main.c

/*******************************************************************************
 * This file is part of SWIFT.
 * Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
 *                    Matthieu Schaller (matthieu.schaller@durham.ac.uk)
 *               2015 Peter W. Draper (p.w.draper@durham.ac.uk)
 *                    Angus Lepper (angus.lepper@ed.ac.uk)
 *               2016 John A. Regan (john.a.regan@durham.ac.uk)
 *                    Tom Theuns (tom.theuns@durham.ac.uk)
 *
 * This program 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 3 of the License, or
 * (at your option) any later version.
 *
 * This program 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 General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/

/* Config parameters. */
#include "../config.h"

/* Some standard headers. */
#include <errno.h>
#include <fenv.h>
#include <libgen.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <unistd.h>

/* MPI headers. */
#ifdef WITH_MPI
#include <mpi.h>
#endif

/* Local headers. */
#include "argparse.h"
#include "swift.h"

/* Engine policy flags. */
#ifndef ENGINE_POLICY
#define ENGINE_POLICY engine_policy_none
#endif

/* Global profiler. */
struct profiler prof;

/*  Usage string. */
static const char *const swift_usage[] = {
    "swift [options] [[--] param-file]",
    "swift [options] param-file",
    "swift_mpi [options] [[--] param-file]",
    "swift_mpi [options] param-file",
    NULL,
};

/* Function to handle multiple -P arguments. */
struct cmdparams {
  const char *param[PARSER_MAX_NO_OF_PARAMS];
  int nparam;
};

static int handle_cmdparam(struct argparse *self,
                           const struct argparse_option *opt) {
  struct cmdparams *cmdps = (struct cmdparams *)opt->data;
  cmdps->param[cmdps->nparam] = *(char **)opt->value;
  cmdps->nparam++;
  return 1;
}

/**
 * @brief Main routine that loads a few particles and generates some output.
 *
 */
int main(int argc, char *argv[]) {

  struct clocks_time tic, toc;
  struct engine e;

  /* Structs used by the engine. Declare now to make sure these are always in
   * scope.  */
  struct chemistry_global_data chemistry;
  struct cooling_function_data cooling_func;
  struct cosmology cosmo;
  struct external_potential potential;
  struct star_formation starform;
  struct pm_mesh mesh;
  struct gpart *gparts = NULL;
  struct gravity_props gravity_properties;
  struct hydro_props hydro_properties;
  struct stars_props stars_properties;
  struct feedback_props feedback_properties;
  struct entropy_floor_properties entropy_floor;
  struct black_holes_props black_holes_properties;
  struct fof_props fof_properties;
  struct part *parts = NULL;
  struct phys_const prog_const;
  struct space s;
  struct spart *sparts = NULL;
  struct bpart *bparts = NULL;
  struct unit_system us;

  int nr_nodes = 1, myrank = 0;

#ifdef WITH_MPI
  /* Start by initializing MPI. */
  int res = 0, prov = 0;
  if ((res = MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &prov)) !=
      MPI_SUCCESS)
    error("Call to MPI_Init failed with error %i.", res);
  if (prov != MPI_THREAD_MULTIPLE)
    error(
        "MPI does not provide the level of threading"
        " required (MPI_THREAD_MULTIPLE).");
  if ((res = MPI_Comm_size(MPI_COMM_WORLD, &nr_nodes)) != MPI_SUCCESS)
    error("MPI_Comm_size failed with error %i.", res);
  if ((res = MPI_Comm_rank(MPI_COMM_WORLD, &myrank)) != MPI_SUCCESS)
    error("Call to MPI_Comm_rank failed with error %i.", res);

  /* Make sure messages are stamped with the correct rank and step. */
  engine_rank = myrank;
  engine_current_step = 0;

  if ((res = MPI_Comm_set_errhandler(MPI_COMM_WORLD, MPI_ERRORS_RETURN)) !=
      MPI_SUCCESS)
    error("Call to MPI_Comm_set_errhandler failed with error %i.", res);
  if (myrank == 0)
    printf("[0000] [00000.0] main: MPI is up and running with %i node(s).\n\n",
           nr_nodes);
  if (nr_nodes == 1) {
    message("WARNING: you are running with one MPI rank.");
    message("WARNING: you should use the non-MPI version of this program.");
  }
  fflush(stdout);

#endif

  /* Welcome to SWIFT, you made the right choice */
  if (myrank == 0) greetings(/*fof=*/0);

  int with_aff = 0;
  int dry_run = 0;
  int dump_tasks = 0;
  int dump_threadpool = 0;
  int nsteps = -2;
  int restart = 0;
  int with_cosmology = 0;
  int with_external_gravity = 0;
  int with_temperature = 0;
  int with_cooling = 0;
  int with_self_gravity = 0;
  int with_hydro = 0;
  int with_stars = 0;
  int with_fof = 0;
  int with_star_formation = 0;
  int with_feedback = 0;
  int with_black_holes = 0;
  int with_limiter = 0;
  int with_fp_exceptions = 0;
  int with_drift_all = 0;
  int with_mpole_reconstruction = 0;
  int with_structure_finding = 0;
  int verbose = 0;
  int nr_threads = 1;
  int with_verbose_timers = 0;
  char *output_parameters_filename = NULL;
  char *cpufreqarg = NULL;
  char *param_filename = NULL;
  char restart_file[200] = "";
  unsigned long long cpufreq = 0;
  struct cmdparams cmdps;
  cmdps.nparam = 0;
  cmdps.param[0] = NULL;
  char *buffer = NULL;

  /* Parse the command-line parameters. */
  struct argparse_option options[] = {
      OPT_HELP(),

      OPT_GROUP("  Simulation options:\n"),
      OPT_BOOLEAN('b', "feedback", &with_feedback, "Run with stars feedback.",
                  NULL, 0, 0),
      OPT_BOOLEAN('c', "cosmology", &with_cosmology,
                  "Run with cosmological time integration.", NULL, 0, 0),
      OPT_BOOLEAN(0, "temperature", &with_temperature,
                  "Run with temperature calculation.", NULL, 0, 0),
      OPT_BOOLEAN('C', "cooling", &with_cooling,
                  "Run with cooling (also switches on --temperature).", NULL, 0,
                  0),
      OPT_BOOLEAN('D', "drift-all", &with_drift_all,
                  "Always drift all particles even the ones far from active "
                  "particles. This emulates Gadget-[23] and GIZMO's default "
                  "behaviours.",
                  NULL, 0, 0),
      OPT_BOOLEAN('F', "star-formation", &with_star_formation,
                  "Run with star formation.", NULL, 0, 0),
      OPT_BOOLEAN('g', "external-gravity", &with_external_gravity,
                  "Run with an external gravitational potential.", NULL, 0, 0),
      OPT_BOOLEAN('G', "self-gravity", &with_self_gravity,
                  "Run with self-gravity.", NULL, 0, 0),
      OPT_BOOLEAN('M', "multipole-reconstruction", &with_mpole_reconstruction,
                  "Reconstruct the multipoles every time-step.", NULL, 0, 0),
      OPT_BOOLEAN('s', "hydro", &with_hydro, "Run with hydrodynamics.", NULL, 0,
                  0),
      OPT_BOOLEAN('S', "stars", &with_stars, "Run with stars.", NULL, 0, 0),
      OPT_BOOLEAN('B', "black-holes", &with_black_holes,
                  "Run with black holes.", NULL, 0, 0),
      OPT_BOOLEAN(
          'u', "fof", &with_fof,
          "Run Friends-of-Friends algorithm to perform black hole seeding.",
          NULL, 0, 0),
      OPT_BOOLEAN('x', "velociraptor", &with_structure_finding,
                  "Run with structure finding.", NULL, 0, 0),
      OPT_BOOLEAN(0, "limiter", &with_limiter, "Run with time-step limiter.",
                  NULL, 0, 0),

      OPT_GROUP("  Control options:\n"),
      OPT_BOOLEAN('a', "pin", &with_aff,
                  "Pin runners using processor affinity.", NULL, 0, 0),
      OPT_BOOLEAN('d', "dry-run", &dry_run,
                  "Dry run. Read the parameter file, allocates memory but does "
                  "not read the particles from ICs. Exits before the start of "
                  "time integration. Checks the validity of parameters and IC "
                  "files as well as memory limits.",
                  NULL, 0, 0),
      OPT_BOOLEAN('e', "fpe", &with_fp_exceptions,
                  "Enable floating-point exceptions (debugging mode).", NULL, 0,
                  0),
      OPT_STRING('f', "cpu-frequency", &cpufreqarg,
                 "Overwrite the CPU "
                 "frequency (Hz) to be used for time measurements.",
                 NULL, 0, 0),
      OPT_INTEGER('n', "steps", &nsteps,
                  "Execute a fixed number of time steps. When unset use the "
                  "time_end parameter to stop.",
                  NULL, 0, 0),
      OPT_STRING('o', "output-params", &output_parameters_filename,
                 "Generate a parameter file with the options for selecting the "
                 "output fields.",
                 NULL, 0, 0),
      OPT_STRING('P', "param", &buffer,
                 "Set parameter value, overiding the value read from the "
                 "parameter file. Can be used more than once {sec:par:value}.",
                 handle_cmdparam, (intptr_t)&cmdps, 0),
      OPT_BOOLEAN('r', "restart", &restart, "Continue using restart files.",
                  NULL, 0, 0),
      OPT_INTEGER('t', "threads", &nr_threads,
                  "The number of threads to use on each MPI rank. Defaults to "
                  "1 if not specified.",
                  NULL, 0, 0),
      OPT_INTEGER('T', "timers", &with_verbose_timers,
                  "Print timers every time-step.", NULL, 0, 0),
      OPT_INTEGER('v', "verbose", &verbose,
                  "Run in verbose mode, in MPI mode 2 outputs from all ranks.",
                  NULL, 0, 0),
      OPT_INTEGER('y', "task-dumps", &dump_tasks,
                  "Time-step frequency at which task graphs are dumped.", NULL,
                  0, 0),
      OPT_INTEGER('Y', "threadpool-dumps", &dump_threadpool,
                  "Time-step frequency at which threadpool tasks are dumped.",
                  NULL, 0, 0),
      OPT_END(),
  };
  struct argparse argparse;
  argparse_init(&argparse, options, swift_usage, 0);
  argparse_describe(&argparse, "\nParameters:",
                    "\nSee the file examples/parameter_example.yml for an "
                    "example of parameter file.");
  int nargs = argparse_parse(&argparse, argc, (const char **)argv);

  /* Write output parameter file */
  if (myrank == 0 && output_parameters_filename != NULL) {
    io_write_output_field_parameter(output_parameters_filename);
    printf("End of run.\n");
    return 0;
  }

  /* Need a parameter file. */
  if (nargs != 1) {
    if (myrank == 0) argparse_usage(&argparse);
    printf("\nError: no parameter file was supplied.\n");
    return 1;
  }
  param_filename = argv[0];

  /* Checks of options. */
#if !defined(HAVE_SETAFFINITY) || !defined(HAVE_LIBNUMA)
  if (with_aff) {
    printf("Error: no NUMA support for thread affinity\n");
    return 1;
  }
#endif

#ifndef HAVE_FE_ENABLE_EXCEPT
  if (with_fp_exceptions) {
    printf("Error: no support for floating point exceptions\n");
    return 1;
  }
#endif

#ifndef HAVE_VELOCIRAPTOR
  if (with_structure_finding) {
    printf("Error: VELOCIraptor is not available\n");
    return 1;
  }
#endif

#ifndef SWIFT_DEBUG_TASKS
  if (dump_tasks) {
    if (myrank == 0) {
      message(
          "WARNING: complete task dumps are only created when "
          "configured with --enable-task-debugging.");
      message("         Basic task statistics will be output.");
    }
  }
#endif

#ifndef SWIFT_DEBUG_THREADPOOL
  if (dump_threadpool) {
    printf(
        "Error: threadpool dumping is only possible if SWIFT was "
        "configured with the --enable-threadpool-debugging option.\n");
    return 1;
  }
#endif

  /* The CPU frequency is a long long, so we need to parse that ourselves. */
  if (cpufreqarg != NULL) {
    if (sscanf(cpufreqarg, "%llu", &cpufreq) != 1) {
      if (myrank == 0)
        printf("Error parsing CPU frequency (%s).\n", cpufreqarg);
      return 1;
    }
  }

  if (!with_self_gravity && !with_hydro && !with_external_gravity) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf("\nError: At least one of -s, -g or -G must be chosen.\n");
    }
    return 1;
  }
  if (with_stars && !with_external_gravity && !with_self_gravity) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf(
          "\nError: Cannot process stars without gravity, -g or -G "
          "must be chosen.\n");
    }
    return 1;
  }

  if (with_black_holes && !with_self_gravity) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf(
          "\nError: Cannot process black holes without self-gravity, -G must "
          "be chosen.\n");
    }
    return 1;
  }

  if (with_fof && !with_self_gravity) {
    if (myrank == 0)
      printf(
          "Error: Cannot perform FOF search without gravity, -g or -G must be "
          "chosen.\n");
    return 1;
  }

  if (with_fof && !with_black_holes) {
    if (myrank == 0)
      printf(
          "Error: Cannot perform FOF seeding without black holes being in use, "
          "-B must be chosen.\n");
    return 1;
  }

  if (!with_stars && with_star_formation) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf(
          "\nError: Cannot process star formation without stars, --stars must "
          "be chosen.\n");
    }
    return 1;
  }

  if (!with_stars && with_feedback) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf(
          "\nError: Cannot process feedback without stars, --stars must be "
          "chosen.\n");
    }
    return 1;
  }

  if (!with_hydro && with_feedback) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf(
          "\nError: Cannot process feedback without gas, --hydro must be "
          "chosen.\n");
    }
    return 1;
  }

  if (!with_hydro && with_black_holes) {
    if (myrank == 0) {
      argparse_usage(&argparse);
      printf(
          "\nError: Cannot process black holes without gas, --hydro must be "
          "chosen.\n");
    }
    return 1;
  }

/* Let's pin the main thread, now we know if affinity will be used. */
#if defined(HAVE_SETAFFINITY) && defined(HAVE_LIBNUMA) && defined(_GNU_SOURCE)
  if (with_aff &&
      ((ENGINE_POLICY)&engine_policy_setaffinity) == engine_policy_setaffinity)
    engine_pin();
#endif

  /* Genesis 1.1: And then, there was time ! */
  clocks_set_cpufreq(cpufreq);

  /* How vocal are we ? */
  const int talking = (verbose == 1 && myrank == 0) || (verbose == 2);

  if (myrank == 0 && dry_run)
    message(
        "Executing a dry run. No i/o or time integration will be performed.");

  /* Report CPU frequency.*/
  cpufreq = clocks_get_cpufreq();
  if (myrank == 0) {
    message("CPU frequency used for tick conversion: %llu Hz", cpufreq);
  }

/* Report host name(s). */
#ifdef WITH_MPI
  if (talking) {
    message("Rank %d running on: %s", myrank, hostname());
  }
#else
  message("Running on: %s", hostname());
#endif

/* Do we have debugging checks ? */
#ifdef SWIFT_DEBUG_CHECKS
  if (myrank == 0)
    message("WARNING: Debugging checks activated. Code will be slower !");
#endif

/* Do we have debugging checks ? */
#ifdef SWIFT_USE_NAIVE_INTERACTIONS
  if (myrank == 0)
    message(
        "WARNING: Naive cell interactions activated. Code will be slower !");
#endif

/* Do we have gravity accuracy checks ? */
#ifdef SWIFT_GRAVITY_FORCE_CHECKS
  if (myrank == 0)
    message(
        "WARNING: Checking 1/%d of all gpart for gravity accuracy. Code will "
        "be slower !",
        SWIFT_GRAVITY_FORCE_CHECKS);
#endif

  /* Do we choke on FP-exceptions ? */
  if (with_fp_exceptions) {
#ifdef HAVE_FE_ENABLE_EXCEPT
    feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
#endif
    if (myrank == 0)
      message("WARNING: Floating point exceptions will be reported.");
  }

/* Do we have slow barriers? */
#ifndef HAVE_PTHREAD_BARRIERS
  if (myrank == 0)
    message("WARNING: Non-optimal thread barriers are being used.");
#endif

  /* How large are the parts? */
  if (myrank == 0) {
    message("sizeof(part)        is %4zi bytes.", sizeof(struct part));
    message("sizeof(xpart)       is %4zi bytes.", sizeof(struct xpart));
    message("sizeof(spart)       is %4zi bytes.", sizeof(struct spart));
    message("sizeof(bpart)       is %4zi bytes.", sizeof(struct bpart));
    message("sizeof(gpart)       is %4zi bytes.", sizeof(struct gpart));
    message("sizeof(multipole)   is %4zi bytes.", sizeof(struct multipole));
    message("sizeof(grav_tensor) is %4zi bytes.", sizeof(struct grav_tensor));
    message("sizeof(task)        is %4zi bytes.", sizeof(struct task));
    message("sizeof(cell)        is %4zi bytes.", sizeof(struct cell));
  }

  /* Read the parameter file */
  struct swift_params *params =
      (struct swift_params *)malloc(sizeof(struct swift_params));
  if (params == NULL) error("Error allocating memory for the parameter file.");
  if (myrank == 0) {
    message("Reading runtime parameters from file '%s'", param_filename);
    parser_read_file(param_filename, params);

    /* Handle any command-line overrides. */
    if (cmdps.nparam > 0) {
      message(
          "Overwriting values read from the YAML file with command-line "
          "values.");
      for (int k = 0; k < cmdps.nparam; k++)
        parser_set_param(params, cmdps.param[k]);
    }
  }
#ifdef WITH_MPI
  /* Broadcast the parameter file */
  MPI_Bcast(params, sizeof(struct swift_params), MPI_BYTE, 0, MPI_COMM_WORLD);
#endif

  /* Temporary early aborts for modes not supported over MPI. */
#ifdef WITH_MPI
  if (with_mpole_reconstruction && nr_nodes > 1)
    error("Cannot reconstruct m-poles every step over MPI (yet).");
  if (with_limiter) error("Can't run with time-step limiter over MPI (yet)");
#endif

    /* Temporary early aborts for modes not supported with hand-vec. */
#if defined(WITH_VECTORIZATION) && defined(GADGET2_SPH) && \
    !defined(CHEMISTRY_NONE)
  error(
      "Cannot run with chemistry and hand-vectorization (yet). "
      "Use --disable-hand-vec at configure time.");
#endif

  /* Check that we can write the snapshots by testing if the output
   * directory exists and is searchable and writable. */
  char basename[PARSER_MAX_LINE_SIZE];
  parser_get_param_string(params, "Snapshots:basename", basename);
  const char *dirp = dirname(basename);
  if (access(dirp, W_OK | X_OK) != 0) {
    error("Cannot write snapshots in directory %s (%s)", dirp, strerror(errno));
  }

  /* Check that we can write the structure finding catalogues by testing if the
   * output directory exists and is searchable and writable. */
  if (with_structure_finding) {
    char stfbasename[PARSER_MAX_LINE_SIZE];
    parser_get_param_string(params, "StructureFinding:basename", stfbasename);
    const char *stfdirp = dirname(stfbasename);
    if (access(stfdirp, W_OK | X_OK) != 0) {
      error("Cannot write stf catalogues in directory %s (%s)", stfdirp,
            strerror(errno));
    }
  }

  /* Prepare the domain decomposition scheme */
  struct repartition reparttype;
#ifdef WITH_MPI
  struct partition initial_partition;
  partition_init(&initial_partition, &reparttype, params, nr_nodes);

  /* Let's report what we did */
  if (myrank == 0) {
#if defined(HAVE_PARMETIS)
    if (reparttype.usemetis)
      message("Using METIS serial partitioning:");
    else
      message("Using ParMETIS partitioning:");
#elif defined(HAVE_METIS)
    message("Using METIS serial partitioning:");
#else
    message("Non-METIS partitioning:");
#endif
    message("  initial partitioning: %s",
            initial_partition_name[initial_partition.type]);
    if (initial_partition.type == INITPART_GRID)
      message("    grid set to [ %i %i %i ].", initial_partition.grid[0],
              initial_partition.grid[1], initial_partition.grid[2]);
    message("  repartitioning: %s", repartition_name[reparttype.type]);
  }
#endif

  /* Common variables for restart and IC sections. */
  int clean_smoothing_length_values = 0;
  int flag_entropy_ICs = 0;

  /* Work out where we will read and write restart files. */
  char restart_dir[PARSER_MAX_LINE_SIZE];
  parser_get_opt_param_string(params, "Restarts:subdir", restart_dir,
                              "restart");

  /* The directory must exist. */
  if (myrank == 0) {
    if (access(restart_dir, W_OK | X_OK) != 0) {
      if (restart) {
        error("Cannot restart as no restart subdirectory: %s (%s)", restart_dir,
              strerror(errno));
      } else {
        if (mkdir(restart_dir, 0777) != 0)
          error("Failed to create restart directory: %s (%s)", restart_dir,
                strerror(errno));
      }
    }
  }

  /* Basename for any restart files. */
  char restart_name[PARSER_MAX_LINE_SIZE];
  parser_get_opt_param_string(params, "Restarts:basename", restart_name,
                              "swift");

  /* How often to check for the stop file and dump restarts and exit the
   * application. */
  const int restart_stop_steps =
      parser_get_opt_param_int(params, "Restarts:stop_steps", 100);

  /* Get the maximal wall-clock time of this run */
  const float restart_max_hours_runtime =
      parser_get_opt_param_float(params, "Restarts:max_run_time", FLT_MAX);

  /* Do we want to resubmit when we hit the limit? */
  const int resubmit_after_max_hours =
      parser_get_opt_param_int(params, "Restarts:resubmit_on_exit", 0);

  /* What command should we run to resubmit at the end? */
  char resubmit_command[PARSER_MAX_LINE_SIZE];
  if (resubmit_after_max_hours)
    parser_get_param_string(params, "Restarts:resubmit_command",
                            resubmit_command);

  /* If restarting, look for the restart files. */
  if (restart) {

    /* Attempting a restart. */
    char **restart_files = NULL;
    int restart_nfiles = 0;

    if (myrank == 0) {
      message("Restarting SWIFT");

      /* Locate the restart files. */
      restart_files =
          restart_locate(restart_dir, restart_name, &restart_nfiles);
      if (restart_nfiles == 0)
        error("Failed to locate any restart files in %s", restart_dir);

      /* We need one file per rank. */
      if (restart_nfiles != nr_nodes)
        error("Incorrect number of restart files, expected %d found %d",
              nr_nodes, restart_nfiles);

      if (verbose > 0)
        for (int i = 0; i < restart_nfiles; i++)
          message("found restart file: %s", restart_files[i]);
    }

#ifdef WITH_MPI
    /* Distribute the restart files, need one for each rank. */
    if (myrank == 0) {

      for (int i = 1; i < nr_nodes; i++) {
        strcpy(restart_file, restart_files[i]);
        MPI_Send(restart_file, 200, MPI_BYTE, i, 0, MPI_COMM_WORLD);
      }

      /* Keep local file. */
      strcpy(restart_file, restart_files[0]);

      /* Finished with the list. */
      restart_locate_free(restart_nfiles, restart_files);

    } else {
      MPI_Recv(restart_file, 200, MPI_BYTE, 0, 0, MPI_COMM_WORLD,
               MPI_STATUS_IGNORE);
    }
    if (verbose > 1) message("local restart file = %s", restart_file);
#else

    /* Just one restart file. */
    strcpy(restart_file, restart_files[0]);
#endif

    /* Now read it. */
    restart_read(&e, restart_file);

    /* And initialize the engine with the space and policies. */
    if (myrank == 0) clocks_gettime(&tic);
    engine_config(/*restart=*/1, /*fof=*/0, &e, params, nr_nodes, myrank,
                  nr_threads, with_aff, talking, restart_file);
    if (myrank == 0) {
      clocks_gettime(&toc);
      message("engine_config took %.3f %s.", clocks_diff(&tic, &toc),
              clocks_getunit());
      fflush(stdout);
    }

    /* Check if we are already done when given steps on the command-line. */
    if (e.step >= nsteps && nsteps > 0)
      error("Not restarting, already completed %d steps", e.step);

  } else {

    /* Not restarting so look for the ICs. */
    /* Initialize unit system and constants */
    units_init_from_params(&us, params, "InternalUnitSystem");
    phys_const_init(&us, params, &prog_const);
    if (myrank == 0) {
      message("Internal unit system: U_M = %e g.", us.UnitMass_in_cgs);
      message("Internal unit system: U_L = %e cm.", us.UnitLength_in_cgs);
      message("Internal unit system: U_t = %e s.", us.UnitTime_in_cgs);
      message("Internal unit system: U_I = %e A.", us.UnitCurrent_in_cgs);
      message("Internal unit system: U_T = %e K.", us.UnitTemperature_in_cgs);
      phys_const_print(&prog_const);
    }

    /* Read particles and space information from ICs */
    char ICfileName[200] = "";
    parser_get_param_string(params, "InitialConditions:file_name", ICfileName);
    const int periodic =
        parser_get_param_int(params, "InitialConditions:periodic");
    const int replicate =
        parser_get_opt_param_int(params, "InitialConditions:replicate", 1);
    clean_smoothing_length_values = parser_get_opt_param_int(
        params, "InitialConditions:cleanup_smoothing_lengths", 0);
    const int cleanup_h = parser_get_opt_param_int(
        params, "InitialConditions:cleanup_h_factors", 0);
    const int cleanup_sqrt_a = parser_get_opt_param_int(
        params, "InitialConditions:cleanup_velocity_factors", 0);
    const int generate_gas_in_ics = parser_get_opt_param_int(
        params, "InitialConditions:generate_gas_in_ics", 0);

    /* Some checks that we are not doing something stupid */
    if (generate_gas_in_ics && flag_entropy_ICs)
      error("Can't generate gas if the entropy flag is set in the ICs.");
    if (generate_gas_in_ics && !with_cosmology)
      error("Can't generate gas if the run is not cosmological.");

    /* Initialise the cosmology */
    if (with_cosmology)
      cosmology_init(params, &us, &prog_const, &cosmo);
    else
      cosmology_init_no_cosmo(&cosmo);
    if (myrank == 0 && with_cosmology) cosmology_print(&cosmo);

    /* Initialise the hydro properties */
    if (with_hydro)
      hydro_props_init(&hydro_properties, &prog_const, &us, params);
    else
      bzero(&hydro_properties, sizeof(struct hydro_props));

    /* Initialise the equation of state */
    if (with_hydro)
      eos_init(&eos, &prog_const, &us, params);
    else
      bzero(&eos, sizeof(struct eos_parameters));

    /* Initialise the entropy floor */
    if (with_hydro)
      entropy_floor_init(&entropy_floor, &prog_const, &us, &hydro_properties,
                         params);
    else
      bzero(&entropy_floor, sizeof(struct entropy_floor_properties));

    /* Initialise the stars properties */
    if (with_stars)
      stars_props_init(&stars_properties, &prog_const, &us, params,
                       &hydro_properties, &cosmo);
    else
      bzero(&stars_properties, sizeof(struct stars_props));

    /* Initialise the feedback properties */
    if (with_feedback) {
#ifdef FEEDBACK_NONE
      error("ERROR: Running with feedback but compiled without it.");
#endif
      feedback_props_init(&feedback_properties, &prog_const, &us, params,
                          &hydro_properties, &cosmo);
    } else
      bzero(&feedback_properties, sizeof(struct feedback_props));

    /* Initialise the black holes properties */
    if (with_black_holes) {
#ifdef BLACK_HOLES_NONE
      error("ERROR: Running with black_holes but compiled without it.");
#endif
      black_holes_props_init(&black_holes_properties, &prog_const, &us, params,
                             &hydro_properties, &cosmo);
    } else
      bzero(&black_holes_properties, sizeof(struct black_holes_props));

    /* Initialise the gravity properties */
    bzero(&gravity_properties, sizeof(struct gravity_props));
    if (with_self_gravity)
      gravity_props_init(&gravity_properties, params, &prog_const, &cosmo,
                         with_cosmology, periodic);

      /* Initialise the cooling function properties */
#ifdef COOLING_NONE
    if (with_cooling || with_temperature) {
      error(
          "ERROR: Running with cooling / temperature calculation"
          " but compiled without it.");
    }
#else
    if (!with_cooling && !with_temperature) {
      error(
          "ERROR: Compiled with cooling but running without it. "
          "Did you forget the --cooling or --temperature flags?");
    }
#endif
    bzero(&cooling_func, sizeof(struct cooling_function_data));
    if (with_cooling || with_temperature) {
      cooling_init(params, &us, &prog_const, &hydro_properties, &cooling_func);
    }
    if (myrank == 0) cooling_print(&cooling_func);

    /* Initialise the star formation law and its properties */
    bzero(&starform, sizeof(struct star_formation));
    if (with_star_formation) {
#ifdef STAR_FORMATION_NONE
      error("ERROR: Running with star formation but compiled without it!");
#endif
      starformation_init(params, &prog_const, &us, &hydro_properties,
                         &starform);
    }
    if (with_star_formation && myrank == 0) starformation_print(&starform);

    /* Initialise the chemistry */
    bzero(&chemistry, sizeof(struct chemistry_global_data));
    chemistry_init(params, &us, &prog_const, &chemistry);
    if (myrank == 0) chemistry_print(&chemistry);

    /* Initialise the FOF properties */
    bzero(&fof_properties, sizeof(struct fof_props));
    if (with_fof) fof_init(&fof_properties, params, &prog_const, &us);

    /* Be verbose about what happens next */
    if (myrank == 0) message("Reading ICs from file '%s'", ICfileName);
    if (myrank == 0 && cleanup_h)
      message("Cleaning up h-factors (h=%f)", cosmo.h);
    if (myrank == 0 && cleanup_sqrt_a)
      message("Cleaning up a-factors from velocity (a=%f)", cosmo.a);
    fflush(stdout);

    /* Get ready to read particles of all kinds */
    size_t Ngas = 0, Ngpart = 0, Nspart = 0, Nbpart = 0;
    double dim[3] = {0., 0., 0.};
    if (myrank == 0) clocks_gettime(&tic);
#if defined(HAVE_HDF5)
#if defined(WITH_MPI)
#if defined(HAVE_PARALLEL_HDF5)
    read_ic_parallel(ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts,
                     &Ngas, &Ngpart, &Nspart, &Nbpart, &flag_entropy_ICs,
                     with_hydro, (with_external_gravity || with_self_gravity),
                     with_stars, with_black_holes, cleanup_h, cleanup_sqrt_a,
                     cosmo.h, cosmo.a, myrank, nr_nodes, MPI_COMM_WORLD,
                     MPI_INFO_NULL, nr_threads, dry_run);
#else