src/gromacs/mdrunutility/handlerestart.cpp

   1 /*
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   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 /*! \internal \file
  36  *
  37  * \brief This file declares functions for mdrun to call to manage the
  38  * details of doing a restart (ie. reading checkpoints, appending
  39  * output files).
  40  *
  41  * \todo Clean up the error-prone logic here. Add doxygen.
  42  *
  43  * \author Berk Hess <hess@kth.se>
  44  * \author Erik Lindahl <erik@kth.se>
  45  * \author Mark Abraham <mark.j.abraham@gmail.com>
  46  *
  47  * \ingroup module_mdrunutility
  48  */
  49
  50 #include "gmxpre.h"
  51
  52 #include "handlerestart.h"
  53
  54 #include <string.h>
  55
  56 #include "gromacs/commandline/filenm.h"
  57 #include "gromacs/fileio/checkpoint.h"
  58 #include "gromacs/fileio/gmxfio.h"
  59 #include "gromacs/gmxlib/network.h"
  60 #include "gromacs/mdlib/main.h"
  61 #include "gromacs/mdtypes/commrec.h"
  62 #include "gromacs/utility/basedefinitions.h"
  63 #include "gromacs/utility/fatalerror.h"
  64 #include "gromacs/utility/smalloc.h"
  65
  66 /*! \brief Search for \p fnm_cp in fnm and return true iff found
  67  *
  68  * \todo This could be implemented sanely with a for loop. */
  69 static gmx_bool exist_output_file(const char *fnm_cp, int nfile, const t_filenm fnm[])
  70 {
  71     int i;
  72
  73     /* Check if the output file name stored in the checkpoint file
  74      * is one of the output file names of mdrun.
  75      */
  76     i = 0;
  77     while (i < nfile &&
  78            !(is_output(&fnm[i]) && strcmp(fnm_cp, fnm[i].fns[0]) == 0))
  79     {
  80         i++;
  81     }
  82
  83     return (i < nfile && gmx_fexist(fnm_cp));
  84 }
  85
  86 /*! \brief Support handling restarts
  87  *
  88  * \todo Clean this up (next patch)
  89  *
  90  * Read just the simulation 'generation' and with bTryToAppendFiles check files.
  91  * This is is needed at the beginning of mdrun,
  92  * to be able to rename the logfile correctly.
  93  * When file appending is requested, checks which output files are present,
  94  * and issue a fatal error if some are not.
  95  * Upon return, bAddPart will tell whether the simulation part
  96  * needs to be added to the output file name, i.e. when we are doing checkpoint
  97  * continuation without appending.
  98  *
  99  * This routine cannot print tons of data, since it is called before
 100  * the log file is opened. */
 101 static void
 102 read_checkpoint_data(const char *filename, int *simulation_part,
 103                      t_commrec *cr,
 104                      gmx_bool bTryToAppendFiles,
 105                      int nfile, const t_filenm fnm[],
 106                      const char *part_suffix,
 107                      gmx_bool *bAddPart,
 108                      bool *bDoAppendFiles)
 109 {
 110     t_fileio            *fp;
 111     int                  nfiles;
 112     gmx_file_position_t *outputfiles;
 113     int                  nexist, f;
 114     char                *fn, suf_up[STRLEN];
 115
 116     *bDoAppendFiles = FALSE;
 117
 118     if (SIMMASTER(cr))
 119     {
 120         if (!gmx_fexist(filename) || (!(fp = gmx_fio_open(filename, "r")) ))
 121         {
 122             *simulation_part = 0;
 123             /* We have already warned the user that no checkpoint file existed before, don't
 124              * need to do it again
 125              */
 126         }
 127         else
 128         {
 129             read_checkpoint_simulation_part_and_filenames(fp,
 130                                                           simulation_part,
 131                                                           &nfiles,
 132                                                           &outputfiles);
 133
 134             if (bTryToAppendFiles)
 135             {
 136                 nexist = 0;
 137                 for (f = 0; f < nfiles; f++)
 138                 {
 139                     if (exist_output_file(outputfiles[f].filename, nfile, fnm))
 140                     {
 141                         nexist++;
 142                     }
 143                 }
 144                 if (nexist == nfiles)
 145                 {
 146                     *bDoAppendFiles = bTryToAppendFiles;
 147                 }
 148                 else
 149                 {
 150                     // If we get here, the user requested restarting from a checkpoint file, that checkpoint
 151                     // file was found (so it is not the first part of a new run), but we are still missing
 152                     // some or all checkpoint files. In this case we issue a fatal error since there are
 153                     // so many special cases we cannot keep track of, and better safe than sorry.
 154                     fprintf(stderr,
 155                             "Output file appending has been requested,\n"
 156                             "but some output files listed in the checkpoint file %s\n"
 157                             "are not present or not named as the output files by the current program:\n",
 158                             filename);
 159                     fprintf(stderr, "Expect output files present:\n");
 160                     for (f = 0; f < nfiles; f++)
 161                     {
 162                         if (exist_output_file(outputfiles[f].filename,
 163                                               nfile, fnm))
 164                         {
 165                             fprintf(stderr, "  %s\n", outputfiles[f].filename);
 166                         }
 167                     }
 168                     fprintf(stderr, "\n");
 169                     fprintf(stderr, "Expected output files not present or named differently:\n");
 170                     for (f = 0; f < nfiles; f++)
 171                     {
 172                         if (!exist_output_file(outputfiles[f].filename,
 173                                                nfile, fnm))
 174                         {
 175                             fprintf(stderr, "  %s\n", outputfiles[f].filename);
 176                         }
 177                     }
 178
 179                     gmx_fatal(FARGS,
 180                               "File appending requested, but %d of the %d output files are not present or are named differently. "
 181                               "For safety reasons, GROMACS-2016 and later only allows file appending to be used when all files "
 182                               "have the same names as they had in the original run. "
 183                               "Checkpointing is merely intended for plain continuation of runs. "
 184                               "For safety reasons you must specify all file names (e.g. with -deffnm), "
 185                               "and all these files must match the names used in the run prior to checkpointing "
 186                               "since we will append to them by default. If you used -deffnm and the files listed above as not "
 187                               "present are in fact present, try explicitly specifying them in respective mdrun options. "
 188                               "If the files are not available, you "
 189                               "can add the -noappend flag to mdrun and write separate new parts. "
 190                               "For mere concatenation of files, you should use the gmx trjcat tool instead.",
 191                               nfiles-nexist, nfiles);
 192                 }
 193             }
 194
 195             if (*bDoAppendFiles)
 196             {
 197                 if (nfiles == 0)
 198                 {
 199                     gmx_fatal(FARGS, "File appending requested, but no output file information is stored in the checkpoint file");
 200                 }
 201                 fn = outputfiles[0].filename;
 202                 if (strlen(fn) < 4 ||
 203                     gmx_strcasecmp(fn+strlen(fn)-4, ftp2ext(efLOG)) == 0)
 204                 {
 205                     gmx_fatal(FARGS, "File appending requested, but the log file is not the first file listed in the checkpoint file");
 206                 }
 207                 /* Set bAddPart to whether the suffix string '.part' is present
 208                  * in the log file name.
 209                  */
 210                 strcpy(suf_up, part_suffix);
 211                 upstring(suf_up);
 212                 *bAddPart = (strstr(fn, part_suffix) != nullptr ||
 213                              strstr(fn, suf_up) != nullptr);
 214             }
 215
 216             sfree(outputfiles);
 217         }
 218     }
 219     if (PAR(cr))
 220     {
 221         // Make sure all settings are in sync
 222         gmx_bcast(sizeof(*simulation_part), simulation_part, cr);
 223
 224         if (*simulation_part > 0 && bTryToAppendFiles)
 225         {
 226             gmx_bcast(sizeof(*bDoAppendFiles), bDoAppendFiles, cr);
 227             gmx_bcast(sizeof(*bAddPart), bAddPart, cr);
 228         }
 229     }
 230 }
 231
 232 /* This routine cannot print tons of data, since it is called before the log file is opened. */
 233 void
 234 handleRestart(t_commrec            *cr,
 235               const gmx_multisim_t *ms,
 236               gmx_bool              bTryToAppendFiles,
 237               const int             NFILE,
 238               t_filenm              fnm[],
 239               bool                 *bDoAppendFiles,
 240               bool                 *bStartFromCpt)
 241 {
 242     gmx_bool        bAddPart;
 243     int             sim_part, sim_part_fn;
 244     const char     *part_suffix = ".part";
 245     FILE           *fpmulti;
 246
 247
 248     /* Check if there is ANY checkpoint file available */
 249     sim_part    = 1;
 250     sim_part_fn = sim_part;
 251     if (opt2bSet("-cpi", NFILE, fnm))
 252     {
 253         bAddPart = !bTryToAppendFiles;
 254
 255         read_checkpoint_data(opt2fn_master("-cpi", NFILE, fnm, cr),
 256                              &sim_part_fn, cr,
 257                              bTryToAppendFiles, NFILE, fnm,
 258                              part_suffix, &bAddPart, bDoAppendFiles);
 259         if (sim_part_fn == 0 && isMasterSimMasterRank(ms, cr))
 260         {
 261             fprintf(stdout, "No previous checkpoint file present with -cpi option, assuming this is a new run.\n");
 262         }
 263         else
 264         {
 265             sim_part = sim_part_fn + 1;
 266         }
 267
 268         // Master ranks of multi simulations should check that the
 269         // simulation part number is consistent across the
 270         // simulations.
 271         if (isMultiSim(ms) && MASTER(cr))
 272         {
 273             // Only the master simulation should report on problems.
 274             if (isMasterSimMasterRank(ms, cr))
 275             {
 276                 /* Log file is not yet available, so if there's a
 277                  * problem we can only write to stderr. */
 278                 fpmulti = stderr;
 279             }
 280             else
 281             {
 282                 fpmulti = nullptr;
 283             }
 284             check_multi_int(fpmulti, ms, sim_part, "simulation part", TRUE);
 285         }
 286     }
 287     else
 288     {
 289         *bDoAppendFiles = false;
 290         bAddPart        = false;
 291     }
 292
 293     *bStartFromCpt = sim_part > 1;
 294
 295     if (!*bDoAppendFiles)
 296     {
 297         sim_part_fn = sim_part;
 298     }
 299
 300     if (bAddPart)
 301     {
 302         char suffix[STRLEN];
 303
 304         /* Rename all output files (except checkpoint files) */
 305         /* create new part name first (zero-filled) */
 306         sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
 307
 308         add_suffix_to_output_names(fnm, NFILE, suffix);
 309         if (isMasterSimMasterRank(ms, cr))
 310         {
 311             fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
 312         }
 313     }
 314 }