Merge branch 'Parameter-File' into 'master'

First version of main() using a parameter file to get constants.

That's pretty big but does not touch the physics, the parallelisation nor MPI.

In brief:
 - Latest version of the parser from @jwillis 
 - More uniform name of functions in the unit module.
 - Added the ability for the `engine`, `space`, `unit` and `partition` objects to construct themselves from a parsed parameter file.
 - Added an example yaml file with full documentation.
 - Added yaml files and run scripts for the Sedov, Sod and uniform examples. 
 - General tidying of the `main()`.
 - Dropped the dependency on z-lib which we don't use.
 - Updated the README to reflect the new command-line parameters.
 - Cleaned-up the `main()` such that the only command-line parameters read in are policies and debugging options. 
 - Added the option to do a 'dry run'. This reads the parameter file, allocates the memory required by the ICs but does not read anything and constructs a space and engine. This allows us to check the validity of a given parameter file.

Happy to guide you through the changes if need be. 

This closes #81.

See merge request !140

.gitignore

@@ -43,6 +43,7 @@ tests/testTimeIntegration
 tests/testSPHStep
 tests/testKernel
 tests/testParser
+tests/parser_output.yml
 
 theory/latex/swift.pdf
 theory/kernel/kernels.pdf

README

- Welcome to the cosmological code
+ Welcome to the cosmological hydrodynamical code
     ______       _________________
    / ___/ |     / /  _/ ___/_  __/
    \__ \| | /| / // // /_   / /   
@@ -6,8 +6,26 @@
  /____/ |__/|__/___/_/    /_/     
  SPH With Inter-dependent Fine-grained Tasking
 
-Website: www.swiftsim.com
-Twitter: @SwiftSimulation
+ Website: www.swiftsim.com
+ Twitter: @SwiftSimulation
 
-See INSTALL.swift for instructions.
+See INSTALL.swift for install instructions.
 
+Usage: swift [OPTION] PARAMFILE
+
+Valid options are:
+  -c          Run with cosmological time integration
+  -d          Dry run. Read the parameter file, allocate memory but does not read 
+              the particles from ICs and exit before the start of time integration.
+              Allows user to check validy of parameter and IC files as well as memory limits.
+  -e          Enable floating-point exceptions (debugging mode)
+  -f    {int} Overwrite the CPU frequency (Hz) to be used for time measurements
+  -g          Run with an external gravitational potential
+  -G          Run with self-gravity
+  -s          Run with SPH
+  -v     [12] Increase the level of verbosity 1: MPI-rank 0 writes 
+              2: All MPI-ranks write
+  -y    {int} Time-step frequency at which task graphs are dumped
+  -h          Print this help message and exit
+
+See the file examples/parameter_example.yml for an example of parameter file.

configure.ac

@@ -287,11 +287,11 @@ AC_SUBST([METIS_LIBS])
 AC_SUBST([METIS_INCS])
 AM_CONDITIONAL([HAVEMETIS],[test -n "$METIS_LIBS"])
 
-# Check for zlib.
-AC_CHECK_LIB([z],[gzopen],[
-    AC_DEFINE([HAVE_LIBZ],[1],[Set to 1 if zlib is installed.])
-    LDFLAGS="$LDFLAGS -lz"
-    ],[])
+# # Check for zlib.
+# AC_CHECK_LIB([z],[gzopen],[
+#     AC_DEFINE([HAVE_LIBZ],[1],[Set to 1 if zlib is installed.])
+#     LDFLAGS="$LDFLAGS -lz"
+#     ],[])
 
 
 # Check for HDF5. This is required.

examples/CosmoVolume/cosmoVolume.yml

+
+# Define the system of units to use internally. 
+UnitSystem:
+  UnitMass_in_cgs:     1   # Grams
+  UnitLength_in_cgs:   1   # Centimeters
+  UnitVelocity_in_cgs: 1   # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters for the task scheduling
+Scheduler:
+  nr_threads:       16        # The number of threads per MPI rank to use.
+  nr_queues:        0        # The number of task queues to use. Use 0  to let the system decide.
+  cell_max_size:    8000000  # Maximal number of interactions per task (this is the default value).
+  cell_sub_size:    5000     # Maximal number of interactions per sub-task  (this is the default value).
+  cell_split_size:  400      # Maximal number of particles per cell (this is the default value).
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.    # The end time of the simulation (in internal units).
+  dt_min:     1e-6  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      1.       # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  max_ghost_iterations:  30       # Maximal number of iterations allowed to converge towards the smoothing length.
+  max_smoothing_length:  0.6      # Maximal smoothing length allowed (in internal units).
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./cosmoVolume.hdf5     # The file to read
+  h_scaling:  1.                    # A scaling factor to apply to all smoothing lengths in the ICs.
+  shift_x:    0.                    # A shift to apply to all particles read from the ICs (in internal units).
+  shift_y:    0.
+  shift_z:    0.
+
+# Parameters govering domain decomposition
+DomainDecomposition:
+  initial_type:       m     # The initial strategy ("g", "m", "w", or "v"). See documentation for details.
+  initial_grid_x:    10     # Grid size if the 'g' strategy is chosen.
+  initial_grid_y:    10
+  initial_grid_z:    10
+  repartition_type:   b     # The re-decomposition strategy ("n", "b", "v", "e" or "x"). See documentation for details.
+ 

examples/CosmoVolume/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e cosmoVolume.hdf5 ]
+then
+    echo "Fetching initial conditions for the cosmo volume example..."
+    ./getIC.sh
+fi
+
+../swift -s cosmoVolume.yml

examples/SedovBlast/run.sh

+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e sedov.hdf5 ]
+then
+    echo "Generating initial conditions for the SedovBlast example..."
+    python makeIC_fcc.py
+fi
+
+../swift -s sedov.yml

examples/SedovBlast/sedov.yml

+
+# Define the system of units to use internally. 
+UnitSystem:
+  UnitMass_in_cgs:     1   # Grams
+  UnitLength_in_cgs:   1   # Centimeters
+  UnitVelocity_in_cgs: 1   # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters for the task scheduling
+Scheduler:
+  nr_threads:       16       # The number of threads per MPI rank to use.
+  nr_queues:        0        # The number of task queues to use. Use 0  to let the system decide.
+  cell_max_size:    8000000  # Maximal number of interactions per task (this is the default value).
+  cell_sub_size:    5000     # Maximal number of interactions per sub-task  (this is the default value).
+  cell_split_size:  400      # Maximal number of particles per cell (this is the default value).
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.    # The end time of the simulation (in internal units).
+  dt_min:     1e-7  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      1.       # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  max_ghost_iterations:  30       # Maximal number of iterations allowed to converge towards the smoothing length.
+  max_smoothing_length:  1.       # Maximal smoothing length allowed (in internal units).
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./sedov.hdf5          # The file to read
+  h_scaling:  1.                    # A scaling factor to apply to all smoothing lengths in the ICs.
+  shift_x:    0.                    # A shift to apply to all particles read from the ICs (in internal units).
+  shift_y:    0.
+  shift_z:    0.
+
+# Parameters govering domain decomposition
+DomainDecomposition:
+  initial_type:       m     # The initial strategy ("g", "m", "w", or "v"). See documentation for details.
+  initial_grid_x:    10     # Grid size if the 'g' strategy is chosen.
+  initial_grid_y:    10
+  initial_grid_z:    10
+  repartition_type:   b     # The re-decomposition strategy ("n", "b", "v", "e" or "x"). See documentation for details.
+ 

examples/SodShock/run.sh

+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e sodShock.hdf5 ]
+then
+    echo "Generating initial conditions for the SodShock example..."
+    python makeIC.py
+fi
+
+../swift -s sodShock.yml

examples/SodShock/sodShock.yml

+
+# Define the system of units to use internally. 
+UnitSystem:
+  UnitMass_in_cgs:     1   # Grams
+  UnitLength_in_cgs:   1   # Centimeters
+  UnitVelocity_in_cgs: 1   # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters for the task scheduling
+Scheduler:
+  nr_threads:       16        # The number of threads per MPI rank to use.
+  nr_queues:        0        # The number of task queues to use. Use 0  to let the system decide.
+  cell_max_size:    8000000  # Maximal number of interactions per task (this is the default value).
+  cell_sub_size:    5000     # Maximal number of interactions per sub-task.
+  cell_split_size:  400      # Maximal number of particles per cell (this is the default value).
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.    # The end time of the simulation (in internal units).
+  dt_min:     1e-7  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      1.       # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  max_ghost_iterations:  30       # Maximal number of iterations allowed to converge towards the smoothing length.
+  max_smoothing_length:  0.01     # Maximal smoothing length allowed (in internal units).
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./sodShock.hdf5       # The file to read
+  h_scaling:  1.                    # A scaling factor to apply to all smoothing lengths in the ICs.
+  shift_x:    0.                    # A shift to apply to all particles read from the ICs (in internal units).
+  shift_y:    0.
+  shift_z:    0.
+
+# Parameters govering domain decomposition
+DomainDecomposition:
+  initial_type:       m     # The initial strategy ("g", "m", "w", or "v"). See documentation for details.
+  initial_grid_x:    10     # Grid size if the 'g' strategy is chosen.
+  initial_grid_y:    10
+  initial_grid_z:    10
+  repartition_type:   b     # The re-decomposition strategy ("n", "b", "v", "e" or "x"). See documentation for details.
+ 

examples/UniformBox/run.sh

+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e uniformBox.hdf5 ]
+then
+    echo "Generating initial conditions for the uniform box example..."
+    python makeIC.py 100
+fi
+
+../swift -s uniformBox.yml

examples/UniformBox/uniformBox.yml

+
+# Define the system of units to use internally. 
+UnitSystem:
+  UnitMass_in_cgs:     1   # Grams
+  UnitLength_in_cgs:   1   # Centimeters
+  UnitVelocity_in_cgs: 1   # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters for the task scheduling
+Scheduler:
+  nr_threads:       16        # The number of threads per MPI rank to use.
+  nr_queues:        0        # The number of task queues to use. Use 0  to let the system decide.
+  cell_max_size:    8000000  # Maximal number of interactions per task (this is the default value).
+  cell_sub_size:    5000     # Maximal number of interactions per sub-task  (this is the default value).
+  cell_split_size:  400      # Maximal number of particles per cell (this is the default value).
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.    # The end time of the simulation (in internal units).
+  dt_min:     1e-6  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      1.       # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  max_ghost_iterations:  30       # Maximal number of iterations allowed to converge towards the smoothing length.
+  max_smoothing_length:  0.1      # Maximal smoothing length allowed (in internal units).
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./uniformBox.hdf5     # The file to read
+  h_scaling:  1.                    # A scaling factor to apply to all smoothing lengths in the ICs.
+  shift_x:    0.                    # A shift to apply to all particles read from the ICs (in internal units).
+  shift_y:    0.
+  shift_z:    0.
+
+# Parameters govering domain decomposition
+DomainDecomposition:
+  initial_type:       m     # The initial strategy ("g", "m", "w", or "v"). See documentation for details.
+  initial_grid_x:    10     # Grid size if the 'g' strategy is chosen.
+  initial_grid_y:    10
+  initial_grid_z:    10
+  repartition_type:   b     # The re-decomposition strategy ("n", "b", "v", "e" or "x"). See documentation for details.
+ 

examples/parameter_example.yml

+
+# Define the system of units to use internally. 
+UnitSystem:
+  UnitMass_in_cgs:     1   # Grams
+  UnitLength_in_cgs:   1   # Centimeters
+  UnitVelocity_in_cgs: 1   # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters for the task scheduling
+Scheduler:
+  nr_threads:       2        # The number of threads per MPI rank to use.
+  nr_queues:        0        # The number of task queues to use. Use 0  to let the system decide.
+  cell_max_size:    8000000  # Maximal number of interactions per task (this is the default value).
+  cell_sub_size:    8000000  # Maximal number of interactions per sub-task  (this is the default value).
+  cell_split_size:  400      # Maximal number of particles per cell (this is the default value).
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.    # The end time of the simulation (in internal units).
+  dt_min:     1e-6  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      1.       # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  max_ghost_iterations:  30       # Maximal number of iterations allowed to converge towards the smoothing length.
+  max_smoothing_length:  3.       # Maximal smoothing length allowed (in internal units).
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  SedovBlast/sedov.hdf5 # The file to read
+  h_scaling:  1.                    # A scaling factor to apply to all smoothing lengths in the ICs.
+  shift_x:    0.                    # A shift to apply to all particles read from the ICs (in internal units).
+  shift_y:    0.
+  shift_z:    0.
+
+# Parameters govering domain decomposition
+DomainDecomposition:
+  initial_type:       m     # The initial strategy ("g", "m", "w", or "v"). See documentation for details.
+  initial_grid_x:    10     # Grid size if the 'g' strategy is chosen.
+  initial_grid_y:    10
+  initial_grid_z:    10
+  repartition_type:   b     # The re-decomposition strategy ("n", "b", "v", "e" or "x"). See documentation for details.
+ 

examples/runs.sh

-#!/bin/bash
-
-# Set some global stuff
-export OMP_WAIT_POLICY=PASSIVE
-
-# Generate the initial conditions if they are not present.
-if [ ! -e SodShock/sodShock.hdf5 ]
-then
-    echo "Generating initial conditions for the SodShock example..."
-    cd SodShock
-    python makeIC.py
-    cd ..
-fi
-if [ ! -e SedovBlast/sedov.hdf5 ]
-then
-    echo "Generating initial conditions for the SedovBlast example..."
-    cd SedovBlast/
-    python makeIC_fcc.py
-    cd ..
-fi
-if [ ! -e CosmoVolume/cosmoVolume.hdf5 ]
-then
-    echo "Downloading initial conditions for the CosmoVolume example..."
-    cd CosmoVolume
-    ./getIC.sh
-    cd ..
-fi
-
-
-# Loop over number of cores
-for cpu in {1..32}
-do
-
-    # Sod-Shock runs
-    if [ ! -e SodShock_${cpu}.dump ]
-    then
-        ./swift -t $cpu -f SodShock/sodShock.hdf5 -m 0.01 -w 5000 -c 1. -d 1e-7 -e 0.01 > SodShock_fixed_${cpu}.dump
-    fi
-    
-    # Sedov blast
-    if [ ! -e SedovBlast_${cpu}.dump ]
-    then
-        ./swift -t $cpu -f SedovBlast/sedov.hdf5 -m 0.02 -w 5000 -c 1. -d 1e-7 -e 0.01 > SedovBlast_fixed_${cpu}.dump
-    fi
-    
-    # Cosmological volume
-    if [ ! -e CosmoVolume_${cpu}.dump ]
-    then
-        ./swift -t $cpu -f CosmoVolume/cosmoVolume.hdf5 -m 0.6 -w 5000 -c 1. -d 1e-7 -e 0.01 > CosmoVolume_fixed_${cpu}.dump
-    fi
-
-done
-

src/common_io.c

@@ -282,15 +282,15 @@ void writeUnitSystem(hid_t h_file, struct UnitSystem* us) {
   if (h_grpunit < 0) error("Error while creating Unit System group");
 
   writeAttribute_d(h_grpunit, "Unit mass in cgs (U_M)",
-                   getBaseUnit(us, UNIT_MASS));
+                   units_get_base_unit(us, UNIT_MASS));
   writeAttribute_d(h_grpunit, "Unit length in cgs (U_L)",
-                   getBaseUnit(us, UNIT_LENGTH));
+                   units_get_base_unit(us, UNIT_LENGTH));
   writeAttribute_d(h_grpunit, "Unit time in cgs (U_t)",
-                   getBaseUnit(us, UNIT_TIME));
+                   units_get_base_unit(us, UNIT_TIME));
   writeAttribute_d(h_grpunit, "Unit current in cgs (U_I)",
-                   getBaseUnit(us, UNIT_CURRENT));
+                   units_get_base_unit(us, UNIT_CURRENT));
   writeAttribute_d(h_grpunit, "Unit temperature in cgs (U_T)",
-                   getBaseUnit(us, UNIT_TEMPERATURE));
+                   units_get_base_unit(us, UNIT_TEMPERATURE));
 
   H5Gclose(h_grpunit);
 }

src/const.h

@@ -70,9 +70,4 @@
 #define GADGET2_SPH
 //#define DEFAULT_SPH
 
-/* System of units */
-#define const_unit_length_in_cgs 1   /* 3.08567810e16  /\* 1Mpc *\/ */
-#define const_unit_mass_in_cgs 1     /* 1.9891e33      /\* 1 M_sun *\/ */
-#define const_unit_velocity_in_cgs 1 /* 1e5            /\* km s^-1 *\/ */
-
 #endif /* SWIFT_CONST_H */

src/engine.c

@@ -56,10 +56,11 @@
 #include "partition.h"
 #include "timers.h"
 
-const char *engine_policy_names[12] = {
-    "none",          "rand",   "steal",        "keep",
-    "block",         "fix_dt", "cpu_tight",    "mpi",
-    "numa_affinity", "hydro",  "self_gravity", "external_gravity"};
+const char *engine_policy_names[13] = {
+    "none",                 "rand",   "steal",        "keep",
+    "block",                "fix_dt", "cpu_tight",    "mpi",
+    "numa_affinity",        "hydro",  "self_gravity", "external_gravity",
+    "cosmology_integration"};
 
 /** The rank of the engine as a global variable (for messages). */
 int engine_rank;
@@ -1650,7 +1651,7 @@ void engine_rebuild(struct engine *e) {
     error("engine_marktasks failed after space_rebuild.");
 
   /* Print the status of the system */
-  engine_print_task_counts(e);
+  if (e->verbose) engine_print_task_counts(e);
 
   if (e->verbose)
     message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
@@ -2026,8 +2027,8 @@ void engine_step(struct engine *e) {
   if (e->nodeID == 0) {
 
     /* Print some information to the screen */
-    printf("%d %e %e %d %d %.3f\n", e->step, e->time, e->timeStep, updates,
-           g_updates, e->wallclock_time);
+    printf("  %6d %14e %14e %10d %10d %21.3f\n", e->step, e->time, e->timeStep,
+           updates, g_updates, e->wallclock_time);
     fflush(stdout);
 
     /* Write some energy statistics */
@@ -2320,30 +2321,25 @@ static bool hyperthreads_present(void) {
  *
  * @param e The #engine.
  * @param s The #space in which this #runner will run.
- * @param dt The initial time step to use.
- * @param nr_threads The number of threads to spawn.
- * @param nr_queues The number of task queues to create.
+ * @param params The parsed parameter file.
  * @param nr_nodes The number of MPI ranks.
  * @param nodeID The MPI rank of this node.
  * @param policy The queuing policy to use.
- * @param timeBegin Time at the begininning of the simulation.
- * @param timeEnd Time at the end of the simulation.
- * @param dt_min Minimal allowed timestep (unsed with fixdt policy)
- * @param dt_max Maximal allowed timestep
  * @param verbose Is this #engine talkative ?
  */
 
-void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
-                 int nr_queues, int nr_nodes, int nodeID, int policy,
-                 float timeBegin, float timeEnd, float dt_min, float dt_max,
-                 int verbose) {
+void engine_init(struct engine *e, struct space *s,
+                 const struct swift_params *params, int nr_nodes, int nodeID,
+                 int policy, int verbose) {
+
+  /* Clean-up everything */
+  bzero(e, sizeof(struct engine));
 
   /* Store the values. */
   e->s = s;
-  e->nr_threads = nr_threads;
+  e->nr_threads = parser_get_param_int(params, "Scheduler:nr_threads");
   e->policy = policy;
   e->step = 0;
-  e->nullstep = 0;
   e->nr_nodes = nr_nodes;
   e->nodeID = nodeID;
   e->proxy_ind = NULL;
@@ -2352,15 +2348,15 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
   e->forcerepart = REPART_NONE;
   e->links = NULL;
   e->nr_links = 0;
-  e->timeBegin = timeBegin;
-  e->timeEnd = timeEnd;
-  e->timeOld = timeBegin;
-  e->time = timeBegin;
+  e->timeBegin = parser_get_param_double(params, "TimeIntegration:time_begin");
+  e->timeEnd = parser_get_param_double(params, "TimeIntegration:time_end");
+  e->timeOld = e->timeBegin;
+  e->time = e->timeBegin;
   e->ti_old = 0;
   e->ti_current = 0;
   e->timeStep = 0.;
-  e->dt_min = dt_min;
-  e->dt_max = dt_max;
+  e->dt_min = parser_get_param_double(params, "TimeIntegration:dt_min");
+  e->dt_max = parser_get_param_double(params, "TimeIntegration:dt_max");
   e->file_stats = NULL;
   e->verbose = verbose;
   e->count_step = 0;
@@ -2370,6 +2366,11 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
   /* Make the space link back to the engine. */
   s->e = e;
 
+  /* Get the number of queues */
+  int nr_queues = parser_get_param_int(params, "Scheduler:nr_queues");
+  if (nr_queues <= 0) nr_queues = e->nr_threads;
+  s->nr_queues = nr_queues;
+
 #if defined(HAVE_SETAFFINITY)
   const int nr_cores = sysconf(_SC_NPROCESSORS_ONLN);
   int cpuid[nr_cores];
@@ -2465,15 +2466,19 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
   engine_print_policy(e);
 
   /* Print information about the hydro scheme */
-  if (e->nodeID == 0) message("Hydrodynamic scheme: %s", SPH_IMPLEMENTATION);
-  if (e->nodeID == 0) message("Hydrodynamic kernel: %s", kernel_name);
+  if ((e->policy & engine_policy_hydro) == engine_policy_hydro) {
+    if (e->nodeID == 0) message("Hydrodynamic scheme: %s.", SPH_IMPLEMENTATION);
+    if (e->nodeID == 0)
+      message("Hydrodynamic kernel: %s with %.2f +/- %.2f neighbours.",
+              kernel_name, kernel_nwneigh, const_delta_nwneigh);
+  }
 
   /* Check we have sensible time bounds */
-  if (timeBegin >= timeEnd)
+  if (e->timeBegin >= e->timeEnd)
     error(
         "Final simulation time (t_end = %e) must be larger than the start time "
         "(t_beg = %e)",
-        timeEnd, timeBegin);
+        e->timeEnd, e->timeBegin);
 
   /* Check we have sensible time-step values */
   if (e->dt_min > e->dt_max)
@@ -2483,7 +2488,7 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
         e->dt_min, e->dt_max);
 
   /* Deal with timestep */
-  e->timeBase = (timeEnd - timeBegin) / max_nr_timesteps;
+  e->timeBase = (e->timeEnd - e->timeBegin) / max_nr_timesteps;
   e->ti_current = 0;
 
   /* Fixed time-step case */
@@ -2502,12 +2507,12 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
     if (e->nodeID == 0) {
       message("Absolute minimal timestep size: %e", e->timeBase);
 
-      float dt_min = timeEnd - timeBegin;
+      float dt_min = e->timeEnd - e->timeBegin;
       while (dt_min > e->dt_min) dt_min /= 2.f;
 
       message("Minimal timestep size (on time-line): %e", dt_min);
 
-      float dt_max = timeEnd - timeBegin;
+      float dt_max = e->timeEnd - e->timeBegin;
       while (dt_max > e->dt_max) dt_max /= 2.f;
 
       message("Maximal timestep size (on time-line): %e", dt_max);
@@ -2541,10 +2546,9 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
   e->barrier_launchcount = 0;
 
   /* Init the scheduler with enough tasks for the initial sorting tasks. */
-  int nr_tasks = 2 * s->tot_cells + e->nr_threads;
+  const int nr_tasks = 2 * s->tot_cells + 2 * e->nr_threads;
   scheduler_init(&e->sched, e->s, nr_tasks, nr_queues, scheduler_flag_steal,
                  e->nodeID);
-  s->nr_queues = nr_queues;
 
   /* Create the sorting tasks. */
   for (int i = 0; i < e->nr_threads; i++) {
@@ -2558,10 +2562,10 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
   scheduler_ranktasks(&e->sched);
 
   /* Allocate and init the threads. */
-  if ((e->runners =
-           (struct runner *)malloc(sizeof(struct runner) * nr_threads)) == NULL)
+  if ((e->runners = (struct runner *)malloc(sizeof(struct runner) *
+                                            e->nr_threads)) == NULL)
     error("Failed to allocate threads array.");
-  for (int k = 0; k < nr_threads; k++) {
+  for (int k = 0; k < e->nr_threads; k++) {
     e->runners[k].id = k;
     e->runners[k].e = e;
     e->barrier_running += 1;
@@ -2573,7 +2577,7 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
 
       /* Set a reasonable queue ID. */
       e->runners[k].cpuid = cpuid[k % nr_cores];
-      if (nr_queues < nr_threads)
+      if (nr_queues < e->nr_threads)
         e->runners[k].qid = cpuid[k % nr_cores] * nr_queues / nr_cores;
       else
         e->runners[k].qid = k;
@@ -2592,7 +2596,7 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
 #endif
     } else {
       e->runners[k].cpuid = k;
-      e->runners[k].qid = k * nr_queues / nr_threads;
+      e->runners[k].qid = k * nr_queues / e->nr_threads;
     }
     // message( "runner %i on cpuid=%i with qid=%i." , e->runners[k].id ,
     // e->runners[k].cpuid , e->runners[k].qid );

src/engine.h

@@ -38,6 +38,7 @@
 #include "scheduler.h"
 #include "space.h"
 #include "task.h"
+#include "parser.h"
 #include "partition.h"
 
 /* Some constants. */
@@ -53,7 +54,8 @@ enum engine_policy {
   engine_policy_setaffinity = (1 << 7),
   engine_policy_hydro = (1 << 8),
   engine_policy_self_gravity = (1 << 9),
-  engine_policy_external_gravity = (1 << 10)
+  engine_policy_external_gravity = (1 << 10),
+  engine_policy_cosmology = (1 << 11)
 };
 
 extern const char *engine_policy_names[];
@@ -126,7 +128,7 @@ struct engine {
   FILE *file_stats;
 
   /* The current step number. */
-  int step, nullstep;
+  int step;
 
   /* The number of particles updated in the previous step. */
   int count_step;
@@ -166,10 +168,9 @@ struct engine {
 
 /* Function prototypes. */
 void engine_barrier(struct engine *e, int tid);
-void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
-                 int nr_queues, int nr_nodes, int nodeID, int policy,
-                 float timeBegin, float timeEnd, float dt_min, float dt_max,
-                 int verbose);
+void engine_init(struct engine *e, struct space *s,
+                 const struct swift_params *params, int nr_nodes, int nodeID,
+                 int policy, int verbose);
 void engine_launch(struct engine *e, int nr_runners, unsigned int mask,
                    unsigned int submask);
 void engine_prepare(struct engine *e);

src/parallel_io.c

@@ -274,11 +274,11 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
                  type);
 
   /* Write unit conversion factors for this data set */
-  conversionString(buffer, us, convFactor);
+  units_conversion_string(buffer, us, convFactor);
   writeAttribute_d(h_data, "CGS conversion factor",
-                   conversionFactor(us, convFactor));
-  writeAttribute_f(h_data, "h-scale exponent", hFactor(us, convFactor));
-  writeAttribute_f(h_data, "a-scale exponent", aFactor(us, convFactor));
+                   units_conversion_factor(us, convFactor));
+  writeAttribute_f(h_data, "h-scale exponent", units_h_factor(us, convFactor));
+  writeAttribute_f(h_data, "a-scale exponent", units_a_factor(us, convFactor));
   writeAttribute_s(h_data, "Conversion factor", buffer);
 
   /* Free and close everything */
@@ -349,6 +349,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
  * @param parts (output) The array of #part read from the file.
  * @param N (output) The number of particles read from the file.
  * @param periodic (output) 1 if the volume is periodic, 0 if not.
+ * @param dry_run If 1, don't read the particle. Only allocates the arrays.
  *
  * Opens the HDF5 file fileName and reads the particles contained
  * in the parts array. N is the returned number of particles found
@@ -363,7 +364,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
 void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
                       struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
                       int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
-                      MPI_Info info) {
+                      MPI_Info info, int dry_run) {
   hid_t h_file = 0, h_grp = 0;
   /* GADGET has only cubic boxes (in cosmological mode) */
   double boxSize[3] = {0.0, -1.0, -1.0};
@@ -469,13 +470,15 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
     switch (ptype) {
 
       case GAS:
-        hydro_read_particles(h_grp, N[ptype], N_total[ptype], offset[ptype],
-                             *parts);
+        if (!dry_run)
+          hydro_read_particles(h_grp, N[ptype], N_total[ptype], offset[ptype],
+                               *parts);
         break;
 
       case DM:
-        darkmatter_read_particles(h_grp, N[ptype], N_total[ptype],
-                                  offset[ptype], *gparts);
+        if (!dry_run)
+          darkmatter_read_particles(h_grp, N[ptype], N_total[ptype],
+                                    offset[ptype], *gparts);
         break;
 
       default:
@@ -487,10 +490,10 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
   }
 
   /* Prepare the DM particles */
-  prepare_dm_gparts(*gparts, Ndm);
+  if (!dry_run) prepare_dm_gparts(*gparts, Ndm);
 
   /* Now duplicate the hydro particle into gparts */
-  duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+  if (!dry_run) duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
 
   /* message("Done Reading particles..."); */
 

src/parallel_io.h

@@ -34,7 +34,7 @@
 void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
                       struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
                       int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
-                      MPI_Info info);
+                      MPI_Info info, int dry_run);
 
 void write_output_parallel(struct engine* e, struct UnitSystem* us,
                            int mpi_rank, int mpi_size, MPI_Comm comm,