Merge release-4-6 into release-5-0

[gromacs.git] / src / gromacs / gmxlib / checkpoint.c

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */

/* The source code in this file should be thread-safe.
   Please keep it that way. */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <string.h>
#include <time.h>

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

#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif

#ifdef GMX_NATIVE_WINDOWS
/* _chsize_s */
#include <io.h>
#include <sys/locking.h>
#endif

#include "copyrite.h"
#include "names.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "gromacs/utility/smalloc.h"
#include "txtdump.h"
#include "vec.h"
#include "network.h"
#include "checkpoint.h"
#include "main.h"
#include "gromacs/utility/cstringutil.h"
#include <fcntl.h>

#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xdrf.h"
#include "gromacs/fileio/xdr_datatype.h"
#include "gromacs/utility/baseversion.h"
#include "gmx_fatal.h"

#include "buildinfo.h"

#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif

#define CPT_MAGIC1 171817
#define CPT_MAGIC2 171819
#define CPTSTRLEN 1024

#ifdef GMX_DOUBLE
#define GMX_CPT_BUILD_DP 1
#else
#define GMX_CPT_BUILD_DP 0
#endif

/* cpt_version should normally only be changed
 * when the header of footer format changes.
 * The state data format itself is backward and forward compatible.
 * But old code can not read a new entry that is present in the file
 * (but can read a new format when new entries are not present).
 */
static const int cpt_version = 16;


const char *est_names[estNR] =
{
    "FE-lambda",
    "box", "box-rel", "box-v", "pres_prev",
    "nosehoover-xi", "thermostat-integral",
    "x", "v", "SDx", "CGp", "LD-rng", "LD-rng-i",
    "disre_initf", "disre_rm3tav",
    "orire_initf", "orire_Dtav",
    "svir_prev", "nosehoover-vxi", "v_eta", "vol0", "nhpres_xi", "nhpres_vxi", "fvir_prev", "fep_state", "MC-rng", "MC-rng-i"
};

enum {
    eeksEKIN_N, eeksEKINH, eeksDEKINDL, eeksMVCOS, eeksEKINF, eeksEKINO, eeksEKINSCALEF, eeksEKINSCALEH, eeksVSCALE, eeksEKINTOTAL, eeksNR
};

const char *eeks_names[eeksNR] =
{
    "Ekin_n", "Ekinh", "dEkindlambda", "mv_cos",
    "Ekinf", "Ekinh_old", "EkinScaleF_NHC", "EkinScaleH_NHC", "Vscale_NHC", "Ekin_Total"
};

enum {
    eenhENERGY_N, eenhENERGY_AVER, eenhENERGY_SUM, eenhENERGY_NSUM,
    eenhENERGY_SUM_SIM, eenhENERGY_NSUM_SIM,
    eenhENERGY_NSTEPS, eenhENERGY_NSTEPS_SIM,
    eenhENERGY_DELTA_H_NN,
    eenhENERGY_DELTA_H_LIST,
    eenhENERGY_DELTA_H_STARTTIME,
    eenhENERGY_DELTA_H_STARTLAMBDA,
    eenhNR
};

const char *eenh_names[eenhNR] =
{
    "energy_n", "energy_aver", "energy_sum", "energy_nsum",
    "energy_sum_sim", "energy_nsum_sim",
    "energy_nsteps", "energy_nsteps_sim",
    "energy_delta_h_nn",
    "energy_delta_h_list",
    "energy_delta_h_start_time",
    "energy_delta_h_start_lambda"
};

/* free energy history variables -- need to be preserved over checkpoint */
enum {
    edfhBEQUIL, edfhNATLAMBDA, edfhWLHISTO, edfhWLDELTA, edfhSUMWEIGHTS, edfhSUMDG, edfhSUMMINVAR, edfhSUMVAR,
    edfhACCUMP, edfhACCUMM, edfhACCUMP2, edfhACCUMM2, edfhTIJ, edfhTIJEMP, edfhNR
};
/* free energy history variable names  */
const char *edfh_names[edfhNR] =
{
    "bEquilibrated", "N_at_state", "Wang-Landau Histogram", "Wang-Landau Delta", "Weights", "Free Energies", "minvar", "variance",
    "accumulated_plus", "accumulated_minus", "accumulated_plus_2",  "accumulated_minus_2", "Tij", "Tij_empirical"
};

#ifdef GMX_NATIVE_WINDOWS
static int
gmx_wintruncate(const char *filename, __int64 size)
{
#ifdef GMX_FAHCORE
    /*we do this elsewhere*/
    return 0;
#else
    FILE *fp;
    int   rc;

    fp = fopen(filename, "rb+");

    if (fp == NULL)
    {
        return -1;
    }

    return _chsize_s( fileno(fp), size);
#endif
}
#endif


enum {
    ecprREAL, ecprRVEC, ecprMATRIX
};

enum {
    cptpEST, cptpEEKS, cptpEENH, cptpEDFH
};
/* enums for the different components of checkpoint variables, replacing the hard coded ones.
   cptpEST - state variables.
   cptpEEKS - Kinetic energy state variables.
   cptpEENH - Energy history state variables.
   cptpEDFH - free energy history variables.
 */


static const char *st_names(int cptp, int ecpt)
{
    switch (cptp)
    {
        case cptpEST: return est_names [ecpt]; break;
        case cptpEEKS: return eeks_names[ecpt]; break;
        case cptpEENH: return eenh_names[ecpt]; break;
        case cptpEDFH: return edfh_names[ecpt]; break;
    }

    return NULL;
}

static void cp_warning(FILE *fp)
{
    fprintf(fp, "\nWARNING: Checkpoint file is corrupted or truncated\n\n");
}

static void cp_error()
{
    gmx_fatal(FARGS, "Checkpoint file corrupted/truncated, or maybe you are out of disk space?");
}

static void do_cpt_string_err(XDR *xd, gmx_bool bRead, const char *desc, char **s, FILE *list)
{
    bool_t res = 0;

    if (bRead)
    {
        snew(*s, CPTSTRLEN);
    }
    res = xdr_string(xd, s, CPTSTRLEN);
    if (res == 0)
    {
        cp_error();
    }
    if (list)
    {
        fprintf(list, "%s = %s\n", desc, *s);
        sfree(*s);
    }
}

static int do_cpt_int(XDR *xd, const char *desc, int *i, FILE *list)
{
    bool_t res = 0;

    res = xdr_int(xd, i);
    if (res == 0)
    {
        return -1;
    }
    if (list)
    {
        fprintf(list, "%s = %d\n", desc, *i);
    }
    return 0;
}

static int do_cpt_u_chars(XDR *xd, const char *desc, int n, unsigned char *i, FILE *list)
{
    bool_t res = 1;
    int    j;
    if (list)
    {
        fprintf(list, "%s = ", desc);
    }
    for (j = 0; j < n && res; j++)
    {
        res &= xdr_u_char(xd, &i[j]);
        if (list)
        {
            fprintf(list, "%02x", i[j]);
        }
    }
    if (list)
    {
        fprintf(list, "\n");
    }
    if (res == 0)
    {
        return -1;
    }

    return 0;
}

static void do_cpt_int_err(XDR *xd, const char *desc, int *i, FILE *list)
{
    if (do_cpt_int(xd, desc, i, list) < 0)
    {
        cp_error();
    }
}

static void do_cpt_step_err(XDR *xd, const char *desc, gmx_int64_t *i, FILE *list)
{
    bool_t res = 0;
    char   buf[STEPSTRSIZE];

    res = xdr_int64(xd, i);
    if (res == 0)
    {
        cp_error();
    }
    if (list)
    {
        fprintf(list, "%s = %s\n", desc, gmx_step_str(*i, buf));
    }
}

static void do_cpt_double_err(XDR *xd, const char *desc, double *f, FILE *list)
{
    bool_t res = 0;

    res = xdr_double(xd, f);
    if (res == 0)
    {
        cp_error();
    }
    if (list)
    {
        fprintf(list, "%s = %f\n", desc, *f);
    }
}

static void do_cpt_real_err(XDR *xd, real *f)
{
    bool_t res = 0;

#ifdef GMX_DOUBLE
    res = xdr_double(xd, f);
#else
    res = xdr_float(xd, f);
#endif
    if (res == 0)
    {
        cp_error();
    }
}

static void do_cpt_n_rvecs_err(XDR *xd, const char *desc, int n, rvec f[], FILE *list)
{
    int i, j;

    for (i = 0; i < n; i++)
    {
        for (j = 0; j < DIM; j++)
        {
            do_cpt_real_err(xd, &f[i][j]);
        }
    }

    if (list)
    {
        pr_rvecs(list, 0, desc, f, n);
    }
}

/* If nval >= 0, nval is used; on read this should match the passed value.
 * If nval n<0, *nptr is used; on read the value is stored in nptr
 */
static int do_cpte_reals_low(XDR *xd, int cptp, int ecpt, int sflags,
                             int nval, int *nptr, real **v,
                             FILE *list, int erealtype)
{
    bool_t  res = 0;
#ifndef GMX_DOUBLE
    int     dtc = xdr_datatype_float;
#else
    int     dtc = xdr_datatype_double;
#endif
    real   *vp, *va = NULL;
    float  *vf;
    double *vd;
    int     nf, dt, i;

    if (list == NULL)
    {
        if (nval >= 0)
        {
            nf = nval;
        }
        else
        {
            if (nptr == NULL)
            {
                gmx_incons("*ntpr=NULL in do_cpte_reals_low");
            }
            nf = *nptr;
        }
    }
    res = xdr_int(xd, &nf);
    if (res == 0)
    {
        return -1;
    }
    if (list == NULL)
    {
        if (nval >= 0)
        {
            if (nf != nval)
            {
                gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), nval, nf);
            }
        }
        else
        {
            *nptr = nf;
        }
    }
    dt  = dtc;
    res = xdr_int(xd, &dt);
    if (res == 0)
    {
        return -1;
    }
    if (dt != dtc)
    {
        fprintf(stderr, "Precision mismatch for state entry %s, code precision is %s, file precision is %s\n",
                st_names(cptp, ecpt), xdr_datatype_names[dtc],
                xdr_datatype_names[dt]);
    }
    if (list || !(sflags & (1<<ecpt)))
    {
        snew(va, nf);
        vp = va;
    }
    else
    {
        if (*v == NULL)
        {
            snew(*v, nf);
        }
        vp = *v;
    }
    if (dt == xdr_datatype_float)
    {
        if (dtc == xdr_datatype_float)
        {
            vf = (float *)vp;
        }
        else
        {
            snew(vf, nf);
        }
        res = xdr_vector(xd, (char *)vf, nf,
                         (unsigned int)sizeof(float), (xdrproc_t)xdr_float);
        if (res == 0)
        {
            return -1;
        }
        if (dtc != xdr_datatype_float)
        {
            for (i = 0; i < nf; i++)
            {
                vp[i] = vf[i];
            }
            sfree(vf);
        }
    }
    else
    {
        if (dtc == xdr_datatype_double)
        {
            vd = (double *)vp;
        }
        else
        {
            snew(vd, nf);
        }
        res = xdr_vector(xd, (char *)vd, nf,
                         (unsigned int)sizeof(double), (xdrproc_t)xdr_double);
        if (res == 0)
        {
            return -1;
        }
        if (dtc != xdr_datatype_double)
        {
            for (i = 0; i < nf; i++)
            {
                vp[i] = vd[i];
            }
            sfree(vd);
        }
    }

    if (list)
    {
        switch (erealtype)
        {
            case ecprREAL:
                pr_reals(list, 0, st_names(cptp, ecpt), vp, nf);
                break;
            case ecprRVEC:
                pr_rvecs(list, 0, st_names(cptp, ecpt), (rvec *)vp, nf/3);
                break;
            default:
                gmx_incons("Unknown checkpoint real type");
        }
    }
    if (va)
    {
        sfree(va);
    }

    return 0;
}


/* This function stores n along with the reals for reading,
 * but on reading it assumes that n matches the value in the checkpoint file,
 * a fatal error is generated when this is not the case.
 */
static int do_cpte_reals(XDR *xd, int cptp, int ecpt, int sflags,
                         int n, real **v, FILE *list)
{
    return do_cpte_reals_low(xd, cptp, ecpt, sflags, n, NULL, v, list, ecprREAL);
}

/* This function does the same as do_cpte_reals,
 * except that on reading it ignores the passed value of *n
 * and stored the value read from the checkpoint file in *n.
 */
static int do_cpte_n_reals(XDR *xd, int cptp, int ecpt, int sflags,
                           int *n, real **v, FILE *list)
{
    return do_cpte_reals_low(xd, cptp, ecpt, sflags, -1, n, v, list, ecprREAL);
}

static int do_cpte_real(XDR *xd, int cptp, int ecpt, int sflags,
                        real *r, FILE *list)
{
    int n;

    return do_cpte_reals_low(xd, cptp, ecpt, sflags, 1, NULL, &r, list, ecprREAL);
}

static int do_cpte_ints(XDR *xd, int cptp, int ecpt, int sflags,
                        int n, int **v, FILE *list)
{
    bool_t res = 0;
    int    dtc = xdr_datatype_int;
    int   *vp, *va = NULL;
    int    nf, dt, i;

    nf  = n;
    res = xdr_int(xd, &nf);
    if (res == 0)
    {
        return -1;
    }
    if (list == NULL && v != NULL && nf != n)
    {
        gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), n, nf);
    }
    dt  = dtc;
    res = xdr_int(xd, &dt);
    if (res == 0)
    {
        return -1;
    }
    if (dt != dtc)
    {
        gmx_fatal(FARGS, "Type mismatch for state entry %s, code type is %s, file type is %s\n",
                  st_names(cptp, ecpt), xdr_datatype_names[dtc],
                  xdr_datatype_names[dt]);
    }
    if (list || !(sflags & (1<<ecpt)) || v == NULL)
    {
        snew(va, nf);
        vp = va;
    }
    else
    {
        if (*v == NULL)
        {
            snew(*v, nf);
        }
        vp = *v;
    }
    res = xdr_vector(xd, (char *)vp, nf,
                     (unsigned int)sizeof(int), (xdrproc_t)xdr_int);
    if (res == 0)
    {
        return -1;
    }
    if (list)
    {
        pr_ivec(list, 0, st_names(cptp, ecpt), vp, nf, TRUE);
    }
    if (va)
    {
        sfree(va);
    }

    return 0;
}

static int do_cpte_int(XDR *xd, int cptp, int ecpt, int sflags,
                       int *i, FILE *list)
{
    return do_cpte_ints(xd, cptp, ecpt, sflags, 1, &i, list);
}

static int do_cpte_doubles(XDR *xd, int cptp, int ecpt, int sflags,
                           int n, double **v, FILE *list)
{
    bool_t  res = 0;
    int     dtc = xdr_datatype_double;
    double *vp, *va = NULL;
    int     nf, dt, i;

    nf  = n;
    res = xdr_int(xd, &nf);
    if (res == 0)
    {
        return -1;
    }
    if (list == NULL && nf != n)
    {
        gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), n, nf);
    }
    dt  = dtc;
    res = xdr_int(xd, &dt);
    if (res == 0)
    {
        return -1;
    }
    if (dt != dtc)
    {
        gmx_fatal(FARGS, "Precision mismatch for state entry %s, code precision is %s, file precision is %s\n",
                  st_names(cptp, ecpt), xdr_datatype_names[dtc],
                  xdr_datatype_names[dt]);
    }
    if (list || !(sflags & (1<<ecpt)))
    {
        snew(va, nf);
        vp = va;
    }
    else
    {
        if (*v == NULL)
        {
            snew(*v, nf);
        }
        vp = *v;
    }
    res = xdr_vector(xd, (char *)vp, nf,
                     (unsigned int)sizeof(double), (xdrproc_t)xdr_double);
    if (res == 0)
    {
        return -1;
    }
    if (list)
    {
        pr_doubles(list, 0, st_names(cptp, ecpt), vp, nf);
    }
    if (va)
    {
        sfree(va);
    }

    return 0;
}

static int do_cpte_double(XDR *xd, int cptp, int ecpt, int sflags,
                          double *r, FILE *list)
{
    return do_cpte_doubles(xd, cptp, ecpt, sflags, 1, &r, list);
}


static int do_cpte_rvecs(XDR *xd, int cptp, int ecpt, int sflags,
                         int n, rvec **v, FILE *list)
{
    int n3;

    return do_cpte_reals_low(xd, cptp, ecpt, sflags,
                             n*DIM, NULL, (real **)v, list, ecprRVEC);
}

static int do_cpte_matrix(XDR *xd, int cptp, int ecpt, int sflags,
                          matrix v, FILE *list)
{
    real *vr;
    real  ret;

    vr  = (real *)&(v[0][0]);
    ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
                            DIM*DIM, NULL, &vr, NULL, ecprMATRIX);

    if (list && ret == 0)
    {
        pr_rvecs(list, 0, st_names(cptp, ecpt), v, DIM);
    }

    return ret;
}


static int do_cpte_nmatrix(XDR *xd, int cptp, int ecpt, int sflags,
                           int n, real **v, FILE *list)
{
    int   i;
    real *vr;
    real  ret, reti;
    char  name[CPTSTRLEN];

    ret = 0;
    if (v == NULL)
    {
        snew(v, n);
    }
    for (i = 0; i < n; i++)
    {
        reti = 0;
        vr   = v[i];
        reti = do_cpte_reals_low(xd, cptp, ecpt, sflags, n, NULL, &(v[i]), NULL, ecprREAL);
        if (list && reti == 0)
        {
            sprintf(name, "%s[%d]", st_names(cptp, ecpt), i);
            pr_reals(list, 0, name, v[i], n);
        }
        if (reti == 0)
        {
            ret = 0;
        }
    }
    return ret;
}

static int do_cpte_matrices(XDR *xd, int cptp, int ecpt, int sflags,
                            int n, matrix **v, FILE *list)
{
    bool_t  res = 0;
    matrix *vp, *va = NULL;
    real   *vr;
    int     nf, i, j, k;
    int     ret;

    nf  = n;
    res = xdr_int(xd, &nf);
    if (res == 0)
    {
        return -1;
    }
    if (list == NULL && nf != n)
    {
        gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), n, nf);
    }
    if (list || !(sflags & (1<<ecpt)))
    {
        snew(va, nf);
        vp = va;
    }
    else
    {
        if (*v == NULL)
        {
            snew(*v, nf);
        }
        vp = *v;
    }
    snew(vr, nf*DIM*DIM);
    for (i = 0; i < nf; i++)
    {
        for (j = 0; j < DIM; j++)
        {
            for (k = 0; k < DIM; k++)
            {
                vr[(i*DIM+j)*DIM+k] = vp[i][j][k];
            }
        }
    }
    ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
                            nf*DIM*DIM, NULL, &vr, NULL, ecprMATRIX);
    for (i = 0; i < nf; i++)
    {
        for (j = 0; j < DIM; j++)
        {
            for (k = 0; k < DIM; k++)
            {
                vp[i][j][k] = vr[(i*DIM+j)*DIM+k];
            }
        }
    }
    sfree(vr);

    if (list && ret == 0)
    {
        for (i = 0; i < nf; i++)
        {
            pr_rvecs(list, 0, st_names(cptp, ecpt), vp[i], DIM);
        }
    }
    if (va)
    {
        sfree(va);
    }

    return ret;
}

static void do_cpt_header(XDR *xd, gmx_bool bRead, int *file_version,
                          char **version, char **btime, char **buser, char **bhost,
                          int *double_prec,
                          char **fprog, char **ftime,
                          int *eIntegrator, int *simulation_part,
                          gmx_int64_t *step, double *t,
                          int *nnodes, int *dd_nc, int *npme,
                          int *natoms, int *ngtc, int *nnhpres, int *nhchainlength,
                          int *nlambda, int *flags_state,
                          int *flags_eks, int *flags_enh, int *flags_dfh,
                          int *nED, int *eSwapCoords,
                          FILE *list)
{
    bool_t res = 0;
    int    magic;
    int    idum = 0;
    int    i;
    char  *fhost;

    if (bRead)
    {
        magic = -1;
    }
    else
    {
        magic = CPT_MAGIC1;
    }
    res = xdr_int(xd, &magic);
    if (res == 0)
    {
        gmx_fatal(FARGS, "The checkpoint file is empty/corrupted, or maybe you are out of disk space?");
    }
    if (magic != CPT_MAGIC1)
    {
        gmx_fatal(FARGS, "Start of file magic number mismatch, checkpoint file has %d, should be %d\n"
                  "The checkpoint file is corrupted or not a checkpoint file",
                  magic, CPT_MAGIC1);
    }
    if (!bRead)
    {
        snew(fhost, 255);
        gmx_gethostname(fhost, 255);
    }
    do_cpt_string_err(xd, bRead, "GROMACS version", version, list);
    do_cpt_string_err(xd, bRead, "GROMACS build time", btime, list);
    do_cpt_string_err(xd, bRead, "GROMACS build user", buser, list);
    do_cpt_string_err(xd, bRead, "GROMACS build host", bhost, list);
    do_cpt_string_err(xd, bRead, "generating program", fprog, list);
    do_cpt_string_err(xd, bRead, "generation time", ftime, list);
    *file_version = cpt_version;
    do_cpt_int_err(xd, "checkpoint file version", file_version, list);
    if (*file_version > cpt_version)
    {
        gmx_fatal(FARGS, "Attempting to read a checkpoint file of version %d with code of version %d\n", *file_version, cpt_version);
    }
    if (*file_version >= 13)
    {
        do_cpt_int_err(xd, "GROMACS double precision", double_prec, list);
    }
    else
    {
        *double_prec = -1;
    }
    if (*file_version >= 12)
    {
        do_cpt_string_err(xd, bRead, "generating host", &fhost, list);
        if (list == NULL)
        {
            sfree(fhost);
        }
    }
    do_cpt_int_err(xd, "#atoms", natoms, list);
    do_cpt_int_err(xd, "#T-coupling groups", ngtc, list);
    if (*file_version >= 10)
    {
        do_cpt_int_err(xd, "#Nose-Hoover T-chains", nhchainlength, list);
    }
    else
    {
        *nhchainlength = 1;
    }
    if (*file_version >= 11)
    {
        do_cpt_int_err(xd, "#Nose-Hoover T-chains for barostat ", nnhpres, list);
    }
    else
    {
        *nnhpres = 0;
    }
    if (*file_version >= 14)
    {
        do_cpt_int_err(xd, "# of total lambda states ", nlambda, list);
    }
    else
    {
        *nlambda = 0;
    }
    do_cpt_int_err(xd, "integrator", eIntegrator, list);
    if (*file_version >= 3)
    {
        do_cpt_int_err(xd, "simulation part #", simulation_part, list);
    }
    else
    {
        *simulation_part = 1;
    }
    if (*file_version >= 5)
    {
        do_cpt_step_err(xd, "step", step, list);
    }
    else
    {
        do_cpt_int_err(xd, "step", &idum, list);
        *step = idum;
    }
    do_cpt_double_err(xd, "t", t, list);
    do_cpt_int_err(xd, "#PP-nodes", nnodes, list);
    idum = 1;
    do_cpt_int_err(xd, "dd_nc[x]", dd_nc ? &(dd_nc[0]) : &idum, list);
    do_cpt_int_err(xd, "dd_nc[y]", dd_nc ? &(dd_nc[1]) : &idum, list);
    do_cpt_int_err(xd, "dd_nc[z]", dd_nc ? &(dd_nc[2]) : &idum, list);
    do_cpt_int_err(xd, "#PME-only nodes", npme, list);
    do_cpt_int_err(xd, "state flags", flags_state, list);
    if (*file_version >= 4)
    {
        do_cpt_int_err(xd, "ekin data flags", flags_eks, list);
        do_cpt_int_err(xd, "energy history flags", flags_enh, list);
    }
    else
    {
        *flags_eks   = 0;
        *flags_enh   = (*flags_state >> (estORIRE_DTAV+1));
        *flags_state = (*flags_state & ~((1<<(estORIRE_DTAV+1)) |
                                         (1<<(estORIRE_DTAV+2)) |
                                         (1<<(estORIRE_DTAV+3))));
    }
    if (*file_version >= 14)
    {
        do_cpt_int_err(xd, "df history flags", flags_dfh, list);
    }
    else
    {
        *flags_dfh = 0;
    }

    if (*file_version >= 15)
    {
        do_cpt_int_err(xd, "ED data sets", nED, list);
    }
    else
    {
        *nED = 0;
    }
    if (*file_version >= 16)
    {
        do_cpt_int_err(xd, "swap", eSwapCoords, list);
    }
}

static int do_cpt_footer(XDR *xd, int file_version)
{
    bool_t res = 0;
    int    magic;

    if (file_version >= 2)
    {
        magic = CPT_MAGIC2;
        res   = xdr_int(xd, &magic);
        if (res == 0)
        {
            cp_error();
        }
        if (magic != CPT_MAGIC2)
        {
            return -1;
        }
    }

    return 0;
}

static int do_cpt_state(XDR *xd, gmx_bool bRead,
                        int fflags, t_state *state,
                        FILE *list)
{
    int    sflags;
    int    i;
    int    ret;
    int    nnht, nnhtp;

    ret = 0;

    nnht  = state->nhchainlength*state->ngtc;
    nnhtp = state->nhchainlength*state->nnhpres;

    if (bRead) /* we need to allocate space for dfhist if we are reading */
    {
        init_df_history(&state->dfhist, state->dfhist.nlambda);
    }

    sflags = state->flags;
    for (i = 0; (i < estNR && ret == 0); i++)
    {
        if (fflags & (1<<i))
        {
            switch (i)
            {
                case estLAMBDA:  ret      = do_cpte_reals(xd, cptpEST, i, sflags, efptNR, &(state->lambda), list); break;
                case estFEPSTATE: ret     = do_cpte_int (xd, cptpEST, i, sflags, &state->fep_state, list); break;
                case estBOX:     ret      = do_cpte_matrix(xd, cptpEST, i, sflags, state->box, list); break;
                case estBOX_REL: ret      = do_cpte_matrix(xd, cptpEST, i, sflags, state->box_rel, list); break;
                case estBOXV:    ret      = do_cpte_matrix(xd, cptpEST, i, sflags, state->boxv, list); break;
                case estPRES_PREV: ret    = do_cpte_matrix(xd, cptpEST, i, sflags, state->pres_prev, list); break;
                case estSVIR_PREV:  ret   = do_cpte_matrix(xd, cptpEST, i, sflags, state->svir_prev, list); break;
                case estFVIR_PREV:  ret   = do_cpte_matrix(xd, cptpEST, i, sflags, state->fvir_prev, list); break;
                case estNH_XI:   ret      = do_cpte_doubles(xd, cptpEST, i, sflags, nnht, &state->nosehoover_xi, list); break;
                case estNH_VXI:  ret      = do_cpte_doubles(xd, cptpEST, i, sflags, nnht, &state->nosehoover_vxi, list); break;
                case estNHPRES_XI:   ret  = do_cpte_doubles(xd, cptpEST, i, sflags, nnhtp, &state->nhpres_xi, list); break;
                case estNHPRES_VXI:  ret  = do_cpte_doubles(xd, cptpEST, i, sflags, nnhtp, &state->nhpres_vxi, list); break;
                case estTC_INT:  ret      = do_cpte_doubles(xd, cptpEST, i, sflags, state->ngtc, &state->therm_integral, list); break;
                case estVETA:    ret      = do_cpte_real(xd, cptpEST, i, sflags, &state->veta, list); break;
                case estVOL0:    ret      = do_cpte_real(xd, cptpEST, i, sflags, &state->vol0, list); break;
                case estX:       ret      = do_cpte_rvecs(xd, cptpEST, i, sflags, state->natoms, &state->x, list); break;
                case estV:       ret      = do_cpte_rvecs(xd, cptpEST, i, sflags, state->natoms, &state->v, list); break;
                case estSDX:     ret      = do_cpte_rvecs(xd, cptpEST, i, sflags, state->natoms, &state->sd_X, list); break;
                /* The RNG entries are no longer written,
                 * the next 4 lines are only for reading old files.
                 */
                case estLD_RNG:  ret      = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
                case estLD_RNGI: ret      = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
                case estMC_RNG:  ret      = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
                case estMC_RNGI: ret      = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
                case estDISRE_INITF:  ret = do_cpte_real (xd, cptpEST, i, sflags, &state->hist.disre_initf, list); break;
                case estDISRE_RM3TAV: ret = do_cpte_n_reals(xd, cptpEST, i, sflags, &state->hist.ndisrepairs, &state->hist.disre_rm3tav, list); break;
                case estORIRE_INITF:  ret = do_cpte_real (xd, cptpEST, i, sflags, &state->hist.orire_initf, list); break;
                case estORIRE_DTAV:   ret = do_cpte_n_reals(xd, cptpEST, i, sflags, &state->hist.norire_Dtav, &state->hist.orire_Dtav, list); break;
                default:
                    gmx_fatal(FARGS, "Unknown state entry %d\n"
                              "You are probably reading a new checkpoint file with old code", i);
            }
        }
    }

    return ret;
}

static int do_cpt_ekinstate(XDR *xd, int fflags, ekinstate_t *ekins,
                            FILE *list)
{
    int  i;
    int  ret;

    ret = 0;

    for (i = 0; (i < eeksNR && ret == 0); i++)
    {
        if (fflags & (1<<i))
        {
            switch (i)
            {

                case eeksEKIN_N:     ret = do_cpte_int(xd, cptpEEKS, i, fflags, &ekins->ekin_n, list); break;
                case eeksEKINH:     ret  = do_cpte_matrices(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinh, list); break;
                case eeksEKINF:      ret = do_cpte_matrices(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinf, list); break;
                case eeksEKINO:      ret = do_cpte_matrices(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinh_old, list); break;
                case eeksEKINTOTAL:  ret = do_cpte_matrix(xd, cptpEEKS, i, fflags, ekins->ekin_total, list); break;
                case eeksEKINSCALEF: ret = do_cpte_doubles(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinscalef_nhc, list); break;
                case eeksVSCALE:     ret = do_cpte_doubles(xd, 1, cptpEEKS, fflags, ekins->ekin_n, &ekins->vscale_nhc, list); break;
                case eeksEKINSCALEH: ret = do_cpte_doubles(xd, 1, cptpEEKS, fflags, ekins->ekin_n, &ekins->ekinscaleh_nhc, list); break;
                case eeksDEKINDL:   ret  = do_cpte_real(xd, 1, cptpEEKS, fflags, &ekins->dekindl, list); break;
                case eeksMVCOS:      ret = do_cpte_real(xd, 1, cptpEEKS, fflags, &ekins->mvcos, list); break;
                default:
                    gmx_fatal(FARGS, "Unknown ekin data state entry %d\n"
                              "You are probably reading a new checkpoint file with old code", i);
            }
        }
    }

    return ret;
}


static int do_cpt_swapstate(XDR *xd, gmx_bool bRead, swapstate_t *swapstate, FILE *list)
{
    int ii, ic, j;
    int ret              = 0;
    int swap_cpt_version = 1;


    if (eswapNO == swapstate->eSwapCoords)
    {
        return ret;
    }

    swapstate->bFromCpt = bRead;

    do_cpt_int_err(xd, "swap checkpoint version", &swap_cpt_version, list);
    do_cpt_int_err(xd, "swap coupling steps", &swapstate->nAverage, list);

    /* When reading, init_swapcoords has not been called yet,
     * so we have to allocate memory first. */

    for (ic = 0; ic < eCompNR; ic++)
    {
        for (ii = 0; ii < eIonNR; ii++)
        {
            if (bRead)
            {
                do_cpt_int_err(xd, "swap requested atoms", &swapstate->nat_req[ic][ii], list);
            }
            else
            {
                do_cpt_int_err(xd, "swap requested atoms p", swapstate->nat_req_p[ic][ii], list);
            }

            if (bRead)
            {
                do_cpt_int_err(xd, "swap influx netto", &swapstate->inflow_netto[ic][ii], list);
            }
            else
            {
                do_cpt_int_err(xd, "swap influx netto p", swapstate->inflow_netto_p[ic][ii], list);
            }

            if (bRead && (NULL == swapstate->nat_past[ic][ii]) )
            {
                snew(swapstate->nat_past[ic][ii], swapstate->nAverage);
            }

            for (j = 0; j < swapstate->nAverage; j++)
            {
                if (bRead)
                {
                    do_cpt_int_err(xd, "swap past atom counts", &swapstate->nat_past[ic][ii][j], list);
                }
                else
                {
                    do_cpt_int_err(xd, "swap past atom counts p", &swapstate->nat_past_p[ic][ii][j], list);
                }
            }
        }
    }

    /* Ion flux per channel */
    for (ic = 0; ic < eChanNR; ic++)
    {
        for (ii = 0; ii < eIonNR; ii++)
        {
            if (bRead)
            {
                do_cpt_int_err(xd, "channel flux", &swapstate->fluxfromAtoB[ic][ii], list);
            }
            else
            {
                do_cpt_int_err(xd, "channel flux p", swapstate->fluxfromAtoB_p[ic][ii], list);
            }
        }
    }

    /* Ion flux leakage */
    if (bRead)
    {
        snew(swapstate->fluxleak, 1);
    }
    do_cpt_int_err(xd, "flux leakage", swapstate->fluxleak, list);

    /* Ion history */
    do_cpt_int_err(xd, "number of ions", &swapstate->nions, list);

    if (bRead)
    {
        snew(swapstate->channel_label, swapstate->nions);
        snew(swapstate->comp_from, swapstate->nions);
    }

    do_cpt_u_chars(xd, "channel history", swapstate->nions, swapstate->channel_label, list);
    do_cpt_u_chars(xd, "domain history", swapstate->nions, swapstate->comp_from, list);

    /* Save the last known whole positions to checkpoint
     * file to be able to also make multimeric channels whole in PBC */
    do_cpt_int_err(xd, "Ch0 atoms", &swapstate->nat[eChan0], list);
    do_cpt_int_err(xd, "Ch1 atoms", &swapstate->nat[eChan1], list);
    if (bRead)
    {
        snew(swapstate->xc_old_whole[eChan0], swapstate->nat[eChan0]);
        snew(swapstate->xc_old_whole[eChan1], swapstate->nat[eChan1]);
        do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0], swapstate->xc_old_whole[eChan0], list);
        do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1], swapstate->xc_old_whole[eChan1], list);
    }
    else
    {
        do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0], *swapstate->xc_old_whole_p[eChan0], list);
        do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1], *swapstate->xc_old_whole_p[eChan1], list);
    }

    return ret;
}


static int do_cpt_enerhist(XDR *xd, gmx_bool bRead,
                           int fflags, energyhistory_t *enerhist,
                           FILE *list)
{
    int  i;
    int  j;
    int  ret;

    ret = 0;

    if (bRead)
    {
        enerhist->nsteps     = 0;
        enerhist->nsum       = 0;
        enerhist->nsteps_sim = 0;
        enerhist->nsum_sim   = 0;
        enerhist->dht        = NULL;

        if (fflags & (1<< eenhENERGY_DELTA_H_NN) )
        {
            snew(enerhist->dht, 1);
            enerhist->dht->ndh              = NULL;
            enerhist->dht->dh               = NULL;
            enerhist->dht->start_lambda_set = FALSE;
        }
    }

    for (i = 0; (i < eenhNR && ret == 0); i++)
    {
        if (fflags & (1<<i))
        {
            switch (i)
            {
                case eenhENERGY_N:     ret = do_cpte_int(xd, cptpEENH, i, fflags, &enerhist->nener, list); break;
                case eenhENERGY_AVER:  ret = do_cpte_doubles(xd, cptpEENH, i, fflags, enerhist->nener, &enerhist->ener_ave, list); break;
                case eenhENERGY_SUM:   ret = do_cpte_doubles(xd, cptpEENH, i, fflags, enerhist->nener, &enerhist->ener_sum, list); break;
                case eenhENERGY_NSUM:  do_cpt_step_err(xd, eenh_names[i], &enerhist->nsum, list); break;
                case eenhENERGY_SUM_SIM: ret = do_cpte_doubles(xd, cptpEENH, i, fflags, enerhist->nener, &enerhist->ener_sum_sim, list); break;
                case eenhENERGY_NSUM_SIM:   do_cpt_step_err(xd, eenh_names[i], &enerhist->nsum_sim, list); break;
                case eenhENERGY_NSTEPS:     do_cpt_step_err(xd, eenh_names[i], &enerhist->nsteps, list); break;
                case eenhENERGY_NSTEPS_SIM: do_cpt_step_err(xd, eenh_names[i], &enerhist->nsteps_sim, list); break;
                case eenhENERGY_DELTA_H_NN: do_cpt_int_err(xd, eenh_names[i], &(enerhist->dht->nndh), list);
                    if (bRead) /* now allocate memory for it */
                    {
                        snew(enerhist->dht->dh, enerhist->dht->nndh);
                        snew(enerhist->dht->ndh, enerhist->dht->nndh);
                        for (j = 0; j < enerhist->dht->nndh; j++)
                        {
                            enerhist->dht->ndh[j] = 0;
                            enerhist->dht->dh[j]  = NULL;
                        }
                    }
                    break;
                case eenhENERGY_DELTA_H_LIST:
                    for (j = 0; j < enerhist->dht->nndh; j++)
                    {
                        ret = do_cpte_n_reals(xd, cptpEENH, i, fflags, &enerhist->dht->ndh[j], &(enerhist->dht->dh[j]), list);
                    }
                    break;
                case eenhENERGY_DELTA_H_STARTTIME:
                    ret = do_cpte_double(xd, cptpEENH, i, fflags, &(enerhist->dht->start_time), list); break;
                case eenhENERGY_DELTA_H_STARTLAMBDA:
                    ret = do_cpte_double(xd, cptpEENH, i, fflags, &(enerhist->dht->start_lambda), list); break;
                default:
                    gmx_fatal(FARGS, "Unknown energy history entry %d\n"
                              "You are probably reading a new checkpoint file with old code", i);
            }
        }
    }

    if ((fflags & (1<<eenhENERGY_SUM)) && !(fflags & (1<<eenhENERGY_SUM_SIM)))
    {
        /* Assume we have an old file format and copy sum to sum_sim */
        srenew(enerhist->ener_sum_sim, enerhist->nener);
        for (i = 0; i < enerhist->nener; i++)
        {
            enerhist->ener_sum_sim[i] = enerhist->ener_sum[i];
        }
        fflags |= (1<<eenhENERGY_SUM_SIM);
    }

    if ( (fflags & (1<<eenhENERGY_NSUM)) &&
         !(fflags & (1<<eenhENERGY_NSTEPS)))
    {
        /* Assume we have an old file format and copy nsum to nsteps */
        enerhist->nsteps = enerhist->nsum;
        fflags          |= (1<<eenhENERGY_NSTEPS);
    }
    if ( (fflags & (1<<eenhENERGY_NSUM_SIM)) &&
         !(fflags & (1<<eenhENERGY_NSTEPS_SIM)))
    {
        /* Assume we have an old file format and copy nsum to nsteps */
        enerhist->nsteps_sim = enerhist->nsum_sim;
        fflags              |= (1<<eenhENERGY_NSTEPS_SIM);
    }

    return ret;
}

static int do_cpt_df_hist(XDR *xd, int fflags, df_history_t *dfhist, FILE *list)
{
    int  i, nlambda;
    int  ret;

    nlambda = dfhist->nlambda;
    ret     = 0;

    for (i = 0; (i < edfhNR && ret == 0); i++)
    {
        if (fflags & (1<<i))
        {
            switch (i)
            {
                case edfhBEQUIL:       ret = do_cpte_int(xd, cptpEDFH, i, fflags, &dfhist->bEquil, list); break;
                case edfhNATLAMBDA:    ret = do_cpte_ints(xd, cptpEDFH, i, fflags, nlambda, &dfhist->n_at_lam, list); break;
                case edfhWLHISTO:      ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->wl_histo, list); break;
                case edfhWLDELTA:      ret = do_cpte_real(xd, cptpEDFH, i, fflags, &dfhist->wl_delta, list); break;
                case edfhSUMWEIGHTS:   ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_weights, list); break;
                case edfhSUMDG:        ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_dg, list); break;
                case edfhSUMMINVAR:    ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_minvar, list); break;
                case edfhSUMVAR:       ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_variance, list); break;
                case edfhACCUMP:       ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_p, list); break;
                case edfhACCUMM:       ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_m, list); break;
                case edfhACCUMP2:      ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_p2, list); break;
                case edfhACCUMM2:      ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_m2, list); break;
                case edfhTIJ:          ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->Tij, list); break;
                case edfhTIJEMP:       ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->Tij_empirical, list); break;

                default:
                    gmx_fatal(FARGS, "Unknown df history entry %d\n"
                              "You are probably reading a new checkpoint file with old code", i);
            }
        }
    }

    return ret;
}


/* This function stores the last whole configuration of the reference and
 * average structure in the .cpt file
 */
static int do_cpt_EDstate(XDR *xd, gmx_bool bRead,
                          edsamstate_t *EDstate, FILE *list)
{
    int  i, j;
    int  ret = 0;
    char buf[STRLEN];


    EDstate->bFromCpt = bRead;

    if (EDstate->nED <= 0)
    {
        return ret;
    }

    /* When reading, init_edsam has not been called yet,
     * so we have to allocate memory first. */
    if (bRead)
    {
        snew(EDstate->nref, EDstate->nED);
        snew(EDstate->old_sref, EDstate->nED);
        snew(EDstate->nav, EDstate->nED);
        snew(EDstate->old_sav, EDstate->nED);
    }

    /* Read/write the last whole conformation of SREF and SAV for each ED dataset (usually only one) */
    for (i = 0; i < EDstate->nED; i++)
    {
        /* Reference structure SREF */
        sprintf(buf, "ED%d # of atoms in reference structure", i+1);
        do_cpt_int_err(xd, buf, &EDstate->nref[i], list);
        sprintf(buf, "ED%d x_ref", i+1);
        if (bRead)
        {
            snew(EDstate->old_sref[i], EDstate->nref[i]);
            do_cpt_n_rvecs_err(xd, buf, EDstate->nref[i], EDstate->old_sref[i], list);
        }
        else
        {
            do_cpt_n_rvecs_err(xd, buf, EDstate->nref[i], EDstate->old_sref_p[i], list);
        }

        /* Average structure SAV */
        sprintf(buf, "ED%d # of atoms in average structure", i+1);
        do_cpt_int_err(xd, buf, &EDstate->nav[i], list);
        sprintf(buf, "ED%d x_av", i+1);
        if (bRead)
        {
            snew(EDstate->old_sav[i], EDstate->nav[i]);
            do_cpt_n_rvecs_err(xd, buf, EDstate->nav[i], EDstate->old_sav[i], list);
        }
        else
        {
            do_cpt_n_rvecs_err(xd, buf, EDstate->nav[i], EDstate->old_sav_p[i], list);
        }
    }

    return ret;
}


static int do_cpt_files(XDR *xd, gmx_bool bRead,
                        gmx_file_position_t **p_outputfiles, int *nfiles,
                        FILE *list, int file_version)
{
    int                  i, j;
    gmx_off_t            offset;
    gmx_off_t            mask = 0xFFFFFFFFL;
    int                  offset_high, offset_low;
    char                *buf;
    gmx_file_position_t *outputfiles;

    if (do_cpt_int(xd, "number of output files", nfiles, list) != 0)
    {
        return -1;
    }

    if (bRead)
    {
        snew(*p_outputfiles, *nfiles);
    }

    outputfiles = *p_outputfiles;

    for (i = 0; i < *nfiles; i++)
    {
        /* 64-bit XDR numbers are not portable, so it is stored as separate high/low fractions */
        if (bRead)
        {
            do_cpt_string_err(xd, bRead, "output filename", &buf, list);
            strncpy(outputfiles[i].filename, buf, CPTSTRLEN-1);
            if (list == NULL)
            {
                sfree(buf);
            }

            if (do_cpt_int(xd, "file_offset_high", &offset_high, list) != 0)
            {
                return -1;
            }
            if (do_cpt_int(xd, "file_offset_low", &offset_low, list) != 0)
            {
                return -1;
            }
            outputfiles[i].offset = ( ((gmx_off_t) offset_high) << 32 ) | ( (gmx_off_t) offset_low & mask );
        }
        else
        {
            buf = outputfiles[i].filename;
            do_cpt_string_err(xd, bRead, "output filename", &buf, list);
            /* writing */
            offset      = outputfiles[i].offset;
            if (offset == -1)
            {
                offset_low  = -1;
                offset_high = -1;
            }
            else
            {
                offset_low  = (int) (offset & mask);
                offset_high = (int) ((offset >> 32) & mask);
            }
            if (do_cpt_int(xd, "file_offset_high", &offset_high, list) != 0)
            {
                return -1;
            }
            if (do_cpt_int(xd, "file_offset_low", &offset_low, list) != 0)
            {
                return -1;
            }
        }
        if (file_version >= 8)
        {
            if (do_cpt_int(xd, "file_checksum_size", &(outputfiles[i].chksum_size),
                           list) != 0)
            {
                return -1;
            }
            if (do_cpt_u_chars(xd, "file_checksum", 16, outputfiles[i].chksum, list) != 0)
            {
                return -1;
            }
        }
        else
        {
            outputfiles[i].chksum_size = -1;
        }
    }
    return 0;
}


void write_checkpoint(const char *fn, gmx_bool bNumberAndKeep,
                      FILE *fplog, t_commrec *cr,
                      int eIntegrator, int simulation_part,
                      gmx_bool bExpanded, int elamstats,
                      gmx_int64_t step, double t, t_state *state)
{
    t_fileio            *fp;
    int                  file_version;
    char                *version;
    char                *btime;
    char                *buser;
    char                *bhost;
    int                  double_prec;
    char                *fprog;
    char                *fntemp; /* the temporary checkpoint file name */
    time_t               now;
    char                 timebuf[STRLEN];
    int                  nppnodes, npmenodes, flag_64bit;
    char                 buf[1024], suffix[5+STEPSTRSIZE], sbuf[STEPSTRSIZE];
    gmx_file_position_t *outputfiles;
    int                  noutputfiles;
    char                *ftime;
    int                  flags_eks, flags_enh, flags_dfh, i;
    t_fileio            *ret;

    if (DOMAINDECOMP(cr))
    {
        nppnodes  = cr->dd->nnodes;
        npmenodes = cr->npmenodes;
    }
    else
    {
        nppnodes  = 1;
        npmenodes = 0;
    }

#ifndef GMX_NO_RENAME
    /* make the new temporary filename */
    snew(fntemp, strlen(fn)+5+STEPSTRSIZE);
    strcpy(fntemp, fn);
    fntemp[strlen(fn) - strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
    sprintf(suffix, "_%s%s", "step", gmx_step_str(step, sbuf));
    strcat(fntemp, suffix);
    strcat(fntemp, fn+strlen(fn) - strlen(ftp2ext(fn2ftp(fn))) - 1);
#else
    /* if we can't rename, we just overwrite the cpt file.
     * dangerous if interrupted.
     */
    snew(fntemp, strlen(fn));
    strcpy(fntemp, fn);
#endif
    time(&now);
    gmx_ctime_r(&now, timebuf, STRLEN);

    if (fplog)
    {
        fprintf(fplog, "Writing checkpoint, step %s at %s\n\n",
                gmx_step_str(step, buf), timebuf);
    }

    /* Get offsets for open files */
    gmx_fio_get_output_file_positions(&outputfiles, &noutputfiles);

    fp = gmx_fio_open(fntemp, "w");

    if (state->ekinstate.bUpToDate)
    {
        flags_eks =
            ((1<<eeksEKIN_N) | (1<<eeksEKINH) | (1<<eeksEKINF) |
             (1<<eeksEKINO) | (1<<eeksEKINSCALEF) | (1<<eeksEKINSCALEH) |
             (1<<eeksVSCALE) | (1<<eeksDEKINDL) | (1<<eeksMVCOS));
    }
    else
    {
        flags_eks = 0;
    }

    flags_enh = 0;
    if (state->enerhist.nsum > 0 || state->enerhist.nsum_sim > 0)
    {
        flags_enh |= (1<<eenhENERGY_N);
        if (state->enerhist.nsum > 0)
        {
            flags_enh |= ((1<<eenhENERGY_AVER) | (1<<eenhENERGY_SUM) |
                          (1<<eenhENERGY_NSTEPS) | (1<<eenhENERGY_NSUM));
        }
        if (state->enerhist.nsum_sim > 0)
        {
            flags_enh |= ((1<<eenhENERGY_SUM_SIM) | (1<<eenhENERGY_NSTEPS_SIM) |
                          (1<<eenhENERGY_NSUM_SIM));
        }
        if (state->enerhist.dht)
        {
            flags_enh |= ( (1<< eenhENERGY_DELTA_H_NN) |
                           (1<< eenhENERGY_DELTA_H_LIST) |
                           (1<< eenhENERGY_DELTA_H_STARTTIME) |
                           (1<< eenhENERGY_DELTA_H_STARTLAMBDA) );
        }
    }

    if (bExpanded)
    {
        flags_dfh = ((1<<edfhBEQUIL) | (1<<edfhNATLAMBDA) | (1<<edfhSUMWEIGHTS) |  (1<<edfhSUMDG)  |
                     (1<<edfhTIJ) | (1<<edfhTIJEMP));
        if (EWL(elamstats))
        {
            flags_dfh |= ((1<<edfhWLDELTA) | (1<<edfhWLHISTO));
        }
        if ((elamstats == elamstatsMINVAR) || (elamstats == elamstatsBARKER) || (elamstats == elamstatsMETROPOLIS))
        {
            flags_dfh |= ((1<<edfhACCUMP) | (1<<edfhACCUMM) | (1<<edfhACCUMP2) | (1<<edfhACCUMM2)
                          | (1<<edfhSUMMINVAR) | (1<<edfhSUMVAR));
        }
    }
    else
    {
        flags_dfh = 0;
    }

    /* We can check many more things now (CPU, acceleration, etc), but
     * it is highly unlikely to have two separate builds with exactly
     * the same version, user, time, and build host!
     */

    version = gmx_strdup(gmx_version());
    btime   = gmx_strdup(BUILD_TIME);
    buser   = gmx_strdup(BUILD_USER);
    bhost   = gmx_strdup(BUILD_HOST);

    double_prec = GMX_CPT_BUILD_DP;
    fprog       = gmx_strdup(Program());

    ftime   = &(timebuf[0]);

    do_cpt_header(gmx_fio_getxdr(fp), FALSE, &file_version,
                  &version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
                  &eIntegrator, &simulation_part, &step, &t, &nppnodes,
                  DOMAINDECOMP(cr) ? cr->dd->nc : NULL, &npmenodes,
                  &state->natoms, &state->ngtc, &state->nnhpres,
                  &state->nhchainlength, &(state->dfhist.nlambda), &state->flags, &flags_eks, &flags_enh, &flags_dfh,
                  &state->edsamstate.nED, &state->swapstate.eSwapCoords,
                  NULL);

    sfree(version);
    sfree(btime);
    sfree(buser);
    sfree(bhost);
    sfree(fprog);

    if ((do_cpt_state(gmx_fio_getxdr(fp), FALSE, state->flags, state, NULL) < 0)        ||
        (do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, NULL) < 0) ||
        (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, flags_enh, &state->enerhist, NULL) < 0)  ||
        (do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL) < 0)  ||
        (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, &state->edsamstate, NULL) < 0)      ||
        (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, &state->swapstate, NULL) < 0) ||
        (do_cpt_files(gmx_fio_getxdr(fp), FALSE, &outputfiles, &noutputfiles, NULL,
                      file_version) < 0))
    {
        gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
    }

    do_cpt_footer(gmx_fio_getxdr(fp), file_version);

    /* we really, REALLY, want to make sure to physically write the checkpoint,
       and all the files it depends on, out to disk. Because we've
       opened the checkpoint with gmx_fio_open(), it's in our list
       of open files.  */
    ret = gmx_fio_all_output_fsync();

    if (ret)
    {
        char buf[STRLEN];
        sprintf(buf,
                "Cannot fsync '%s'; maybe you are out of disk space?",
                gmx_fio_getname(ret));

        if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == NULL)
        {
            gmx_file(buf);
        }
        else
        {
            gmx_warning(buf);
        }
    }

    if (gmx_fio_close(fp) != 0)
    {
        gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
    }

    /* we don't move the checkpoint if the user specified they didn't want it,
       or if the fsyncs failed */
#ifndef GMX_NO_RENAME
    if (!bNumberAndKeep && !ret)
    {
        if (gmx_fexist(fn))
        {
            /* Rename the previous checkpoint file */
            strcpy(buf, fn);
            buf[strlen(fn) - strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
            strcat(buf, "_prev");
            strcat(buf, fn+strlen(fn) - strlen(ftp2ext(fn2ftp(fn))) - 1);
#ifndef GMX_FAHCORE
            /* we copy here so that if something goes wrong between now and
             * the rename below, there's always a state.cpt.
             * If renames are atomic (such as in POSIX systems),
             * this copying should be unneccesary.
             */
            gmx_file_copy(fn, buf, FALSE);
            /* We don't really care if this fails:
             * there's already a new checkpoint.
             */
#else
            gmx_file_rename(fn, buf);
#endif
        }
        if (gmx_file_rename(fntemp, fn) != 0)
        {
            gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
        }
    }
#endif  /* GMX_NO_RENAME */

    sfree(outputfiles);
    sfree(fntemp);

#ifdef GMX_FAHCORE
    /*code for alternate checkpointing scheme.  moved from top of loop over
       steps */
    fcRequestCheckPoint();
    if (fcCheckPointParallel( cr->nodeid, NULL, 0) == 0)
    {
        gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", step );
    }
#endif /* end GMX_FAHCORE block */
}

static void print_flag_mismatch(FILE *fplog, int sflags, int fflags)
{
    int i;

    fprintf(fplog, "\nState entry mismatch between the simulation and the checkpoint file\n");
    fprintf(fplog, "Entries which are not present in the checkpoint file will not be updated\n");
    fprintf(fplog, "  %24s    %11s    %11s\n", "", "simulation", "checkpoint");
    for (i = 0; i < estNR; i++)
    {
        if ((sflags & (1<<i)) || (fflags & (1<<i)))
        {
            fprintf(fplog, "  %24s    %11s    %11s\n",
                    est_names[i],
                    (sflags & (1<<i)) ? "  present  " : "not present",
                    (fflags & (1<<i)) ? "  present  " : "not present");
        }
    }
}

static void check_int(FILE *fplog, const char *type, int p, int f, gmx_bool *mm)
{
    FILE *fp = fplog ? fplog : stderr;

    if (p != f)
    {
        fprintf(fp, "  %s mismatch,\n", type);
        fprintf(fp, "    current program: %d\n", p);
        fprintf(fp, "    checkpoint file: %d\n", f);
        fprintf(fp, "\n");
        *mm = TRUE;
    }
}

static void check_string(FILE *fplog, const char *type, const char *p,
                         const char *f, gmx_bool *mm)
{
    FILE *fp = fplog ? fplog : stderr;

    if (strcmp(p, f) != 0)
    {
        fprintf(fp, "  %s mismatch,\n", type);
        fprintf(fp, "    current program: %s\n", p);
        fprintf(fp, "    checkpoint file: %s\n", f);
        fprintf(fp, "\n");
        *mm = TRUE;
    }
}

static void check_match(FILE *fplog,
                        char *version,
                        char *btime, char *buser, char *bhost, int double_prec,
                        char *fprog,
                        t_commrec *cr, int npp_f, int npme_f,
                        ivec dd_nc, ivec dd_nc_f)
{
    int      npp;
    gmx_bool mm                 = FALSE;
    gmx_bool patchlevel_differs = FALSE;
    gmx_bool version_differs    = FALSE;

    check_string(fplog, "Version", gmx_version(), version, &mm);
    patchlevel_differs = mm;

    if (patchlevel_differs)
    {
        /* Gromacs should be able to continue from checkpoints between
         * different patch level versions, but we do not guarantee
         * compatibility between different major/minor versions - check this.
         */
        int   gmx_major, gmx_minor;
        int   cpt_major, cpt_minor;
        sscanf(gmx_version(), "VERSION %d.%d", &gmx_major, &gmx_minor);
        sscanf(version, "VERSION %d.%d", &cpt_major, &cpt_minor);
        version_differs = (gmx_major != cpt_major || gmx_minor != cpt_minor);
    }

    check_string(fplog, "Build time", BUILD_TIME, btime, &mm);
    check_string(fplog, "Build user", BUILD_USER, buser, &mm);
    check_string(fplog, "Build host", BUILD_HOST, bhost, &mm);
    check_int   (fplog, "Double prec.", GMX_CPT_BUILD_DP, double_prec, &mm);
    check_string(fplog, "Program name", Program(), fprog, &mm);

    check_int   (fplog, "#nodes", cr->nnodes, npp_f+npme_f, &mm);
    if (cr->nnodes > 1)
    {
        check_int (fplog, "#PME-nodes", cr->npmenodes, npme_f, &mm);

        npp = cr->nnodes;
        if (cr->npmenodes >= 0)
        {
            npp -= cr->npmenodes;
        }
        if (npp == npp_f)
        {
            check_int (fplog, "#DD-cells[x]", dd_nc[XX], dd_nc_f[XX], &mm);
            check_int (fplog, "#DD-cells[y]", dd_nc[YY], dd_nc_f[YY], &mm);
            check_int (fplog, "#DD-cells[z]", dd_nc[ZZ], dd_nc_f[ZZ], &mm);
        }
    }

    if (mm)
    {
        const char msg_version_difference[] =
            "The current Gromacs major & minor version are not identical to those that\n"
            "generated the checkpoint file. In principle Gromacs does not support\n"
            "continuation from checkpoints between different versions, so we advise\n"
            "against this. If you still want to try your luck we recommend that you use\n"
            "the -noappend flag to keep your output files from the two versions separate.\n"
            "This might also work around errors where the output fields in the energy\n"
            "file have changed between the different major & minor versions.\n";

        const char msg_mismatch_notice[] =
            "Gromacs patchlevel, binary or parallel settings differ from previous run.\n"
            "Continuation is exact, but not guaranteed to be binary identical.\n";

        const char msg_logdetails[] =
            "See the log file for details.\n";

        if (version_differs)
        {
            fprintf(stderr, "%s%s\n", msg_version_difference, fplog ? msg_logdetails : "");

            if (fplog)
            {
                fprintf(fplog, "%s\n", msg_version_difference);
            }
        }
        else
        {
            /* Major & minor versions match at least, but something is different. */
            fprintf(stderr, "%s%s\n", msg_mismatch_notice, fplog ? msg_logdetails : "");
            if (fplog)
            {
                fprintf(fplog, "%s\n", msg_mismatch_notice);
            }
        }
    }
}

static void read_checkpoint(const char *fn, FILE **pfplog,
                            t_commrec *cr, ivec dd_nc,
                            int eIntegrator, int *init_fep_state, gmx_int64_t *step, double *t,
                            t_state *state, gmx_bool *bReadEkin,
                            int *simulation_part,
                            gmx_bool bAppendOutputFiles, gmx_bool bForceAppend)
{
    t_fileio            *fp;
    int                  i, j, rc;
    int                  file_version;
    char                *version, *btime, *buser, *bhost, *fprog, *ftime;
    int                  double_prec;
    char                 filename[STRLEN], buf[STEPSTRSIZE];
    int                  nppnodes, eIntegrator_f, nppnodes_f, npmenodes_f;
    ivec                 dd_nc_f;
    int                  natoms, ngtc, nnhpres, nhchainlength, nlambda, fflags, flags_eks, flags_enh, flags_dfh;
    int                  d;
    int                  ret;
    gmx_file_position_t *outputfiles;
    int                  nfiles;
    t_fileio            *chksum_file;
    FILE               * fplog = *pfplog;
    unsigned char        digest[16];
#if !defined __native_client__ && !defined GMX_NATIVE_WINDOWS
    struct flock         fl; /* don't initialize here: the struct order is OS
                                dependent! */
#endif

    const char *int_warn =
        "WARNING: The checkpoint file was generated with integrator %s,\n"
        "         while the simulation uses integrator %s\n\n";

#if !defined __native_client__ && !defined GMX_NATIVE_WINDOWS
    fl.l_type   = F_WRLCK;
    fl.l_whence = SEEK_SET;
    fl.l_start  = 0;
    fl.l_len    = 0;
    fl.l_pid    = 0;
#endif

    fp = gmx_fio_open(fn, "r");
    do_cpt_header(gmx_fio_getxdr(fp), TRUE, &file_version,
                  &version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
                  &eIntegrator_f, simulation_part, step, t,
                  &nppnodes_f, dd_nc_f, &npmenodes_f,
                  &natoms, &ngtc, &nnhpres, &nhchainlength, &nlambda,
                  &fflags, &flags_eks, &flags_enh, &flags_dfh,
                  &state->edsamstate.nED, &state->swapstate.eSwapCoords, NULL);

    if (bAppendOutputFiles &&
        file_version >= 13 && double_prec != GMX_CPT_BUILD_DP)
    {
        gmx_fatal(FARGS, "Output file appending requested, but the code and checkpoint file precision (single/double) don't match");
    }

    if (cr == NULL || MASTER(cr))
    {
        fprintf(stderr, "\nReading checkpoint file %s generated: %s\n\n",
                fn, ftime);
    }

    /* This will not be written if we do appending, since fplog is still NULL then */
    if (fplog)
    {
        fprintf(fplog, "\n");
        fprintf(fplog, "Reading checkpoint file %s\n", fn);
        fprintf(fplog, "  file generated by:     %s\n", fprog);
        fprintf(fplog, "  file generated at:     %s\n", ftime);
        fprintf(fplog, "  GROMACS build time:    %s\n", btime);
        fprintf(fplog, "  GROMACS build user:    %s\n", buser);
        fprintf(fplog, "  GROMACS build host:    %s\n", bhost);
        fprintf(fplog, "  GROMACS double prec.:  %d\n", double_prec);
        fprintf(fplog, "  simulation part #:     %d\n", *simulation_part);
        fprintf(fplog, "  step:                  %s\n", gmx_step_str(*step, buf));
        fprintf(fplog, "  time:                  %f\n", *t);
        fprintf(fplog, "\n");
    }

    if (natoms != state->natoms)
    {
        gmx_fatal(FARGS, "Checkpoint file is for a system of %d atoms, while the current system consists of %d atoms", natoms, state->natoms);
    }
    if (ngtc != state->ngtc)
    {
        gmx_fatal(FARGS, "Checkpoint file is for a system of %d T-coupling groups, while the current system consists of %d T-coupling groups", ngtc, state->ngtc);
    }
    if (nnhpres != state->nnhpres)
    {
        gmx_fatal(FARGS, "Checkpoint file is for a system of %d NH-pressure-coupling variables, while the current system consists of %d NH-pressure-coupling variables", nnhpres, state->nnhpres);
    }

    if (nlambda != state->dfhist.nlambda)
    {
        gmx_fatal(FARGS, "Checkpoint file is for a system with %d lambda states, while the current system consists of %d lambda states", nlambda, state->dfhist.nlambda);
    }

    init_gtc_state(state, state->ngtc, state->nnhpres, nhchainlength); /* need to keep this here to keep the tpr format working */
    /* write over whatever was read; we use the number of Nose-Hoover chains from the checkpoint */

    if (eIntegrator_f != eIntegrator)
    {
        if (MASTER(cr))
        {
            fprintf(stderr, int_warn, EI(eIntegrator_f), EI(eIntegrator));
        }
        if (bAppendOutputFiles)
        {
            gmx_fatal(FARGS,
                      "Output file appending requested, but input/checkpoint integrators do not match.\n"
                      "Stopping the run to prevent you from ruining all your data...\n"
                      "If you _really_ know what you are doing, try with the -noappend option.\n");
        }
        if (fplog)
        {
            fprintf(fplog, int_warn, EI(eIntegrator_f), EI(eIntegrator));
        }
    }

    if (!PAR(cr))
    {
        nppnodes      = 1;
        cr->npmenodes = 0;
    }
    else if (cr->nnodes == nppnodes_f + npmenodes_f)
    {
        if (cr->npmenodes < 0)
        {
            cr->npmenodes = npmenodes_f;
        }
        nppnodes = cr->nnodes - cr->npmenodes;
        if (nppnodes == nppnodes_f)
        {
            for (d = 0; d < DIM; d++)
            {
                if (dd_nc[d] == 0)
                {
                    dd_nc[d] = dd_nc_f[d];
                }
            }
        }
    }
    else
    {
        /* The number of PP nodes has not been set yet */
        nppnodes = -1;
    }

    if (fflags != state->flags)
    {

        if (MASTER(cr))
        {
            if (bAppendOutputFiles)
            {
                gmx_fatal(FARGS,
                          "Output file appending requested, but input and checkpoint states are not identical.\n"
                          "Stopping the run to prevent you from ruining all your data...\n"
                          "You can try with the -noappend option, and get more info in the log file.\n");
            }

            if (getenv("GMX_ALLOW_CPT_MISMATCH") == NULL)
            {
                gmx_fatal(FARGS, "You seem to have switched ensemble, integrator, T and/or P-coupling algorithm between the cpt and tpr file. The recommended way of doing this is passing the cpt file to grompp (with option -t) instead of to mdrun. If you know what you are doing, you can override this error by setting the env.var. GMX_ALLOW_CPT_MISMATCH");
            }
            else
            {
                fprintf(stderr,
                        "WARNING: The checkpoint state entries do not match the simulation,\n"
                        "         see the log file for details\n\n");
            }
        }

        if (fplog)
        {
            print_flag_mismatch(fplog, state->flags, fflags);
        }
    }
    else
    {
        if (MASTER(cr))
        {
            check_match(fplog, version, btime, buser, bhost, double_prec, fprog,
                        cr, nppnodes_f, npmenodes_f, dd_nc, dd_nc_f);
        }
    }
    ret             = do_cpt_state(gmx_fio_getxdr(fp), TRUE, fflags, state, NULL);
    *init_fep_state = state->fep_state;  /* there should be a better way to do this than setting it here.
                                            Investigate for 5.0. */
    if (ret)
    {
        cp_error();
    }
    ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, NULL);
    if (ret)
    {
        cp_error();
    }
    *bReadEkin = ((flags_eks & (1<<eeksEKINH)) || (flags_eks & (1<<eeksEKINF)) || (flags_eks & (1<<eeksEKINO)) ||
                  ((flags_eks & (1<<eeksEKINSCALEF)) | (flags_eks & (1<<eeksEKINSCALEH)) | (flags_eks & (1<<eeksVSCALE))));

    ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE,
                          flags_enh, &state->enerhist, NULL);
    if (ret)
    {
        cp_error();
    }

    if (file_version < 6)
    {
        const char *warn = "Reading checkpoint file in old format, assuming that the run that generated this file started at step 0, if this is not the case the averages stored in the energy file will be incorrect.";

        fprintf(stderr, "\nWARNING: %s\n\n", warn);
        if (fplog)
        {
            fprintf(fplog, "\nWARNING: %s\n\n", warn);
        }
        state->enerhist.nsum     = *step;
        state->enerhist.nsum_sim = *step;
    }

    ret = do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state->swapstate, NULL);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state->edsamstate, NULL);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE, &outputfiles, &nfiles, NULL, file_version);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_footer(gmx_fio_getxdr(fp), file_version);
    if (ret)
    {
        cp_error();
    }
    if (gmx_fio_close(fp) != 0)
    {
        gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
    }

    sfree(fprog);
    sfree(ftime);
    sfree(btime);
    sfree(buser);
    sfree(bhost);

    /* If the user wants to append to output files,
     * we use the file pointer positions of the output files stored
     * in the checkpoint file and truncate the files such that any frames
     * written after the checkpoint time are removed.
     * All files are md5sum checked such that we can be sure that
     * we do not truncate other (maybe imprortant) files.
     */
    if (bAppendOutputFiles)
    {
        if (fn2ftp(outputfiles[0].filename) != efLOG)
        {
            /* make sure first file is log file so that it is OK to use it for
             * locking
             */
            gmx_fatal(FARGS, "The first output file should always be the log "
                      "file but instead is: %s. Cannot do appending because of this condition.", outputfiles[0].filename);
        }
        for (i = 0; i < nfiles; i++)
        {
            if (outputfiles[i].offset < 0)
            {
                gmx_fatal(FARGS, "The original run wrote a file called '%s' which "
                          "is larger than 2 GB, but mdrun did not support large file"
                          " offsets. Can not append. Run mdrun with -noappend",
                          outputfiles[i].filename);
            }
#ifdef GMX_FAHCORE
            chksum_file = gmx_fio_open(outputfiles[i].filename, "a");

#else
            chksum_file = gmx_fio_open(outputfiles[i].filename, "r+");

            /* lock log file */
            if (i == 0)
            {
                /* Note that there are systems where the lock operation
                 * will succeed, but a second process can also lock the file.
                 * We should probably try to detect this.
                 */
#if defined __native_client__
                errno = ENOSYS;
                if (1)

#elif defined GMX_NATIVE_WINDOWS
                if (_locking(fileno(gmx_fio_getfp(chksum_file)), _LK_NBLCK, LONG_MAX) == -1)
#else
                if (fcntl(fileno(gmx_fio_getfp(chksum_file)), F_SETLK, &fl) == -1)
#endif
                {
                    if (errno == ENOSYS)
                    {
                        if (!bForceAppend)
                        {
                            gmx_fatal(FARGS, "File locking is not supported on this system. Use -noappend or specify -append explicitly to append anyhow.");
                        }
                        else
                        {
                            fprintf(stderr, "\nNOTE: File locking is not supported on this system, will not lock %s\n\n", outputfiles[i].filename);
                            if (fplog)
                            {
                                fprintf(fplog, "\nNOTE: File locking not supported on this system, will not lock %s\n\n", outputfiles[i].filename);
                            }
                        }
                    }
                    else if (errno == EACCES || errno == EAGAIN)
                    {
                        gmx_fatal(FARGS, "Failed to lock: %s. Already running "
                                  "simulation?", outputfiles[i].filename);
                    }
                    else
                    {
                        gmx_fatal(FARGS, "Failed to lock: %s. %s.",
                                  outputfiles[i].filename, strerror(errno));
                    }
                }
            }

            /* compute md5 chksum */
            if (outputfiles[i].chksum_size != -1)
            {
                if (gmx_fio_get_file_md5(chksum_file, outputfiles[i].offset,
                                         digest) != outputfiles[i].chksum_size) /*at the end of the call the file position is at the end of the file*/
                {
                    gmx_fatal(FARGS, "Can't read %d bytes of '%s' to compute checksum. The file has been replaced or its contents have been modified. Cannot do appending because of this condition.",
                              outputfiles[i].chksum_size,
                              outputfiles[i].filename);
                }
            }
            if (i == 0)  /*log file needs to be seeked in case we need to truncate (other files are truncated below)*/
            {
                if (gmx_fio_seek(chksum_file, outputfiles[i].offset))
                {
                    gmx_fatal(FARGS, "Seek error! Failed to truncate log-file: %s.", strerror(errno));
                }
            }
#endif

            if (i == 0) /*open log file here - so that lock is never lifted
                           after chksum is calculated */
            {
                *pfplog = gmx_fio_getfp(chksum_file);
            }
            else
            {
                gmx_fio_close(chksum_file);
            }
#ifndef GMX_FAHCORE
            /* compare md5 chksum */
            if (outputfiles[i].chksum_size != -1 &&
                memcmp(digest, outputfiles[i].chksum, 16) != 0)
            {
                if (debug)
                {
                    fprintf(debug, "chksum for %s: ", outputfiles[i].filename);
                    for (j = 0; j < 16; j++)
                    {
                        fprintf(debug, "%02x", digest[j]);
                    }
                    fprintf(debug, "\n");
                }
                gmx_fatal(FARGS, "Checksum wrong for '%s'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition.",
                          outputfiles[i].filename);
            }
#endif


            if (i != 0) /*log file is already seeked to correct position */
            {
#ifdef GMX_NATIVE_WINDOWS
                rc = gmx_wintruncate(outputfiles[i].filename, outputfiles[i].offset);
#else
                rc = truncate(outputfiles[i].filename, outputfiles[i].offset);
#endif
                if (rc != 0)
                {
                    gmx_fatal(FARGS, "Truncation of file %s failed. Cannot do appending because of this failure.", outputfiles[i].filename);
                }
            }
        }
    }

    sfree(outputfiles);
}


void load_checkpoint(const char *fn, FILE **fplog,
                     t_commrec *cr, ivec dd_nc,
                     t_inputrec *ir, t_state *state,
                     gmx_bool *bReadEkin,
                     gmx_bool bAppend, gmx_bool bForceAppend)
{
    gmx_int64_t     step;
    double          t;

    if (SIMMASTER(cr))
    {
        /* Read the state from the checkpoint file */
        read_checkpoint(fn, fplog,
                        cr, dd_nc,
                        ir->eI, &(ir->fepvals->init_fep_state), &step, &t, state, bReadEkin,
                        &ir->simulation_part, bAppend, bForceAppend);
    }
    if (PAR(cr))
    {
        gmx_bcast(sizeof(cr->npmenodes), &cr->npmenodes, cr);
        gmx_bcast(DIM*sizeof(dd_nc[0]), dd_nc, cr);
        gmx_bcast(sizeof(step), &step, cr);
        gmx_bcast(sizeof(*bReadEkin), bReadEkin, cr);
    }
    ir->bContinuation    = TRUE;
    if (ir->nsteps >= 0)
    {
        ir->nsteps          += ir->init_step - step;
    }
    ir->init_step        = step;
    ir->simulation_part += 1;
}

static void read_checkpoint_data(t_fileio *fp, int *simulation_part,
                                 gmx_int64_t *step, double *t, t_state *state,
                                 int *nfiles, gmx_file_position_t **outputfiles)
{
    int                  file_version;
    char                *version, *btime, *buser, *bhost, *fprog, *ftime;
    int                  double_prec;
    int                  eIntegrator;
    int                  nppnodes, npme;
    ivec                 dd_nc;
    int                  flags_eks, flags_enh, flags_dfh;
    int                  nfiles_loc;
    gmx_file_position_t *files_loc = NULL;
    int                  ret;

    do_cpt_header(gmx_fio_getxdr(fp), TRUE, &file_version,
                  &version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
                  &eIntegrator, simulation_part, step, t, &nppnodes, dd_nc, &npme,
                  &state->natoms, &state->ngtc, &state->nnhpres, &state->nhchainlength,
                  &(state->dfhist.nlambda), &state->flags, &flags_eks, &flags_enh, &flags_dfh,
                  &state->edsamstate.nED, &state->swapstate.eSwapCoords, NULL);
    ret =
        do_cpt_state(gmx_fio_getxdr(fp), TRUE, state->flags, state, NULL);
    if (ret)
    {
        cp_error();
    }
    ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, NULL);
    if (ret)
    {
        cp_error();
    }
    ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE,
                          flags_enh, &state->enerhist, NULL);
    if (ret)
    {
        cp_error();
    }
    ret = do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state->edsamstate, NULL);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state->swapstate, NULL);
    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE,
                       outputfiles != NULL ? outputfiles : &files_loc,
                       outputfiles != NULL ? nfiles : &nfiles_loc,
                       NULL, file_version);
    if (files_loc != NULL)
    {
        sfree(files_loc);
    }

    if (ret)
    {
        cp_error();
    }

    ret = do_cpt_footer(gmx_fio_getxdr(fp), file_version);
    if (ret)
    {
        cp_error();
    }

    sfree(fprog);
    sfree(ftime);
    sfree(btime);
    sfree(buser);
    sfree(bhost);
}

void
read_checkpoint_state(const char *fn, int *simulation_part,
                      gmx_int64_t *step, double *t, t_state *state)
{
    t_fileio *fp;

    fp = gmx_fio_open(fn, "r");
    read_checkpoint_data(fp, simulation_part, step, t, state, NULL, NULL);
    if (gmx_fio_close(fp) != 0)
    {
        gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
    }
}

void read_checkpoint_trxframe(t_fileio *fp, t_trxframe *fr)
{
    /* This next line is nasty because the sub-structures of t_state
     * cannot be assumed to be zeroed (or even initialized in ways the
     * rest of the code might assume). Using snew would be better, but
     * this will all go away for 5.0. */
    t_state         state;
    int             simulation_part;
    gmx_int64_t     step;
    double          t;

    init_state(&state, 0, 0, 0, 0, 0);

    read_checkpoint_data(fp, &simulation_part, &step, &t, &state, NULL, NULL);

    fr->natoms  = state.natoms;
    fr->bTitle  = FALSE;
    fr->bStep   = TRUE;
    fr->step    = gmx_int64_to_int(step,
                                   "conversion of checkpoint to trajectory");
    fr->bTime      = TRUE;
    fr->time       = t;
    fr->bLambda    = TRUE;
    fr->lambda     = state.lambda[efptFEP];
    fr->fep_state  = state.fep_state;
    fr->bAtoms     = FALSE;
    fr->bX         = (state.flags & (1<<estX));
    if (fr->bX)
    {
        fr->x     = state.x;
        state.x   = NULL;
    }
    fr->bV      = (state.flags & (1<<estV));
    if (fr->bV)
    {
        fr->v     = state.v;
        state.v   = NULL;
    }
    fr->bF      = FALSE;
    fr->bBox    = (state.flags & (1<<estBOX));
    if (fr->bBox)
    {
        copy_mat(state.box, fr->box);
    }
    done_state(&state);
}

void list_checkpoint(const char *fn, FILE *out)
{
    t_fileio            *fp;
    int                  file_version;
    char                *version, *btime, *buser, *bhost, *fprog, *ftime;
    int                  double_prec;
    int                  eIntegrator, simulation_part, nppnodes, npme;
    gmx_int64_t          step;
    double               t;
    ivec                 dd_nc;
    t_state              state;
    int                  flags_eks, flags_enh, flags_dfh;
    int                  indent;
    int                  i, j;
    int                  ret;
    gmx_file_position_t *outputfiles;
    int                  nfiles;

    init_state(&state, -1, -1, -1, -1, 0);

    fp = gmx_fio_open(fn, "r");
    do_cpt_header(gmx_fio_getxdr(fp), TRUE, &file_version,
                  &version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
                  &eIntegrator, &simulation_part, &step, &t, &nppnodes, dd_nc, &npme,
                  &state.natoms, &state.ngtc, &state.nnhpres, &state.nhchainlength,
                  &(state.dfhist.nlambda), &state.flags,
                  &flags_eks, &flags_enh, &flags_dfh, &state.edsamstate.nED,
                  &state.swapstate.eSwapCoords, out);
    ret = do_cpt_state(gmx_fio_getxdr(fp), TRUE, state.flags, &state, out);
    if (ret)
    {
        cp_error();
    }
    ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state.ekinstate, out);
    if (ret)
    {
        cp_error();
    }
    ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE,
                          flags_enh, &state.enerhist, out);

    if (ret == 0)
    {
        ret = do_cpt_df_hist(gmx_fio_getxdr(fp),
                             flags_dfh, &state.dfhist, out);
    }

    if (ret == 0)
    {
        ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state.edsamstate, out);
    }

    if (ret == 0)
    {
        ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state.swapstate, out);
    }

    if (ret == 0)
    {
        do_cpt_files(gmx_fio_getxdr(fp), TRUE, &outputfiles, &nfiles, out, file_version);
    }

    if (ret == 0)
    {
        ret = do_cpt_footer(gmx_fio_getxdr(fp), file_version);
    }

    if (ret)
    {
        cp_warning(out);
    }
    if (gmx_fio_close(fp) != 0)
    {
        gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
    }

    done_state(&state);
}


static gmx_bool exist_output_file(const char *fnm_cp, int nfile, const t_filenm fnm[])
{
    int i;

    /* Check if the output file name stored in the checkpoint file
     * is one of the output file names of mdrun.
     */
    i = 0;
    while (i < nfile &&
           !(is_output(&fnm[i]) && strcmp(fnm_cp, fnm[i].fns[0]) == 0))
    {
        i++;
    }

    return (i < nfile && gmx_fexist(fnm_cp));
}

/* This routine cannot print tons of data, since it is called before the log file is opened. */
gmx_bool read_checkpoint_simulation_part(const char *filename, int *simulation_part,
                                         gmx_int64_t *cpt_step, t_commrec *cr,
                                         gmx_bool bAppendReq,
                                         int nfile, const t_filenm fnm[],
                                         const char *part_suffix, gmx_bool *bAddPart)
{
    t_fileio            *fp;
    gmx_int64_t          step = 0;
    double               t;
    /* This next line is nasty because the sub-structures of t_state
     * cannot be assumed to be zeroed (or even initialized in ways the
     * rest of the code might assume). Using snew would be better, but
     * this will all go away for 5.0. */
    t_state              state;
    int                  nfiles;
    gmx_file_position_t *outputfiles;
    int                  nexist, f;
    gmx_bool             bAppend;
    char                *fn, suf_up[STRLEN];

    bAppend = FALSE;

    if (SIMMASTER(cr))
    {
        if (!gmx_fexist(filename) || (!(fp = gmx_fio_open(filename, "r")) ))
        {
            *simulation_part = 0;
        }
        else
        {
            init_state(&state, 0, 0, 0, 0, 0);

            read_checkpoint_data(fp, simulation_part, &step, &t, &state,
                                 &nfiles, &outputfiles);
            if (gmx_fio_close(fp) != 0)
            {
                gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
            }
            done_state(&state);

            if (bAppendReq)
            {
                nexist = 0;
                for (f = 0; f < nfiles; f++)
                {
                    if (exist_output_file(outputfiles[f].filename, nfile, fnm))
                    {
                        nexist++;
                    }
                }
                if (nexist == nfiles)
                {
                    bAppend = bAppendReq;
                }
                else if (nexist > 0)
                {
                    fprintf(stderr,
                            "Output file appending has been requested,\n"
                            "but some output files listed in the checkpoint file %s\n"
                            "are not present or are named differently by the current program:\n",
                            filename);
                    fprintf(stderr, "output files present:");
                    for (f = 0; f < nfiles; f++)
                    {
                        if (exist_output_file(outputfiles[f].filename,
                                              nfile, fnm))
                        {
                            fprintf(stderr, " %s", outputfiles[f].filename);
                        }
                    }
                    fprintf(stderr, "\n");
                    fprintf(stderr, "output files not present or named differently:");
                    for (f = 0; f < nfiles; f++)
                    {
                        if (!exist_output_file(outputfiles[f].filename,
                                               nfile, fnm))
                        {
                            fprintf(stderr, " %s", outputfiles[f].filename);
                        }
                    }
                    fprintf(stderr, "\n");

                    gmx_fatal(FARGS, "File appending requested, but %d of the %d output files are not present or are named differently", nfiles-nexist, nfiles);
                }
            }

            if (bAppend)
            {
                if (nfiles == 0)
                {
                    gmx_fatal(FARGS, "File appending requested, but no output file information is stored in the checkpoint file");
                }
                fn = outputfiles[0].filename;
                if (strlen(fn) < 4 ||
                    gmx_strcasecmp(fn+strlen(fn)-4, ftp2ext(efLOG)) == 0)
                {
                    gmx_fatal(FARGS, "File appending requested, but the log file is not the first file listed in the checkpoint file");
                }
                /* Set bAddPart to whether the suffix string '.part' is present
                 * in the log file name.
                 */
                strcpy(suf_up, part_suffix);
                upstring(suf_up);
                *bAddPart = (strstr(fn, part_suffix) != NULL ||
                             strstr(fn, suf_up) != NULL);
            }

            sfree(outputfiles);
        }
    }
    if (PAR(cr))
    {
        gmx_bcast(sizeof(*simulation_part), simulation_part, cr);

        if (*simulation_part > 0 && bAppendReq)
        {
            gmx_bcast(sizeof(bAppend), &bAppend, cr);
            gmx_bcast(sizeof(*bAddPart), bAddPart, cr);
        }
    }
    if (NULL != cpt_step)
    {
        *cpt_step = step;
    }

    return bAppend;
}