Merge branch 'new_cosmo_ICs' into 'master'

New cosmo ICs

New ICs to replace the BigCosmoVolume at some point.
They contain corrected smoothing lengths such that the initialisation step is much shorter. They also contain the DM particles and further species for when we are ready to have them in SWIFT.

The EAGLE_25 case is almost the old BigCosmoVolume.

See merge request !188

.gitignore

@@ -28,6 +28,7 @@ examples/*.xmf
 examples/used_parameters.yml
 examples/energy.txt
 examples/*/*.xmf
+examples/*/*.hdf5
 examples/*/used_parameters.yml
 examples/*/energy.txt
 

examples/BigCosmoVolume/makeIC.py

@@ -47,7 +47,7 @@ if downsample > 1. or downsample <= 0.:
 # Download the tile
 if (not os.path.isfile("tile.hdf5")):
     print "Downloading initial tile..."
-    urllib.urlretrieve ("http://icc.dur.ac.uk/~jlvc76/Files/SWIFT/tile.hdf5", "tile.hdf5")
+    urllib.urlretrieve ("http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/tile.hdf5", "tile.hdf5")
     print "Done."
 else:
     print "Tile already exists. No need to download..."

examples/CosmoVolume/getIC.sh

 #!/bin/bash
-wget http://icc.dur.ac.uk/~jlvc76/Files/SWIFT/cosmoVolume.hdf5
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/cosmoVolume.hdf5

examples/EAGLE_12/README

+ICs extracted from the EAGLE suite of simulations. 
+
+WARNING: The ICs are 460MB in size. They contain ~6.5M DM particles,
+~6M gas particles and ~250k star particles.
+
+The particle distribution here is the snapshot 27 (z=0.1) of the 12Mpc
+Ref-model. h- and a- factors from the original Gadget code have been
+corrected for. Variables not used in a pure hydro & gravity code have
+been removed.  Everything is ready to be run without cosmological
+integration.
+
+The particle load of the main EAGLE simulation can be reproduced by
+running these ICs on 8 cores.

examples/EAGLE_12/eagle_12.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  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:
+  cell_sub_size:    6000     # Value used for the original scaling tests
+  cell_split_size:  300      # Value used for the original scaling tests
+
+# 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 governing the snapshots
+Snapshots:
+  basename:            eagle # Common part of the name of output files
+  time_first:          0.    # Time of the first output (in internal units)
+  delta_time:          0.05  # Time difference between consecutive outputs (in internal units)
+  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 governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  max_smoothing_length:  0.1    # Maximal smoothing length allowed (in internal units).
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./EAGLE_ICs_12.hdf5     # The file to read
+

examples/EAGLE_12/getIC.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs_12.hdf5

examples/EAGLE_12/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e EAGLE_ICs_12.hdf5 ]
+then
+    echo "Fetching initial conditions for the EAGLE 12Mpc example..."
+    ./getIC.sh
+fi
+
+../swift -s -t 16 eagle_12.yml
+

examples/EAGLE_25/README

+ICs extracted from the EAGLE suite of simulations. 
+
+WARNING: The ICs are 3.6GB in size. They contain ~52M DM particles,
+~50M gas particles and ~2M star particles.
+
+The particle distribution here is the snapshot 27 (z=0.1) of the 25Mpc
+Ref-model. h- and a- factors from the original Gadget code have been
+corrected for. Variables not used in a pure hydro & gravity code have
+been removed. 
+Everything is ready to be run without cosmological integration. 
+
+The particle load of the main EAGLE simulation can be reproduced by
+running these ICs on 64 cores.

examples/EAGLE_25/eagle_25.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  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:
+  cell_sub_size:    6000     # Value used for the original scaling tests
+  cell_split_size:  300      # Value used for the original scaling tests
+
+# 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 governing the snapshots
+Snapshots:
+  basename:            eagle # Common part of the name of output files
+  time_first:          0.    # Time of the first output (in internal units)
+  delta_time:          0.05  # Time difference between consecutive outputs (in internal units)
+  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 governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  max_smoothing_length:  0.1    # Maximal smoothing length allowed (in internal units).
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./EAGLE_ICs_25.hdf5     # The file to read
+

examples/EAGLE_25/getIC.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs_25.hdf5

examples/EAGLE_25/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e EAGLE_ICs_25.hdf5 ]
+then
+    echo "Fetching initial conditions for the EAGLE 25Mpc example..."
+    ./getIC.sh
+fi
+
+../swift -s -t 16 eagle_25.yml
+

examples/EAGLE_50/README

+ICs extracted from the EAGLE suite of simulations. 
+
+WARNING: The ICs are 28GB in size. They contain ~425M DM particles,
+~405M gas particles and ~20M star particles
+
+The particle distribution here is the snapshot 27 (z=0.1) of the 50Mpc
+Ref-model. h- and a- factors from the original Gadget code have been
+corrected for. Variables not used in a pure hydro & gravity code have
+been removed. 
+Everything is ready to be run without cosmological integration. 
+
+The particle load of the main EAGLE simulation can be reproduced by
+running these ICs on 512 cores.

examples/EAGLE_50/eagle_50.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  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:
+  cell_sub_size:    6000     # Value used for the original scaling tests
+  cell_split_size:  300      # Value used for the original scaling tests
+
+# 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 governing the snapshots
+Snapshots:
+  basename:            eagle # Common part of the name of output files
+  time_first:          0.    # Time of the first output (in internal units)
+  delta_time:          0.05  # Time difference between consecutive outputs (in internal units)
+  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 governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  max_smoothing_length:  0.1    # Maximal smoothing length allowed (in internal units).
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./EAGLE_ICs_50.hdf5     # The file to read
+

examples/EAGLE_50/getIC.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs_50.hdf5

examples/EAGLE_50/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e EAGLE_ICs_50.hdf5 ]
+then
+    echo "Fetching initial conditions for the EAGLE 50Mpc example..."
+    ./getIC.sh
+fi
+
+../swift -s -t 16 eagle_50.yml
+

examples/mkplots.m

-
-%% Scaling and efficiency plots for the first test
-datadir = 'Opteron8380';
-test = importdata( [ datadir '/snap_C90.totals' ]);
-ncores = size( test , 1 );
-col = 11;
-
-clf
-subplot('position',[ 0.05 , 0.1 , 0.4 , 0.8 ]);
-plot( 1:ncores , test(1,col) ./ test(:,col) , '-k' , 'LineWidth' , 2 ); hold on;
-xlabel('nr. cores');
-plot( [1,ncores] , [1,ncores] , ':k' , 'LineWidth' , 1.4 );
-hold off;
-title('Speedup GadgetSMP');
-axis([ 1 , ncores , 0 , ncores ]);
-
-subplot('position',[ 0.52 0.1 , 0.4 , 0.8 ]);
-plot( 1:ncores , test(1,col) ./ test(:,col) ./ (1:ncores)' , '-k' , 'LineWidth' , 2 ); hold on;
-plot( [1,ncores] , [1,1] , ':k' , 'LineWidth' , 1.4 );
-% text(4*ncores/5,1,sprintf('%.2f',min(test(:,10))),'BackgroundColor',[1,1,1],'FontSize',12);
-xlabel('nr. cores');
-hold off;
-title('Efficiency GadgetSMP');
-axis([ 1 , ncores , 0 , 1.2 ]);
-
-% Print this plot
-set( gcf , 'PaperSize' , 2.3*[ 8.5 4.5 ] );
-set( gcf , 'PaperPosition' , 2.3*[ 0.25 0.25 8 4 ] );
-print -depsc2 test.eps
-!epstopdf test.eps 
-
-
-%% Scaling and efficiency plots for the second test
-test2 = importdata( 'test2.totals');
-ncores = size( test2 , 1 );
-
-clf
-subplot('position',[ 0.05 , 0.1 , 0.4 , 0.8 ]);
-plot( 1:ncores , test2(1,10) ./ test2(:,10) , '-k' , 'LineWidth' , 2 ); hold on;
-xlabel('nr. cores');
-plot( [1,ncores] , [1,ncores] , ':k' , 'LineWidth' , 1.4 );
-hold off;
-title('Speedup');
-axis([ 1 , ncores , 0 , ncores ]);
-
-subplot('position',[ 0.52 0.1 , 0.4 , 0.8 ]);
-plot( 1:ncores , test2(1,10) ./ test2(:,10) ./ (1:ncores)' , '-k' , 'LineWidth' , 2 ); hold on;
-plot( [1,ncores] , [1,1] , ':k' , 'LineWidth' , 1.4 );
-text(4*ncores/5,1,sprintf('%.2f',min(test2(:,10))),'BackgroundColor',[1,1,1],'FontSize',12);
-xlabel('nr. cores');
-hold off;
-title('Efficiency');
-axis([ 1 , ncores , 0 , 1.2 ]);
-
-% Print this plot
-set( gcf , 'PaperSize' , 2.3*[ 8.5 4.5 ] );
-set( gcf , 'PaperPosition' , 2.3*[ 0.25 0.25 8 4 ] );
-print -depsc2 test2.eps
-!epstopdf test2.eps 
-
-
-%% Components of the first test
-test = importdata( 'test_nosort.totals');
-ncores = size( test , 1 );
-cols = [ 1 , 2 , 3 , 5 ];
-
-clf
-subplot('position',[ 0.1 , 0.1 , 0.8 , 0.8 ]);
-plot( 1:ncores , test(:,cols) , 'LineWidth' , 2 ); hold on;
-legend( 'sort' , 'self' , 'pair' , 'get task' , 'Location' , 'NorthWest' );
-xlabel('nr. cores');
-hold off;
-title('ms per task type');
-axis([ 1 , ncores , 0 , max(max(test(:,cols)))*1.1 ]);
-
-% Print this plot
-set( gcf , 'PaperSize' , 2.3*[ 4.5 4 ] );
-set( gcf , 'PaperPosition' , 2.3*[ 0.25 0.25 4 4 ] );
-print -depsc2 parts.eps
-!epstopdf parts.eps 
-
-
-%% Components of the second test
-test2 = importdata( 'test2.totals');
-ncores = size( test2 , 1 );
-cols = [ 1 , 2 , 3 , 5 ];
-
-clf
-subplot('position',[ 0.1 , 0.1 , 0.8 , 0.8 ]);
-plot( 1:ncores , test2(:,cols) , 'LineWidth' , 2 ); hold on;
-legend( 'sort' , 'self' , 'pair' , 'get task' , 'Location' , 'NorthWest' );
-xlabel('nr. cores');
-hold off;
-title('ms per task type');
-axis([ 1 , ncores , 0 , max(max(test2(:,cols)))*1.1 ]);
-
-% Print this plot
-set( gcf , 'PaperSize' , 2.3*[ 4.5 4 ] );
-set( gcf , 'PaperPosition' , 2.3*[ 0.25 0.25 4 4 ] );
-print -depsc2 parts2.eps
-!epstopdf parts2.eps 
-

src/parallel_io.c

@@ -487,7 +487,7 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
         break;
 
       default:
-        error("Particle Type %d not yet supported. Aborting", ptype);
+        message("Particle Type %d not yet supported. Particles ignored", ptype);
     }
 
     /* Close particle group */

src/serial_io.c

@@ -564,7 +564,8 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
             break;
 
           default:
-            error("Particle Type %d not yet supported. Aborting", ptype);
+            message("Particle Type %d not yet supported. Particles ignored",
+                    ptype);
         }
 
         /* Close particle group */

src/single_io.c

@@ -439,7 +439,7 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
         break;
 
       default:
-        error("Particle Type %d not yet supported. Aborting", ptype);
+        message("Particle Type %d not yet supported. Particles ignored", ptype);
     }
 
     /* Close particle group */