Move executable out of examples

Makefile.am

@@ -30,5 +30,74 @@ SUBDIRS += examples/Cooling/CoolingRates
 endif
 DIST_SUBDIRS = $(SUBDIRS) examples/Cooling/CoolingRates
 
+# Common flags
+MYFLAGS =
+
+# Add the source directory and the non-standard paths to the included library headers to CFLAGS
+AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/argparse $(HDF5_CPPFLAGS) \
+	$(GSL_INCS) $(FFTW_INCS) $(NUMA_INCS) $(GRACKLE_INCS) $(OPENMP_CFLAGS) \
+	$(CHEALPIX_CFLAGS)
+
+AM_LDFLAGS = $(HDF5_LDFLAGS)
+
+# Extra libraries.
+EXTRA_LIBS = $(GSL_LIBS) $(HDF5_LIBS) $(FFTW_LIBS) $(NUMA_LIBS) $(PROFILER_LIBS) \
+	$(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) \
+	$(CHEALPIX_LIBS)
+
+# MPI libraries.
+MPI_LIBS = $(PARMETIS_LIBS) $(METIS_LIBS) $(MPI_THREAD_LIBS) $(FFTW_MPI_LIBS)
+MPI_FLAGS = -DWITH_MPI $(PARMETIS_INCS) $(METIS_INCS) $(FFTW_MPI_INCS)
+
+# Programs.
+bin_PROGRAMS = swift
+
+# Also build the FOF tool?
+if HAVESTANDALONEFOF
+bin_PROGRAMS += fof
+endif
+
+# Do we have the CSDS?
+if HAVECSDS
+LD_CSDS = csds/src/.libs/libcsds_writer.a
+else
+LD_CSDS =
+endif
+
+# Build MPI versions as well?
+if HAVEMPI
+bin_PROGRAMS += swift_mpi
+if HAVESTANDALONEFOF
+bin_PROGRAMS += fof_mpi
+endif
+endif
+
+# engine_policy_setaffinity is available?
+if HAVESETAFFINITY
+ENGINE_POLICY_SETAFFINITY=| engine_policy_setaffinity
+else
+ENGINE_POLICY_SETAFFINITY=
+endif
+
+# Sources for swift
+swift_SOURCES = swift.c
+swift_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+swift_LDADD =  src/libswiftsim.la argparse/libargparse.la $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
+# Sources for swift_mpi, do we need an affinity policy for MPI?
+swift_mpi_SOURCES = swift.c
+swift_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+swift_mpi_LDADD =  src/libswiftsim_mpi.la argparse/libargparse.la $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
+# Sources for fof
+fof_SOURCES = swift_fof.c
+fof_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+fof_LDADD =  src/.libs/libswiftsim.a argparse/.libs/libargparse.a $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
+# Sources for fof_mpi, do we need an affinity policy for MPI?
+fof_mpi_SOURCES = swift_fof.c
+fof_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+fof_mpi_LDADD =  src/.libs/libswiftsim_mpi.a argparse/.libs/libargparse.a $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
 # Non-standard files that should be part of the distribution.
 EXTRA_DIST = INSTALL.swift .clang-format format.sh

doc/RTD/source/GettingStarted/compiling_code.rst

@@ -107,15 +107,14 @@ This may be required as a dependency of HEALPix.
 Initial Setup
 -------------
 
-We use autotools for setup. To get a basic running version of the code
-(the binary is created in swiftsim/examples) on most platforms, run
-
+We use autotools for setup. To get a basic running version of the code use:
 .. code-block:: bash
 
   ./autogen.sh
   ./configure
   make
 
+the executable binaries are found in the top directory.
 
 MacOS Specific Oddities
 ~~~~~~~~~~~~~~~~~~~~~~~

examples/Cooling/ConstantCosmoTempEvolution/run.sh

@@ -20,7 +20,7 @@ then
 fi
 
 # Run SWIFT
-../../swift --hydro --cosmology --cooling --threads=4 const_cosmo_temp_evol.yml 2>&1 | tee output.log
+../../../swift --hydro --cosmology --cooling --threads=4 const_cosmo_temp_evol.yml 2>&1 | tee output.log
 
 # Plot the result
 python3 plot_thermal_history.py cooling_box

examples/Cooling/CoolingBox/run.sh

@@ -21,7 +21,7 @@ then
 fi
 
 # Run SWIFT
-../../swift --hydro --cooling --threads=4 -n 1000 coolingBox.yml
+../../../swift --hydro --cooling --threads=4 -n 1000 coolingBox.yml
 
 # Check energy conservation and cooling rate
 python3 plotEnergy.py

examples/Cooling/CoolingHalo/run.sh

@@ -4,7 +4,7 @@
 echo "Generating initial conditions for the isothermal potential box example..."
 python3 makeIC.py 10000 
 
-../../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
+../../../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
 
 python3 radial_profile.py 2. 200 100
 

examples/Cooling/CoolingHaloWithSpin/run.sh

@@ -5,7 +5,7 @@ echo "Generating initial conditions for the isothermal potential box example..."
 python3 makeIC.py 10000 
 
 # Run SWIFT with external potential, SPH and cooling
-../../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
+../../../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
 
 # python3 radial_profile.py 10
 

examples/Cooling/CoolingRedshiftDependence/run.sh

@@ -14,7 +14,7 @@ then
     python3 makeIC.py
 fi
 
-swift_location="../../swift"
+swift_location="../../../swift"
 
 rm data/redshift_dependence_*_z_*.hdf5
 

examples/Cooling/FeedbackEvent_3D/run.sh

@@ -12,7 +12,7 @@ if [ ! -f feedback.hdf5 ]; then
 fi
 
 # Run SWIFT
-../../swift --hydro --cooling --limiter --threads=4 feedback.yml 2>&1 | tee output.log
+../../../swift --hydro --cooling --limiter --threads=4 feedback.yml 2>&1 | tee output.log
 
 # Plot the solution
 python3 plotSolution.py 5

examples/Cooling/FeedbackEvent_3D/runs.sh

@@ -17,7 +17,7 @@ do
 
     cd default_diffmax_$diffusion_alpha_max
 
-    ../../../swift --hydro --cooling --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log 
+    ../../../../swift --hydro --cooling --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log 
 
     cd ..
     
@@ -25,7 +25,7 @@ do
 
     cd nocool_diffmax_$diffusion_alpha_max
 
-    ../../../swift --hydro --temperature --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log 
+    ../../../../swift --hydro --temperature --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log 
 
     cd ..
 done

examples/Cosmology/ComovingSodShock_1D/run.sh

@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Plot the result
 python3 plotSolution.py 1

examples/Cosmology/ComovingSodShock_2D/run.sh

@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 python3 plotSolution.py 1

examples/Cosmology/ComovingSodShock_3D/run.sh

@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 python3 plotSolution.py 1

examples/Cosmology/ComovingToroTest2_1D/run.sh

@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../../swift --cosmology --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
 
 # Plot the result
 python3 plotSolution.py 1

examples/Cosmology/ConstantCosmoVolume/run.sh

@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../../swift --hydro --cosmology --self-gravity --threads=8 constant_volume.yml 2>&1 | tee output.log
+../../../swift --hydro --cosmology --self-gravity --threads=8 constant_volume.yml 2>&1 | tee output.log
 
 # Plot the result
 python3 plotSolution.py $i

examples/Cosmology/NeutrinoCosmo/run.sh

@@ -8,4 +8,4 @@ then
 fi
 
 # Run SWIFT
-../../swift -c -G --threads=8 neutrino_cosmo.yml 2>&1 | tee output.log
+../../../swift -c -G --threads=8 neutrino_cosmo.yml 2>&1 | tee output.log

examples/Cosmology/ZeldovichPancake_3D/run.sh

@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../../swift --hydro --cosmology --self-gravity --threads=8 zeldovichPancake.yml 2>&1 | tee output.log
+../../../swift --hydro --cosmology --self-gravity --threads=8 zeldovichPancake.yml 2>&1 | tee output.log
 
 # Plot the result
 for i in {0..119}

examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../../swift --cosmology --self-gravity --threads=16 eagle_100.yml 2>&1 | tee output.log
+../../../swift --cosmology --self-gravity --threads=16 eagle_100.yml 2>&1 | tee output.log
 

examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../../swift --cosmology --self-gravity --threads=16 eagle_12.yml 2>&1 | tee output.log
+../../../swift --cosmology --self-gravity --threads=16 eagle_12.yml 2>&1 | tee output.log
 

examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../../swift --cosmology --self-gravity --threads=16 eagle_25.yml 2>&1 | tee output.log
+../../../swift --cosmology --self-gravity --threads=16 eagle_25.yml 2>&1 | tee output.log
 

examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../../swift --cosmology --self-gravity --threads=16 eagle_50.yml 2>&1 | tee output.log
+../../../swift --cosmology --self-gravity --threads=16 eagle_50.yml 2>&1 | tee output.log