Merge branch 'master' into io_unit_conversion

.gitignore

@@ -28,6 +28,8 @@ examples/*.xmf
 examples/used_parameters.yml
 examples/energy.txt
 examples/*/*.xmf
+examples/*/*.dat
+examples/*/*.hdf5
 examples/*/used_parameters.yml
 examples/*/energy.txt
 

README

@@ -26,6 +26,8 @@ Valid options are:
   -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
+  -n    {int} Execute a fixed number of time steps. When unset use the time_end
+              parameter to stop. 
   -s          Run with SPH
   -t    {int} The number of threads to use on each MPI rank. Defaults to 1 if not specified.
   -v     [12] Increase the level of verbosity 1: MPI-rank 0 writes 

configure.ac

@@ -72,9 +72,6 @@ if test "$enable_ipo" = "yes"; then
    fi
 fi
 
-# Add libtool support.
-LT_INIT
-
 # Check for MPI. Need to do this before characterising the compiler (C99 mode),
 # as this changes the compiler.
 # We should consider using AX_PROG_CC_MPI to replace AC_PROG_CC when compiling
@@ -151,6 +148,9 @@ AM_CONDITIONAL([HAVEMPI],[test $enable_mpi = "yes"])
 # Indicate that MPIRUN can be modified by an environement variable
 AC_ARG_VAR(MPIRUN, Path to the mpirun command if non-standard)
 
+# Add libtool support (now that CC is defined).
+LT_INIT
+
 # Need C99 and inline support.
 AC_PROG_CC_C99
 AC_C_INLINE
@@ -179,7 +179,7 @@ if test "$enable_opt" = "yes" ; then
    ac_test_CFLAGS="yes"
    CFLAGS="$old_CFLAGS $CFLAGS"
 
-   # Check SSE & AVX support (some overlap with AX_CC_MAXOPT). 
+   # Check SSE & AVX support (some overlap with AX_CC_MAXOPT).
    # Don't use the SIMD_FLAGS result with Intel compilers. The -x<code>
    # value from AX_CC_MAXOPT should be sufficient.
    AX_EXT
@@ -287,12 +287,75 @@ 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="$LDFLAGS -lz"
-#     ],[])
+#  Check for tcmalloc a fast malloc that is part of the gperftools.
+have_tcmalloc="no"
+AC_ARG_WITH([tcmalloc],
+   [AS_HELP_STRING([--with-tcmalloc],
+      [use tcmalloc library or specify the directory with lib @<:@yes/no@:>@]
+   )],
+   [with_tcmalloc="$withval"],
+   [with_tcmalloc="no"]
+)
+if test "x$with_tcmalloc" != "xno"; then
+   if test "x$with_tcmalloc" != "xyes" && test "x$with_tcmalloc" != "x"; then
+      tclibs="-L$with_tcmalloc -ltcmalloc"
+   else
+      tclibs="-ltcmalloc"
+   fi
+   AC_CHECK_LIB([tcmalloc],[tc_cfree],[have_tcmalloc="yes"],[have_tcmalloc="no"],
+                $tclibs)
+
+   #  Could just have the minimal version.
+   if test "$have_tcmalloc" = "no"; then
+      if test "x$with_tcmalloc" != "xyes" && test "x$with_tcmalloc" != "x"; then
+         tclibs="-L$with_tcmalloc -ltcmalloc_minimal"
+      else
+         tclibs="-ltcmalloc_minimal"
+      fi
+      AC_CHECK_LIB([tcmalloc],[tc_cfree],[have_tcmalloc="yes"],[have_tcmalloc="no"],
+                   $tclibs)
+   fi
 
+   if test "$have_tcmalloc" = "yes"; then
+      TCMALLOC_LIBS="$tclibs"
+
+      # These are recommended for GCC.
+      if test "$ax_cv_c_compiler_vendor" = "gnu"; then
+         CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
+      fi
+   else
+      TCMALLOC_LIBS=""
+   fi
+fi
+AC_SUBST([TCMALLOC_LIBS])
+AM_CONDITIONAL([HAVETCMALLOC],[test -n "$TCMALLOC_LIBS"])
+
+#  Check for -lprofiler usually part of the gpreftools along with tcmalloc.
+have_profiler="no"
+AC_ARG_WITH([profiler],
+   [AS_HELP_STRING([--with-profiler],
+      [use cpu profiler library or specify the directory with lib @<:@yes/no@:>@]
+   )],
+   [with_profiler="$withval"],
+   [with_profiler="yes"]
+)
+if test "x$with_profiler" != "xno"; then
+   if test "x$with_profiler" != "xyes" && test "x$with_profiler" != "x"; then
+      proflibs="-L$with_profiler -lprofiler"
+   else
+      proflibs="-lprofiler"
+   fi
+   AC_CHECK_LIB([profiler],[ProfilerFlush],[have_profiler="yes"],[have_profiler="no"],
+                $proflibs)
+
+   if test "$have_profiler" = "yes"; then
+      PROFILER_LIBS="$proflibs"
+   else
+      PROFILER_LIBS=""
+   fi
+fi
+AC_SUBST([PROFILER_LIBS])
+AM_CONDITIONAL([HAVEPROFILER],[test -n "$PROFILER_LIBS"])
 
 # Check for HDF5. This is required.
 AX_LIB_HDF5
@@ -410,6 +473,8 @@ AC_MSG_RESULT([
     - parallel     : $have_parallel_hdf5
    Metis enabled   : $have_metis
    libNUMA enabled : $have_numa
+   Using tcmalloc  : $have_tcmalloc
+   CPU profiler    : $have_profiler
 ])
 
 # Generate output.

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/Makefile.am

@@ -21,13 +21,17 @@ MYFLAGS = -DTIMER
 # Add the source directory and debug to CFLAGS
 AM_CFLAGS = -I../src $(HDF5_CPPFLAGS)
 
-AM_LDFLAGS =
+AM_LDFLAGS = $(HDF5_LDFLAGS)
 
-MPI_THREAD_LIBS = @MPI_THREAD_LIBS@
+# Extra libraries.
+EXTRA_LIBS = $(HDF5_LIBS) $(PROFILER_LIBS) $(TCMALLOC_LIBS)
+
+# MPI libraries.
 MPI_LIBS = $(METIS_LIBS) $(MPI_THREAD_LIBS)
 MPI_FLAGS = -DWITH_MPI $(METIS_INCS)
 
-# Set-up the library
+
+# Programs.
 bin_PROGRAMS = swift swift_fixdt
 
 # Build MPI versions as well?
@@ -45,20 +49,20 @@ endif
 # Sources for swift
 swift_SOURCES = main.c
 swift_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-swift_LDADD =  ../src/.libs/libswiftsim.a $(HDF5_LDFLAGS) $(HDF5_LIBS)
+swift_LDADD =  ../src/.libs/libswiftsim.a $(EXTRA_LIBS)
 
 swift_fixdt_SOURCES = main.c
 swift_fixdt_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_fixdt | engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-swift_fixdt_LDADD =  ../src/.libs/libswiftsim.a $(HDF5_LDFLAGS) $(HDF5_LIBS)
+swift_fixdt_LDADD =  ../src/.libs/libswiftsim.a $(EXTRA_LIBS)
 
 # Sources for swift_mpi, do we need an affinity policy for MPI?
 swift_mpi_SOURCES = main.c
 swift_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-swift_mpi_LDADD =  ../src/.libs/libswiftsim_mpi.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(MPI_LIBS)
+swift_mpi_LDADD =  ../src/.libs/libswiftsim_mpi.a $(MPI_LIBS) $(EXTRA_LIBS)
 
 swift_fixdt_mpi_SOURCES = main.c
 swift_fixdt_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_fixdt | engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-swift_fixdt_mpi_LDADD =  ../src/.libs/libswiftsim_mpi.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(MPI_LIBS)
+swift_fixdt_mpi_LDADD =  ../src/.libs/libswiftsim_mpi.a $(MPI_LIBS) $(EXTRA_LIBS)
 
 # Scripts to generate ICs
 EXTRA_DIST = UniformBox/makeIC.py UniformBox/run.sh UniformBox/uniformBox.yml \

examples/MultiTypes/multiTypes.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 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 governing the snapshots
+Snapshots:
+  basename:            multiTypes # Common part of the name of output files
+  time_first:          0.         # Time of the first output (in internal units)
+  delta_time:          0.01       # 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:  ./multiTypes.hdf5     # The file to read
+
+# External potential parameters
+PointMass:
+  position_x:      50.     # location of external point mass in internal units
+  position_y:      50.
+  position_z:      50.	
+  mass:            1e10     # mass of external point mass in internal units

examples/MultiTypes/run.sh

+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e multiTypes.hdf5 ]
+then
+    echo "Generating initial conditions for the multitype box example..."
+    python makeIC.py 50 60
+fi
+
+../swift -s -t 16 multiTypes.yml