != NULL )
        {
            fclose(fp);
            cleandata(perfdata, test_nr);
            return eParselogTerm;
        }

        /* Check whether cycle resetting  worked */
        if (presteps > 0 && !bFoundResetStr)
        {
            if (strstr(line, matchstrcr) != NULL)
            {
                sprintf(dumstring, "Step %s", gmx_large_int_pfmt);
                sscanf(line, dumstring, &resetsteps);
                bFoundResetStr = TRUE;
                if (resetsteps == presteps+cpt_steps)
                {
                    bResetChecked = TRUE;
                }
                else
                {
                    sprintf(dumstring , gmx_large_int_pfmt, resetsteps);
                    sprintf(dumstring2, gmx_large_int_pfmt, presteps+cpt_steps);
                    fprintf(stderr, "WARNING: Time step counters were reset at step %s,\n"
                                    "         though they were supposed to be reset at step %s!\n",
                            dumstring, dumstring2);
                }
            }
        }

        /* Look for strings that appear in a certain order in the log file: */
        switch(iFound)
        {
            case eFoundNothing:
                /* 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",
                            &(perfdata->nx), &(perfdata->ny), &(perfdata->nz), &npme);
                    if (perfdata->nPMEnodes == -1)
                        perfdata->guessPME = npme;
                    else if (perfdata->nPMEnodes != npme)
                        gmx_fatal(FARGS, "PME nodes from command line and output file are not identical");
                    iFound = eFoundDDStr;
                }
                /* Catch a few errors that might have occured: */
                else if (str_starts(line, "There is no domain decomposition for"))
                {
                    fclose(fp);
                    return eParselogNoDDGrid;
                }
                else if (str_starts(line, "reading tpx file"))
                {
                    fclose(fp);
                    return eParselogTPXVersion;
                }
                else if (str_starts(line, "The -dd or -npme option request a parallel simulation"))
                {
                    fclose(fp);
                    return eParselogNotParallel;
                }
                break;
            case eFoundDDStr:
                /* Look for PME mesh/force balance (not necessarily present, though) */
                if (str_starts(line, matchstrbal))
                    sscanf(&line[strlen(matchstrbal)], "%f", &(perfdata->PME_f_load[test_nr]));
                /* Look for matchstring */
                if (str_starts(line, matchstring))
                    iFound = eFoundAccountingStr;
                break;
            case eFoundAccountingStr:
                /* Already found matchstring - look for cycle data */
                if (str_starts(line, "Total  "))
                {
                    sscanf(line,"Total %d %lf",&procs,&(perfdata->Gcycles[test_nr]));
                    iFound = eFoundCycleStr;
                }
                break;
            case eFoundCycleStr:
                /* Already found cycle data - look for remaining performance info and return */
                if (str_starts(line, "Performance:"))
                {
                    sscanf(line,"%s %f %f %f %f", dumstring, &dum1, &dum2, &(perfdata->ns_per_day[test_nr]), &dum3);
                    fclose(fp);
                    if (bResetChecked || presteps == 0)
                        return eParselogOK;
                    else
                        return eParselogResetProblem;
                }
                break;
        }
    } /* while */

    /* Close the log file */
    fclose(fp);

    /* Check why there is no performance data in the log file.
     * Did a fatal errors occur? */
    if (gmx_fexist(errfile))
    {
        fp = fopen(errfile, "r");
        while (fgets(line, STRLEN, fp) != NULL)
        {
            if ( str_starts(line, "Fatal error:") )
            {
                if (fgets(line, STRLEN, fp) != NULL)
                    fprintf(stderr, "\nWARNING: An error occured during this benchmark:\n"
                                    "%s\n", line);
                fclose(fp);
                cleandata(perfdata, test_nr);
                return eParselogFatal;
            }
        }
        fclose(fp);
    }
    else
    {
        fprintf(stderr, "WARNING: Could not find stderr file %s.\n", errfile);
    }

    /* Giving up ... we could not find out why there is no performance data in
     * the log file. */
    fprintf(stdout, "No performance data in log file.\n");
    cleandata(perfdata, test_nr);

    return eParselogNoPerfData;
}


static gmx_bool analyze_data(
        FILE        *fp,
        const char  *fn,
        t_perf      **perfdata,
        int         nnodes,
        int         ntprs,
        int         ntests,
        int         nrepeats,
        t_inputinfo *info,
        int         *index_tpr,    /* OUT: Nr of mdp file with best settings */
        int         *npme_optimal) /* OUT: Optimal number of PME nodes */
{
    int  i,j,k;
    int line=0, line_win=-1;
    int  k_win=-1, i_win=-1, winPME;
    double s=0.0;  /* standard deviation */
    t_perf *pd;
    char strbuf[STRLEN];
    char str_PME_f_load[13];
    gmx_bool bCanUseOrigTPR;
    gmx_bool bRefinedCoul, bRefinedVdW, bRefinedGrid;


    if (nrepeats > 1)
    {
        sep_line(fp);
        fprintf(fp, "Summary of successful runs:\n");
        fprintf(fp, "Line tpr PME nodes  Gcycles Av.     Std.dev.       ns/day        PME/f");
        if (nnodes > 1)
            fprintf(fp, "    DD grid");
        fprintf(fp, "\n");
    }


    for (k=0; k<ntprs; k++)
    {
        for (i=0; i<ntests; i++)
        {
            /* Select the right dataset: */
            pd = &(perfdata[k][i]);

            pd->Gcycles_Av    = 0.0;
            pd->PME_f_load_Av = 0.0;
            pd->ns_per_day_Av = 0.0;

            if (pd->nPMEnodes == -1)
                sprintf(strbuf, "(%3d)", pd->guessPME);
            else
                sprintf(strbuf, "     ");

            /* Get the average run time of a setting */
            for (j=0; j<nrepeats; j++)
            {
                pd->Gcycles_Av    += pd->Gcycles[j];
                pd->PME_f_load_Av += pd->PME_f_load[j];
            }
            pd->Gcycles_Av    /= nrepeats;
            pd->PME_f_load_Av /= nrepeats;

            for (j=0; j<nrepeats; j++)
            {
                if (pd->ns_per_day[j] > 0.0)
                    pd->ns_per_day_Av += pd->ns_per_day[j];
                else
                {
                    /* Somehow the performance number was not aquired for this run,
                     * therefor set the average to some negative value: */
                    pd->ns_per_day_Av = -1.0f*nrepeats;
                    break;
                }
            }
            pd->ns_per_day_Av /= nrepeats;

            /* Nicer output: */
            if (pd->PME_f_load_Av > 0.0)
                sprintf(str_PME_f_load, "%12.3f", pd->PME_f_load_Av);
            else
                sprintf(str_PME_f_load, "%s", "         -  ");


            /* We assume we had a successful run if both averages are positive */
            if (pd->Gcycles_Av > 0.0 && pd->ns_per_day_Av > 0.0)
            {
                /* Output statistics if repeats were done */
                if (nrepeats > 1)
                {
                    /* Calculate the standard deviation */
                    s = 0.0;
                    for (j=0; j<nrepeats; j++)
                        s += pow( pd->Gcycles[j] - pd->Gcycles_Av, 2 );
                    s /= (nrepeats - 1);
                    s = sqrt(s);

                    fprintf(fp, "%4d %3d %4d%s %12.3f %12.3f %12.3f %s",
                            line, k, pd->nPMEnodes, strbuf, pd->Gcycles_Av, s,
                            pd->ns_per_day_Av, str_PME_f_load);
                    if (nnodes > 1)
                        fprintf(fp, "  %3d %3d %3d", pd->nx, pd->ny, pd->nz);
                    fprintf(fp, "\n");
                }
                /* Store the index of the best run found so far in 'winner': */
                if ( (k_win == -1) || (pd->Gcycles_Av < perfdata[k_win][i_win].Gcycles_Av) )
                {
                    k_win = k;
                    i_win = i;
                    line_win = line;
                }
                line++;
            }
        }
    }

    if (k_win == -1)
        gmx_fatal(FARGS, "None of the runs was successful! Check %s for problems.", fn);

    sep_line(fp);

    winPME = perfdata[k_win][i_win].nPMEnodes;

    if (1 == ntests)
    {
        /* We stuck to a fixed number of PME-only nodes */
        sprintf(strbuf, "settings No. %d", k_win);
    }
    else
    {
        /* We have optimized the number of PME-only nodes */
        if (winPME == -1)
            sprintf(strbuf, "%s", "the automatic number of PME nodes");
        else
            sprintf(strbuf, "%d PME nodes", winPME);
    }
    fprintf(fp, "Best performance was achieved with %s", strbuf);
    if ((nrepeats > 1) && (ntests > 1))
        fprintf(fp, " (see line %d)", line_win);
    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]    );
    bRefinedGrid = !(info->nkx[k_win] == info->nkx[0] &&
                     info->nky[k_win] == info->nky[0] &&
                     info->nkz[k_win] == info->nkz[0]);

    if (bRefinedCoul || bRefinedVdW || bRefinedGrid)
    {
        fprintf(fp, "Optimized PME settings:\n");
        bCanUseOrigTPR = FALSE;
    }
    else
    {
        bCanUseOrigTPR = TRUE;
    }

    if (bRefinedCoul)
        fprintf(fp, "   New Coulomb radius: %f nm (was %f nm)\n", info->rcoulomb[k_win], info->rcoulomb[0]);

    if (bRefinedVdW)
        fprintf(fp, "   New Van der Waals radius: %f nm (was %f nm)\n", info->rvdw[k_win], info->rvdw[0]);

    if (bRefinedGrid)
        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],
                                                                          info->nkx[0], info->nky[0], info->nkz[0]);

    if (bCanUseOrigTPR && ntprs > 1)
        fprintf(fp, "and original PME settings.\n");

    fflush(fp);

    /* Return the index of the mdp file that showed the highest performance
     * and the optimal number of PME nodes */
    *index_tpr    = k_win;
    *npme_optimal = winPME;

    return bCanUseOrigTPR;
}


/* Get the commands we need to set up the runs from environment variables */
static void get_program_paths(gmx_bool bThreads, char *cmd_mpirun[], char cmd_np[],
                              char *cmd_mdrun[], int repeats)
{
    char *command=NULL;
    char *cp;
    char *cp2;
    char line[STRLEN];
    FILE *fp;
    const char def_mpirun[] = "mpirun";
    const char def_mdrun[]  = "mdrun";
    const char filename[]   = "benchtest.log";
    const char match_mpi[]  = "NNODES=";
    const char match_mdrun[]= "Program: ";
    const char empty_mpirun[] = "";
    gmx_bool  bMdrun = FALSE;
    gmx_bool  bMPI   = FALSE;


    /* Get the commands we need to set up the runs from environment variables */
    if (!bThreads)
    {
        if ( (cp = getenv("MPIRUN")) != NULL)
            *cmd_mpirun = strdup(cp);
        else
            *cmd_mpirun = strdup(def_mpirun);
    }
    else
    {
        *cmd_mpirun = strdup(empty_mpirun);
    }

    if ( (cp = getenv("MDRUN" )) != NULL )
        *cmd_mdrun  = strdup(cp);
    else
        *cmd_mdrun  = strdup(def_mdrun);


    /* If no simulations have to be performed, we are done here */
    if (repeats <= 0)
        return;

    /* Run a small test to see whether mpirun + mdrun work  */
    fprintf(stdout, "Making sure that mdrun can be executed. ");
    if (bThreads)
    {
        snew(command, strlen(*cmd_mdrun) + strlen(cmd_np) + strlen(filename) + 50);
        sprintf(command, "%s%s-version -maxh 0.001 1> %s 2>&1", *cmd_mdrun, cmd_np, filename);
    }   
    else
    {
        snew(command, strlen(*cmd_mpirun) + strlen(cmd_np) + strlen(*cmd_mdrun) + strlen(filename) + 50);
        sprintf(command, "%s%s%s -version -maxh 0.001 1> %s 2>&1", *cmd_mpirun, cmd_np, *cmd_mdrun, filename);
    }
    fprintf(stdout, "Trying '%s' ... ", command);
    make_backup(filename);
    gmx_system_call(command);

    /* Check if we find the characteristic string in the output: */
    if (!gmx_fexist(filename))
        gmx_fatal(FARGS, "Output from test run could not be found.");

    fp = fopen(filename, "r");
    /* We need to scan the whole output file, since sometimes the queuing system
     * also writes stuff to stdout/err */
    while ( !feof(fp) )
    {
        cp2=fgets(line, STRLEN, fp);
        if (cp2!=NULL)
        {
            if ( str_starts(line, match_mdrun) )
                bMdrun = TRUE;
            if ( str_starts(line, match_mpi) )
                bMPI = TRUE;
        }
    }
    fclose(fp);

    if (bThreads)
    {
        if (bMPI)
        {
            gmx_fatal(FARGS, "Need a threaded version of mdrun. This one\n"
                    "(%s)\n"
                    "seems to have been compiled with MPI instead.",
                    *cmd_mdrun);
        }
    }
    else
    {
        if (bMdrun && !bMPI)
        {
            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);
        }
    }

    if (!bMdrun)
    {
        gmx_fatal(FARGS, "Cannot execute mdrun. Please check %s for problems!",
                filename);
    }

    fprintf(stdout, "passed.\n");

    /* Clean up ... */
    remove(filename);
    sfree(command);
}


static void launch_simulation(
        gmx_bool bLaunch,       /* Should the simulation be launched? */
        FILE *fp,               /* General log file */
        gmx_bool bThreads,      /* whether to use threads */
        char *cmd_mpirun,       /* Command for mpirun */
        char *cmd_np,           /* Switch for -np or -nt or empty */
        char *cmd_mdrun,        /* Command for mdrun */
        char *args_for_mdrun,   /* Arguments for mdrun */
        const char *simulation_tpr,   /* This tpr will be simulated */
        int  nnodes,            /* Number of nodes to run on */
        int  nPMEnodes)         /* Number of PME nodes to use */
{
    char  *command;


    /* Make enough space for the system call command,
     * (100 extra chars for -npme ... etc. options should suffice): */
    snew(command, strlen(cmd_mpirun)+strlen(cmd_mdrun)+strlen(cmd_np)+strlen(args_for_mdrun)+strlen(simulation_tpr)+100);

    /* Note that the -passall options requires args_for_mdrun to be at the end
     * of the command line string */
    if (bThreads)
    {
        sprintf(command, "%s%s-npme %d -s %s %s",
                cmd_mdrun, cmd_np, nPMEnodes, simulation_tpr, args_for_mdrun);
    }
    else
    {
        sprintf(command, "%s%s%s -npme %d -s %s %s",
                cmd_mpirun, cmd_np, cmd_mdrun, nPMEnodes, simulation_tpr, args_for_mdrun);
    }

    fprintf(fp, "%s this command line to launch the simulation:\n\n%s", bLaunch? "Using":"Please use", command);
    sep_line(fp);
    fflush(fp);

    /* Now the real thing! */
    if (bLaunch)
    {
        fprintf(stdout, "\nLaunching simulation with best parameters now.\nExecuting '%s'", command);
        sep_line(stdout);
        fflush(stdout);
        gmx_system_call(command);
    }
}


static void modify_PMEsettings(
        gmx_large_int_t simsteps,  /* Set this value as number of time steps */
        const char *fn_best_tpr,   /* tpr file with the best performance */
        const char *fn_sim_tpr)    /* name of tpr file to be launched */
{
    t_inputrec   *ir;
    t_state      state;
    gmx_mtop_t   mtop;
    char         buf[200];

    snew(ir,1);
    read_tpx_state(fn_best_tpr,ir,&state,NULL,&mtop);

    /* Set nsteps to the right value */
    ir->nsteps = simsteps;

    /* Write the tpr file which will be launched */
    sprintf(buf, "Writing optimized simulation file %s with nsteps=%s.\n", fn_sim_tpr, gmx_large_int_pfmt);
    fprintf(stdout,buf,ir->nsteps);
    fflush(stdout);
    write_tpx_state(fn_sim_tpr,ir,&state,&mtop);

    sfree(ir);
}


#define EPME_SWITCHED(e) ((e) == eelPMESWITCH || (e) == eelPMEUSERSWITCH)

/* Make additional TPR files with more computational load for the
 * direct space processors: */
static void make_benchmark_tprs(
        const char *fn_sim_tpr,     /* READ : User-provided tpr file                 */
        char *fn_bench_tprs[],      /* WRITE: Names of benchmark tpr files           */
        gmx_large_int_t benchsteps, /* Number of time steps for benchmark runs       */
        gmx_large_int_t statesteps, /* Step counter in checkpoint file               */
        real rmin,                  /* Minimal Coulomb radius                        */
        real rmax,                  /* Maximal Coulomb radius                        */
        real bScaleRvdw,            /* Scale rvdw along with rcoulomb */
        int *ntprs,                 /* No. of TPRs to write, each with a different
                                       rcoulomb and fourierspacing                   */
        t_inputinfo *info,          /* Contains information about mdp file options   */
        FILE *fp)                   /* Write the output here                         */
{
    int          i,j,d;
    t_inputrec   *ir;
    t_state      state;
    gmx_mtop_t   mtop;
    real         nlist_buffer;      /* Thickness of the buffer regions for PME-switch potentials */
    char         buf[200];
    rvec         box_size;
    gmx_bool     bNote = FALSE;
    real         add;               /* Add this to rcoul for the next test    */
    real         fac = 1.0;         /* Scaling factor for Coulomb radius      */
    real         fourierspacing;    /* Basic fourierspacing from tpr          */


    sprintf(buf, "Making benchmark tpr file%s with %s time step%s",
            *ntprs > 1? "s":"", gmx_large_int_pfmt, benchsteps>1?"s":"");
    fprintf(stdout, buf, benchsteps);
    if (statesteps > 0)
    {
        sprintf(buf, " (adding %s steps from checkpoint file)", gmx_large_int_pfmt);
        fprintf(stdout, buf, statesteps);
        benchsteps += statesteps;
    }
    fprintf(stdout, ".\n");


    snew(ir,1);
    read_tpx_state(fn_sim_tpr,ir,&state,NULL,&mtop);

    /* Check if some kind of PME was chosen */
    if (EEL_PME(ir->coulombtype) == FALSE)
        gmx_fatal(FARGS, "Can only do optimizations for simulations with %s electrostatics.",
                EELTYPE(eelPME));

    /* Check if rcoulomb == rlist, which is necessary for plain PME. */
    if (  (ir->cutoff_scheme != ecutsVERLET) && 
          (eelPME == ir->coulombtype) && !(ir->rcoulomb == ir->rlist))
    {
        gmx_fatal(FARGS, "%s requires rcoulomb (%f) to be equal to rlist (%f).",
                EELTYPE(eelPME), ir->rcoulomb, ir->rlist);
    }
    /* For other PME types, rcoulomb is allowed to be smaller than rlist */
    else if (ir->rcoulomb > ir->rlist)
    {
        gmx_fatal(FARGS, "%s requires rcoulomb (%f) to be equal to or smaller than rlist (%f)",
                EELTYPE(ir->coulombtype), ir->rcoulomb, ir->rlist);
    }

    if (bScaleRvdw && ir->rvdw != ir->rcoulomb)
    {
        fprintf(stdout,"NOTE: input rvdw != rcoulomb, will not scale rvdw\n");
        bScaleRvdw = FALSE;
    }

    /* Reduce the number of steps for the benchmarks */
    info->orig_sim_steps = ir->nsteps;
    ir->nsteps           = benchsteps;

    /* For PME-switch potentials, keep the radial distance of the buffer region */
    nlist_buffer   = ir->rlist - ir->rcoulomb;

    /* Determine length of triclinic box vectors */
    for(d=0; d<DIM; d++)
    {
        box_size[d] = 0;
        for(i=0;i<DIM;i++)
            box_size[d] += state.box[d][i]*state.box[d][i];
        box_size[d] = sqrt(box_size[d]);
    }

    if (ir->fourier_spacing > 0)
    {
        info->fsx[0] = ir->fourier_spacing;
        info->fsy[0] = ir->fourier_spacing;
        info->fsz[0] = ir->fourier_spacing;
    }
    else
    {
        /* Reconstruct fourierspacing per dimension from the number of grid points and box size */
        info->fsx[0] = box_size[XX]/ir->nkx;
        info->fsy[0] = box_size[YY]/ir->nky;
        info->fsz[0] = box_size[ZZ]/ir->nkz;
    }

    /* If no value for the fourierspacing was provided on the command line, we
     * use the reconstruction from the tpr file */
    if (ir->fourier_spacing > 0)
    {
        /* Use the spacing from the tpr */
        fourierspacing = ir->fourier_spacing;
    }
    else
    {
        /* Use the maximum observed spacing */
        fourierspacing = max(max(info->fsx[0],info->fsy[0]),info->fsz[0]);
    }

    fprintf(stdout, "Calculating PME grid points on the basis of a fourierspacing of %f nm\n", fourierspacing);

    /* For performance comparisons the number of particles is useful to have */
    fprintf(fp, "   Number of particles  : %d\n", mtop.natoms);

    /* Print information about settings of which some are potentially modified: */
    fprintf(fp, "   Coulomb type         : %s\n", EELTYPE(ir->coulombtype));
    fprintf(fp, "   Grid spacing x y z   : %f %f %f\n",
            box_size[XX]/ir->nkx, box_size[YY]/ir->nky, box_size[ZZ]/ir->nkz);
    fprintf(fp, "   Van der Waals type   : %s\n", EVDWTYPE(ir->vdwtype));
    if (EVDW_SWITCHED(ir->vdwtype))
        fprintf(fp, "   rvdw_switch          : %f nm\n", ir->rvdw_switch);
    if (EPME_SWITCHED(ir->coulombtype))
        fprintf(fp, "   rlist                : %f nm\n", ir->rlist);
    if (ir->rlistlong != max_cutoff(ir->rvdw,ir->rcoulomb))
        fprintf(fp, "   rlistlong            : %f nm\n", ir->rlistlong);

    /* Print a descriptive line about the tpr settings tested */
    fprintf(fp, "\nWill try these real/reciprocal workload settings:\n");
    fprintf(fp, " No.   scaling  rcoulomb");
    fprintf(fp, "  nkx  nky  nkz");
    fprintf(fp, "   spacing");
    if (evdwCUT == ir->vdwtype)
        fprintf(fp, "      rvdw");
    if (EPME_SWITCHED(ir->coulombtype))
        fprintf(fp, "     rlist");
    if ( ir->rlistlong != max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb)) )
        fprintf(fp, " rlistlong");
    fprintf(fp, "  tpr file\n");

    /* Loop to create the requested number of tpr input files */
    for (j = 0; j < *ntprs; j++)
    {
        /* The first .tpr is the provided one, just need to modify nsteps,
         * so skip the following block */
        if (j != 0)
        {
            /* Determine which Coulomb radii rc to use in the benchmarks */
            add = (rmax-rmin)/(*ntprs-1);
            if (is_equal(rmin,info->rcoulomb[0]))
            {
                ir->rcoulomb = rmin + j*add;
            }
            else if (is_equal(rmax,info->rcoulomb[0]))
            {
                ir->rcoulomb = rmin + (j-1)*add;
            }
            else
            {
                /* rmin != rcoul != rmax, ergo test between rmin and rmax */
                add = (rmax-rmin)/(*ntprs-2);
                ir->rcoulomb = rmin + (j-1)*add;
            }

            /* Determine the scaling factor fac */
            fac = ir->rcoulomb/info->rcoulomb[0];

            /* Scale the Fourier grid spacing */
            ir->nkx = ir->nky = ir->nkz = 0;
            calc_grid(NULL,state.box,fourierspacing*fac,&ir->nkx,&ir->nky,&ir->nkz);

            /* Adjust other radii since various conditions neet to be fulfilled */
            if (eelPME == ir->coulombtype)
            {
                /* plain PME, rcoulomb must be equal to rlist */
                ir->rlist = ir->rcoulomb;
            }
            else
            {
                /* rlist must be >= rcoulomb, we keep the size of the buffer region */
                ir->rlist = ir->rcoulomb + nlist_buffer;
            }

            if (bScaleRvdw && evdwCUT == ir->vdwtype)
            {
                /* For vdw cutoff, rvdw >= rlist */
                ir->rvdw = max(info->rvdw[0], ir->rlist);
            }

            ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));

        } /* end of "if (j != 0)" */

        /* for j==0: Save the original settings
         * for j >0: Save modified radii and Fourier grids */
        info->rcoulomb[j]  = ir->rcoulomb;
        info->rvdw[j]      = ir->rvdw;
        info->nkx[j]       = ir->nkx;
        info->nky[j]       = ir->nky;
        info->nkz[j]       = ir->nkz;
        info->rlist[j]     = ir->rlist;
        info->rlistlong[j] = ir->rlistlong;
        info->fsx[j]       = fac*fourierspacing;
        info->fsy[j]       = fac*fourierspacing;
        info->fsz[j]       = fac*fourierspacing;

        /* Write the benchmark tpr file */
        strncpy(fn_bench_tprs[j],fn_sim_tpr,strlen(fn_sim_tpr)-strlen(".tpr"));
        sprintf(buf, "_bench%.2d.tpr", j);
        strcat(fn_bench_tprs[j], buf);
        fprintf(stdout,"Writing benchmark tpr %s with nsteps=", fn_bench_tprs[j]);
        fprintf(stdout, gmx_large_int_pfmt, ir->nsteps);
        if (j > 0)
            fprintf(stdout,", scaling factor %f\n", fac);
        else
            fprintf(stdout,", unmodified settings\n");

        write_tpx_state(fn_bench_tprs[j],ir,&state,&mtop);

        /* Write information about modified tpr settings to log file */
        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)
            fprintf(fp, "%10f", ir->rvdw);
        if (EPME_SWITCHED(ir->coulombtype))
            fprintf(fp, "%10f", ir->rlist);
        if ( info->rlistlong[0] != max_cutoff(info->rlist[0],max_cutoff(info->rvdw[0],info->rcoulomb[0])) )
            fprintf(fp, "%10f", ir->rlistlong);
        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]) )
        {
            bNote = TRUE;
        }
    }
    if (bNote)
        fprintf(fp, "\nNote that in addition to the Coulomb radius and the Fourier grid\n"
                    "other input settings were also changed (see table above).\n"
                    "Please check if the modified settings are appropriate.\n");
    fflush(stdout);
    fflush(fp);
    sfree(ir);
}


/* Rename the files we want to keep to some meaningful filename and
 * delete the rest */
static void cleanup(const t_filenm *fnm, int nfile, int k, int nnodes,
                    int nPMEnodes, int nr, gmx_bool bKeepStderr)
{
    char numstring[STRLEN];
    char newfilename[STRLEN];
    const char *fn=NULL;
    int i;
    const char *opt;


    fprintf(stdout, "Cleaning up, deleting benchmark temp files ...\n");

    for (i=0; i<nfile; i++)
    {
        opt = (char *)fnm[i].opt;
        if ( strcmp(opt, "-p") == 0 )
        {
            /* do nothing; keep this file */
            ;
        }
        else if (strcmp(opt, "-bg") == 0)
        {
            /* Give the log file a nice name so one can later see which parameters were used */
            numstring[0] = '\0';
            if (nr > 0)
                sprintf(numstring, "_%d", nr);
            sprintf(newfilename, "%s_no%d_np%d_npme%d%s", opt2fn("-bg",nfile,fnm), k, nnodes, nPMEnodes, numstring);
            if (gmx_fexist(opt2fn("-bg",nfile,fnm)))
            {
                fprintf(stdout, "renaming log file to %s\n", newfilename);
                make_backup(newfilename);
                rename(opt2fn("-bg",nfile,fnm), newfilename);
            }
        }
        else if (strcmp(opt, "-err") == 0)
        {
            /* This file contains the output of stderr. We want to keep it in
             * cases where there have been problems. */
            fn = opt2fn(opt, nfile, fnm);
            numstring[0] = '\0';
            if (nr > 0)
                sprintf(numstring, "_%d", nr);
            sprintf(newfilename, "%s_no%d_np%d_npme%d%s", fn, k, nnodes, nPMEnodes, numstring);
            if (gmx_fexist(fn))
            {
                if (bKeepStderr)
                {
                    fprintf(stdout, "Saving stderr output in %s\n", newfilename);
                    make_backup(newfilename);
                    rename(fn, newfilename);
                }
                else
                {
                    fprintf(stdout, "Deleting %s\n", fn);
                    remove(fn);
                }
            }
        }
        /* 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);
            }
        }
    }
}


/* 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};

/* Create a list of numbers of PME nodes to test */
static void make_npme_list(
        const char *npmevalues_opt,  /* Make a complete list with all
                           * possibilities or a short list that keeps only
                           * reasonable numbers of PME nodes                  */
        int *nentries,    /* Number of entries we put in the nPMEnodes list   */
        int *nPMEnodes[], /* Each entry contains the value for -npme          */
        int nnodes,       /* Total number of nodes to do the tests on         */
        int minPMEnodes,  /* Minimum number of PME nodes                      */
        int maxPMEnodes)  /* Maximum number of PME nodes                      */
{
    int i,npme,npp;
    int min_factor=1;     /* We request that npp and npme have this minimal
                           * largest common factor (depends on npp)           */
    int nlistmax;         /* Max. list size                                   */
    int nlist;            /* Actual number of entries in list                 */
    int eNPME=0;


    /* Do we need to check all possible values for -npme or is a reduced list enough? */
    if ( 0 == strcmp(npmevalues_opt, "all") )
    {
        eNPME = eNpmeAll;
    }
    else if ( 0 == strcmp(npmevalues_opt, "subset") )
    {
        eNPME = eNpmeSubset;
    }
    else /* "auto" or "range" */
    {
        if (nnodes <= 64)
            eNPME = eNpmeAll;
        else if (nnodes < 128)
            eNPME = eNpmeReduced;
        else
            eNPME = eNpmeSubset;
    }

    /* Calculate how many entries we could possibly have (in case of -npme all) */
    if (nnodes > 2)
    {
        nlistmax = maxPMEnodes - minPMEnodes + 3;
        if (0 == minPMEnodes)
            nlistmax--;
    }
    else
        nlistmax = 1;

    /* Now make the actual list which is at most of size nlist */
    snew(*nPMEnodes, nlistmax);
    nlist = 0; /* start counting again, now the real entries in the list */
    for (i = 0; i < nlistmax - 2; i++)
    {
        npme = maxPMEnodes - i;
        npp  = nnodes-npme;
        switch (eNPME)
        {
            case eNpmeAll:
                min_factor = 1;
                break;
            case eNpmeReduced:
                min_factor = 2;
                break;
            case eNpmeSubset:
                /* For 2d PME we want a common largest factor of at least the cube
                 * root of the number of PP nodes */
                min_factor = (int) pow(npp, 1.0/3.0);
                break;
            default:
                gmx_fatal(FARGS, "Unknown option for eNPME in make_npme_list");
                break;
        }
        if (largest_common_factor(npp, npme) >= min_factor)
        {
            (*nPMEnodes)[nlist] = npme;
            nlist++;
        }
    }
    /* We always test 0 PME nodes and the automatic number */
    *nentries = nlist + 2;
    (*nPMEnodes)[nlist  ] =  0;
    (*nPMEnodes)[nlist+1] = -1;

    fprintf(stderr, "Will try the following %d different values for -npme:\n", *nentries);
    for (i=0; i<*nentries-1; i++)
        fprintf(stderr, "%d, ", (*nPMEnodes)[i]);
    fprintf(stderr, "and %d (auto).\n", (*nPMEnodes)[*nentries-1]);
}


/* Allocate memory to store the performance data */
static void init_perfdata(t_perf *perfdata[], int ntprs, int datasets, int repeats)
{
    int i, j, k;


    for (k=0; k<ntprs; k++)
    {
        snew(perfdata[k], datasets);
        for (i=0; i<datasets; i++)
        {
            for (j=0; j<repeats; j++)
            {
                snew(perfdata[k][i].Gcycles   , repeats);
                snew(perfdata[k][i].ns_per_day, repeats);
                snew(perfdata[k][i].PME_f_load, repeats);
            }
        }
    }
}


/* Check for errors on mdrun -h */
static void make_sure_it_runs(char *mdrun_cmd_line, int length, FILE *fp)
{
    char *command, *msg;
    int  ret;


    snew(command, length +  15);
    snew(msg    , length + 500);

    fprintf(stdout, "Making shure the benchmarks can be executed ...\n");
    sprintf(command, "%s-h -quiet", mdrun_cmd_line);
    ret = gmx_system_call(command);

    if (0 != ret)
    {
        /* 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"
                        "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"
                        "\n%s\n\n", command);

        fprintf(stderr, "%s", msg);
        sep_line(fp);
        fprintf(fp    , "%s", msg);

        exit(ret);
    }

    sfree(command);
    sfree(msg    );
}


static void do_the_tests(
        FILE *fp,                   /* General g_tune_pme output file         */
        char **tpr_names,           /* Filenames of the input files to test   */
        int maxPMEnodes,            /* Max fraction of nodes to use for PME   */
        int minPMEnodes,            /* Min fraction of nodes to use for PME   */
        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     */
        int *pmeentries,            /* Entries in the nPMEnodes list          */
        int repeats,                /* Repeat each test this often            */
        int nnodes,                 /* Total number of nodes = nPP + nPME     */
        int nr_tprs,                /* Total number of tpr files to test      */
        gmx_bool bThreads,          /* Threads or MPI?                        */
        char *cmd_mpirun,           /* mpirun command string                  */
        char *cmd_np,               /* "-np", "-n", whatever mpirun needs     */
        char *cmd_mdrun,            /* mdrun command string                   */
        char *cmd_args_bench,       /* arguments for mdrun in a string        */
        const t_filenm *fnm,        /* List of filenames from command line    */
        int nfile,                  /* Number of files specified on the cmdl. */
        int sim_part,               /* For checkpointing                      */
        int presteps,               /* DLB equilibration steps, is checked    */
        gmx_large_int_t cpt_steps)  /* Time step counter in the checkpoint    */
{
    int     i,nr,k,ret,count=0,totaltests;
    int     *nPMEnodes=NULL;
    t_perf  *pd=NULL;
    int     cmdline_length;
    char    *command, *cmd_stub;
    char    buf[STRLEN];
    gmx_bool bResetProblem=FALSE;
    gmx_bool bFirst=TRUE;


    /* This string array corresponds to the eParselog enum type at the start
     * of this file */
    const char* ParseLog[] = {"OK.",
                              "Logfile not found!",
                              "No timings, logfile truncated?",
                              "Run was terminated.",
                              "Counters were not reset properly.",
                              "No DD grid found for these settings.",
                              "TPX version conflict!",
                              "mdrun was not started in parallel!",
                              "An error occured." };
    char    str_PME_f_load[13];


    /* Allocate space for the mdrun command line. 100 extra characters should
       be more than enough for the -npme etcetera arguments */
    cmdline_length =  strlen(cmd_mpirun)
                    + strlen(cmd_np)
                    + strlen(cmd_mdrun)
                    + strlen(cmd_args_bench)
                    + strlen(tpr_names[0]) + 100;
    snew(command , cmdline_length);
    snew(cmd_stub, cmdline_length);

    /* Construct the part of the command line that stays the same for all tests: */
    if (bThreads)
    {
        sprintf(cmd_stub, "%s%s", cmd_mdrun, cmd_np);
    }
    else
    {
        sprintf(cmd_stub, "%s%s%s ", cmd_mpirun, cmd_np, cmd_mdrun);
    }

    /* Create a list of numbers of PME nodes to test */
    if (npme_fixed < -1)
    {
        make_npme_list(npmevalues_opt, pmeentries, &nPMEnodes,
                nnodes, minPMEnodes, maxPMEnodes);
    }
    else
    {
        *pmeentries  = 1;
        snew(nPMEnodes, 1);
        nPMEnodes[0] = npme_fixed;
        fprintf(stderr, "Will use a fixed number of %d PME-only nodes.\n", nPMEnodes[0]);
    }

    if (0 == repeats)
    {
        fprintf(fp, "\nNo benchmarks done since number of repeats (-r) is 0.\n");
        ffclose(fp);
        finalize(opt2fn("-p", nfile, fnm));
        exit(0);
    }

    /* Allocate one dataset for each tpr input file: */
    init_perfdata(perfdata, nr_tprs, *pmeentries, repeats);

    /*****************************************/
    /* Main loop over all tpr files to test: */
    /*****************************************/
    totaltests = nr_tprs*(*pmeentries)*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");
        /* Loop over various numbers of PME nodes: */
        for (i = 0; i < *pmeentries; i++)
        {
            pd = &perfdata[k][i];

            /* Loop over the repeats for each scenario: */
            for (nr = 0; nr < repeats; nr++)
            {
                pd->nPMEnodes = nPMEnodes[i];

                /* Add -npme and -s to the command line and save it. Note that
                 * the -passall (if set) options requires cmd_args_bench to be
                 * at the end of the command line string */
                snew(pd->mdrun_cmd_line, cmdline_length);
                sprintf(pd->mdrun_cmd_line, "%s-npme %d -s %s %s",
                        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 */
                if (bFirst)
                    make_sure_it_runs(pd->mdrun_cmd_line, cmdline_length, fp);
                bFirst = FALSE;

                /* Do a benchmark simulation: */
                if (repeats > 1)
                    sprintf(buf, ", pass %d/%d", nr+1, repeats);
                else
                    buf[0]='\0';
                fprintf(stdout, "\n=== Progress %2.0f%%, tpr %d/%d, run %d/%d%s:\n",
                        (100.0*count)/totaltests,
                        k+1, nr_tprs, i+1, *pmeentries, buf);
                make_backup(opt2fn("-err",nfile,fnm));
                sprintf(command, "%s 1> /dev/null 2>%s", pd->mdrun_cmd_line, opt2fn("-err",nfile,fnm));
                fprintf(stdout, "%s\n", pd->mdrun_cmd_line);
                gmx_system_call(command);

                /* Collect the performance data from the log file; also check stderr
                 * for fatal errors */
                ret = parse_logfile(opt2fn("-bg",nfile,fnm), opt2fn("-err",nfile,fnm),
                        pd, nr, presteps, cpt_steps, nnodes);
                if ((presteps > 0) && (ret == eParselogResetProblem))
                    bResetProblem = TRUE;

                if (-1 == pd->nPMEnodes)
                    sprintf(buf, "(%3d)", pd->guessPME);
                else
                    sprintf(buf, "     ");

                /* Nicer output */
                if (pd->PME_f_load[nr] > 0.0)
                    sprintf(str_PME_f_load, "%12.3f", pd->PME_f_load[nr]);
                else
                    sprintf(str_PME_f_load, "%s", "         -  ");

                /* Write the data we got to disk */
                fprintf(fp, "%4d%s %12.3f %12.3f %s    %s", pd->nPMEnodes,
                        buf, pd->Gcycles[nr], pd->ns_per_day[nr], str_PME_f_load, ParseLog[ret]);
                if (! (ret==eParselogOK || ret==eParselogNoDDGrid || ret==eParselogNotFound) )
                    fprintf(fp, " Check %s file for problems.", ret==eParselogFatal? "err":"log");
                fprintf(fp, "\n");
                fflush(fp);
                count++;

                /* Do some cleaning up and delete the files we do not need any more */
                cleanup(fnm, nfile, k, nnodes, pd->nPMEnodes, nr, ret==eParselogFatal);

                /* If the first run with this number of processors already failed, do not try again: */
                if (pd->Gcycles[0] <= 0.0 && repeats > 1)
                {
                    fprintf(stdout, "Skipping remaining passes of unsuccessful setting, see log file for details.\n");
                    count += repeats-(nr+1);
                    break;
                }
            } /* end of repeats loop */
        } /* end of -npme loop */
    } /* end of tpr file loop */

    if (bResetProblem)
    {
        sep_line(fp);
        fprintf(fp, "WARNING: The cycle and time step counters could not be reset\n"
                    "properly. The reason could be that mpirun did not manage to\n"
                    "export the environment variable GMX_RESET_COUNTER. You might\n"
                    "have to give a special switch to mpirun for that.\n"
                    "Alternatively, you can manually set GMX_RESET_COUNTER to the\n"
                    "value normally provided by -presteps.");
        sep_line(fp);
    }
    sfree(command);
    sfree(cmd_stub);
}


static void check_input(
        int nnodes,
        int repeats,
        int *ntprs,
        real *rmin,
        real rcoulomb,
        real *rmax,
        real maxPMEfraction,
        real minPMEfraction,
        int  npme_fixed,
        gmx_large_int_t bench_nsteps,
        const t_filenm *fnm,
        int nfile,
        int sim_part,
        int presteps,
        int npargs,
        t_pargs *pa)
{
    int old;


    /* Make sure the input file exists */
    if (!gmx_fexist(opt2fn("-s",nfile,fnm)))
        gmx_fatal(FARGS, "File %s not found.", opt2fn("-s",nfile,fnm));

    /* Make sure that the checkpoint file is not overwritten during benchmarking */
    if ( (0 == strcmp(opt2fn("-cpi",nfile,fnm), opt2fn("-bcpo",nfile,fnm)) ) && (sim_part > 1) )
        gmx_fatal(FARGS, "Checkpoint input (-cpi) and benchmark checkpoint output (-bcpo) files must not be identical.\n"
                         "The checkpoint input file must not be overwritten during the benchmarks.\n");

    /* Make sure that repeats is >= 0 (if == 0, only write tpr files) */
    if (repeats < 0)
        gmx_fatal(FARGS, "Number of repeats < 0!");

    /* Check number of nodes */
    if (nnodes < 1)
        gmx_fatal(FARGS, "Number of nodes/threads must be a positive integer.");

    /* Automatically choose -ntpr if not set */
    if (*ntprs < 1)
    {
        if (nnodes < 16)
            *ntprs = 1;
        else
        {
            *ntprs = 3;
            /* Set a reasonable scaling factor for rcoulomb */
            if (*rmax <= 0)
                *rmax = rcoulomb * 1.2;
        }
        fprintf(stderr, "Will test %d tpr file%s.\n", *ntprs, *ntprs==1?"":"s");
    }
    else
    {
        if (1 == *ntprs)
            fprintf(stderr, "Note: Choose ntpr>1 to shift PME load between real and reciprocal space.\n");
    }

    /* Make shure that rmin <= rcoulomb <= rmax */
    if (*rmin <= 0) *rmin = rcoulomb;
    if (*rmax <= 0) *rmax = rcoulomb;
    if ( !(*rmin <= *rmax) )
    {
        gmx_fatal(FARGS, "Please choose the Coulomb radii such that rmin <= rmax.\n"
                         "rmin = %g, rmax = %g, actual rcoul from .tpr file = %g\n", *rmin, *rmax, rcoulomb);
    }
    /* Add test scenarios if rmin or rmax were set */
    if (*ntprs <= 2)
    {
        if ( !is_equal(*rmin, rcoulomb) && (*ntprs == 1) )
        {
            (*ntprs)++;
            fprintf(stderr, "NOTE: Setting -rmin to %g changed -ntpr to %d\n",
                    *rmin, *ntprs);
        }
        if (!is_equal(*rmax, rcoulomb) && (*ntprs == 1) )
        {
            (*ntprs)++;
            fprintf(stderr, "NOTE: Setting -rmax to %g changed -ntpr to %d\n",
                    *rmax, *ntprs);
        }
    }
    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) )
        *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) )
        *ntprs = max(*ntprs, 3);

    if (old != *ntprs)
    {
        fprintf(stderr, "NOTE: Your rmin, rmax setting changed -ntpr to %d\n", *ntprs);
    }

    if (*ntprs > 1)
    {
        if (is_equal(*rmin,rcoulomb) && is_equal(rcoulomb,*rmax)) /* 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"
                            "with correspondingly adjusted PME grid settings\n");
            *ntprs = 1;
        }
    }

    /* Check whether max and min fraction are within required values */
    if (maxPMEfraction > 0.5 || maxPMEfraction < 0)
        gmx_fatal(FARGS, "-max must be between 0 and 0.5");
    if (minPMEfraction > 0.5 || minPMEfraction < 0)
        gmx_fatal(FARGS, "-min must be between 0 and 0.5");
    if (maxPMEfraction < minPMEfraction)
        gmx_fatal(FARGS, "-max must be larger or equal to -min");

    /* Check whether the number of steps - if it was set - has a reasonable value */
    if (bench_nsteps < 0)
        gmx_fatal(FARGS, "Number of steps must be positive.");

    if (bench_nsteps > 10000 || bench_nsteps < 100)
    {
        fprintf(stderr, "WARNING: steps=");
        fprintf(stderr, gmx_large_int_pfmt, bench_nsteps);
        fprintf(stderr, ". Are you sure you want to perform so %s steps for each benchmark?\n", (bench_nsteps < 100)? "few" : "many");
    }

    if (presteps < 0)
    {
        gmx_fatal(FARGS, "Cannot have a negative number of presteps.\n");
    }

    /* Check for rcoulomb scaling if more than one .tpr file is tested */
    if (*ntprs > 1)
    {
        if (*rmin/rcoulomb < 0.75 || *rmax/rcoulomb > 1.25)
            fprintf(stderr, "WARNING: Applying extreme scaling factor. I hope you know what you are doing.\n");
    }

    /* If a fixed number of PME nodes is set we do rcoulomb and PME gird tuning
     * only. We need to check whether the requested number of PME-only nodes
     * makes sense. */
    if (npme_fixed > -1)
    {
        /* 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",
                             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",
                             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");
        }
    }
}


/* Returns TRUE when "opt" is needed at launch time */
static gmx_bool is_launch_file(char *opt, gmx_bool bSet)
{
    /* Apart from the input .tpr we need all options that were set
     * on the command line and that do not start with -b */
    if (0 == strncmp(opt,"-b", 2) || 0 == strncmp(opt,"-s", 2))
        return FALSE;

    if (bSet)
        return TRUE;
    else
        return FALSE;
}


/* Returns TRUE when "opt" defines a file which is needed for the benchmarks runs */
static gmx_bool is_bench_file(char *opt, gmx_bool bSet, gmx_bool bOptional, gmx_bool bIsOutput)
{
    /* Apart from the input .tpr, all files starting with "-b" are for
     * _b_enchmark files exclusively */
    if (0 == strncmp(opt,"-s", 2)) return FALSE;
    if (0 == strncmp(opt,"-b", 2) || 0 == strncmp(opt,"-s", 2))
    {
        if (!bOptional || bSet)
            return TRUE;
        else
            return FALSE;
    }
    else
    {
        if (bIsOutput)
            return FALSE;
        else
            if (bSet) /* These are additional input files like -cpi -ei */
                return TRUE;
            else
                return FALSE;
    }
}


/* Adds 'buf' to 'str' */
static void add_to_string(char **str, char *buf)
{
    int len;


    len = strlen(*str) + strlen(buf) + 1;
    srenew(*str, len);
    strcat(*str, buf);
}


/* Create the command line for the benchmark as well as for the real run */
static void create_command_line_snippets(
        gmx_bool bThreads,
        gmx_bool bAppendFiles,
        gmx_bool bKeepAndNumCPT,
        gmx_bool bResetHWay,
        int      presteps,
        int      nfile,
        t_filenm fnm[],
        int      npargs,
        t_pargs  *pa,
        const char *procstring,      /* How to pass the number of processors to $MPIRUN */
        char     *cmd_np[],          /* Actual command line snippet, e.g. '-np <N>' */
        char     *cmd_args_bench[],  /* command line arguments for benchmark runs */
        char     *cmd_args_launch[], /* command line arguments for simulation run */
        char     extra_args[])       /* Add this to the end of the command line */
{
    int        i;
    char       *opt;
    const char *name;
    char       strbuf[STRLEN];


    /* strlen needs at least '\0' as a string: */
    snew(*cmd_args_bench ,1);
    snew(*cmd_args_launch,1);
    *cmd_args_launch[0]='\0';
    *cmd_args_bench[0] ='\0';


    /*******************************************/
    /* 1. Process other command line arguments */
    /*******************************************/
    if (presteps > 0)
    {
        /* Add equilibration steps to benchmark options */
        sprintf(strbuf, "-resetstep %d ", presteps);
        add_to_string(cmd_args_bench, strbuf);
    }
    /* These switches take effect only at launch time */
    if (FALSE == bAppendFiles)
    {
        add_to_string(cmd_args_launch, "-noappend ");
    }
    if (bKeepAndNumCPT)
    {
        add_to_string(cmd_args_launch, "-cpnum ");
    }
    if (bResetHWay)
    {
        add_to_string(cmd_args_launch, "-resethway ");
    }

    /********************/
    /* 2. Process files */
    /********************/
    for (i=0; i<nfile; i++)
    {
        opt  = (char *)fnm[i].opt;
        name = opt2fn(opt,nfile,fnm);

        /* Strbuf contains the options, now let's sort out where we need that */
        sprintf(strbuf, "%s %s ", opt, name);

        if ( is_bench_file(opt, opt2bSet(opt,nfile,fnm), is_optional(&fnm[i]), is_output(&fnm[i])) )
        {
            /* All options starting with -b* need the 'b' removed,
             * therefore overwrite strbuf */
            if (0 == strncmp(opt, "-b", 2))
                sprintf(strbuf, "-%s %s ", &opt[2], name);

            add_to_string(cmd_args_bench, strbuf);
        }

        if ( is_launch_file(opt,opt2bSet(opt,nfile,fnm)) )
            add_to_string(cmd_args_launch, strbuf);
    }

    add_to_string(cmd_args_bench , extra_args);
    add_to_string(cmd_args_launch, extra_args);
}


/* Set option opt */
static void setopt(const char *opt,int nfile,t_filenm fnm[])
{
  int i;

  for(i=0; (i<nfile); i++)
    if (strcmp(opt,fnm[i].opt)==0)
      fnm[i].flag |= ffSET;
}


/* This routine inspects the tpr file and ...
 * 1. checks for output files that get triggered by a tpr option. These output
 *    files are marked as 'set' to allow for a proper cleanup after each
 *    tuning run.
 * 2. returns the PME:PP load ratio
 * 3. returns rcoulomb from the tpr */
static float inspect_tpr(int nfile, t_filenm fnm[], real *rcoulomb)
{
    gmx_bool     bPull;     /* Is pulling requested in .tpr file?             */
    gmx_bool     bTpi;      /* Is test particle insertion requested?          */
    gmx_bool     bFree;     /* Is a free energy simulation requested?         */
    gmx_bool     bNM;       /* Is a normal mode analysis requested?           */
    t_inputrec   ir;
    t_state      state;
    gmx_mtop_t   mtop;


    /* Check tpr file for options that trigger extra output files */
    read_tpx_state(opt2fn("-s",nfile,fnm),&ir,&state,NULL,&mtop);
    bPull = (epullNO != ir.ePull);
    bFree = (efepNO  != ir.efep );
    bNM   = (eiNM    == ir.eI   );
    bTpi  = EI_TPI(ir.eI);

    /* Set these output files on the tuning command-line */
    if (bPull)
    {
        setopt("-pf"  , nfile, fnm);
        setopt("-px"  , nfile, fnm);
    }
    if (bFree)
    {
        setopt("-dhdl", nfile, fnm);
    }
    if (bTpi)
    {
        setopt("-tpi" , nfile, fnm);
        setopt("-tpid", nfile, fnm);
    }
    if (bNM)
    {
        setopt("-mtx" , nfile, fnm);
    }

    *rcoulomb = ir.rcoulomb;

    /* Return the estimate for the number of PME nodes */
    return pme_load_estimate(&mtop,&ir,state.box);
}


static void couple_files_options(int nfile, t_filenm fnm[])
{
    int i;
    gmx_bool bSet,bBench;
    char *opt;
    char buf[20];


    for (i=0; i<nfile; i++)
    {
        opt  = (char *)fnm[i].opt;
        bSet = ((fnm[i].flag & ffSET) != 0);
        bBench = (0 == strncmp(opt,"-b", 2));

        /* Check optional files */
        /* If e.g. -eo is set, then -beo also needs to be set */
        if (is_optional(&fnm[i]) && bSet && !bBench)
        {
            sprintf(buf, "-b%s", &opt[1]);
            setopt(buf,nfile,fnm);
        }
        /* If -beo is set, then -eo also needs to be! */
        if (is_optional(&fnm[i]) && bSet && bBench)
        {
            sprintf(buf, "-%s", &opt[2]);
            setopt(buf,nfile,fnm);
        }
    }
}


static double gettime()
{
#ifdef HAVE_GETTIMEOFDAY
    struct timeval t;
    double seconds;

    gettimeofday(&t,NULL);

    seconds = (double) t.tv_sec + 1e-6*(double)t.tv_usec;

    return seconds;
#else
    double  seconds;

    seconds = time(NULL);

    return seconds;
#endif
}


#define BENCHSTEPS (1000)

int gmx_tune_pme(int argc,char *argv[])
{
    const char *desc[] = {
            "For a given number [TT]-np[tt] or [TT]-nt[tt] of processors/threads, this program systematically",
            "times [TT]mdrun[tt] with various numbers of PME-only nodes 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. ",
            "Simply pass your [TT].tpr[tt] file to [TT]g_tune_pme[tt] together with other options",
            "for [TT]mdrun[tt] as needed.[PAR]",
            "Which executables are used can be set in the environment variables",
            "MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
            "will be used as defaults. Note that for certain MPI frameworks you",
            "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]",
            "Please call [TT]g_tune_pme[tt] with the normal options you would pass to",
            "[TT]mdrun[tt] and add [TT]-np[tt] for the number of processors to perform the",
            "tests on, or [TT]-nt[tt] for the number of threads. You can also add [TT]-r[tt]",
            "to repeat each test several times to get better statistics. [PAR]",
            "[TT]g_tune_pme[tt] can test various real space / reciprocal space workloads",
            "for you. With [TT]-ntpr[tt] you control how many extra [TT].tpr[tt] files will be",
            "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. ",
            "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",
            "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",
            "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.",
            "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]g_tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
            "After calling [TT]mdrun[tt] several times, detailed performance information",
            "is available in the output file [TT]perf.out.[tt] ",
            "[BB]Note[bb] that during the benchmarks, a couple of temporary files are written",
            "(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
            "If you want the simulation to be started automatically with the",
            "optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
    };

    int        nnodes =1;
    int        repeats=2;
    int        pmeentries=0; /* How many values for -npme do we actually test for each tpr file */
    real       maxPMEfraction=0.50;
    real       minPMEfraction=0.25;
    int        maxPMEnodes, minPMEnodes;
    float      guessPMEratio;   /* guessed PME:PP ratio based on the tpr file */
    float      guessPMEnodes;
    int        npme_fixed=-2;             /* If >= -1, use only this number
                                           * of PME-only nodes                */
    int        ntprs=0;
    real       rmin=0.0,rmax=0.0;  /* min and max value for rcoulomb if scaling is requested */
    real       rcoulomb=-1.0;             /* Coulomb radius as set in .tpr file */
    gmx_bool   bScaleRvdw=TRUE;
    gmx_large_int_t bench_nsteps=BENCHSTEPS;
    gmx_large_int_t new_sim_nsteps=-1;   /* -1 indicates: not set by the user */
    gmx_large_int_t cpt_steps=0;         /* Step counter in .cpt input file   */
    int        presteps=100;    /* Do a full cycle reset after presteps steps */
    gmx_bool   bOverwrite=FALSE, bKeepTPR;
    gmx_bool   bLaunch=FALSE;
    char       *ExtraArgs=NULL;
    char       **tpr_names=NULL;
    const char *simulation_tpr=NULL;
    int        best_npme, best_tpr;
    int        sim_part = 1;     /* For benchmarks with checkpoint files */
    char       bbuf[STRLEN];

    /* Default program names if nothing else is found */
    char        *cmd_mpirun=NULL, *cmd_mdrun=NULL;
    char        *cmd_args_bench, *cmd_args_launch;
    char        *cmd_np=NULL;

    t_perf      **perfdata=NULL;
    t_inputinfo *info;
    int         i;
    FILE        *fp;
    t_commrec   *cr;

    /* Print out how long the tuning took */
    double      seconds;

    static t_filenm fnm[] = {
      /* g_tune_pme */
      { efOUT, "-p",      "perf",     ffWRITE },
      { efLOG, "-err",    "bencherr", ffWRITE },
      { efTPX, "-so",     "tuned",    ffWRITE },
      /* mdrun: */
      { efTPX, NULL,      NULL,       ffREAD },
      { efTRN, "-o",      NULL,       ffWRITE },
      { efXTC, "-x",      NULL,       ffOPTWR },
      { efCPT, "-cpi",    NULL,       ffOPTRD },
      { efCPT, "-cpo",    NULL,       ffOPTWR },
      { efSTO, "-c",      "confout",  ffWRITE },
      { efEDR, "-e",      "ener",     ffWRITE },
      { efLOG, "-g",      "md",       ffWRITE },
      { efXVG, "-dhdl",   "dhdl",     ffOPTWR },
      { efXVG, "-field",  "field",    ffOPTWR },
      { efXVG, "-table",  "table",    ffOPTRD },
      { efXVG, "-tabletf", "tabletf",   ffOPTRD },
      { efXVG, "-tablep", "tablep",   ffOPTRD },
      { efXVG, "-tableb", "table",    ffOPTRD },
      { efTRX, "-rerun",  "rerun",    ffOPTRD },
      { efXVG, "-tpi",    "tpi",      ffOPTWR },
      { efXVG, "-tpid",   "tpidist",  ffOPTWR },
      { efEDI, "-ei",     "sam",      ffOPTRD },
      { efEDO, "-eo",     "sam",      ffOPTWR },
      { efGCT, "-j",      "wham",     ffOPTRD },
      { efGCT, "-jo",     "bam",      ffOPTWR },
      { efXVG, "-ffout",  "gct",      ffOPTWR },
      { efXVG, "-devout", "deviatie", ffOPTWR },
      { efXVG, "-runav",  "runaver",  ffOPTWR },
      { efXVG, "-px",     "pullx",    ffOPTWR },
      { efXVG, "-pf",     "pullf",    ffOPTWR },
      { efXVG, "-ro",     "rotation", ffOPTWR },
      { efLOG, "-ra",     "rotangles",ffOPTWR },
      { efLOG, "-rs",     "rotslabs", ffOPTWR },
      { efLOG, "-rt",     "rottorque",ffOPTWR },
      { efMTX, "-mtx",    "nm",       ffOPTWR },
      { efNDX, "-dn",     "dipole",   ffOPTWR },
      /* Output files that are deleted after each benchmark run */
      { efTRN, "-bo",     "bench",    ffWRITE },
      { efXTC, "-bx",     "bench",    ffWRITE },
      { efCPT, "-bcpo",   "bench",    ffWRITE },
      { efSTO, "-bc",     "bench",    ffWRITE },
      { efEDR, "-be",     "bench",    ffWRITE },
      { efLOG, "-bg",     "bench",    ffWRITE },
      { efEDO, "-beo",    "bench",    ffOPTWR },
      { efXVG, "-bdhdl",  "benchdhdl",ffOPTWR },
      { efXVG, "-bfield", "benchfld" ,ffOPTWR },
      { efXVG, "-btpi",   "benchtpi", ffOPTWR },
      { efXVG, "-btpid",  "benchtpid",ffOPTWR },
      { efGCT, "-bjo",    "bench",    ffOPTWR },
      { efXVG, "-bffout", "benchgct", ffOPTWR },
      { efXVG, "-bdevout","benchdev", ffOPTWR },
      { efXVG, "-brunav", "benchrnav",ffOPTWR },
      { efXVG, "-bpx",    "benchpx",  ffOPTWR },
      { efXVG, "-bpf",    "benchpf",  ffOPTWR },
      { efXVG, "-bro",    "benchrot", ffOPTWR },
      { efLOG, "-bra",    "benchrota",ffOPTWR },
      { efLOG, "-brs",    "benchrots",ffOPTWR },
      { efLOG, "-brt",    "benchrott",ffOPTWR },
      { efMTX, "-bmtx",   "benchn",   ffOPTWR },
      { efNDX, "-bdn",    "bench",    ffOPTWR }
    };

    gmx_bool bThreads     = FALSE;

    int  nthreads=1;

    const char *procstring[] =
      { NULL, "-np", "-n", "none", NULL };
    const char *npmevalues_opt[] =
      { NULL, "auto", "all", "subset", NULL };

    gmx_bool bAppendFiles=TRUE;
    gmx_bool bKeepAndNumCPT=FALSE;
    gmx_bool bResetCountersHalfWay=FALSE;
    gmx_bool bBenchmark=TRUE;

    output_env_t oenv=NULL;

    t_pargs pa[] = {
      /***********************/
      /* g_tune_pme options: */
      /***********************/
      { "-np",       FALSE, etINT,  {&nnodes},
        "Number of nodes to run the tests on (must be > 2 for separate PME nodes)" },
      { "-npstring", FALSE, etENUM, {procstring},
        "Specify the number of processors to [TT]$MPIRUN[tt] using this string"},
      { "-nt",       FALSE, etINT,  {&nthreads},
        "Number of 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" },
      { "-min",      FALSE, etREAL, {&minPMEfraction},
        "Min fraction of PME nodes 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."},
      { "-rmax",     FALSE, etREAL, {&rmax},
        "If >0, maximal rcoulomb for -ntpr>1 (rcoulomb upscaling results in fourier grid downscaling)" },
      { "-rmin",     FALSE, etREAL, {&rmin},
        "If >0, minimal rcoulomb for -ntpr>1" },
      { "-scalevdw",  FALSE, etBOOL, {&bScaleRvdw},
        "Scale rvdw along with rcoulomb"},
      { "-ntpr",     FALSE, etINT,  {&ntprs},
        "Number of [TT].tpr[tt] files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. "
        "If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
      { "-steps",    FALSE, etGMX_LARGE_INT, {&bench_nsteps},
        "Take timings for this many steps in the benchmark runs" },
      { "-resetstep",FALSE, etINT,  {&presteps},
        "Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
      { "-simsteps", FALSE, etGMX_LARGE_INT, {&new_sim_nsteps},
        "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
      { "-launch",   FALSE, etBOOL, {&bLaunch},
        "Launch the real simulation after optimization" },
      { "-bench",    FALSE, etBOOL, {&bBenchmark},
        "Run the benchmarks or just create the input [TT].tpr[tt] files?" },
      /******************/
      /* mdrun options: */
      /******************/
      /* We let g_tune_pme parse and understand these options, because we need to
       * prevent that they appear on the mdrun command line for the benchmarks */
      { "-append",   FALSE, etBOOL, {&bAppendFiles},
        "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only)" },
      { "-cpnum",    FALSE, etBOOL, {&bKeepAndNumCPT},
        "Keep and number checkpoint files (launch only)" },
      { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
        "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt] (launch only)" }
    };


#define NFILE asize(fnm)

    CopyRight(stderr,argv[0]);

    seconds = gettime();

    parse_common_args(&argc,argv,PCA_NOEXIT_ON_ARGS,
                      NFILE,fnm,asize(pa),pa,asize(desc),desc,
                      0,NULL,&oenv);

    /* Store the remaining unparsed command line entries in a string which
     * is then attached to the mdrun command line */
    snew(ExtraArgs, 1);
    ExtraArgs[0] = '\0';
    for (i=1; i<argc; i++) /* argc will now be 1 if everything was understood */
    {
        add_to_string(&ExtraArgs, argv[i]);
        add_to_string(&ExtraArgs, " ");
    }

    if (opt2parg_bSet("-nt",asize(pa),pa))
    {
        bThreads=TRUE;
        if (opt2parg_bSet("-npstring",asize(pa),pa))
            fprintf(stderr, "WARNING: -npstring has no effect when using threads.\n");

        if (nnodes > 1)
            gmx_fatal(FARGS, "Can't run multi-threaded MPI simulation yet!");
        /* and now we just set this; a bit of an ugly hack*/
        nnodes=nthreads;
    }
    /* Check for PME:PP ratio and whether tpr triggers additional output files */
    guessPMEratio = inspect_tpr(NFILE,fnm,&rcoulomb);

    /* Automatically set -beo options if -eo is set etc. */
    couple_files_options(NFILE,fnm);

    /* Construct the command line arguments for benchmark runs
     * as well as for the simulation run */
    if (bThreads)
        sprintf(bbuf," -nt %d ", nthreads);
    else
        sprintf(bbuf," -np %d ", nnodes);

    cmd_np = bbuf;

    create_command_line_snippets(bThreads,bAppendFiles,bKeepAndNumCPT,bResetCountersHalfWay,presteps,
                                 NFILE,fnm,asize(pa),pa,procstring[0],
                                 &cmd_np, &cmd_args_bench, &cmd_args_launch,
                                 ExtraArgs);

    /* Read in checkpoint file if requested */
    sim_part = 1;
    if(opt2bSet("-cpi",NFILE,fnm))
    {
        snew(cr,1);
        cr->duty=DUTY_PP; /* makes the following routine happy */
        read_checkpoint_simulation_part(opt2fn("-cpi",NFILE,fnm),
                    &sim_part,&cpt_steps,cr,
                    FALSE,NFILE,fnm,NULL,NULL);
        sfree(cr);
        sim_part++;
        /* sim_part will now be 1 if no checkpoint file was found */
        if (sim_part<=1)
            gmx_fatal(FARGS, "Checkpoint file %s not found!", opt2fn("-cpi",NFILE,fnm));
    }

    /* Open performance output file and write header info */
    fp = ffopen(opt2fn("-p",NFILE,fnm),"w");

    /* Make a quick consistency check of command line parameters */
    check_input(nnodes, repeats, &ntprs, &rmin, rcoulomb, &rmax,
                maxPMEfraction, minPMEfraction, npme_fixed,
                bench_nsteps, fnm, NFILE, sim_part, presteps,
                asize(pa),pa);

    /* Determine the maximum and minimum number of PME nodes to test,
     * the actual list of settings is build in do_the_tests(). */
    if ((nnodes > 2) && (npme_fixed < -1))
    {
        if (0 == strcmp(npmevalues_opt[0], "auto"))
        {
            /* Determine the npme range automatically based on the PME:PP load guess */
            if (guessPMEratio > 1.0)
            {
                /* More PME than PP work, probably we do not need separate PME nodes at all! */
                maxPMEnodes=nnodes/2;
                minPMEnodes=nnodes/2;
            }
            else
            {
                /* PME : PP load is in the range 0..1, let's test around the guess */
                guessPMEnodes = nnodes/(1.0 + 1.0/guessPMEratio);
                minPMEnodes = floor(0.7*guessPMEnodes);
                maxPMEnodes =  ceil(1.6*guessPMEnodes);
                maxPMEnodes = min(maxPMEnodes, nnodes/2);
            }
        }
        else
        {
            /* Determine the npme range based on user input */
            maxPMEnodes = floor(maxPMEfraction*nnodes);
            minPMEnodes = max(floor(minPMEfraction*nnodes), 0);
            fprintf(stdout, "Will try runs with %d ", minPMEnodes);
            if (maxPMEnodes != minPMEnodes)
                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");
        }
    }
    else
    {
        maxPMEnodes = 0;
        minPMEnodes = 0;
    }

    /* Get the commands we need to set up the runs from environment variables */
    get_program_paths(bThreads, &cmd_mpirun, cmd_np, &cmd_mdrun, repeats);

    /* Print some header info to file */
    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());
    if (!bThreads)
    {
        fprintf(fp, "Number of nodes         : %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]);
        else
            fprintf(fp, "Not setting number of nodes in system call\n");
    }
    else
        fprintf(fp, "Number of threads       : %d\n", nnodes);

    fprintf(fp, "The mdrun  command is   : %s\n", cmd_mdrun);
    fprintf(fp, "mdrun args benchmarks   : %s\n", cmd_args_bench);
    fprintf(fp, "Benchmark steps         : ");
    fprintf(fp, gmx_large_int_pfmt, bench_nsteps);
    fprintf(fp, "\n");
    fprintf(fp, "dlb equilibration steps : %d\n", presteps);
    if (sim_part > 1)
    {
        fprintf(fp, "Checkpoint time step    : ");
        fprintf(fp, gmx_large_int_pfmt, cpt_steps);
        fprintf(fp, "\n");
    }
    fprintf(fp, "mdrun args at launchtime: %s\n", cmd_args_launch);

    if (new_sim_nsteps >= 0)
    {
        bOverwrite = TRUE;
        fprintf(stderr, "Note: Simulation input file %s will have ", opt2fn("-so",NFILE,fnm));
        fprintf(stderr, gmx_large_int_pfmt, new_sim_nsteps+cpt_steps);
        fprintf(stderr, " steps.\n");
        fprintf(fp, "Simulation steps        : ");
        fprintf(fp, gmx_large_int_pfmt, new_sim_nsteps);
        fprintf(fp, "\n");
    }
    if (repeats > 1)
        fprintf(fp, "Repeats for each test   : %d\n", repeats);

    if (npme_fixed >= -1)
    {
        fprintf(fp, "Fixing -npme at         : %d\n", npme_fixed);
    }

    fprintf(fp, "Input file              : %s\n", opt2fn("-s",NFILE,fnm));
    fprintf(fp, "   PME/PP load estimate : %g\n", guessPMEratio);

    /* Allocate memory for the inputinfo struct: */
    snew(info, 1);
    info->nr_inputfiles = ntprs;
    for (i=0; i<ntprs; i++)
    {
        snew(info->rcoulomb , ntprs);
        snew(info->rvdw     , ntprs);
        snew(info->rlist    , ntprs);
        snew(info->rlistlong, ntprs);
        snew(info->nkx      , ntprs);
        snew(info->nky      , ntprs);
        snew(info->nkz      , ntprs);
        snew(info->fsx      , ntprs);
        snew(info->fsy      , ntprs);
        snew(info->fsz      , ntprs);
    }
    /* Make alternative tpr files to test: */
    snew(tpr_names, ntprs);
    for (i=0; i<ntprs; i++)
        snew(tpr_names[i], STRLEN);

    /* It can be that ntprs is reduced by make_benchmark_tprs if not enough
     * different grids could be found. */
    make_benchmark_tprs(opt2fn("-s",NFILE,fnm), tpr_names, bench_nsteps+presteps,
                        cpt_steps, rmin, rmax, bScaleRvdw, &ntprs, info, fp);

    /********************************************************************************/
    /* Main loop over all scenarios we need to test: tpr files, PME nodes, repeats  */
    /********************************************************************************/
    snew(perfdata, ntprs);
    if (bBenchmark)
    {
        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, sim_part, presteps, cpt_steps);

        fprintf(fp, "\nTuning took%8.1f minutes.\n", (gettime()-seconds)/60.0);

        /* Analyse the results and give a suggestion for optimal settings: */
        bKeepTPR = analyze_data(fp, opt2fn("-p", NFILE, fnm), perfdata, nnodes, ntprs, pmeentries,
                repeats, info, &best_tpr, &best_npme);

        /* Take the best-performing tpr file and enlarge nsteps to original value */
        if ( bKeepTPR && !bOverwrite )
        {
            simulation_tpr = opt2fn("-s",NFILE,fnm);
        }
        else
        {
            simulation_tpr = opt2fn("-so",NFILE,fnm);
            modify_PMEsettings(bOverwrite? (new_sim_nsteps+cpt_steps) :
                    info->orig_sim_steps, tpr_names[best_tpr],
                    simulation_tpr);
        }

        /* Let's get rid of the temporary benchmark input files */
        for (i=0; i<ntprs; i++)
        {
            fprintf(stdout, "Deleting temporary benchmark input file %s\n", tpr_names[i]);
            remove(tpr_names[i]);
        }

        /* Now start the real simulation if the user requested it ... */
        launch_simulation(bLaunch, fp, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
                cmd_args_launch, simulation_tpr, nnodes, best_npme);
    }
    ffclose(fp);

    /* ... or simply print the performance results to screen: */
    if (!bLaunch)
        finalize(opt2fn("-p", NFILE, fnm));

    return 0;
}