Update AGORA test problem: High-res ICs [Reviewed]

example/grackle/Make.mach.eureka-intel

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+#=======================================================================
+#
+# FILE:        Make.mach.eureka-intel
+#
+# DESCRIPTION: Makefile for the calab-ntu Eureka GPU cluster with Intel
+#              compiler and OpenMP support
+#
+# AUTHOR:      Hsi-Yu Schive (modified by Guan-Ming Su, Barry T. Chiang,
+#              and Chun-Yen Chen)
+#
+# DATE:        April 1, 2016 (August 28, 2024)
+#=======================================================================
+
+MACH_TEXT  = Eureka Intel
+MACH_VALID = 0
+MACH_FILE  = Make.mach.eureka-intel
+
+#-----------------------------------------------------------------------
+# Install paths (local variables)
+#-----------------------------------------------------------------------
+
+LOCAL_HDF5_INSTALL = /software/hdf5/default
+LOCAL_FC_INSTALL   = /software/intel/oneapi/compiler/default/linux/compiler/lib/intel64
+
+#-----------------------------------------------------------------------
+# Compiler settings
+#-----------------------------------------------------------------------
+
+MACH_CPP       = icpc # C preprocessor command
+
+# Compilers
+MACH_CC_NOMPI  = icc # C compiler
+MACH_CXX_NOMPI = icpc # C++ compiler
+MACH_FC_NOMPI  = ifort # Fortran 77
+MACH_F90_NOMPI = ifort # Fortran 90
+MACH_LD_NOMPI  = icpc # Linker
+MACH_LIBTOOL   = libtool
+
+#-----------------------------------------------------------------------
+# Machine-dependent defines
+#-----------------------------------------------------------------------
+
+# Note: When compiling against HDF5 version 1.8 or greater, you need to
+# compile HDF5 with --with-default-api-version=v16, or specify with
+# -DH5_USE_16_API.
+
+MACH_DEFINES   = -DLINUX -DH5_USE_16_API
+
+#-----------------------------------------------------------------------
+# Compiler flag settings
+#-----------------------------------------------------------------------
+
+MACH_OMPFLAGS = -fopenmp # OpenMP flags
+MACH_CPPFLAGS = -P -traditional # C preprocessor flags
+MACH_CFLAGS   = -mp1 -prec_div -fp_port -align # C compiler flags
+MACH_CXXFLAGS = -mp1 -prec_div -fp_port -align # C++ compiler flags
+MACH_FFLAGS   = # Fortran 77 compiler flags
+MACH_F90FLAGS = -mp1 -prec_div -fp_port -align #-save -zero # Fortran 90 compiler flags
+MACH_LDFLAGS  = #-lifcore -lifport -lpthread -ldl # Linker flags
+
+#-----------------------------------------------------------------------
+# Optimization flags
+#-----------------------------------------------------------------------
+
+MACH_OPT_WARN        = # Flags for verbose compiler warnings
+MACH_OPT_DEBUG       = -g -O0 # Flags for debugging
+MACH_OPT_HIGH        = -O2 # Flags for high conservative optimization
+MACH_OPT_AGGRESSIVE  = -O3 #-Mfptrap -Mflushz -fastsse -Mdaz -Mnontemporal -Mnofprelaxed -Mvect=altcode,assoc,prefetch -Kieee # Flags for aggressive optimization
+
+#-----------------------------------------------------------------------
+# Includes
+#-----------------------------------------------------------------------
+
+LOCAL_INCLUDES_HDF5   = -I$(LOCAL_HDF5_INSTALL)/include # HDF5 includes
+MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5)
+
+#-----------------------------------------------------------------------
+# Libraries
+#-----------------------------------------------------------------------
+
+LOCAL_LIBS_HDF5   = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 # HDF5 libraries
+LOCAL_LIBS_MACH   = -L$(LOCAL_FC_INSTALL) -lm -lifcore -lifport # Machine-dependent libraries
+
+MACH_LIBS         = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)
+
+#-----------------------------------------------------------------------
+# Installation
+#-----------------------------------------------------------------------
+
+# if $(HOME)/local does not exist, mkdir before `make install`
+
+### Use this when make omp-on is set
+MACH_INSTALL_PREFIX = <local_grackle_directory>/grackle_eureka_single_omp
+### Use this when make omp-off is set
+#MACH_INSTALL_PREFIX = <local_grackle_directory>/grackle_no_omp_single_precision
+MACH_INSTALL_LIB_DIR =
+MACH_INSTALL_INCLUDE_DIR =

example/grackle/Make.mach.spock-intel

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+#=======================================================================
+#
+# FILE:        Make.mach.spock-intel
+#
+# DESCRIPTION: Makefile for the calab-ntu Spock GPU cluster with Intel
+#              compiler and OpenMP support
+#
+# AUTHOR:      Hsi-Yu Schive (modified by Guan-Ming Su, Barry T. Chiang,
+#              and Chun-Yen Chen)
+#
+# DATE:        April 1, 2016 (August 28, 2024)
+#=======================================================================
+
+MACH_TEXT  = Spock Intel
+MACH_VALID = 0
+MACH_FILE  = Make.mach.spock-intel
+
+#-----------------------------------------------------------------------
+# Install paths (local variables)
+#-----------------------------------------------------------------------
+
+LOCAL_HDF5_INSTALL = /software/hdf5/1.10.6-intel-2023.1.0
+LOCAL_FC_INSTALL   = /software/intel/oneapi/compiler/latest/linux/compiler/lib/intel64
+
+#-----------------------------------------------------------------------
+# Compiler settings
+#-----------------------------------------------------------------------
+
+MACH_CPP       = icpc # C preprocessor command
+
+# Compilers
+MACH_CC_NOMPI  = icc # C compiler
+MACH_CXX_NOMPI = icpc # C++ compiler
+MACH_FC_NOMPI  = ifort # Fortran 77
+MACH_F90_NOMPI = ifort # Fortran 90
+MACH_LD_NOMPI  = icpc # Linker
+MACH_LIBTOOL   = libtool
+
+#-----------------------------------------------------------------------
+# Machine-dependent defines
+#-----------------------------------------------------------------------
+
+# Note: When compiling against HDF5 version 1.8 or greater, you need to
+# compile HDF5 with --with-default-api-version=v16, or specify with
+# -DH5_USE_16_API.
+
+MACH_DEFINES   = -DLINUX -DH5_USE_16_API
+
+#-----------------------------------------------------------------------
+# Compiler flag settings
+#-----------------------------------------------------------------------
+
+MACH_OMPFLAGS = -fopenmp # OpenMP flags
+MACH_CPPFLAGS = -P -traditional # C preprocessor flags
+MACH_CFLAGS   = -mp1 -prec_div -fp_port -align # C compiler flags
+MACH_CXXFLAGS = -mp1 -prec_div -fp_port -align # C++ compiler flags
+MACH_FFLAGS   = # Fortran 77 compiler flags
+MACH_F90FLAGS = -mp1 -prec_div -fp_port -align #-save -zero # Fortran 90 compiler flags
+MACH_LDFLAGS  = #-lifcore -lifport -lpthread -ldl # Linker flags
+
+#-----------------------------------------------------------------------
+# Optimization flags
+#-----------------------------------------------------------------------
+
+MACH_OPT_WARN        = # Flags for verbose compiler warnings
+MACH_OPT_DEBUG       = -g -O0 # Flags for debugging
+MACH_OPT_HIGH        = -O2 # Flags for high conservative optimization
+MACH_OPT_AGGRESSIVE  = -O3 #-Mfptrap -Mflushz -fastsse -Mdaz -Mnontemporal -Mnofprelaxed -Mvect=altcode,assoc,prefetch -Kieee # Flags for aggressive optimization
+
+#-----------------------------------------------------------------------
+# Includes
+#-----------------------------------------------------------------------
+
+LOCAL_INCLUDES_HDF5   = -I$(LOCAL_HDF5_INSTALL)/include # HDF5 includes
+MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5)
+
+#-----------------------------------------------------------------------
+# Libraries
+#-----------------------------------------------------------------------
+
+LOCAL_LIBS_HDF5   = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 # HDF5 libraries
+LOCAL_LIBS_MACH   = -L$(LOCAL_FC_INSTALL) -lm -lifcore -lifport # Machine-dependent libraries
+
+MACH_LIBS         = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)
+
+#-----------------------------------------------------------------------
+# Installation
+#-----------------------------------------------------------------------
+
+# if $(HOME)/local does not exist, mkdir before `make install`
+
+### Use this when make omp-on is set
+MACH_INSTALL_PREFIX = <local_grackle_directory>/grackle_spock_single_omp
+### Use this when make omp-off is set
+#MACH_INSTALL_PREFIX = <local_grackle_directory>/grackle_no_omp_single_precision
+MACH_INSTALL_LIB_DIR =
+MACH_INSTALL_INCLUDE_DIR =

example/grackle/README

@@ -0,0 +1,14 @@
+First-time GRACKLE installation guide (on calab-ntu gpu-clusters as an example):
+========================================
+1. First download the source code by executing "git clone https://github.com/grackle-project/grackle"
+2. Next navigate to "cd grackle". The required UVB interpolation tables can be downloaded via "git submodule update --init"
+3. Next navigate to "./configure; cd src/clib"
+4. Copy into the config files "Make.mach.eureka-intel" or "Make.mach.spock-intel" (from the directory "<your_gamer_directory>/example/grackle/") and change the prefix: "MACH_INSTALL_PREFIX = <your_grackle_directory>/grackle_spock" in "Make.mach.spock-intel" to the path you wish to install the package
+5. Next execute "make clean; make machine-spock-intel" or "make clean; make machine-eureka-intel"
+6. Next execute "make show-config" and "make precision-32" (single precision is more compatible with gaming GPUs on eureka and spock) and "make omp-on" (GAMER does utilize OpenMP)
+7. Next execute "make save-config-gamer" (save this GAMER-spock specific config setting) and "make load-config-gamer" (load this GAMER-spock specific config setting)
+8. Lastly for code compilation, execute "make; make install"
+9. To compile the corresponding gamer executable:
+    (1) Add the path "GRACKLE_PATH    <your_grackle_directory>/grackle_spock_single_omp" to "<your_gamer_directory>/configs/spock_intel.config"
+    (2) Copy "generate_make.sh" from the AGORA test problem and change "--machine=spock_intel" in that file, and then execute "sh generate_make.sh"
+    (3) Generate a gamer executable via "make clean; make -j 4"

example/test_problem/Hydro/AGORA_IsolatedGalaxy/Input_Options/Input__Flag_Jeans.high-res

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+# Level          Jeans_length/cell_size
+      0                            64.0
+      1                            64.0
+      2                            64.0
+      3                            64.0
+      4                            64.0
+      5                            64.0
+      6                            64.0
+      7                            64.0
+      8                            64.0
+      9                            64.0
+     10                            64.0
+     11                            64.0

example/test_problem/Hydro/AGORA_IsolatedGalaxy/Input_Options/Input__Flag_ParMassCell.high-res

@@ -0,0 +1,13 @@
+# Level    Total_particle_mass_per_cell
+      0                    1.0035496e-3
+      1                    1.0035496e-3
+      2                    1.0035496e-3
+      3                    1.0035496e-3
+      4                    1.0035496e-3
+      5                    1.0035496e-3
+      6                    1.0035496e-3
+      7                    1.0035496e-3
+      8                    1.0035496e-3
+      9                    1.0035496e-3
+     10                    1.0035496e-3
+     11                    1.0035496e-3

example/test_problem/Hydro/AGORA_IsolatedGalaxy/Input_Options/Input__Flag_Rho.high-res

@@ -0,0 +1,12 @@
+# Level                         Density
+      0           3.125751391053200e-10
+      1           2.500601112842560e-09
+      2           2.000480890274048e-08
+      3           1.600384712219238e-07
+      4           1.280307769775391e-06
+      5           1.024246215820313e-05
+      6           8.193969726562500e-05
+      7           6.555175781250000e-04
+      8           5.244140625000000e-03
+      9           4.195312500000000e-02
+     10           3.356250000000000e-01