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Object-oriented Utilitarian Functionality for Large-scale Physics Simulations
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README: BUILDING GENASIS APPLICATIONS, EXAMPLES, AND/OR UNIT TESTS -------------------------------------------------------------------------- A machine-specific Makefile is needed to build GenASiS programs. Several sample Makefiles are provided under the subdirectory Build/Machines. Minor modifications of one of the provided Makefiles that most approximates one's computing environment is often sufficient to get started. The essential information needed includes the name of the compiler wrapper to compile MPI-based code (e.g. commonly 'mpif90' for Fortran), compiler-specific flags for various debugging and optimization options, and the flags and locations to include and link with third-party libraries such as Silo. Once the machine-specific Makefile is set up, the environment variable GENASIS_MACHINE has to be set to tell the GenASiS build system to use the corresponding Makefile. For example, to use the Makefile for the GNU compiler on a Linux machine (i.e. Makefile_Linux_GNU), in a Bash Unix shell one can type: > export GENASIS_MACHINE=Linux_GNU In most common computing environments with a generic MPI library, the fluid dynamics example programs (described in the accompanying paper) can then be built and executed (here with 8 MPI processes) with the following commands: > cd Programs/Examples/Basics/FluidDynamics/Executables > make PURPOSE=OPTIMIZE all > mpirun -np 8 ./SineWaveAdvection_Linux_GNU nCells=128,128,128 > mpirun -np 8 ./SawtoothWaveAdvection_Linux_GNU nCells=128,128,128 \ nWavelengths=2,2,2 > mpirun -np 8 ./RiemannProblem_Linux_GNU nCells=128,128,128 \ FinishTime=0.25 (To compile in a manner that is unoptimized but useful for debuggers, replace 'PURPOSE=OPTIMIZE' with 'PURPOSE=DEBUG'. Or omit it altogether; in the absence of a specification of PURPOSE, the Makefile in FluidDynamics/Executables sets PURPOSE=DEBUG as a default.) Note that in these examples, the optional non-default parameter values for nCells, nWavelengths, and FinishTime---which were used in generating the figures in the accompanying paper---are passed to the programs in this case via command-line options. The 1D and 2D cases of these programs can also be executed by specifying fewer elements for nCells, for example > mpirun -np 2 ./RiemannProblem_Linux_GNU nCells=128 Dimensionality=1D \ FinishTime=0.25 > mpirun -np 4 ./RiemannProblem_Linux_GNU nCells=128,128 Dimensionality=2D \ FinishTime=0.25 where the 'Dimensionality' option here is only used as an appendix to the name of the output file (it should be consistent with the number of elements given to nCells, which the program uses to determine the desired dimensionality of the mesh). By default the output files are written in the directory "Output" that resides on the same level as the "Executables" directory, but this can be changed with an optional 'OutputDirectory' command line option. If the VisIt visualization package is available, plots similar to the Figures in the accompanying paper can be generated using the supplied visualization script called from the "Output" directory. The script takes one argument, which is the program name appended with the "Dimensionality" string. Assuming the executable "visit" is available, the visualization script can be called, for example, as the follows: > cd Programs/Examples/Basics/FluidDynamics/Output > visit -cli -s ../PlaneWaveAdvection.visit.py SineWaveAdvection_3D > visit -cli -s ../PlaneWaveAdvection.visit.py SawtoothWaveAdvection_2D > visit -cli -s ../PlaneWaveAdvection.visit.py RiemannProblem_1D The molecular dynamics programs described in the accompanying paper can be built and executed in a manner similar to those in FluidDynamics. The directory MolecularDynamics is also found under Programs/Examples/Basics. A blanket "make all" command in the Executables subdirectory compiles both ArgonEquilibrium and ClusterFormation}. For both programs, all results presented in the accompanying paper were obtained with parameters nSteps=10000 and nWrite=1000. Various numbers of particles and processes used for different runs are mentioned in the accompanying paper. In the case of ClusterFormation, the number of particles is directly specified by a parameter nParticles. For ArgonEquilibrium a parameter nUnitCellsRoot is used instead; the number of particles is 4 * ( nUnitCellsRoot ** 3 ). Thus the values 8, 12, 16, and 20 for nUnitCellsRoot correspond to 2048, 6912, 16384, and 32000 particles respectively. Specification of the number density and temperature parameters for different phases of argon is discussed in the accompanying paper. Unit test programs exercising individual GenASIS classes can similarly be built and executed inside the "Executables" directory of each leaf division of the code under "Programs/UnitTests". For example, the following commands build and execute the unit test programs for classes in the "Runtime" division: > cd Programs/UnitTests/Basics/Runtime/Executables > make all > mpirun -np 1 [program_name] This blanket "make all" builds all the unit test targets in the Makefile fragment Programs/Basics/Runtime/Makefile_Runtime. Individual targets of course also can be built. GenASiS Basics Version 2 has been tested with the following compilers: GNU Fortran compiler (gfortran, part of GCC) version 6.1.0, Intel Fortran 16.0.03, and Cray Compiler Environment version 8.5.3. Newer versions of these compilers are likely to work as well. GenASiS Basics is written in full compliance with the Fortran 2003 standard (with the addition of a couple of minor new features of Fortan 2008, including the "impure" attribute and finding a new unit number in the "open" statement) to enhance portability. Authors: Christian Cardall (firstname.lastname@example.org) Reuben Budiardja (email@example.com)